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  • 1.
    Aguida, Blanche
    et al.
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Babo, Jonathan
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Baouz, Soria
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Jourdan, Nathalie
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France.
    Procopio, Maria
    Department of Biophysics, Faculty of Arts and Sciences, Johns Hopkins University, MD, Baltimore, United States.
    El-Esawi, Mohamed A.
    Botany Department, Faculty of Science, Tanta University, Tanta, Egypt.
    Engle, Dorothy
    Biology Department, Xavier University, OH, Cincinnati, United States.
    Mills, Stephen
    Chemistry Department, Xavier University, OH, Cincinnati, United States.
    Wenkel, Stephan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Huck, Alexander
    DTU Physics, Technical University of Denmark, Kongens Lyngby, Denmark.
    Berg-Sørensen, Kirstine
    DTU Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
    Kampranis, Sotirios C.
    Biochemical Engineering Group, Plant Biochemistry Section, Department of Plant and Environment Sciences, University of Copenhagen, Frederiksberg, Denmark.
    Link, Justin
    Physics and Engineering Department, OH, Cincinnati, United States.
    Ahmad, Margaret
    Unite Mixed de Recherche (UMR) Centre Nationale de la Recherche Scientifique (CNRS) 8256 (B2A), Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, Paris, France; Biology Department, Xavier University, OH, Cincinnati, United States.
    'Seeing' the electromagnetic spectrum: spotlight on the cryptochrome photocycle2024In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 15, article id 1340304Article, review/survey (Refereed)
    Abstract [en]

    Cryptochromes are widely dispersed flavoprotein photoreceptors that regulate numerous developmental responses to light in plants, as well as to stress and entrainment of the circadian clock in animals and humans. All cryptochromes are closely related to an ancient family of light-absorbing flavoenzymes known as photolyases, which use light as an energy source for DNA repair but themselves have no light sensing role. Here we review the means by which plant cryptochromes acquired a light sensing function. This transition involved subtle changes within the flavin binding pocket which gave rise to a visual photocycle consisting of light-inducible and dark-reversible flavin redox state transitions. In this photocycle, light first triggers flavin reduction from an initial dark-adapted resting state (FADox). The reduced state is the biologically active or ‘lit’ state, correlating with biological activity. Subsequently, the photoreduced flavin reoxidises back to the dark adapted or ‘resting’ state. Because the rate of reoxidation determines the lifetime of the signaling state, it significantly modulates biological activity. As a consequence of this redox photocycle Crys respond to both the wavelength and the intensity of light, but are in addition regulated by factors such as temperature, oxygen concentration, and cellular metabolites that alter rates of flavin reoxidation even independently of light. Mechanistically, flavin reduction is correlated with conformational change in the protein, which is thought to mediate biological activity through interaction with biological signaling partners. In addition, a second, entirely independent signaling mechanism arises from the cryptochrome photocycle in the form of reactive oxygen species (ROS). These are synthesized during flavin reoxidation, are known mediators of biotic and abiotic stress responses, and have been linked to Cry biological activity in plants and animals. Additional special properties arising from the cryptochrome photocycle include responsivity to electromagnetic fields and their applications in optogenetics. Finally, innovations in methodology such as the use of Nitrogen Vacancy (NV) diamond centers to follow cryptochrome magnetic field sensitivity in vivo are discussed, as well as the potential for a whole new technology of ‘magneto-genetics’ for future applications in synthetic biology and medicine.

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  • 2. Akhter, Shirin
    et al.
    Kretzschmar, Warren W.
    Nordal, Veronika
    Delhomme, Nicolas
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nilsson, Ove
    Emanuelsson, Olof
    Sundström, Jens F.
    Integrative analysis of three RNA sequencing methods identifies mutually exclusive exons of MADS-box isoforms during early bud development in Picea abies2018In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 9, article id 1625Article in journal (Refereed)
    Abstract [en]

    Recent efforts to sequence the genomes and transcriptomes of several gymnosperm species have revealed an increased complexity in certain gene families in gymnosperms as compared to angiosperms. One example of this is the gymnosperm sister Glade to angiosperm TM3-like MADS-box genes, which at least in the conifer lineage has expanded in number of genes. We have previously identified a member of this subclade, the conifer gene DEFICIENS AGAMOUS LIKE 19 (DAL19), as being specifically upregulated in cone-setting shoots. Here, we show through Sanger sequencing of mRNA-derived cDNA and mapping to assembled conifer genomic sequences that DAL19 produces six mature mRNA splice variants in Picea abies. These splice variants use alternate first and last exons, while their four central exons constitute a core region present in all six transcripts. Thus, they are likely to be transcript isoforms. Quantitative Real-Time PCR revealed that two mutually exclusive first DAL19 exons are differentially expressed across meristems that will form either male or female cones, or vegetative shoots. Furthermore, mRNA in situ hybridization revealed that two mutually exclusive last DAL19 exons were expressed in a cell-specific pattern within bud meristems. Based on these findings in DAL19, we developed a sensitive approach to transcript isoform assembly from short-read sequencing of mRNA. We applied this method to 42 putative MADS-box core regions in P abies, from which we assembled 1084 putative transcripts. We manually curated these transcripts to arrive at 933 assembled transcript isoforms of 38 putative MADS-box genes. 152 of these isoforms, which we assign to 28 putative MADS-box genes, were differentially expressed across eight female, male, and vegetative buds. We further provide evidence of the expression of 16 out of the 38 putative MADS-box genes by mapping PacBio Iso-Seq circular consensus reads derived from pooled sample sequencing to assembled transcripts. In summary, our analyses reveal the use of mutually exclusive exons of MADS-box gene isoforms during early bud development in P. abies, and we find that the large number of identified MADS-box transcripts in P. abies results not only from expansion of the gene family through gene duplication events but also from the generation of numerous splice variants.

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  • 3. Alagna, F.
    et al.
    Caceres, M. E.
    Pandolfi, S.
    Collani, Silvio
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Mousavi, S.
    Mariotti, R.
    Cultrera, N. G. M.
    Baldoni, L.
    Barcaccia, G.
    The Paradox of Self-Fertile Varieties in the Context of Self-Incompatible Genotypes in Olive2019In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 10, article id 725Article, review/survey (Refereed)
    Abstract [en]

    Olive, representing one of the most important fruit crops of the Mediterranean area, is characterized by a general low fruit yield, due to numerous constraints, including alternate bearing, low flower viability, male-sterility, inter-incompatibility, and self-incompatibility (SI). Early efforts to clarify the genetic control of SI in olive gave conflicting results, and only recently, the genetic control of SI has been disclosed, revealing that olive possesses an unconventional homomorphic sporophytic diallelic system of SI, dissimilar from other described plants. This system, characterized by the presence of two SI groups, prevents self-fertilization and regulates inter-compatibility between cultivars, such that cultivars bearing the same incompatibility group are incompatible. Despite the presence of a functional SI, some varieties, in particular conditions, are able to set seeds following self-fertilization, a mechanism known as pseudo-self-compatibility (PSC), as widely reported in previous literature. Here, we summarize the results of previous works on SI in olive, particularly focusing on the occurrence of self-fertility, and offer a new perspective in view of the recent elucidation of the genetic architecture of the SI system in olive. Recent advances in research aimed at unraveling the molecular bases of SI and its breakdown in olive are also presented. The clarification of these mechanisms may have a huge impact on orchard management and will provide fundamental information for the future of olive breeding programs.

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  • 4.
    Alallaq, Sanaria
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Biology, College of Science for Women, Baghdad University, Baghdad, Iraq.
    Ranjan, Alok
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Brunoni, Federica
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Novak, Ondrej
    Lakehal, Abdellah
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Universite´ Paris-Saclay, Versailles, France.
    Red Light Controls Adventitious Root Regeneration by Modulating Hormone Homeostasis in Picea abies Seedlings2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, article id 586140Article in journal (Refereed)
    Abstract [en]

    Vegetative propagation relies on the capacity of plants to regeneratede novoadventitious roots (ARs), a quantitative trait controlled by the interaction of endogenous factors, such as hormones and environmental cues among which light plays a central role. However, the physiological and molecular components mediating light cues during AR initiation (ARI) remain largely elusive. Here, we explored the role of red light (RL) on ARI in de-rooted Norway spruce seedlings. We combined investigation of hormone metabolism and gene expression analysis to identify potential signaling pathways. We also performed extensive anatomical characterization to investigate ARI at the cellular level. We showed that in contrast to white light, red light promoted ARI likely by reducing jasmonate (JA) and JA-isoleucine biosynthesis and repressing the accumulation of isopentyl-adenine-type cytokinins. We demonstrated that exogenously applied JA and/or CK inhibit ARI in a dose-dependent manner and found that they possibly act in the same pathway. The negative effect of JA on ARI was confirmed at the histological level. We showed that JA represses the early events of ARI. In conclusion, RL promotes ARI by repressing the accumulation of the wound-induced phytohormones JA and CK.

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  • 5. Asaf, Sajjad
    et al.
    Waqas, Muhammad
    Khan, Abdul L.
    Khan, Muhammad A.
    Kang, Sang-Mo
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Shahzad, Raheem
    Bilal, Saqib
    Yun, Byung-Wook
    Lee, In-Jung
    The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, article id 304Article in journal (Refereed)
    Abstract [en]

    Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the Ominuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete Ominuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

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  • 6. Bakker, Elisabeth S.
    et al.
    Veen, Ciska G. F.
    Ter Heerdt, Gerard J. N.
    Huig, Naomi
    Sarneel, Judith M
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Ecology and Biodiversity Group, Utrecht University, Utrecht, Netherlands; Plant Ecophysiology Group, Utrecht University, Utrecht, Netherlands.
    High grazing pressure of geese threatens conservation and restoration of reed belts2018In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 9, article id 1649Article in journal (Refereed)
    Abstract [en]

    Reed (Phragmites australis (Cav.) Trin. ex Steud.) beds are important habitat for marsh birds, but are declining throughout Europe. Increasing numbers of the native marsh bird, the Greylag goose (Anser anser L.), are hypothesized to cause reed bed decline and inhibit restoration of reed beds, but data are largely lacking. In this study, we experimentally tested the effect of grazing by Greylag geese on the growth and expansion of reed growing in belts along lake shorelines. After 5 years of protecting reed from-grazing with exclosures, reed stems were over 4-fold denser and taller than in the grazed plots. Grazing pressure was intense with 50-100% of the stems being grazed among years in the control plots open to grazing. After 5 years of protection we opened half of the exclosures and the geese immediately grazed almost 100% of the reed stems. Whereas this did not affect the reed stem density, the stem height was strongly reduced and similar to permanently grazed reed. The next year geese were actively chased away by management from mid-March to mid-June, which changed the maximum amount of geese from over 2300 to less than 50. As a result, reed stem density and height increased and the reed belt had recovered over the full 6 m length of the experimental plots. Lastly, we introduced reed plants in an adjacent lake where no reed was growing and geese did visit this area. After two years, the density of the planted reed was six to nine-fold higher and significantly taller in exclosures compared to control plots where geese had access to the reed plants. We conclude that there is a conservation dilemma regarding how to preserve and restore reed belts in the presence of high densities of Greylag geese as conservation of both reed belts and high goose numbers seems infeasible. We suggest that there are three possible solutions for this dilemma: (1) effects of the geese can be mediated by goose population management, (2) the robustness of the reed marshes can be increased, and (3) at the landscape level, spatial planning can be used to configure landscapes with large reed bed reserves surrounded by unmown, unfertilized meadows.

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  • 7.
    Bannoud, Florencia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France.
    Adventitious Rooting in Populus Species: Update and Perspectives2021In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 12, article id 668837Article, review/survey (Refereed)
    Abstract [en]

    Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.

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  • 8. Bilal, Saqib
    et al.
    Shahzad, Raheem
    Khan, Abdul L
    Kang, Sang-Mo
    Imran, Qari Muhammad
    Al-Harrasi, Ahmed
    Yun, Byung-Wook
    Lee, In-Jung
    Endophytic microbial consortia of phytohormones-producing fungus Paecilomyces formosus LHL10 and bacteria Sphingomonas sp. LK11 to Glycine max L. regulates physio-hormonal changes to attenuate aluminum and zinc stresses2018In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 9, article id 1273Article in journal (Refereed)
    Abstract [en]

    The compatible microbial consortia containing fungal and bacterial symbionts acting synergistically are applied to improve plant growth and eco-physiological responses in extreme crop growth conditions. However, the interactive effects of phytohormones-producing endophytic fungal and bacterial symbionts plant growth and stress tolerance under heavy metal stress have been least known. In the current study, the phytohormones-producing endophytic Paecilomyces formosus LHL10 and Sphingomonas sp. LK11 revealed potent growth and tolerance during their initial screening against combined Al and Zn (2.5 mM each) stress. This was followed with their co-inoculation in the Al- and Zn-stressed Glycine max L. plants, showing significantly higher plant growth attributes (shoot/root length, fresh/dry weight, and chlorophyll content) than the plants solely inoculated with LHL10 or LK11 and the non-inoculated (control) plants under metal stresses. Interestingly, under metal stress, the consortia exhibited lower metal uptake and inhibited metal transport in roots. Metal-induced oxidative stresses were modulated in co-inoculated plants through reduced hydrogen peroxide, lipid peroxidation, and antioxidant enzymes (catalase and superoxide dismutase) in comparison to the non-inoculated plants. In addition, endophytic co-inoculation enhanced plant macronutrient uptake (P, K, S, and N) and modulated soil enzymatic activities under stress conditions. It significantly downregulated the expression of heavy metal ATPase genes GmHMA13, GmHMA18, GmHMA19, and GmPHA1 and upregulated the expression of an ariadne-like ubiquitin ligase gene GmARI1 under heavy metals stress. Furthermore, the endogenous phytohormonal contents of co-inoculated plants revealed significantly enhanced gibberellins and reduced abscisic acid and jasmonic acid contents, suggesting that this endophytic interaction mitigated the adverse effect of metal stresses in host plants. In conclusion, the co-inoculation of the endophytic fungus LHL10 and bacteria LK11 actively contributed to the tripartite mutualistic symbiosis in G. max under heavy metal stresses; this could be used an excellent strategy for sustainable agriculture in the heavy metal-contaminated fields.

  • 9. Bitocchi, Elena
    et al.
    Rau, Domenico
    Benazzo, Andrea
    Bellucci, Elisa
    Goretti, Daniela
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Biagetti, Eleonora
    Panziera, Alex
    Laido, Giovanni
    Rodriguez, Monica
    Gioia, Tania
    Attene, Giovanna
    McClean, Phillip
    Lee, Rian K.
    Jackson, Scott A.
    Bertorelle, Giorgio
    Papa, Roberto
    High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 2005Article in journal (Refereed)
    Abstract [en]

    Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of Phaseolus vulgaris by sequencing 49 gene fragments from a sample of 45 P. vulgaris wild and domesticated accessions, and as controls, two accessions each of the closely related species Phaseolus coccineus and Phaseolus dumosus. An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.

  • 10. Blaschek, Leonard
    et al.
    Champagne, Antoine
    Dimotakis, Charilaos
    Nuoendagula,
    Decou, Raphaël
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hishiyama, Shojiro
    Kratzer, Susanne
    Kajita, Shinya
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Arrhenius Laboratories, Department of Ecology, Environment and Plant Sciences (DEEP), Stockholm University, Stockholm, Sweden.
    Cellular and Genetic Regulation of Coniferaldehyde Incorporation in Lignin of Herbaceous and Woody Plants by Quantitative Wiesner Staining2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, article id 109Article in journal (Refereed)
    Abstract [en]

    Lignin accumulates in the cell walls of specialized cell types to enable plants to stand upright and conduct water and minerals, withstand abiotic stresses, and defend themselves against pathogens. These functions depend on specific lignin concentrations and subunit composition in different cell types and cell wall layers. However, the mechanisms controlling the accumulation of specific lignin subunits, such as coniferaldehyde, during the development of these different cell types are still poorly understood. We herein validated the Wiesner test (phloroglucinol/HCl) for the restrictive quantitative in situ analysis of coniferaldehyde incorporation in lignin. Using this optimized tool, we investigated the genetic control of coniferaldehyde incorporation in the different cell types of genetically-engineered herbaceous and woody plants with modified lignin content and/or composition. Our results demonstrate that the incorporation of coniferaldehyde in lignified cells is controlled by (a) autonomous biosynthetic routes for each cell type, combined with (b) distinct cell-to-cell cooperation between specific cell types, and (c) cell wall layer-specific accumulation capacity. This process tightly regulates coniferaldehyde residue accumulation in specific cell types to adapt their property and/or function to developmental and/or environmental changes.

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  • 11.
    Boussardon, Clément
    et al.
    Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France.
    Martin-Magniette, Marie-Laure
    Godin, Béatrice
    Benamar, Abdelilah
    Vittrant, Benjamin
    Citerne, Sylvie
    Mary-Huard, Tristan
    Macherel, David
    Rajjou, Loïc
    Budar, Françoise
    Novel Cytonuclear Combinations Modify Arabidopsis thaliana Seed Physiology and Vigor2019In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 10, article id 32Article in journal (Refereed)
    Abstract [en]

    Dormancy and germination vigor are complex traits of primary importance for adaptation and agriculture. Intraspecific variation in cytoplasmic genomes and cytonuclear interactions were previously reported to affect germination in Arabidopsis using novel cytonuclear combinations that disrupt co-adaptation between natural variants of nuclear and cytoplasmic genomes. However, specific aspects of dormancy and germination vigor were not thoroughly explored, nor the parental contributions to the genetic effects. Here, we specifically assessed dormancy, germination performance and longevity of seeds from Arabidopsis plants with natural and new genomic compositions. All three traits were modified by cytonuclear reshuffling. Both depth and release rate of dormancy could be modified by a changing of cytoplasm. Significant changes on dormancy and germination performance due to specific cytonuclear interacting combinations mainly occurred in opposite directions, consistent with the idea that a single physiological consequence of the new genetic combination affected both traits oppositely. However, this was not always the case. Interestingly, the ability of parental accessions to contribute to significant cytonuclear interactions modifying the germination phenotype was different depending on whether they provided the nuclear or cytoplasmic genetic compartment. The observed deleterious effects of novel cytonuclear combinations (in comparison with the nuclear parent) were consistent with a contribution of cytonuclear interactions to germination adaptive phenotypes. More surprisingly, we also observed favorable effects of novel cytonuclear combinations, suggesting suboptimal genetic combinations exist in natural populations for these traits. Reduced sensitivity to exogenous ABA and faster endogenous ABA decay during germination were observed in a novel cytonuclear combination that also exhibited enhanced longevity and better germination performance, compared to its natural nuclear parent. Taken together, our results strongly support that cytoplasmic genomes represent an additional resource of natural variation for breeding seed vigor traits.

  • 12.
    Cardoso, Hélia
    et al.
    MED – Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, Évora, Portugal.
    Peixe, Augusto
    MED – Mediterranean Institute for Agriculture, Environment and Development, Department of Plant Science, School of Science and Technology, University of Évora, Évora, Portugal.
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, Versailles, France.
    Porfírio, Sara
    Complex Carbohydrate Research Center, University of Georgia Athens, GA, Athens, United States.
    Druege, Uwe
    Erfurt Research Centre for Horticultural Crops, University of Applied Sciences Erfurt, Erfurt, Germany.
    Editorial: Advances on the Biological Mechanisms Involved in Adventitious Root Formation: From Signaling to Morphogenesis2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 867651Article in journal (Other academic)
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  • 13. Catalá, Rafael
    et al.
    Carrasco-López, Cristian
    Perea-Resa, Carlos
    Hernández-Verdeja, Tamara
    Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas-CSIC, Madrid, Spain.
    Salinas, Julio
    Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress2019In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 10, article id 167Article, review/survey (Refereed)
    Abstract [en]

    It has long been assumed that the wide reprogramming of gene expression that modulates plant response to unfavorable environmental conditions is mainly controlled at the transcriptional level. A growing body of evidence, however, indicates that posttranscriptional regulatory mechanisms also play a relevant role in this control. Thus, the LSMs, a family of proteins involved in mRNA metabolism highly conserved in eukaryotes, have emerged as prominent regulators of plant tolerance to abiotic stress. Arabidopsis contains two main LSM ring-shaped heteroheptameric complexes, LSM1-7 and LSM2-8, with different subcellular localization and function. The LSM1-7 ring is part of the cytoplasmic decapping complex that regulates mRNA stability. On the other hand, the LSM2-8 complex accumulates in the nucleus to ensure appropriate levels of U6 snRNA and, therefore, correct pre-mRNA splicing. Recent studies reported unexpected results that led to a fundamental change in the assumed consideration that LSM complexes are mere components of the mRNA decapping and splicing cellular machineries. Indeed, these data have demonstrated that LSM1-7 and LSM2-8 rings operate in Arabidopsis by selecting specific RNA targets, depending on the environmental conditions. This specificity allows them to actively imposing particular gene expression patterns that fine-tune plant responses to abiotic stresses. In this review, we will summarize current and past knowledge on the role of LSM rings in modulating plant physiology, with special focus on their function in abiotic stress responses.

  • 14.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wagner, Raik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Insights into the Cyanobacterial Deg/HtrA Proteases2016In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 694Article in journal (Refereed)
    Abstract [en]

    Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serinetype ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.

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  • 15.
    Chowdhury, Jamil
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Ferdous, Jannatul
    Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Lihavainen, Jenna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Albrectsen, Benedicte Riber
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lundberg-Felten, Judith
    Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Fluorogenic properties of 4-dimethylaminocinnamaldehyde (DMACA) enable high resolution imaging of cell-wall-bound proanthocyanidins in plant root tissues2023In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 1060804Article in journal (Refereed)
    Abstract [en]

    Proanthocyanidins (PAs) are polymeric phenolic compounds found in plants and used in many industrial applications. Despite strong evidence of herbivore and pathogen resistance-related properties of PAs, their in planta function is not fully understood. Determining the location and dynamics of PAs in plant tissues and cellular compartments is crucial to understand their mode of action. Such an approach requires microscopic localization with fluorescent dyes that specifically bind to PAs. Such dyes have hitherto been lacking. Here, we show that 4-dimethylaminocinnamaldehyde (DMACA) can be used as a PA-specific fluorescent dye that allows localization of PAs at high resolution in cell walls and inside cells using confocal microscopy, revealing features of previously unreported wall-bound PAs. We demonstrate several novel usages of DMACA as a fluorophore by taking advantage of its double staining compatibility with other fluorescent dyes. We illustrate the use of the dye alone and its co-localization with cell wall polymers in different Populus root tissues. The easy-to-use fluorescent staining method, together with its high photostability and compatibility with other fluorogenic dyes, makes DMACA a valuable tool for uncovering the biological function of PAs at a cellular level in plant tissues. DMACA can also be used in other plant tissues than roots, however care needs to be taken when tissues contain compounds that autofluoresce in the red spectral region which can be confounded with the PA-specific DMACA signal.

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  • 16.
    Decker, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Kleczkowski, Leszek
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Substrate Specificity and Inhibitor Sensitivity of Plant UDP-Sugar Producing Pyrophosphorylases2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, article id 1610Article in journal (Refereed)
    Abstract [en]

    UDP-sugars are essential precursors for glycosylation reactions producing cell wall polysaccharides, sucrose, glycoproteins, glycolipids, etc. Primary mechanisms of UDP sugar formation involve the action of at least three distinct pyrophosphorylases using UTP and sugar-1-P as substrates. Here, substrate specificities of barley and Arabidopsis (two isozymes) UDP-glucose pyrophosphorylases (UGPase), Arabidopsis UDP-sugar pyrophosphorylase (USPase) and Arabidopsis UDP-N-acetyl glucosamine pyrophosphorylase2 (UAGPase2) were investigated using a range of sugar-1-phosphates and nucleoside-triphosphates as substrates. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Fru-1-P and Fru-2-P (Km values over 10 mM). Contrary to an earlier report, their activity with Gal-1-P was extremely low. USPase reacted with a range of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P (K-m of 1.3 mM), beta-L-Ara-1-P and alpha-D-Fuc-1-P (K-m of 3.4 mM), but not beta-L-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P (K-m of 1 mM) and, to some extent, D-Glc-1-P (Km of 3.2 mM). Generally, different conformations/substituents at C2, C4, and C5 of the pyranose ring of a sugar were crucial determinants of substrate specificity of a given pyrophosphorylase. Homology models of UDP-sugar binding to UGPase, USPase and UAGPase2 revealed more common amino acids for UDP binding than for sugar binding, reflecting differences in substrate specificity of these proteins. UAGPase2 was inhibited by a salicylate derivative that was earlier shown to affect UGPase and USPase activities, consistent with a common structural architecture of the three pyrophosphorylases. The results are discussed with respect to the role of the pyrophosphorylases in sugar activation for glycosylated end-products.

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  • 17.
    Decker, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kleczkowski, Leszek A.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    UDP-Sugar Producing Pyrophosphorylases: Distinct and Essential Enzymes With Overlapping Substrate Specificities, Providing de novo Precursors for Glycosylation Reactions2019In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 9, article id 1822Article, review/survey (Refereed)
    Abstract [en]

    Nucleotide sugars are the key precursors for all glycosylation reactions and are required both for oligo- and polysaccharides synthesis and protein and lipid glycosylation. Among all nucleotide sugars, UDP-sugars are the most important precursors for biomass production in nature (e.g., synthesis of cellulose, hemicellulose, and pectins for cell wall production). Several recent studies have already suggested a potential role for UDP-Glc in plant growth and development, and UDP-Glc has also been suggested as a signaling molecule, in addition to its precursor function. In this review, we will cover primary mechanisms of formation of UDP-sugars, by focusing on UDP-sugar metabolizing pyrophosphorylases. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase), and UDP-N-acetyl glucosamine pyrophosphorylase (UAGPase), which can be distinguished both by their amino acid sequences and by differences in substrate specificity. Substrate specificities of these enzymes are discussed, along with structure-function relationships, based on their crystal structures and homology modeling. Earlier studies with transgenic plants have revealed that each of the pyrophosphorylases is essential for plant survival, and their loss or a decrease in activity results in reproductive impairment. This constitutes a problem when studying exact in vivo roles of the enzymes using classical reverse genetics approaches. Thus, strategies involving the use of specific inhibitors (reverse chemical genetics) are also discussed. Further characterization of the properties/roles of pyrophosphorylases should address fundamental questions dealing with mechanisms and control of carbohydrate synthesis and may allow to identify targets for manipulation of biomass production in plants.

  • 18. Derba-Maceluch, Marta
    et al.
    Amini, Fariba
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Biology Department, Faculty of Science, Arak University, Arak, Iran.
    Donev, Evgeniy N.
    Pawar, Prashant Mohan-Anupama
    Michaud, Lisa
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Johansson, Ulf
    Albrectsen, Benedicte Riber
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Mellerowicz, Ewa J.
    Cell Wall Acetylation in Hybrid Aspen Affects Field Performance, Foliar Phenolic Composition and Resistance to Biological Stress Factors in a Construct-Dependent Fashion2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, article id 651Article in journal (Refereed)
    Abstract [en]

    The production of biofuels and "green" chemicals from the lignocellulose of fast-growing hardwood species is hampered by extensive acetylation of xylan. Different strategies have been implemented to reduce xylan acetylation, resulting in transgenic plants that show good growth in the greenhouse, improved saccharification and fermentation, but the field performance of such plants has not yet been reported. The aim of this study was to evaluate the impact of reduced acetylation on field productivity and identify the best strategies for decreasing acetylation. Growth and biological stress data were evaluated for 18 hybrid aspen lines with 10-20% reductions in the cell wall acetyl content from a five year field experiment in Southern Sweden. The reduction in acetyl content was achieved either by suppressing the process of acetylation in the Golgi by reducing expression of REDUCED WALL ACETYLATION (RWA) genes, or by post-synthetic acetyl removal by fungal acetyl xylan esterases (AXEs) from two different families, CE1 and CE5, targeting them to cell walls. Transgene expression was regulated by either a constitutive promoter (35S) or a wood-specific promoter (WP). For the majority of transgenic lines, growth was either similar to that in WT and transgenic control (WP:GUS) plants, or slightly reduced. The slight reduction was observed in the AXE-expressing lines regulated by the 35S promoter, not those with the WP promoter which limits expression to cells developing secondary walls. Expressing AXEs regulated by the 35S promoter resulted in increased foliar arthropod chewing, and altered condensed tannins and salicinoid phenolic glucosides (SPGs) profiles. Greater growth inhibition was observed in the case of CE5 than with CE1 AXE, and it was associated with increased foliar necrosis and distinct SPG profiles, suggesting that CE5 AXE could be recognized by the pathogen-associated molecular pattern system. For each of three different constructs, there was a line with dwarfism and growth abnormalities, suggesting random genetic/epigenetic changes. This high frequency of dwarfism (17%) is suggestive of a link between acetyl metabolism and chromatin function. These data represent the first evaluation of acetyl-reduced plants from the field, indicating some possible pitfalls, and identifying the best strategies, when developing highly productive acetyl-reduced feedstocks.

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  • 19.
    Derba-Maceluch, Marta
    et al.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Sivan, Pramod
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden; Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
    Donev, Evgeniy N.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Yassin, Zakiya
    Enhet Produktionssystem och Material, RISE Research Institutes of Sweden, Växjö, Sweden.
    Vaasan, Rakhesh
    Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
    Heinonen, Emilia
    Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden; Wallenberg Wood Science Centre (WWSC), KTH Royal Institute of Technology, Stockholm, Sweden.
    Andersson, Sanna
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Amini, Fariba
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Biology Department, Faculty of Science, Arak University, Arak, Iran.
    Scheepers, Gerhard
    Enhet Produktionssystem och Material, RISE Research Institutes of Sweden, Växjö, Sweden.
    Johansson, Ulf
    Tönnersjöheden Experimental Forest, Swedish University of Agricultural Sciences, Simlångsdalen, Sweden.
    Vilaplana, Francisco J.
    Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden; Wallenberg Wood Science Centre (WWSC), KTH Royal Institute of Technology, Stockholm, Sweden.
    Albrectsen, Benedicte Riber
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hertzberg, Magnus
    SweTree Technologies AB, Umeå, Sweden.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Impact of xylan on field productivity and wood saccharification properties in aspen2023In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 14, article id 1218302Article in journal (Refereed)
    Abstract [en]

    Xylan that comprises roughly 25% of hardwood biomass is undesirable in biorefinery applications involving saccharification and fermentation. Efforts to reduce xylan levels have therefore been made in many species, usually resulting in improved saccharification. However, such modified plants have not yet been tested under field conditions. Here we evaluate the field performance of transgenic hybrid aspen lines with reduced xylan levels and assess their usefulness as short-rotation feedstocks for biorefineries. Three types of transgenic lines were tested in four-year field tests with RNAi constructs targeting either Populus GT43 clades B and C (GT43BC) corresponding to Arabidopsis clades IRX9 and IRX14, respectively, involved in xylan backbone biosynthesis, GATL1.1 corresponding to AtGALT1 involved in xylan reducing end sequence biosynthesis, or ASPR1 encoding an atypical aspartate protease. Their productivity, wood quality traits, and saccharification efficiency were analyzed. The only lines differing significantly from the wild type with respect to growth and biotic stress resistance were the ASPR1 lines, whose stems were roughly 10% shorter and narrower and leaves showed increased arthropod damage. GT43BC lines exhibited no growth advantage in the field despite their superior growth in greenhouse experiments. Wood from the ASPR1 and GT43BC lines had slightly reduced density due to thinner cell walls and, in the case of ASPR1, larger cell diameters. The xylan was less extractable by alkali but more hydrolysable by acid, had increased glucuronosylation, and its content was reduced in all three types of transgenic lines. The hemicellulose size distribution in the GALT1.1 and ASPR1 lines was skewed towards higher molecular mass compared to the wild type. These results provide experimental evidence that GATL1.1 functions in xylan biosynthesis and suggest that ASPR1 may regulate this process. In saccharification without pretreatment, lines of all three constructs provided 8-11% higher average glucose yields than wild-type plants. In saccharification with acid pretreatment, the GT43BC construct provided a 10% yield increase on average. The best transgenic lines of each construct are thus predicted to modestly outperform the wild type in terms of glucose yields per hectare. The field evaluation of transgenic xylan-reduced aspen represents an important step towards more productive feedstocks for biorefineries.

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  • 20.
    Dobrenel, Thomas
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Versailles, France; Université Paris-Sud–Université Paris-Saclay, Orsay, France.
    Mancera-Martinez, Eder
    Forzani, Celine
    Azzopardi, Marianne
    Davanture, Marlene
    Moreau, Manon
    Schepetilnikov, Mikhail
    Chicher, Johana
    Langella, Olivier
    Zivy, Michel
    Robaglia, Christophe
    Ryabova, Lyubov A.
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Meyer, Christian
    The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S62016In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 1611Article in journal (Refereed)
    Abstract [en]

    Protein translation is an energy consuming process that has to be fine-tuned at both the cell and organism levels to match the availability of resources. The target of rapamycin kinase (TOR) is a key regulator of a large range of biological processes in response to environmental cues. In this study, we have investigated the effects of TOR inactivation on the expression and regulation of Arabidopsis ribosomal proteins at different levels of analysis, namely from transcriptomic to phosphoproteomic. TOR inactivation resulted in a coordinated down-regulation of the transcription and translation of nuclear-encoded mRNAs coding for plastidic ribosomal proteins, which could explain the chlorotic phenotype of the TOR silenced plants. We have identified in the 5' untranslated regions (UTRs) of this set of genes a conserved sequence related to the 5' terminal oligopyrimidine motif, which is known to confer translational regulation by the TOR kinase in other eukaryotes. Furthermore, the phosphoproteomic analysis of the ribosomal fraction following TOR inactivation revealed a lower phosphorylation of the conserved Ser240 residue in the C-terminal region of the 40S ribosomal protein S6 (RPS6). These results were confirmed by Western blot analysis using an antibody that specifically recognizes phosphorylated Ser240 in RPS6. Finally, this antibody was used to follow TOR activity in plants. Our results thus uncover a multi-level regulation of plant ribosomal genes and proteins by the TOR kinase.

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  • 21. Donev, Evgeniy
    et al.
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Engineering non-cellulosic polysaccharides of wood for the biorefinery2018In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 9, article id 1537Article, review/survey (Refereed)
    Abstract [en]

    Non-cellulosic polysaccharides constitute approximately one third of usable woody biomass for human exploitation. In contrast to cellulose, these substances are composed of several different types of unit monosaccharides and their backbones are substituted by various groups. Their structural diversity and recent examples of their modification in transgenic plants and mutants suggest they can be targeted for improving wood-processing properties, thereby facilitating conversion of wood in a biorefinery setting. Critical knowledge on their structure-function relationship is slowly emerging, although our understanding of molecular interactions responsible for observed phenomena is still incomplete. This review: (1) provides an overview of structural features of major non-cellulosic polysaccharides of wood, (2) describes the fate of non-cellulosic polysaccharides during biorefinery processing, (3) shows how the non-cellulosic polysaccharides impact lignocellulose processing focused on yields of either sugars or polymers, and (4) discusses outlooks for the improvement of tree species for biorefinery by modifying the structure of non-cellulosic polysaccharides.

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  • 22. Ferrando, Alejandro
    et al.
    Mar Castellano, M.
    Lison, Purificacion
    Leister, Dario
    Stepanova, Anna N.
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Editorial: Relevance of Translational Regulation on Plant Growth and Environmental Responses2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, article id 2170Article in journal (Other academic)
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  • 23.
    Gaur, Rajarshi Kumar
    et al.
    Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India.
    Yadav, Dinesh
    Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India.
    Albrectsen, Benedicte Riber
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Editorial: Omics driven research for the improvement of industrial crops2023In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 14, article id 1143571Article in journal (Other academic)
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  • 24. Hussain, Adil
    et al.
    Mun, Bong-Gyu
    Imran, Qari Muhammad
    Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Kore.
    Lee, Sang-Uk
    Adamu, Teferi A.
    Shahid, Muhammad
    Kim, Kyung-Min
    Yun, Byung-Wook
    Nitric oxide mediated transcriptome profiling reveals activation of multiple regulatory pathways in Arabidopsis thaliana2016In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7Article in journal (Refereed)
    Abstract [en]

    Imbalance between the accumulation and removal of nitric oxide and its derivatives is a challenge faced by all plants at the cellular level, and is especially important under stress conditions. Exposure of plants to various biotic and abiotic stresses causes rapid changes in cellular redox tone potentiated by the rise in reactive nitrogen species that serve as signaling molecules in mediating defensive responses. To understand mechanisms mediated by these signaling molecules, we performed a large-scale analysis of the Arabidopsis transcriptome induced by nitrosative stress. We generated an average of 84 and 91 million reads from three replicates each of control and 1 mM S-nitrosocysteine (CysNO)-infiltrated Arabidopsis leaf samples, respectively. After alignment, more than 95% of all reads successfully mapped to the reference and 32,535 genes and 55,682 transcripts were obtained. CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. After quantile normalization of the FPKM values followed by student's T-test (P < 0.05) we identified 1165 DEGs (463 up-regulated and 702 down-regulated) with at least 2-folds change in expression after CysNO treatment. Expression patterns of selected genes involved in various biological pathways were verified using quantitative real-time PCR. This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.

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  • 25. Igamberdiev, Abir U.
    et al.
    Kleczkowski, Leszek A.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Optimization of ATP synthase function in mitochondria and chloroplasts via the adenylate kinase equilibrium2015In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 6, p. 10-Article in journal (Refereed)
    Abstract [en]

    The bulk of ATP synthesis in plants is performed by ATP synthase, the main bioenergetics engine of cells, operating both in mitochondria and in chloroplasts. The reaction mechanism of ATP synthase has been studied in detail for over half a century; however, its optimal performance depends also on the steady delivery of ATP synthase substrates and the removal of its products. For mitochondrial ATP synthase, we analyze here the provision of stable conditions for (i) the supply of ADP and Mg2+, supported by adenylate kinase (AK) equilibrium in the intermembrane space, (ii) the supply of phosphate via membrane transporter in symport with H+ and (iii) the conditions of outflow of ATP by adenylate transporter carrying out the exchange of free adenylates. We also show that, in chloroplasts, AK equilibrates adenylates and governs Mg2+ contents in the stroma, optimizing ATP synthase and Calvin cycle operation, and affecting the import of inorganic phosphate in exchange with triose phosphates. It is argued that chemiosmosis is not the sole component of ATP synthase performance, which also depends on AK-mediated equilibrium of adenylates and Mg2+, adenylate transport, and phosphate release and supply.

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  • 26. Igamberdiev, Abir U.
    et al.
    Kleczkowski, Leszek A.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism2018In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 9, article id 318Article, review/survey (Refereed)
    Abstract [en]

    Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate serine pathway) is initiated in the cytosol and involves glycerate formation from 3phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

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  • 27.
    Imran, Qari Muhammad
    et al.
    Laboratory of Plant Functional Genomics, School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Falak, Noreen
    Hussain, Adil
    Mun, Bong-Gyu
    Sharma, Arti
    Lee, Sang-Uk
    Kim, Kyung-Min
    Yun, Byung-Wook
    Nitric oxide responsive heavy metal-associated gene AtHMAD1 contributes to development and disease resistance in Arabidopsis thaliana2016In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 712Article in journal (Refereed)
    Abstract [en]

    Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis. Of those 14 genes, the expression of eight HMA genes was significantly increased, whereas that of six genes was significantly reduced. We further validated the RNA-seq results through quantitative real-time PCR analysis. Gene ontology analysis revealed the involvement of these genes in biological processes such as hemostasis and transport. The majority of these nitric oxide (NO)-responsive AtHMA gene products are carrier/transport proteins. AtHMAD1 (At1g51090) showed the highest fold change to S-nitrosocystein. We therefore, further investigated its role in oxidative and nitrosative mediated stress conditions and found that AtHMAD1 has antagonistic role in shoot and root growth. Characterization of AtHMAD1 through functional genomics showed that the knock out mutant athmad1 plants were resistant to virulent Pseudomonas syringae (DC3000) and showed early induction and high transcript accumulation of pathogenesis related gene. Furthermore, inoculation of athamd1 with avirulent strain of the same bacteria showed negative regulation of R-gene mediated resistance. These results were supported by hypersensitive cell death response and cell death induced electrolyte leakage. AtHMAD1 was also observed to negatively regulate systemic acquired resistance SAR as the KO mutant showed induction of SAR marker genes. Overall, these results imply that NO-responsive AtHMA domain containing genes may play an important role in plant development and immunity.

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  • 28.
    Jurca, Manuela
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sjölander, Johan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ibáñez, Cristian
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Departamento de Biología, Universidad de La Serena, La Serena, Chile.
    Matrosova, Anastasia
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Johansson, Mikael
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Bielefeld, Germany.
    Kozarewa, Iwanka
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Takata, Naoki
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Japan.
    Bakó, Laszlo
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Webb, Alex A. R.
    Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
    Israelsson-Nordström, Maria
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Eriksson, Maria E.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
    ZEITLUPE Promotes ABA-Induced Stomatal Closure in Arabidopsis and Populus2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 829121Article in journal (Refereed)
    Abstract [en]

    Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins—which are expressed from dawn to dusk—interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.

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  • 29.
    Klemenčič, Marina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
    Asplund-Samuelsson, Johannes
    Dolinar, Marko
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Phylogenetic Distribution and Diversity of Bacterial Pseudo-Orthocaspases Underline Their Putative Role in Photosynthesis2019In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 10, article id 293Article in journal (Refereed)
    Abstract [en]

    Orthocaspases are prokaryotic caspase homologs – proteases, which cleave their substrates after positively charged residues using a conserved histidine – cysteine (HC) dyad situated in a catalytic p20 domain. However, in orthocaspases pseudo-variants have been identified, which instead of the catalytic HC residues contain tyrosine and serine, respectively. The presence and distribution of these presumably proteolytically inactive p20-containing enzymes has until now escaped attention. We have performed a detailed analysis of orthocaspases in all available prokaryotic genomes, focusing on pseudo-orthocaspases. Surprisingly we identified type I metacaspase homologs in filamentous cyanobacteria. While genes encoding pseudo-orthocaspases seem to be absent in Archaea, our results show conservation of these genes in organisms performing either anoxygenic photosynthesis (orders Rhizobiales, Rhodobacterales, and Rhodospirillales in Alphaproteobacteria) or oxygenic photosynthesis (all sequenced cyanobacteria, except Gloeobacter, Prochlorococcus, and Cyanobium). Contrary to earlier reports, we were able to detect pseudo-orthocaspases in all sequenced strains of the unicellular cyanobacteria Synechococcus and Synechocystis. In silico comparisons of the primary as well as tertiary structures of pseudo-p20 domains with their presumably proteolytically active homologs suggest that differences in their amino acid sequences have no influence on the overall structures. Mutations therefore affect most likely only the proteolytic activity. Our data provide an insight into diversification of pseudo-orthocaspases in Prokaryotes, their taxa-specific distribution, and allow suggestions on their taxa-specific function.

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  • 30.
    Kremnev, Dmitry
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Plastid encoded RNA polymerase activity and expression of photosynthesis genes required for embryo and seed development in Arabidopsis2014In: Frontiers in Plant Science, E-ISSN 1664-462XArticle in journal (Refereed)
    Abstract [en]

    Chloroplast biogenesis and function is essential for proper plant embryo and seed development but the molecular mechanisms underlying the role of plastids during embryogenesis are poorly understood. Expression of plastid encoded genes is dependent on two different transcription machineries; a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. However, the division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear. We show here that PLASTID REDOX INSENSITIVE 2 (PRIN2) and CHLOROPLAST STEM-LOOP BINDING PROTEIN 41 kDa (CSP41b), two proteins identified in plastid nucleoid preparations, are essential for proper plant embryo development. Using Co-IP assays and native PAGE we have shown a direct physical interaction between PRIN2 and CSP41b. Moreover, PRIN2 and CSP41b form a distinct protein complex in vitro that binds DNA. The prin2.2 and csp41b-2 single mutants displayed pale phenotypes, abnormal chloroplasts with reduced transcript levels of photosynthesis genes and defects in embryo development. The respective csp41b-2prin2.2 homo/heterozygote double mutants produced abnormal white colored ovules and shrunken seeds. Thus, the csp41b-2prin2.2 double mutant is embryo lethal. In silico analysis of available array data showed that a large number of genes traditionally classified as PEP dependent genes are transcribed during early embryo development from the pre-globular stage to the mature-green-stage. Taken together, our results suggest that PEP activity and consequently the switch from NEP to PEP activity, is essential during embryo development and that the PRIN2-CSP41b DNA binding protein complex possibly is important for full PEP activity during this process.

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  • 31. Krupinski, Pawel
    et al.
    Bozorg, Behruz
    Larsson, André
    Pietra, Stefano
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Grebe, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Institute of Biochemistry and Biology, Plant Physiology, University of Potsdam, Potsdam, Germany.
    Jönsson, Henrik
    A Model Analysis of Mechanisms for Radial Microtubular Patterns at Root Hair Initiation Sites2016In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 1560Article in journal (Refereed)
    Abstract [en]

    Plant cells have two main modes of growth generating anisotropic structures. Diffuse growth where whole cell walls extend in specific directions, guided by anisotropically positioned cellulose fibers, and tip growth, with inhomogeneous addition of new cell wall material at the tip of the structure. Cells are known to regulate these processes via molecular signals and the cytoskeleton. Mechanical stress has been proposed to provide an input to the positioning of the cellulose fibers via cortical microtubules in diffuse growth. In particular, a stress feedback model predicts a circumferential pattern of fibers surrounding apical tissues and growing primordia, guided by the anisotropic curvature in such tissues. In contrast, during the initiation of tip growing root hairs, a star-like radial pattern has recently been observed. Here, we use detailed finite element models to analyze how a change in mechanical properties at the root hair initiation site can lead to star-like stress patterns in order to understand whether a stress-based feedback model can also explain the microtubule patterns seen during root hair initiation. We show that two independent mechanisms, individually or combined, can be sufficient to generate radial patterns. In the first, new material is added locally at the position of the root hair. In the second, increased tension in the initiation area provides a mechanism. Finally, we describe how a molecular model of Rho-of-plant (ROP) GTPases activation driven by auxin can position a patch of activated ROP protein basally along a 2D root epidermal cell plasma membrane, paving the way for models where mechanical and molecular mechanisms cooperate in the initial placement and outgrowth of root hairs.

  • 32. Kumar, Vikash
    et al.
    Donev, Evgeniy N.
    Barbut, Felix R.
    Kushwah, Sunita
    Mannapperuma, Chanaka
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Urbancsok, Janos
    Mellerowicz, Ewa J.
    Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, p. 1-20, article id 588846Article in journal (Refereed)
    Abstract [en]

    Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.

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  • 33.
    Kunz, Sabine
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Kleczkowski, Leszek
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Hexokinase 1 is required for glucose-induced repression of bZIP63, At5g22920, and BT2 in Arabidopsis2015In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 6, article id 525Article in journal (Refereed)
    Abstract [en]

    Simple sugars, like glucose (Glc) and sucrose (Suc), act as signals to modulate the expression of hundreds of genes in plants. Frequently, however, it remains unclear whether this regulation is induced by the sugars themselves or by their derivatives generated in the course of carbohydrate (CH) metabolism. In the present study, we tested the relevance of different CH metabolism and allocation pathways affecting expression patterns of five selected sugar-responsive genes (bZIP63, At5g22920, BT2, MGD2, and TPS9) in Arabidopsis thaliana. In general, the expression followed diurnal changes in the overall sugar availability. However, under steady growth conditions, this response was hardly impaired in the mutants for CH metabolizing/transporting proteins (adg1, sex1, sus1-4, sus5/6, and tpt2), including also hexokinase1 (HXK1) loss- and gain-of-function plants—gin2.1 and oe3.2, respectively. In addition, transgenic plants carrying pbZIP63::GUS showed no changes in reporter-gene-expression when grown on sugar under steady-state conditions. In contrast, short-term treatments of agar-grown seedlings with 1% Glc or Suc induced pbZIP63::GUS repression, which became even more apparent in seedlings grown in liquid media. Subsequent analyses of liquid-grown gin2.1 and oe3.2 seedlings revealed that Glc -dependent regulation of the five selected genes was not affected in gin2.1, whereas it was enhanced in oe3.2 plants for bZIP63, At5g22920, and BT2. The sugar treatments had no effect on ATP/ADP ratio, suggesting that changes in gene expression were not linked to cellular energy status. Overall, the data suggest that HXK1 does not act as Glc sensor controlling bZIP63, At5g22920, and BT2 expression, but it is nevertheless required for the production of a downstream metabolic signal regulating their expression.

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  • 34. Kusano, Miyako
    et al.
    Jonsson, Pär
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Fukushima, Atsushi
    Gullberg, Jonas
    Sjöström, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Moritz, Thomas
    Metabolite signature during short-day induced growth cessation in populus2011In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 2, article id 29Article in journal (Refereed)
    Abstract [en]

    The photoperiod is an important environmental signal for plants, and influences a wide range of physiological processes. For woody species in northern latitudes, cessation of growth is induced by short photoperiods. In many plant species, short photoperiods stop elongational growth after a few weeks. It is known that plant daylength detection is mediated by Phytochrome A (PHYA) in the woody hybrid aspen species. However, the mechanism of dormancy involving primary metabolism remains unclear. We studied changes in metabolite profiles in hybrid aspen leaves (young, middle, and mature leaves) during short-day-induced growth cessation, using a combination of gas chromatography–time-of-flight mass spectrometry, and multivariate projection methods. Our results indicate that the metabolite profiles in mature source leaves rapidly change when the photoperiod changes. In contrast, the differences in young sink leaves grown under long and short-day conditions are less distinct. We found short daylength induced growth cessation in aspen was associated with rapid changes in the distribution and levels of diverse primary metabolites. In addition, we conducted metabolite profiling of leaves of PHYA overexpressor (PHYAOX) and those of the control to find the discriminative metabolites between PHYAOX and the control under the short-day conditions. The metabolite changes observed in PHYAOX leaves, together with those in the source leaves, identified possible candidates for the metabolite signature (e.g., 2-oxo-glutarate, spermidine, putrescine, 4-amino-butyrate, and tryptophan) during short-day-induced growth cessation in aspen leaves.

  • 35.
    Law, Simon R
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Kellgren, Therese
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Björk, Rafael
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Rydén, Patrik
    Umeå University, Faculty of Science and Technology, Department of Mathematics and Mathematical Statistics.
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Centralization Within Sub-Experiments Enhances the Biological Relevance of Gene Co-expression Networks: A Plant Mitochondrial Case Study2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, article id 524Article in journal (Refereed)
    Abstract [en]

    Gene co-expression networks (GCNs) can be prepared using a variety of mathematical approaches based on data sampled across diverse developmental processes, tissue types, pathologies, mutant backgrounds, and stress conditions. These networks are used to identify genes with similar expression dynamics but are prone to introducing false-positive and false-negative relationships, especially in the instance of large and heterogenous datasets. With the aim of optimizing the relevance of edges in GCNs and enhancing global biological insight, we propose a novel approach that involves a data-centering step performed simultaneously per gene and per sub-experiment, called centralization within sub-experiments (CSE). Using a gene set encoding the plant mitochondrial proteome as a case study, our results show that all CSE-based GCNs assessed had significantly more edges within the majority of the considered functional sub-networks, such as the mitochondrial electron transport chain and its complexes, than GCNs not using CSE; thus demonstrating that CSE-based GCNs are efficient at predicting canonical functions and associated pathways, here referred to as the core gene network. Furthermore, we show that correlation analyses using CSE-processed data can be used to fine-tune prediction of the function of uncharacterized genes; while its use in combination with analyses based on non-CSE data can augment conventional stress analyses with the innate connections underpinning the dynamic system being examined. Therefore, CSE is an effective alternative method to conventional batch correction approaches, particularly when dealing with large and heterogenous datasets. The method is easy to implement into a pre-existing GCN analysis pipeline and can provide enhanced biological relevance to conventional GCNs by allowing users to delineate a core gene network. Author Summary Gene co-expression networks (GCNs) are the product of a variety of mathematical approaches that identify causal relationships in gene expression dynamics but are prone to the misdiagnoses of false-positives and false-negatives, especially in the instance of large and heterogenous datasets. In light of the burgeoning output of next-generation sequencing projects performed on a variety of species, and developmental or clinical conditions; the statistical power and complexity of these networks will undoubtedly increase, while their biological relevance will be fiercely challenged. Here, we propose a novel approach to generate a "core" GCN with enhanced biological relevance. Our method involves a data-centering step that effectively removes all primary treatment/tissue effects, which is simple to employ and can be easily implemented into pre-existing GCN analysis pipelines. The gain in biological relevance resulting from the adoption of this approach was assessed using a plant mitochondrial case study.

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  • 36.
    Le Hir, Rozenn
    et al.
    UMR1318 Institut Jean-Pierre Bourgin, INRA-AgroParisTech, INRA Centre de Versailles, Versailles, France.
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). UMR1318 Institut Jean-Pierre Bourgin, INRA-AgroParisTech, INRA Centre de Versailles, Versailles, France.
    The plant-specific Dof transcription factors family: new players involved in vascular system development and functioning in Arabidopsis2013In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 4, p. Article Number: 164-Article, review/survey (Refereed)
    Abstract [en]

    In higher plants phloem and xylem are responsible for long-distance transport of water, nutrients, and signals that act systemically at short or long-distance to coordinate developmental processes. The formation of the plant vascular system is a complex process that integrates signaling events and gene regulation at transcriptional and posttranscriptional levels. Thanks to transcriptomic and proteomic analysis we start to better understand the mechanisms underlying the formation and the functioning of the vascular system. The role of the DNA-binding with one finger (Dof TFs), a group of plant-specific transcription factors, recently emerged as part of the transcriptional regulatory networks acting on the formation and functioning of the vascular tissues. More than half of the members of this TF family are expressed in the vascular system. In addition some of them have been proposed to be mobile proteins, suggesting a possible role in the control of short- or long-distance signaling as well. This review summarizes the current knowledge on Dof TFs family in Arabidopsis with a special focus on their role in vascular development and functioning.

  • 37.
    Liu, Hui
    et al.
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Yan, Xue-Mei
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Wang, Xin-Rui
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Zhang, Dong-Xu
    Protected Agricultural Technology, R&D Center, Shanxi Datong University, Datong, China.
    Zhou, Qingyuan
    Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
    Shi, Tian-Le
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Jia, Kai-Hua
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Tian, Xue-Chan
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Zhou, Shan-Shan
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Zhang, Ren-Gang
    Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, China.
    Yun, Quan-Zheng
    Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, China.
    Wang, Qing
    Key Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China.
    Xiang, Qiuhong
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Mannapperuma, Chanaka
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Van Zalen, Elena
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Street, Nathaniel R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Porth, Ilga
    Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval Québec, Quebec City, QC, Canada.
    El-Kassaby, Yousry A.
    Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, BC, Vancouver, Canada.
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Guan, Wenbin
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Mao, Jian-Feng
    National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance2021In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 12, article id 766389Article in journal (Refereed)
    Abstract [en]

    In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

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  • 38. Lozanovska, Ivana
    et al.
    Bejarano, Maria Dolores
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Martins, Maria Joao
    Nilsson, Christer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Ferreira, Maria Teresa
    Aguiar, Francisca C.
    Functional Diversity of Riparian Woody Vegetation Is Less Affected by River Regulation in the Mediterranean Than Boreal Region2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, article id 857Article in journal (Refereed)
    Abstract [en]

    River regulation may filter out riparian plants often resulting in reduced functional diversity, i.e., in the range of functions that organisms have in communities and ecosystems. There is, however, little empirical evidence about the magnitude of such reductions in different regions. We investigated the functional diversity patterns of riparian woody vegetation to streamflow regulation in boreal Sweden and Mediterranean Portugal using nine plant functional traits and field data from 109 sampling sites. We evaluated changes in mean plant functional traits as well as in indices of multidimensional functional traits, i.e., functional richness (FRic) and functional redundancy (FRed) within regions and between free-flowing and regulated river reaches. We found that regulation significantly reduced functional diversity in Sweden but not in Portugal. In Sweden, the increased magnitude of variations in water flow and water level in summer, the prolonged duration of extreme hydrological events, the increased frequency of high-water pulses, and the rate of change in water conditions were the likely main drivers of functional diversity change. Small riparian plant species with tiny leaves, poorly lignified stems, and shallow root systems were consistently associated with regulated sites in the boreal region. In Portugal, the similar functional diversity values for free-flowing and regulated rivers likely stem from the smaller streamflow alterations by regulation combined with the species legacy adaptations to the Mediterranean natural hydrological regimes. We conclude that streamflow regulation may reduce the functional diversity of riparian woody vegetation, but the magnitude of these effects will vary depending on the adaptations of the local flora and the patterns of streamflow disturbances. Our study provides insights into functional diversity patterns of riparian woody vegetation affected by regulation in contrasting biomes and encourages further studies of the functional diversity thresholds for maintaining ecosystems.

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  • 39.
    López-López, Alicia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). INRAE, IAM, Université de Lorraine, Nancy, France.
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Rouhier, Nicolas
    INRAE, IAM, Université de Lorraine, Nancy, France.
    Maturation and Assembly of Iron-Sulfur Cluster-Containing Subunits in the Mitochondrial Complex I From Plants2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 916948Article, review/survey (Refereed)
    Abstract [en]

    In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.

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  • 40.
    Milhinhos, Ana
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bollhöner, Benjamin
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Blazquez, Miguel A.
    Novak, Ondrej
    Miguel, Celia M.
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    ACAULIS5 Is Required for Cytokinin Accumulation and Function During Secondary Growth of Populus Trees2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, article id 601858Article in journal (Refereed)
    Abstract [en]

    In the primary root and young hypocotyl of Arabidopsis, ACAULIS5 promotes translation of SUPPRESSOR OF ACAULIS51 (SAC51) and thereby inhibits cytokinin biosynthesis and vascular cell division. In this study, the relationships between ACAULIS5, SAC51 and cytokinin biosynthesis were investigated during secondary growth of Populus stems. Overexpression of ACAULIS5 from the constitutive 35S promoter in hybrid aspen (Populus tremula x Populus tremuloides) trees suppressed the expression level of ACAULIS5, which resulted in low levels of the physiologically active cytokinin bases as well as their direct riboside precursors in the transgenic lines. Low ACAULIS5 expression and low cytokinin levels of the transgenic trees coincided with low cambial activity of the stem. ACAULIS5 therefore, contrary to its function in young seedlings in Arabidopsis, stimulates cytokinin accumulation and cambial activity during secondary growth of the stem. This function is not derived from maturing secondary xylem tissues as transgenic suppression of ACAULIS5 levels in these tissues did not influence secondary growth. Interestingly, evidence was obtained for increased activity of the anticlinal division of the cambial initials under conditions of low ACAULIS5 expression and low cytokinin accumulation. We propose that ACAULIS5 integrates auxin and cytokinin signaling to promote extensive secondary growth of tree stems.

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  • 41.
    Mishra, Laxmi S.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mishra, Sanatkumar
    Caddell, Daniel F.
    Coleman-Derr, Devin
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The Plastid-Localized AtFtsHi3 Pseudo-Protease of Arabidopsis thaliana Has an Impact on Plant Growth and Drought Tolerance2021In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 12, article id 694727Article in journal (Refereed)
    Abstract [en]

    While drought severely affects plant growth and crop production, the molecular mechanisms of the drought response of plants remain unclear. In this study, we demonstrated for the first time the effect of the pseudo-protease AtFtsHi3 of Arabidopsis thaliana on overall plant growth and in drought tolerance. An AtFTSHi3 knock-down mutant [ftshi3-1(kd)] displayed a pale-green phenotype with lower photosynthetic efficiency and Darwinian fitness compared to wild type (Wt). An observed delay in seed germination of ftshi3-1(kd) was attributed to overaccumulation of abscisic acid (ABA); ftshi3-1(kd) seedlings showed partial sensitivity to exogenous ABA. Being exposed to similar severity of soil drying, ftshi3-1(kd) was drought-tolerant up to 20 days after the last irrigation, while wild type plants wilted after 12 days. Leaves of ftshi3-1(kd) contained reduced stomata size, density, and a smaller stomatic aperture. During drought stress, ftshi3-1(kd) showed lowered stomatal conductance, increased intrinsic water-use efficiency (WUEi), and slower stress acclimation. Expression levels of ABA-responsive genes were higher in leaves of ftshi3-1(kd) than Wt; DREB1A, but not DREB2A, was significantly upregulated during drought. However, although ftshi3-1(kd) displayed a drought-tolerant phenotype in aboveground tissue, the root-associated bacterial community responded to drought.

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  • 42. Muola, Anne
    et al.
    Weber, Daniela
    Malm, Lisa E.
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Egan, Paul A.
    Glinwood, Robert
    Parachnowitsch, Amy L.
    Stenberg, Johan A.
    Direct and Pollinator-Mediated Effects of Herbivory on Strawberry and the Potential for Improved Resistance2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, article id 823Article in journal (Refereed)
    Abstract [en]

    The global decline in pollinators has partly been blamed on pesticides, leading some to propose pesticide-free farming as an option to improve pollination. However, herbivores are likely to be more prevalent in pesticide-free environments, requiring knowledge of their effects on pollinators, and alternative crop protection strategies to mitigate any potential pollination reduction. Strawberry leaf beetles (SLB) Galerucella spp. are important strawberry pests in Northern Europe and Russia. Given that SLB attack both leaf and flower tissue, we hypothesized pollinators would discriminate against SLB-damaged strawberry plants (Fragaria vesca, cultivar 'Rugen'), leading to lower pollination success and yield. In addition we screened the most common commercial cultivar 'Rugen' and wild Swedish F. vesca genotypes for SLB resistance to assess the potential for inverse breeding to restore high SLB resistance in cultivated strawberry. Behavioral observations in a controlled experiment revealed that the local pollinator fauna avoided strawberry flowers with SLB-damaged petals. Low pollination, in turn, resulted in smaller more deformed fruits. Furthermore, SLB-damaged flowers produced smaller fruits even when they were hand pollinated, showing herbivore damage also had direct effects on yield, independent of indirect effects on pollination. We found variable resistance in wild woodland strawberry to SLB and more resistant plant genotypes than the cultivar 'Rugen' were identified. Efficient integrated pest management strategies should be employed to mitigate both direct and indirect effects of herbivory for cultivated strawberry, including high intrinsic plant resistance.

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  • 43. Myburg, Alexander A.
    et al.
    Hussey, Steven G.
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Street, Nathaniel R.
    Mizrachi, Eshchar
    Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks2019In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 10, article id 775Article, review/survey (Refereed)
    Abstract [en]

    Fast-growing forest plantations are sustainable feedstocks of plant biomass that can serve as alternatives to fossil carbon resources for materials, chemicals, and energy. Their ability to efficiently harvest light energy and carbon from the atmosphere and sequester this into metabolic precursors for lignocellulosic biopolymers and a wide range of plant specialized metabolites make them excellent biochemical production platforms and living biorefineries. Their large sizes have facilitated multi-omics analyses and systems modeling of key biological processes such as lignin biosynthesis in trees. High-throughput 'omics' approaches have also been applied in segregating tree populations where genetic variation creates abundant genetic perturbations of system components allowing construction of systems genetics models linking genes and pathways to complex trait variation. With this information in hand, it is now possible to start using synthetic biology and genome editing techniques in a bioengineering approach based on a deeper understanding and rational design of biological parts, devices, and integrated systems. However, the complexity of the biology and interacting components will require investment in big data informatics, machine learning, and intuitive visualization to fully explore multi-dimensional patterns and identify emergent properties of biological systems. Predictive systems models could be tested rapidly through high-throughput synthetic biology approaches and multigene editing. Such a bioengineering paradigm, together with accelerated genomic breeding, will be crucial for the development of a new generation of woody biorefinery crops.

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  • 44. Nabi, Rizwana Begum Syed
    et al.
    Tayade, Rupesh
    Imran, Qari Muhammad
    Hussain, Adil
    Shahid, Muhammad
    Yun, Byung-Wook
    Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11Article in journal (Refereed)
  • 45.
    Nickolov, Kaloian
    et al.
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland; Department of Ecology and Genetics, University of Oulu, Oulu, Finland.
    Gauthier, Adrien
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland; UniLaSalle, Agro-Ecology, Hydrogeochemistry, Environments & Resources, UP 2018.C101 of the Ministry in Charge of Agriculture (AGHYLE) Research Unit CS UP 2018.C101, Mont-Saint-Aignan, France.
    Hashimoto, Kenji
    Department of Applied Biological Science, Tokyo University of Science, Noda, Japan.
    Laitinen, Teresa
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    Väisänen, Enni
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    Paasela, Tanja
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland; Natural Resources Institute Finland (Luke), Production Systems, Helsinki, Finland.
    Soliymani, Rabah
    Meilahti Clinical Proteomics Core Facility, Biochemistry & Dev. Biology, University of Helsinki, Biomedicum-Helsinki, Helsinki, Finland.
    Kurusu, Takamitsu
    Department of Applied Biological Science, Tokyo University of Science, Noda, Japan; Department of Mechanical and Electrical Engineering, Suwa University of Science, Chino, Japan.
    Himanen, Kristiina
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    Blokhina, Olga
    Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    Fagerstedt, Kurt V.
    Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    Jokipii-Lukkari, Soile
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Ecology and Genetics, University of Oulu, Oulu, Finland.
    Tuominen, Hannele
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Häggman, Hely
    Department of Ecology and Genetics, University of Oulu, Oulu, Finland.
    Wingsle, Gunnar
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Teeri, Teemu H.
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    Kuchitsu, Kazuyuki
    Department of Applied Biological Science, Tokyo University of Science, Noda, Japan.
    Kärkönen, Anna
    Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland; Natural Resources Institute Finland (Luke), Production Systems, Helsinki, Finland.
    Regulation of PaRBOH1-mediated ROS production in Norway spruce by Ca2+ binding and phosphorylation2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 978586Article in journal (Refereed)
    Abstract [en]

    Plant respiratory burst oxidase homologs (RBOHs) are plasma membrane-localized NADPH oxidases that generate superoxide anion radicals, which then dismutate to H2O2, into the apoplast using cytoplasmic NADPH as an electron donor. PaRBOH1 is the most highly expressed RBOH gene in developing xylem as well as in a lignin-forming cell culture of Norway spruce (Picea abies L. Karst.). Since no previous information about regulation of gymnosperm RBOHs exist, our aim was to resolve how PaRBOH1 is regulated with a focus on phosphorylation. The N-terminal part of PaRBOH1 was found to contain several putative phosphorylation sites and a four-times repeated motif with similarities to the Botrytis-induced kinase 1 target site in Arabidopsis AtRBOHD. Phosphorylation was indicated for six of the sites in in vitro kinase assays using 15 amino-acid-long peptides for each of the predicted phosphotarget site in the presence of protein extracts of developing xylem. Serine and threonine residues showing positive response in the peptide assays were individually mutated to alanine (kinase-inactive) or to aspartate (phosphomimic), and the wild type PaRBOH1 and the mutated constructs transfected to human kidney embryogenic (HEK293T) cells with a low endogenous level of extracellular ROS production. ROS-producing assays with HEK cells showed that Ca2+ and phosphorylation synergistically activate the enzyme and identified several serine and threonine residues that are likely to be phosphorylated including a novel phosphorylation site not characterized in other plant species. These were further investigated with a phosphoproteomic study. Results of Norway spruce, the first gymnosperm species studied in relation to RBOH regulation, show that regulation of RBOH activity is conserved among seed plants.

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  • 46.
    Nie, Shuai
    et al.
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Tian, Xue-Chan
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Kong, Lei
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Zhao, Shi-Wei
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Chen, Zhao-Yang
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Jiao, Si-Qian
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China; Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, China.
    El-Kassaby, Yousry A.
    Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, BC, Vancouver, Canada.
    Porth, Ilga
    Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie de Géographie et Géomatique, Université Laval, QC, Québec, Canada.
    Yang, Fu-Sheng
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China; China National Botanical Garden, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
    Zhao, Wei
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Mao, Jian-Feng
    Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
    Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 1006904Article in journal (Refereed)
    Abstract [en]

    Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.

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  • 47.
    Nogueira, Fabio T. S.
    et al.
    Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo (USP), São Paulo, Piracicaba, Brazil.
    Goretti, Daniela
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Valverde, Federico
    Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Seville, Spain.
    Editorial: CONSTANS – signal integration and development throughout the plant kingdom2024In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 15, article id 1375876Article in journal (Other academic)
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  • 48.
    Ortiz-García, Paloma
    et al.
    Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA /CSIC), Madrid, Spain.
    Pérez-Alonso, Marta-Marina
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA /CSIC), Madrid, Spain.
    González Ortega-Villaizán, Adrián
    Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA /CSIC), Madrid, Spain.
    Sánchez-Parra, Beatriz
    Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA /CSIC), Madrid, Spain; Institute of Biology, University of Graz, Graz, Austria.
    Ludwig-Müller, Jutta
    Institute of Botany, Technische Universität Dresden, Dresden, Germany.
    Wilkinson, Mark D.
    Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA /CSIC), Madrid, Spain.
    Pollmann, Stephan
    Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA /CSIC), Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
    The Indole-3-Acetamide-Induced Arabidopsis Transcription Factor MYB74 Decreases Plant Growth and Contributes to the Control of Osmotic Stress Responses2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 928386Article in journal (Refereed)
    Abstract [en]

    The accumulation of the auxin precursor indole-3-acetamide (IAM) in the ami1 mutant has recently been reported to reduce plant growth and to trigger abiotic stress responses in Arabidopsis thaliana. The observed response includes the induction of abscisic acid (ABA) biosynthesis through the promotion of NCED3 expression. The mechanism by which plant growth is limited, however, remained largely unclear. Here, we investigated the transcriptional responses evoked by the exogenous application of IAM using comprehensive RNA-sequencing (RNA-seq) and reverse genetics approaches. The RNA-seq results highlighted the induction of a small number of genes, including the R2R3 MYB transcription factor genes MYB74 and MYB102. The two MYB factors are known to respond to various stress cues and to ABA. Consistent with a role as negative plant growth regulator, conditional MYB74 overexpressor lines showed a considerable growth reduction. RNA-seq analysis of MYB74 mutants indicated an association of MYB74 with responses to osmotic stress, water deprivation, and seed development, which further linked MYB74 with the observed ami1 osmotic stress and seed phenotype. Collectively, our findings point toward a role for MYB74 in plant growth control and in responses to abiotic stress stimuli.

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  • 49. Plöchinger, Magdalena
    et al.
    Schwenkert, Serena
    von Sydow, Lotta
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Meurer, Jörg
    Functional Update of the Auxiliary Proteins PsbW, PsbY, HCF136, PsbN, TerC and ALB3 in Maintenance and Assembly of PSII2016In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 423Article in journal (Refereed)
    Abstract [en]

    Assembly of Photosystem (PS) II in plants has turned out to be a highly complex process which, at least in part, occurs in a sequential order and requires many more auxiliary proteins than subunits present in the complex. Owing to the high evolutionary conservation of the subunit composition and the three-dimensional structure of the PSII complex, most plant factors involved in the biogenesis of PSII originated from cyanobacteria and only rarely evolved de novo. Furthermore, in chloroplasts the initial assembly steps occur in the non-appressed stroma lamellae, whereas the final assembly including the attachment of the major LHCII antenna proteins takes place in the grana regions. The stroma lamellae are also the place where part of PSII repair occurs, which very likely also involves assembly factors. In cyanobacteria initial PSII assembly also occurs in the thylakoid membrane, in so-called thylakoid centers, which are in contact with the plasma membrane. Here, we provide an update on the structures, localisations, topologies, functions, expression and interactions of the low molecular mass PSII subunits PsbY, PsbW and the auxiliary factors HCF136, PsbN, TerC and ALB3, assisting in PSII complex assembly and protein insertion into the thylakoid membrane.

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  • 50. Ponnu, Jathish
    et al.
    Wahl, Vanessa
    Schmid, Markus
    Max Planck Institute for Developmental Biology, Department of Molecular Biology, Tuebingen, Germany.
    Trehalose-6-phosphate: connecting plant metabolism and development2011In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 2Article in journal (Refereed)
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