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  • 1.
    Ahad, Abdul
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Nick, Peter
    Actin is bundled in activation-tagged tobacco mutants that tolerate aluminum2007Ingår i: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 225, nr 2, s. 451-468Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A panel of aluminum-tolerant (AlRes) mutants was isolated by protoplast-based T-DNA activation tagging in the tobacco cultivar SR1. The mutants fell into two phenotypic classes: a minority of the mutants were fertile and developed similarly to the wild type (type I), the majority was male-sterile and grew as semi-dwarfs (type II). These traits, along with the aluminum tolerance, were inherited in a monogenic dominant manner. Both types of mutants were characterized by excessive bundling of actin microfilaments and by a strongly increased abundance of actin, a phenotype that could be partially phenocopied in the wild type by treatment with aluminum chloride. The actin bundles could be dissociated into finer strands by addition of exogenous auxin in both types of mutants. However, actin microfilaments and leaf expansion were sensitive to blockers of actin assembly in the wild type and in the mutants of type I, whereas they were more tolerant in the mutants of type II. The mutants of type II displayed a hypertrophic development of vasculature, manifest in form of supernumerary leaf veins and extended xylem layers in stems and petioles. Whereas mutants of type I were characterized by a normal, but aluminum-tolerant polar auxin-transport, auxin-transport was strongly promoted in the mutants of type II. The phenotype of these mutants is discussed in terms of reduced endocytosis leading, concomitantly with aluminum tolerance, to changes in polar auxin transport.

  • 2.
    Akhter, Shirin
    et al.
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Westrin, Karl Johan
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Zivi, Nathan
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden; Skogforsk, Uppsala Science Park, Uppsala, Sweden.
    Nordal, Veronika
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Kretzschmar, Warren W.
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Delhomme, Nicolas
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Street, Nathaniel R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Nilsson, Ove
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Emanuelsson, Olof
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Sundström, Jens F.
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway2022Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 236, nr 5, s. 1951-1963Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots.

    We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees.

    A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation.

    In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

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  • 3. Ali, Muhammad Amjad
    et al.
    Azeem, Farrukh
    Nawaz, Muhammad Amjad
    Acet, Tuba
    Abbas, Amjad
    Imran, Qari Muhammad
    Laboratory of Plant Functional Genomics, College of Agriculture & Life Sciences, Kyngpook National University, Buk-gu Daegu, South Korea.
    Shah, Kausar Hussain
    Rehman, Hafiz Mamoon
    Chung, Gyuhwa
    Yang, Seung Hwan
    Transcription factors WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis2018Ingår i: Journal of plant physiology (Print), ISSN 0176-1617, E-ISSN 1618-1328, Vol. 226, s. 12-21Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Plant WRKY transcription factors play a vital role in abiotic stress tolerance and regulation of plant defense responses. This study examined AtWRKY11 and AtWRKY17 expression under ABA, salt, and osmotic stress at different developmental stages in Arabidopsis. We used reverse transcriptase PCR, quantitative real-time PCR, and promoter:GUS lines to analyze expression. Both genes were upregulated in response to abiotic stress. Next, we applied the same stressors to seedlings of T-DNA insertion wrky11 and 17 knock-out mutants (single and double). Under stress, the mutants exhibited slower germination and compromised root growth compared with the wild type. In most cases, double-mutant seedlings were more affected than single mutants. These results suggest that wrky11 and wrky17 are not strictly limited to plant defense responses but are also involved in conferring stress tolerance.

  • 4. Andersson-Gunnerås, Sara
    et al.
    Mellerowicz, Ewa J
    Love, Jonathan
    Segerman, Bo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ohmiya, Yasunori
    Coutinho, Pedro M
    Nilsson, Peter
    Henrissat, Bernard
    Moritz, Thomas
    Sundberg, Björn
    Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis2006Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 45, nr 2, s. 144-165Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) x tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5'-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.

  • 5. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Aaqil Khan, Muhammad
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Kang, Sang-Mo
    Al-Hosni, Khdija
    Jeong, Eun Ju
    Lee, Ko Eun
    Lee, In-Jung
    Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species2017Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 12, nr 8Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of Gsoja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The Gsoja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between Gmax and Ggracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with Gcyrtoloba. The sequence of the accD gene from Gsoja was highly divergent from those of the other species except for Gmax and Ggracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that Gsoja is closely related to Gmax and Ggracilis. The complete Gsoja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.

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  • 6. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Khan, Muhammad Aaqil
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
    Yun, Byung-Wook
    Lee, In-Jung
    Osmoprotective functions conferred to soybean plants via inoculation with Sphingomonas sp. LK11 and exogenous trehalose2017Ingår i: Microbiology Research, ISSN 0944-5013, E-ISSN 1618-0623, Vol. 205, s. 135-145Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Osmotic stress induced by drought can hinder the growth and yield of crop plants. To understand the eco-physiological role of osmoprotectants, the combined utilization of endophytes and osmolytes (trehalose) can be an ideal strategy used to overcome the adverse effects of drought. Hence, in the present study, we aimed to investigate the role of Sphingomonas sp. LK11, which produces phytohormones and synthesizes trehalose, in improving soybean plant growth under drought-induced osmotic stress (−0.4, −0.9, and −1.2 MPa). The results showed that the inoculation of soybean plants with Sphingomonas sp. LK11 significantly increased plant length, dry biomass, photosynthetic pigments, glutathione, amino acids (proline, glycine, and glutamate), and primary sugars as compared to control plants under varying drought stresses. Trehalose applied to the plant with or without endophyte-inoculation also showed similar plant growth-promoting attributes under stress. Stress exposure significantly enhanced endogenous jasmonic (JA) and abscisic (ABA) acid contents in control plants. In contrast, Sphingomonas sp. LK11-inoculation significantly lowered ABA and JA levels in soybean plants, but these phytohormones increased in response to combined treatments during stress. The drought-induced osmotic stress resistance associated with Sphingomonas sp. LK11 and trehalose was also evidenced by increased mRNA gene expression of soybean dehydration responsive element binding protein (DREB)-type transcription factors (GmDREBa and GmDREB2) and the MYB (myeloblastosis) transcription factor (GmMYBJ1) as compared to the control. In conclusion, our findings demonstrated that inoculation with this endophyte and trehalose improved the negative effects of drought-induced osmotic stress, and it enhanced soybean plant growth and tolerance.

  • 7. 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 species2017Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, artikel-id 304Artikel i tidskrift (Refereegranskat)
    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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  • 8.
    Auffret, Alistair G
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Meineri, Eric
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Bruun, Hans Henrik
    Ejrnaes, Rasmus
    Graae, Bente J
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Ontogenetic niche shifts in three Vaccinium species on a sub-alpine mountain side2010Ingår i: Plant Ecology & Diversity, ISSN 1755-0874, E-ISSN 1755-1668, Vol. 3, nr 2, s. 131-139Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Climate warming in arctic and alpine regions is expected to result in the altitudinal migration of plant species, but current predictions neglect differences between species' regeneration niche and established niche.

    Aims: To examine potential recruitment of Vaccinium myrtillus, V. uliginosum and V. vitis-idaea on a mountain slope in northern Sweden in relation to current adult occurrence.

    Methods: We combined a seed-sowing experiment in seven community types with adult occurrence observations and species distribution mapping. Results: Emergence of V. myrtillus and V. vitis-idaea seedlings was significantly related to community type, while V. uliginosum was indifferent, but exhibited the highest average emergence. Adult occurrence was related to community, and ontogenetic niche shifts were observed for all three study species. V. myrtillus was shown to have the highest potential recruitment in habitats at altitudes above its current populations.

    Conclusions: The potential for migration exists, but incongruence between regenerative and established niches presents a challenge for colonisers, as well as for plant migration modelling.

  • 9.
    Barajas-Lopez, Juan de Dios
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Kremnev, Dmitry
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Shaikhali, Jehad
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Pinas-Fernandez, Aurora
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    PAPP5 is involved in the tetrapyrrole mediated plastid signalling during chloroplast development2013Ingår i: PLOS ONE, E-ISSN 1932-6203, Vol. 8, nr 3, artikel-id e60305Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The initiation of chloroplast development in the light is dependent on nuclear encoded components. The nuclear genes encoding key components in the photosynthetic machinery are regulated by signals originating in the plastids. These plastid signals play an essential role in the regulation of photosynthesis associated nuclear genes (PhANGs) when proplastids develop into chloroplasts. One of the plastid signals is linked to the tetrapyrrole biosynthesis and accumulation of the intermediates the Mg-ProtoIX and its methyl ester Mg-ProtoIX-ME. Phytochrome-Associated Protein Phosphatase 5 (PAPP5) was isolated in a previous study as a putative Mg-ProtoIX interacting protein. In order to elucidate if there is a biological link between PAPP5 and the tetrapyrrole mediated signal we generated double mutants between the Arabidopsis papp5 and the crd mutants. The crd mutant over-accumulates Mg-ProtoIX and Mg-ProtoIX-ME and the tetrapyrrole accumulation triggers retrograde signalling. The crd mutant exhibits repression of PhANG expression, altered chloroplast morphology and a pale phenotype. However, in the papp5crd double mutant, the crd phenotype is restored and papp5crd accumulated wild type levels of chlorophyll, developed proper chloroplasts and showed normal induction of PhANG expression in response to light. Tetrapyrrole feeding experiments showed that PAPP5 is required to respond correctly to accumulation of tetrapyrroles in the cell and that PAPP5 is most likely a component in the plastid signalling pathway down stream of the tetrapyrrole Mg-ProtoIX/Mg-ProtoIX-ME. Inhibition of phosphatase activity phenocopied the papp5crd phenotype in the crd single mutant demonstrating that PAPP5 phosphatase activity is essential to mediate the retrograde signal and to suppress PhANG expression in the crd mutant. Thus, our results suggest that PAPP5 receives an inbalance in the tetrapyrrole biosynthesis through the accumulation of Mg-ProtoIX and acts as a negative regulator of PhANG expression during chloroplast biogenesis and development.

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  • 10.
    Bellini, Catherine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.
    A synthetic auxin for cloning mature trees2024Ingår i: Nature Biotechnology, ISSN 1087-0156, E-ISSN 1546-1696Artikel i tidskrift (Övrigt vetenskapligt)
  • 11. Benson, Samuel L
    et al.
    Maheswaran, Pratheesh
    Ware, Maxwell A
    Hunter, C Neil
    Horton, Peter
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ruban, Alexander V
    Johnson, Matthew P
    An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis2015Ingår i: Nature plants, ISSN 2055-026X, Vol. 1, nr 12, artikel-id 15176Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (Delta Lhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and Delta Lhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in Delta Lhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

  • 12. Bitocchi, Elena
    et al.
    Rau, Domenico
    Benazzo, Andrea
    Bellucci, Elisa
    Goretti, Daniela
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 Traits2017Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, artikel-id 2005Artikel i tidskrift (Refereegranskat)
    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.

  • 13.
    Bollhöner, Benjamin
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jokipii-Lukkari, Soile
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bygdell, Joakim
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Stael, Simon
    Adriasola, Mathilda
    Muñiz, Luis
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Van Breusegem, Frank
    Ezcurra, Inés
    Wingsle, Gunnar
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The function of two type II metacaspases in woody tissues of Populus trees2018Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, nr 4, s. 1551-1565Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populustremulaxtremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.

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  • 14. Bot, Phearom
    et al.
    Mun, Bong-Gyu
    Imran, Qari Muhammad
    Hussain, Adil
    Lee, Sang-Uk
    Loake, Gary
    Yun, Byung-Wook
    Differential expression of AtWAKL10 in response to nitric oxide suggests a putative role in biotic and abiotic stress responses2019Ingår i: PeerJ, Vol. 7Artikel i tidskrift (Refereegranskat)
  • 15.
    Boutté, Yohann
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Frescatada-Rosa, Márcia
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Men, Shuzhen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Chow, Cheung-Ming
    Ebine, Kazuo
    Gustavsson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Johansson, Lenore
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ueda, Takashi
    Moore, Ian
    Jürgens, Gerd
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Endocytosis restricts Arabidopsis KNOLLE syntaxin to the cell division plane during late cytokinesis2010Ingår i: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 29, nr 3, s. 546-58Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cytokinesis represents the final stage of eukaryotic cell division during which the cytoplasm becomes partitioned between daughter cells. The process differs to some extent between animal and plant cells, but proteins of the syntaxin family mediate membrane fusion in the plane of cell division in diverse organisms. How syntaxin localization is kept in check remains elusive. Here, we report that localization of the Arabidopsis KNOLLE syntaxin in the plane of cell division is maintained by sterol-dependent endocytosis involving a clathrin- and DYNAMIN-RELATED PROTEIN1A-dependent mechanism. On genetic or pharmacological interference with endocytosis, KNOLLE mis-localizes to lateral plasma membranes after cell-plate fusion. Fluorescence-loss-in-photo-bleaching and fluorescence-recovery-after-photo-bleaching experiments reveal lateral diffusion of GFP-KNOLLE from the plane of division to lateral membranes. In an endocytosis-defective sterol biosynthesis mutant displaying lateral KNOLLE diffusion, KNOLLE secretory trafficking remains unaffected. Thus, restriction of lateral diffusion by endocytosis may serve to maintain specificity of syntaxin localization during late cytokinesis.

  • 16.
    Bygdell, Joakim
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Srivastava, Vaibhav
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Björn
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017Ingår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, nr 13, s. 3405-3417Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

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  • 17. Bünder, Anne
    et al.
    Sundman, Ola
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mahboubi, Amir
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Persson, Staffan
    Mansfield, Shawn D.
    Rüggeberg, Markus
    Niittylä, Totte
    CELLULOSE SYNTHASE INTERACTING 1 is required for wood mechanics and leaf morphology in aspen2020Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 103, nr 5, s. 1858-1868Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cellulose microfibrils synthesized by CELLULOSE SYNTHASE COMPLEXES (CSCs) are the main load‐bearing polymers in wood. CELLULOSE SYNTHASE INTERACTING1 (CSI1) connects CSCs with cortical microtubules, which align with cellulose microfibrils. Mechanical properties of wood are dependent on cellulose microfibril alignment and structure in the cell walls, but the molecular mechanism(s) defining these features is unknown. Herein, we investigated the role of CSI1 in hybrid aspen (Populus tremula  × Populus tremuloides ) by characterizing transgenic lines with significantly reduced CSI1 transcript abundance. Reduction in leaves (50–80%) caused leaf twisting and misshaped pavement cells, while reduction (70–90%) in developing xylem led to impaired mechanical wood properties evident as a decrease in the elastic modulus and rupture. X‐ray diffraction measurements indicate that microfibril angle was not impacted by the altered CSI1 abundance in developing wood fibres. Instead, the augmented wood phenotype of the transgenic trees was associated with a reduced cellulose degree of polymerization. These findings establish a function for CSI1 in wood mechanics and in defining leaf cell shape. Furthermore, the results imply that the microfibril angle in wood is defined by CSI1 independent mechanism(s).

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  • 18.
    Chen, Yang-Er
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. College of Life Sciences, Sichuan Agricultural University, Ya'an, China.
    Yuan, Shu
    Schröder, Wolfgang P.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Comparison of methods for extracting thylakoid membranes of Arabidopsis plants2016Ingår i: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 156, nr 1, s. 3-12Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Robust and reproducible methods for extracting thylakoid membranes are required for the analysis of photosynthetic processes in higher plants such as Arabidopsis. Here, we compare three methods for thylakoid extraction using two different buffers. Method I involves homogenizing the plant material witha metal/glass blender; method II involves manually grinding the plant materialin ice-cold grinding buffer with a mortar and method III entails snap-freezing followed by manual grinding with a mortar, after which the frozen powder is thawed in isolation buffer. Thylakoid membrane samples extracted using each method were analyzed with respect to protein and chlorophyll content, yields relative to starting material, oxygen-evolving activity, protein complex content and phosphorylation. We also examined how the use of fresh and frozen thylakoid material affected the extracts’ contents of protein complexes. The use of different extraction buffers did not significantly alter the protein contentof the extracts in any case. Method I yielded thylakoid membranes with the highest purity and oxygen-evolving activity. Method III used low amounts of starting material and was capable of capturing rapid phosphorylation changes in the sample at the cost of higher levels of contamination. Method II yielded thylakoid membrane extracts with properties intermediate between those obtained with the other two methods. Finally, frozen and freshly isolated thylakoid membranes performed identically in blue native-polyacrylamide gel electrophoresis experiments conducted in order to separate multimeric protein supracomplexes.

  • 19. Chow, Wah Soon
    et al.
    Lee, Hae-Youn
    He, Jie
    Hendrickson, Luke
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia.
    Hong, Young-Nam
    Matsubara, Shizue
    Photoinactivation of photosystem II in leaves2005Ingår i: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 84, nr 1-3, s. 35-41Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Photoinactivation of Photosystem II (PS II), the light-induced loss of ability to evolve oxygen, inevitably occurs under any light environment in nature, counteracted by repair. Under certain conditions, the extent of photoinactivation of PS II depends on the photon exposure (light dosage, x), rather than the irradiance or duration of illumination per se, thus obeying the law of reciprocity of irradiance and duration of illumination, namely, that equal photon exposure produces an equal effect. If the probability of photoinactivation (p) of PS II is directly proportional to an increment in photon exposure (p = kDeltax, where k is the probability per unit photon exposure), it can be deduced that the number of active PS II complexes decreases exponentially as a function of photon exposure: N = Noexp(-kx). Further, since a photon exposure is usually achieved by varying the illumination time (t) at constant irradiance (I), N = Noexp(-kI t), i.e., N decreases exponentially with time, with a rate coefficient of photoinactivation kI, where the product kI is obviously directly proportional to I. Given that N = Noexp(-kx), the quantum yield of photoinactivation of PS II can be defined as -dN/dx = kN, which varies with the number of active PS II complexes remaining. Typically, the quantum yield of photoinactivation of PS II is ca. 0.1micromol PS II per mol photons at low photon exposure when repair is inhibited. That is, when about 10(7) photons have been received by leaf tissue, one PS II complex is inactivated. Some species such as grapevine have a much lower quantum yield of photoinactivation of PS II, even at a chilling temperature. Examination of the longer-term time course of photoinactivation of PS II in capsicum leaves reveals that the decrease in N deviates from a single-exponential decay when the majority of the PS II complexes are inactivated in the absence of repair. This can be attributed to the formation of strong quenchers in severely-photoinactivated PS II complexes, able to dissipate excitation energy efficiently and to protect the remaining active neighbours against damage by light.

  • 20.
    Cocco, Emma
    et al.
    Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; Laboratory of Economic and Pharmaceutical Botany, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy.
    Farci, Domenica
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Haniewicz, Patrycja
    Department of Plant Physiology, Warsaw University of Life Sciences—SGGW, Warsaw, Poland.
    Schröder, Wolfgang P.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Maxia, Andrea
    Laboratory of Economic and Pharmaceutical Botany, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy.
    Piano, Dario
    Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy.
    The Influence of Blue and Red Light on Seed Development and Dormancy in Nicotiana tabacum L.2022Ingår i: Seeds, ISSN 2674-1024, Vol. 1, nr 3, s. 152-163Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The correct development of seeds is a pivotal requirement for species preservation. This process depends on the balance between sensing the environmental stimuli/stressors and hormone-mediated transduction, which results in physiological responses. The red and blue regions of the electromagnetic spectrum are known to influence seed dormancy and germination. Here, we report on the effects induced by the blue (peak at 430 nm) and red (peak at 650 nm) regions of the electromagnetic spectrum on seeds from photo- and skotomorphogenetic capsules developed under white, blue, or red light. Regardless of exposure, seeds from skotomorphogenetic capsules showed an almost absent dormancy in association with altered germination kinetics. Conversely, in seeds from photomorphogenetic capsules, the exposure to the blue region induced skotomorphogenetic-like effects, while the exposure to the whole visible range (350–750 nm), as well as to only the red region, showed a dose-related trend. The observed differences appeared to be dependent on the wavelengths in the red and to be based on transduction mechanisms taking place in fruits. While the molecular bases of this differential effect need to be clarified, the results hint at the role played by different light wavelengths and intensities in seed development and germination. These findings may be relevant for applications in crop production and species safeguarding.

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  • 21.
    Curci, Pasquale Luca
    et al.
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium; Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, Bari, Italy.
    Zhang, Jie
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Mähler, Niklas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Seyfferth, Carolin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Mannapperuma, Chanaka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Diels, Tim
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Van Hautegem, Tom
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Jonsen, David
    SweTree Technologies AB, Skogsmarksgränd 7, Umeå, Sweden.
    Street, Nathaniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Hvidsten, Torgeir R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
    Hertzberg, Magnus
    SweTree Technologies AB, Umeå, Sweden.
    Nilsson, Ove
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden.
    Inzé, Dirk
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Nelissen, Hilde
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Vandepoele, Klaas
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, Belgium.
    Identification of growth regulators using cross-species network analysis in plants2022Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 190, nr 4, s. 2350-2365Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

  • 22. Dauphinee, Adrian N.
    et al.
    Cardoso, Catarina
    Dalman, Kerstin
    Ohlsson, Jonas A.
    Berglund Fick, Stina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Robert, Stephanie
    Hicks, Glenn R.
    Bozhkov, Peter V
    Minina, Elena A.
    Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators2019Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 181, nr 3, s. 855-866Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death, and aging. In plants, autophagy is also known to regulate agronomically important traits such as stress resistance, longevity, vegetative biomass, and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here, we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (1) high-throughput screening of chemical compounds in cell cultures of tobacco (Nicotiana tabacum); (2) confirmation of the identified hits in planta using Arabidopsis (Arabidopsis thaliana); (3) further characterization of the effect using conventional molecular biology methods; and (4) verification of chemical specificity on autophagy in planta. The methods detailed here streamline the identification of specific plant autophagy modulators and aid in unraveling the molecular mechanisms of plant autophagy.

  • 23.
    Decker, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    UDP-sugar metabolizing pyrophosphorylases in plants: formation of precursors for essential glycosylation-reactions2017Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    UDP-sugar metabolizing pyrophosphorylases provide the primary mechanism for de novo synthesis of UDP-sugars, which can then be used for myriads of glycosyltranferase reactions, producing cell wall carbohydrates, sucrose, glycoproteins and glycolipids, as well as many other glycosylated compounds. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase) and UDP-N-acety lglucosamine pyrophosphorylase (UAGPase), which can be discriminated both by differences in accepted substrate range and amino acid sequences.

    This thesis focuses both on experimental examination (and re-examination) of some enzymatic/ biochemical properties of selected members of the UGPases and USPases and UAGPase families and on the design and implementation of a strategy to study in vivo roles of these pyrophosphorylases using specific inhibitors. In the first part, substrate specificities of members of the Arabidopsis UGPase, USPase and UAGPase families were comprehensively surveyed and kinetically analyzed, with barley UGPase also further studied with regard to itspH dependency, regulation by oligomerization, etc. 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 Frc-1-P, whereas USPase reacted with arange of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P, β-L-Ara-1-P and α-D-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P and, to some extent, with D-Glc-1-P. A structure activity relationship was established to connect enzyme activity, the examined sugar-1-phosphates and the three pyrophosphorylases. The UGPase/USPase/UAGPase active sites were subsequently compared in an attempt to identify amino acids which may contribute to the experimentally determined differences in substrate specificities.

    The second part of the thesis deals with identification and characterization of inhibitors of the pyrophosphorylases and with studies on in vivo effects of those inhibitors in Arabidopsis-based systems. A novel luminescence-based high-throughput assay system was designed, which allowed for quantitative measurement of UGPase and USPase activities, down to a pmol per min level. The assay was then used to screen a chemical library (which contained 17,500 potential inhibitors) to identify several compounds affecting UGPase and USPase. Hit-optimization on one of the compounds revealed even stronger inhibitors of UGPase and USPase which also strongly inhibited Arabidopsis pollen germination, by disturbing UDP-sugar metabolism. The inhibitors may represent useful tools to study in vivo roles of the pyrophosphorylases, as a complement to previous genetics-based studies.

    The thesis also includes two review papers on mechanisms of synthesis of NDP-sugars. The first review covered the characterization of USPase from both prokaryotic and eukaryotic organisms, whereas the second review was a comprehensive survey of NDP-sugar producing enzymes (not only UDP-sugar producing and not only pyrophosphorylases). All these enzymes were discussed with respect to their substrate specificities and structural features (if known) and their proposed in vivo functions.

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  • 24.
    Decker, Daniel
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Öberg, Christopher
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kleczkowski, Leszek A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Identification and characterization of inhibitors of UDP-glucose and UDP-sugar pyrophosphorylases for in vivo studies2017Ingår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 90, nr 6, s. 1093-1107Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    UDP-sugars serve as ultimate precursors in hundreds of glycosylation reactions (e.g. for protein and lipid glycosylation, synthesis of sucrose, cell wall polysaccharides, etc.), underlying an important role of UDP-sugar-producing enzymes in cellular metabolism. However, genetic studies on mechanisms of UDP-sugar formation were frequently hampered by reproductive impairment of the resulting mutants, making it difficult to assess an in vivo role of a given enzyme. Here, a chemical library containing 17 500 compounds was separately screened against purified UDP-glucose pyrophosphorylase (UGPase) and UDP-sugar pyrophosphorylase (USPase), both enzymes representing the primary mechanisms of UDP-sugar formation. Several compounds have been identified which, at 50 μm, exerted at least 50% inhibition of the pyrophosphorylase activity. In all cases, both UGPase and USPase activities were inhibited, probably reflecting common structural features of active sites of these enzymes. One of these compounds (cmp #6), a salicylamide derivative, was found as effective inhibitor of Arabidopsis pollen germination and Arabidopsis cell culture growth. Hit optimization on cmp #6 yielded two analogs (cmp #6D and cmp #6D2), which acted as uncompetitive inhibitors against both UGPase and USPase, and were strong inhibitors in the pollen test, with apparent inhibition constants of less than 1 μm. Their effects on pollen germination were relieved by addition of UDP-glucose and UDP-galactose, suggesting that the inhibitors targeted UDP-sugar formation. The results suggest that cmp #6 and its analogs may represent useful tools to study in vivo roles of the pyrophosphorylases, helping to overcome the limitations of genetic approaches.

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  • 25. Derba-Maceluch, Marta
    et al.
    Amini, Fariba
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Biology Department, Faculty of Science, Arak University, Arak, Iran.
    Donev, Evgeniy N.
    Pawar, Prashant Mohan-Anupama
    Michaud, Lisa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Johansson, Ulf
    Albrectsen, Benedicte Riber
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 Fashion2020Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, artikel-id 651Artikel i tidskrift (Refereegranskat)
    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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  • 26.
    Derba-Maceluch, Marta
    et al.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Mitra, Madhusree
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Hedenström, Mattias
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Liu, Xiaokun
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Gandla, Madhavi Latha
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Barbut, Félix R.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Abreu, Ilka N.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Donev, Evgeniy N.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Urbancsok, János
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Moritz, Thomas
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Jönsson, Leif J.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Tsang, Adrian
    Centre for Structural and Functional Genomics, Concordia University, QC, Montreal, Canada.
    Powlowski, Justin
    Centre for Structural and Functional Genomics, Concordia University, QC, Montreal, Canada.
    Master, Emma R.
    Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, ON, Toronto, Canada.
    Mellerowicz, Ewa J.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Xylan glucuronic acid side chains fix suberin-like aliphatic compounds to wood cell walls2023Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 238, nr 1, s. 297-312Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Wood is the most important repository of assimilated carbon in the biosphere, in the form of large polymers (cellulose, hemicelluloses including glucuronoxylan, and lignin) that interactively form a composite, together with soluble extractives including phenolic and aliphatic compounds. Molecular interactions among these compounds are not fully understood.

    We have targeted the expression of a fungal α-glucuronidase to the wood cell wall of aspen (Populus tremula L. × tremuloides Michx.) and Arabidopsis (Arabidopsis thaliana (L.) Heynh), to decrease contents of the 4-O-methyl glucuronopyranose acid (mGlcA) substituent of xylan, to elucidate mGlcA's functions.

    The enzyme affected the content of aliphatic insoluble cell wall components having composition similar to suberin, which required mGlcA for binding to cell walls. Such suberin-like compounds have been previously identified in decayed wood, but here, we show their presence in healthy wood of both hardwood and softwood species. By contrast, γ-ester bonds between mGlcA and lignin were insensitive to cell wall-localized α-glucuronidase, supporting the intracellular formation of these bonds.

    These findings challenge the current view of the wood cell wall composition and reveal a novel function of mGlcA substituent of xylan in fastening of suberin-like compounds to cell wall. They also suggest an intracellular initiation of lignin–carbohydrate complex assembly.

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  • 27.
    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 universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    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 universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Hertzberg, Magnus
    SweTree Technologies AB, Umeå, Sweden.
    Jönsson, Leif J.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    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 aspen2023Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 14, artikel-id 1218302Artikel i tidskrift (Refereegranskat)
    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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  • 28.
    Dob, Asma
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    A novel molecular circuit guides IAA-JA crosstalk during adventitious rooting in Arabidopsis2019Självständigt arbete på avancerad nivå (masterexamen), 80 poäng / 120 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Adventitious rooting is a post embryonic developmental program controlled by a myriad of environmental and endogenous cues. Adventitious roots (ARs) usually initiate from pericycle or cambium-like cells, which undergo reprogramming and cell-fate transition programs. Phytohormones such as indole-3-acetic-acid (IAA) or Jasmonate (JA) play a prominent role in guiding these programs. Indeed, we have previously shown that IAA and JA crosstalk to control early events of adventitious root initiation (ARI) in Arabidopsis thaliana (Arabidopsis). Auxin mediates ARI by controlling the expression of GRETCHEN HAGEN3 (GH3) genes, which modulate the JA pools. JA  in turn negatively regulates ARI in a CORONATINE INSENSITIVE 1 (COI1)-dependent manner. The genetic components acting downstream of JA signalling and the exact mechanistic basis of auxin and JA crosstalk during ARI remains elusive. The present work aimed to bring more insights on the role of JA during ARI and identify its downstream targets. First we adopted  a cell-type-specific complementation approach to unravel where JA signalling inhibits ARI. We found that JA signalling possibly represses the early events occurring in the pericycle cells leading to ARI.  Next, we adopted a comparative transcriptomic approach to unravel the downstream targets of JA signalling during ARI. We identified novel genetic components (DIOXYGENASE FOR AUXIN OXIDATION DAO1 and DAO2) acting downstream of JA. DAO genes control IAA oxidation which leads to an irreversible degradation of IAA. We provide evidence that COI1-dependent JA signalling controls the expression of DAO1 and DAO2.We also show that DAO1 is the major player in ARI, as revealed by the characterization of the double mutant dao1-1dao2C. The mutant dao2C was generated using CRISPR-Cas9 technology. Furthermore, we demonstrated that the loss-of- function mutant dao1-1 exhibited an enhanced AR phenotype compared to the wild type. This phenotype was possibly due to JA and its bioactive form JA-Ile deficiency. Altogether, our data indicates that DAO1 controls a hormonal feedback circuit that maintains and stabilizes the auxin and JA crosstalk during ARI.

  • 29.
    Dobrenel, Thomas
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. 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 universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    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 S62016Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, artikel-id 1611Artikel i tidskrift (Refereegranskat)
    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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  • 30.
    Donev, Evgeniy N.
    et al.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Derba-Maceluch, Marta
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Yassin, Zakiya
    Enhet Produktionssystem och Material, RISE Research Institutes of Sweden, Växjö, Sweden.
    Gandla, Madhavi Latha
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Pramod, Sivan
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden; 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.
    Kumar, Vikash
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Scheepers, Gerhard
    Enhet Produktionssystem och Material, RISE Research Institutes of Sweden, Växjö, Sweden.
    Vilaplana, Francisco
    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.
    Johansson, Ulf
    Tönnersjöheden Experimental Forest, Swedish University of Agricultural Sciences, Simlångsdalen, Sweden.
    Hertzberg, Magnus
    SweTree Technologies AB, Umeå, Sweden.
    Sundberg, Björn
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Winestrand, Sandra
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hörnberg, Andreas
    RISE Processum AB, Örnsköldsvik, Sweden.
    Alriksson, Björn
    RISE Processum AB, Örnsköldsvik, Sweden.
    Jönsson, Leif J.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mellerowicz, Ewa J.
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Field testing of transgenic aspen from large greenhouse screening identifies unexpected winners2023Ingår i: Plant Biotechnology Journal, ISSN 1467-7644, E-ISSN 1467-7652, Vol. 21, nr 5, s. 1005-1021Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H) and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best-performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.

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  • 31.
    Erik, Edlund
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Regulatory Control of Autumn Senescence in Populus tremula2016Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Autumn senescence is a visually spectacular phenomenon in which trees prepare for the oncoming winter. The mechanism for regulation of autumn senescence in trees has been very hard to pinpoint. In this thesis the main focus is to investigate how autumn senescence is regulated in aspens (Populus tremula).

    Previous work has established that autumn senescence in aspens is under daylight control, in this thesis the metabolic status and the effect on autumn senescence was investigated. The metabolic status was altered by girdling which leads to accumulation of photosynthates in the canopy. This resulted in an earlier onset of senescence but also the speed of senescence was changed. At the onset of senescence the girdled trees also accumulated or retained anthocyanins.

    The nitrogen status of aspens during autumn senescence was also investigated, we found that high doses of fertilization could significantly delay the onset of senescence. The effects of various nitrogen forms was investigated by delivering organic and inorganic nitrogen through a precision fertilization delivery system that could inject solutes directly into the xylem of the mature aspens. The study showed that addition of nitrate delayed senescence, addition of arginine did not have any effect on the autumn senescence in aspens, and furthermore the nitrate altered the trees leaf metabolism that was more profound in high dosages of supplied nitrate. 

    Cytokinins are plant hormones believed to delay or block senescence, studies have suggested that the decrease of cytokinins and/or cytokinin signalling may precede senescence in some plants. To investigate how cytokinin regulates autumn senescence in aspens we profiled 34 cytokinin types in a free growing mature aspen. The study begun before autumn senescence was initiated and ended with the shedding of the leaves, and spanned three consecutive years. The study showed that the individual cytokinin profiles varied significantly between the years, this despite that senescence was initiated at the same time each year. Senescence was furthermore not connected to the depletion of either active or total cytokinins levels. The gene pattern of genes known to be associated with cytokinin was also studied, but no gene expression pattern that the profile generated could explain the onset of senescence. These results suggest that the depletion of cytokinins is unlikely to explain the tightly regulated onset of autumn leaf senescence in aspen.

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  • 32.
    Escamez, Sacha
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Latha Gandla, Madhavi
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Derba-Maceluch, Marta
    Lundqvist, Sven-Olof
    Mellerowicz, Ewa J.
    Jönsson, Leif J.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    A collection of genetically engineered Populus trees reveals wood biomass traits that predict glucose yield from enzymatic hydrolysis2017Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 7, artikel-id 15798Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Wood represents a promising source of sugars to produce bio-based renewables, including biofuels. However, breaking down lignocellulose requires costly pretreatments because lignocellulose is recalcitrant to enzymatic saccharification. Increasing saccharification potential would greatly contribute to make wood a competitive alternative to petroleum, but this requires improving wood properties. To identify wood biomass traits associated with saccharification, we analyzed a total of 65 traits related to wood chemistry, anatomy and structure, biomass production and saccharification in 40 genetically engineered Populus tree lines. These lines exhibited broad variation in quantitative traits, allowing for multivariate analyses and mathematical modeling. Modeling revealed that seven wood biomass traits associated in a predictive manner with saccharification of glucose after pretreatment. Four of these seven traits were also negatively associated with biomass production, suggesting a trade-off between saccharification potential and total biomass, which has previously been observed to offset the overall sugar yield from whole trees. We therefore estimated the "total-wood glucose yield" (TWG) from whole trees and found 22 biomass traits predictive of TWG after pretreatment. Both saccharification and TWG were associated with low abundant, often overlooked matrix polysaccharides such as arabinose and rhamnose which possibly represent new markers for improved Populus feedstocks.

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  • 33.
    Escamez, Sacha
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Terryn, Christine
    PICT Platform, Université de Reims Champagne Ardenne, Reims, France.
    Gandla, Madhavi Latha
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Yassin, Zakiya
    RISE AB, Stockholm, Sweden.
    Scheepers, Gerhard
    RISE AB, Stockholm, Sweden.
    Näsholm, Torgny
    Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden; Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Sundman, Ola
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jönsson, Leif J.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Lundberg-Felten, Judith
    Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Tuominen, Hannele
    Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Niittylä, Totte
    Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Paës, Gabriel
    Université de Reims Champagne Ardenne, Reims, France.
    Fluorescence Lifetime Imaging as an in Situ and Label-Free Readout for the Chemical Composition of Lignin2021Ingår i: ACS Sustainable Chemistry and Engineering, E-ISSN 2168-0485, Vol. 9, nr 51, s. 17381-17392Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Naturally fluorescent polymeric molecules such as collagen, resilin, cutin, suberin, or lignin can serve as renewable sources of bioproducts. Theoretical physics predicts that the fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls that form woody biomass. Lignin is composed of different phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured the wood cell wall composition by classical analytical methods in these trees. Using statistical modeling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm (flowering) plants. In a first step toward tailoring lignin biosynthesis toward improvement of woody biomass feedstocks, we show how FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.

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  • 34.
    Fataftah, Nazeer
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bag, Pushan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    André, Domenique
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Lihavainen, Jenna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Zhang, Bo
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Ingvarsson, Pär K.
    Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Nilsson, Ove
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    GIGANTEA influences leaf senescence in trees in two different ways2021Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 187, nr 4, s. 2435-2450Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally-the phenotype followed the genotype of the branch, independent of its position on the tree-and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.

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  • 35. Felten, Judith
    et al.
    Kohler, Annegret
    Morin, Emmanuelle
    Bhalerao, Rishikesh P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Palme, Klaus
    Martin, Francis
    Ditengou, Franck A
    Legue, Valerie
    The ectomycorrhizal fungus laccaria bicolor stimulates lateral root formation in poplar and arabidopsis through auxin transport and signaling2009Ingår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 151, nr 4, s. 1991-2005Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The early phase of the interaction between tree roots and ectomycorrhizal fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We aimed to identify gene networks that regulate LR development during the early signal exchanges between poplar (Populus tremula x Populus alba) and the ectomycorrhizal fungus Laccaria bicolor with a focus on auxin transport and signaling pathways. Our data demonstrated that increased LR development in poplar and Arabidopsis (Arabidopsis thaliana) interacting with L. bicolor is not dependent on the ability of the plant to form ectomycorrhizae. LR stimulation paralleled an increase in auxin accumulation at root apices. Blocking plant polar auxin transport with 1-naphthylphthalamic acid inhibited LR development and auxin accumulation. An oligoarray-based transcript profile of poplar roots exposed to molecules released by L. bicolor revealed the differential expression of 2,945 genes, including several components of polar auxin transport (PtaPIN and PtaAUX genes), auxin conjugation (PtaGH3 genes), and auxin signaling (PtaIAA genes). Transcripts of PtaPIN9, the homolog of Arabidopsis AtPIN2, and several PtaIAAs accumulated specifically during the early interaction phase. Expression of these rapidly induced genes was repressed by 1-naphthylphthalamic acid. Accordingly, LR stimulation upon contact with L. bicolor in Arabidopsis transgenic plants defective in homologs of these genes was decreased or absent. Furthermore, in Arabidopsis pin2, the root apical auxin increase during contact with the fungus was modified. We propose a model in which fungus-induced auxin accumulation at the root apex stimulates LR formation through a mechanism involving PtaPIN9-dependent auxin redistribution together with PtaIAA-based auxin signaling.

  • 36.
    Gandla, Madhavi Latha
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Mähler, Niklas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Escamez, Sacha
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden.
    Skotare, Tomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Obudulu, Ogonna
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Möller, Linus
    SweTree Technologies, Umeå, Sweden.
    Abreu, Ilka N.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Bygdell, Joakim
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hertzberg, Magnus
    SweTree Technologies, Umeå, Sweden.
    Hvidsten, Torgeir R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Moritz, Thomas
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Wingsle, Gunnar
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jönsson, Leif J.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees2021Ingår i: Biotechnology for Biofuels, ISSN 1754-6834, E-ISSN 1754-6834, Vol. 14, nr 1, artikel-id 43Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.

    Results: In this study, we report on transgenic hybrid aspen (Populus tremula × tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.

    Conclusions: The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.

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  • 37.
    Garkava-Gustavsson, L.
    et al.
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Sätra, J. Skytte af
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Odilbekov, F.
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Abreu, I.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Johansson, Annika I.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    van de Weg, E.
    Plant Breeding, Wageningen University & Research, Wageningen, Netherlands.
    Zhebentyayeva, T.
    Department of Ecosystem Science and Management, University Park, The Pennsylvania State University, PA, United States.
    Resistance to Neonectria ditissima in apple: insights from metabolomics and lipidomics analyses2023Ingår i: Xxxi international horticultural congress (ihc2022): International symposium on breeding and effective use of biotechnology and molecular tools in horticultural crops / [ed] V. Bus; M. Causse, International Society for Horticultural Science , 2023, s. 329-335Konferensbidrag (Refereegranskat)
    Abstract [en]

    European canker, caused by the necrotrophic fungus Neonectria ditissima, is the most serious disease in apple production in Sweden. The disease is favored by a relatively cool and rainy climate. The canker damages have a significant economic impact due to reduced bearing surface and increased orchard management costs. The possibilities for chemical and biological control are very limited. Therefore, directed breeding for new resistant cultivars is urgently needed. Knowledge of inheritance of canker resistance and understanding of molecular mechanisms involved in resistant and susceptible responses to fungal attacks would facilitate breeding. In this study, we evaluated the tempo-spatial differences in plant-pathogen interactions in a set of partially resistant and susceptible cultivars by conducting metabolomic and lipidomic analyses. The major trends in metabolomics and lipidomic profiles were common among cultivars, irrespective of the degree of susceptibility. Several metabolites and lipids varied with time point and cultivar under N. ditissima infection. Putative key metabolites such as suberic acid and jasmonic acid were upregulated in all cultivars upon infection. Additionally, several lipids exhibited changes 30 to 45 days post-inoculation. Thus, the approach used seems to have resulted in a rich data set to be further analyzed in light of ongoing QTL-mapping efforts.

  • 38. Gauslaa, Yngvar
    et al.
    Palmqvist, Kristin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Solhaug, Knut Asbjørn
    Hilmo, Olga
    Holien, Håkon
    Nybakken, Line
    Ohlson, Mikael
    Size-dependent growth of two old-growth associated macrolichen species2009Ingår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 181, nr 3, s. 683-692Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Relationships between thallus size and growth variables were analysed for the foliose Lobaria pulmonaria and the pendulous Usnea longissima with the aim of elucidating their morphogenesis and the factors determining thallus area (A) versus biomass (dry weight (DW) gain. Size and growth data originated from a factorial transplantation experiment that included three boreal climate zones (Atlantic, suboceanic and continental), each with three successional forest stands (clear-cut, young and old). When A was replaced by the estimated photobiont layer area in an area-DW scatterplot including all thalli (n = 1080), the two separate species clusters merged into one, suggesting similar allocation patterns between photobionts and mycobionts across growth forms. During transplantation, stand-specific water availability boosted area gain in foliose transplants, consistent with a positive role of water in fungal expansion. In pendulous lichens, A gain greatly exceeded DW gain, particularly in small transplants. The A gain in U. longissima increased with increasing DW:A ratio, consistent with a reallocation of carbon, presumably mobilized from the dense central chord. Pendulous lichens with cylindrical photobiont layers harvest light from all sides. Rapid and flexible three-dimensional A gain allows the colonization of spaces between canopy branches to utilize temporary windows of light in a growing canopy. Foliose lichens with a two-dimensional photobiont layer have more coupled A and DW gains.

  • 39. Granado-Yela, C
    et al.
    García-Verdugo, C
    Carrillo, K
    Rubio DE Casas, R
    Kleczkowski, Leszek A
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Balaguer, L
    Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll Olea europaea L2011Ingår i: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 34, nr 5, s. 800-810Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Trees are modular organisms that adjust their within-crown morphology and physiology in response to within-crown light gradients. However, whether within-plant variation represents a strategy for optimizing light absorption has not been formally tested. We investigated the arrangement of the photosynthetic surface throughout one day and its effects on the photosynthetic process, at the most exposed and most sheltered crown layers of a wild olive tree (Olea europaea L.). Similar measurements were made for cuttings taken from this individual and grown in a greenhouse at contrasted irradiance-levels (100 and 20% full sunlight). Diurnal variations in light interception, carbon fixation and carbohydrate accumulation in sun leaves were negatively correlated with those in shade leaves under field conditions when light intensity was not limiting. Despite genetic identity, these complementary patterns were not found in plants grown in the greenhouse. The temporal disparity among crown positions derived from specialization of the photosynthetic behaviour at different functional and spatial scales: architectural structure (crown level) and carbon budget (leaf level). Our results suggest that the profitability of producing a new module may not only respond to construction costs or light availability, but also rely on its spatio-temporal integration within the productive processes at the whole-crown level.

  • 40. Hartmann, Laura
    et al.
    Pedrotti, Lorenzo
    Weiste, Christoph
    Fekete, Agnes
    Schierstaedt, Jasper
    Göttler, Jasmin
    Kempa, Stefan
    Krischke, Markus
    Dietrich, Katrin
    Mueller, Martin J
    Vicente-Carbajosa, Jesus
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Department of Molecular Plant Physiology, Utrecht University, The Netherlands .
    Dröge-Laser, Wolfgang
    Crosstalk between Two bZIP Signaling Pathways Orchestrates Salt-Induced Metabolic Reprogramming in Arabidopsis Roots2015Ingår i: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 27, nr 8, s. 2244-2260Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.

  • 41.
    Hossain, Mohammad Anwar
    et al.
    Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh.
    Tahjib-Ul-Arif, Md
    Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh, Bangladesh.
    Jahin, Sopnil Ahmed
    Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh.
    Siddique, Abu Bakar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Mim, Mumtarin Haque
    Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh.
    Sharif-Ar-Raffi,
    Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh.
    Haque Bhuiyan, Muhammad Javidul
    Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh, Bangladesh.
    Nowicka, Beatrycze
    Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
    Genetic engineering for heavy metal/metalloid stress tolerance in plants2023Ingår i: Heavy metal toxicity and tolerance in plants: a biological, omics, and genetic engineering approach / [ed] Mohammad Anwar Hossain; AKM Zakir Hossain; Sylvain Bourgerie: Masayuki Fujita; Om Parkash Dhankher; Parvez Haris, John Wiley & Sons, 2023, s. 573-592Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Modern agricultural techniques, anthropogenic activities, fast industrialization and urbanization, and the use of fossil fuels are the sources of significant contamination of the environment with various heavy metals (HMs) and metalloids. HM pollution has an impact on agricultural output and quality. What is more, accumulation of HMs in crops poses a threat to the human health. The problem of contamination of the arable lands with HMs and metalloids has to be addressed in various ways. One of the solutions is plant genetic engineering. Developing and cultivating commercial or industrial crop plants that display increased tolerance to HM-induced stress would let to use HM-affected areas for cultivation. Moreover, HM-tolerant hyperaccumulator plants can be used for phytoremediation of contaminated land. This chapter aims to offer a comprehensive review of current advances in genome transformation for improved plant tolerance to HMs/metalloids with special reference to the overexpression of genes encoding metal transporters, sulfur metabolites, metal chelators, and components of antioxidative system and glyoxalase pathways. In addition, we have discussed the potential of using CRISPR/Cas system in developing HM tolerance in plants.

  • 42. Hussain, Adil
    et al.
    Imran, Qari Muhammad
    School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Republic of Korea.
    Yun, Byung-Wook
    CRISPR/Cas9-mediated gene editing in grain crops2020Ingår i: Recent Advances in Grain Crops Research, IntechOpen , 2020, s. 1-12Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    The development of reliable and efficient techniques for making precise targeted changes in the genome of living organisms has been a long-standing objective of researchers throughout the world. In plants, different methods, each with several different variations, have been developed for this purpose, though many of them are hampered either by providing only temporary modification of gene function or unpredictable off-target results. The recent discovery of clustered regularly interspaced short palindromic repeats (CRISPRs) and the CRISPR-associated 9 (Cas9) nucleases started a new era in genome editing. Basically, the CRISPR/Cas system is a natural immune response of prokaryotes to resist foreign genetic elements entering via plasmids and phages. Through this naturally occurring gene editing system, bacteria create DNA segments known as CRISPR arrays that allow them to "remember" foreign genetic material for protection against it and other similar sequences in the future. This system has now been adopted by researchers in laboratory to create a short guide RNA that binds to specific target sequences of DNA in eukaryotic genome, and the Cas9 enzyme cuts the DNA at the targeted location. Once cut, the cell's endogenous DNA repair machinery is used to add, delete, or replace pieces of genetic material. Though CRISPR/Cas9 technology has been recently developed, it has started to be regularly used for gene editing in plants as well as animals to good success. It has been proved as an efficient transgene-free technique. A simple search on PubMed (NCBI) shows that among all plants, 80 different studies published since 2013 involved CRISPR/Cas9-mediated genome editing in rice. Of these, 20, 13, and 24 papers have been published in 2019, 2018, and 2017, respectively. Furthermore, 20 different studies published since 2014 utilized CRISPR/Cas9 system for gene editing in wheat, where five of these studies were published in 2019 and seven were published in 2018. Genomes of other grain crops edited through this technique include maize, sorghum, barley, etc. This indicates the high utility of this technique for gene editing in grain crops. Here we emphasize on CRISPR/Cas9-mediated gene editing in rice, wheat, and maize.

  • 43. 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 thaliana2016Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7Artikel i tidskrift (Refereegranskat)
    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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  • 44.
    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 thaliana2016Ingår i: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, artikel-id 712Artikel i tidskrift (Refereegranskat)
    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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  • 45.
    Imran, Qari Muhammad
    et al.
    Laboratory of Plant Functional Genomics, School of Applied BioSciences, Kyungpook National University, Daegu, Republic of Korea.
    Hussain, Adil
    Lee, Sang-Uk
    Mun, Bong-Gyu
    Falak, Noreen
    Loake, Gary J.
    Yun, Byung-Wook
    Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes2018Ingår i: Scientific Reports, E-ISSN 2045-2322, Vol. 8, artikel-id 771Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    TFs are important proteins regulating plant responses during environmental stresses. These insults typically induce changes in cellular redox tone driven in part by promoting the production of reactive nitrogen species (RNS). The main source of these RNS is nitric oxide (NO), which serves as a signalling molecule, eliciting defence and resistance responses. To understand how these signalling molecules regulate key biological processes, we performed a large scale S-nitrosocysteine (CySNO)-mediated RNA-seq analysis. The DEGs were analysed to identify potential regulatory TFs. We found a total of 673 (up- and down-regulated) TFs representing a broad range of TF families. GO-enrichment and MapMan analysis suggests that more than 98% of TFs were mapped to the Arabidopsis thaliana genome and classified into pathways like hormone signalling, protein degradation, development, biotic and abiotic stress, etc. A functional analysis of three randomly selected TFs, DDF1RAP2.6, and AtMYB48 identified a regulatory role in plant growth and immunity. Loss-of-function mutations within DDF1 and RAP2.6 showed compromised basal defence and effector triggered immunity, suggesting their positive role in two major plant defence systems. Together, these results imply an important data representing NO-responsive TFs that will help in exploring the core mechanisms involved in biological processes in plants.

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  • 46.
    Imran, Qari Muhammad
    et al.
    Laboratory of Plant Functional Genomics School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Hussain, Adil
    Mun, Bong-Gyu
    Lee, Sang Uk
    Asaf, Sajjad
    Ali, Muhammad Amjad
    Lee, In-Jung
    Yun, Byung-Wook
    Transcriptome wide identification and characterization of NO-responsive WRKY transcription factors in Arabidopsis thaliana L.2018Ingår i: Environmental and Experimental Botany, ISSN 0098-8472, E-ISSN 1873-7307, Vol. 148, s. 128-143Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    WRKY transcription factors are important plant-specific regulatory genes characterized by one or two conserved WRKY domain(s) usually followed by a zinc-finger motif. In this study using Arabidopsis thaliana, the RNA-Seq based transcriptomic analysis showed differential expression of 33 genes encoding WRKY TFs in response to the nitric oxide (NO) donor S-Nitrosocysteine (CySNO). Interestingly, 93.9% of these TFs were up-regulated with at least 2-fold change, suggesting their putative involvement in NO mediated gene regulation. GO- analysis of all the 33 transcriptomic elements showed their putative involvement in biological processes such as abiotic stress tolerance and defense against fungal pathogens (89.39 fold enrichment). Analysis of the NO-responsive AtWRKY TFs promoter region revealed the presence of the cis-acting elements such as ABRE, EIRE, ERE, and MBS involved in osmotic stress response, maximal elicitor-mediated activation, and drought-stress regulation. The analysis of NO-responsive AtWRKY TF motifs and their comparison with rice, soybean, and tomato orthologs suggested that members of the WRKY family belonging to the same group shared similar motifs and phylogenetic tree suggested that these TFs were highly conserved. Validation of transcriptomic data through quantitative real time-PCR showed a high correlation coefficient (0.85) indicating the high reliability and similarity of both types of analysis. Comparison of the NO-responsive and non-responsive WRKYs showed the presence of tyrosine (T) and cysteine (C) residues at a distance of 7 residues from the WRKYGQK motif which may serve as potential targets for modification by NO via tyrosine nitration and S-nitrosylation. We also validated the response of WRKYs through in vivo analysis using atwrky62 loss of function mutant and the results indicated a negative role of AtWRKY62 in plant growth. Furthermore, atwrky62 showed significantly less SNO contents compared to wild type plants indicating putative role of AtWRKY62 in NO metabolism.

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  • 47. Imran, Qari Muhammad
    et al.
    Lee, Sang-Uk
    Mun, Bong-Gyu
    Hussain, Adil
    Asaf, Sajjad
    Lee, In-Jung
    Yun, Byung-Wook
    WRKYs, the Jack-of-various-Trades, Modulate Dehydration Stress in Populus davidiana-A Transcriptomic Approach2019Ingår i: International Journal of Molecular Sciences, ISSN 1661-6596, E-ISSN 1422-0067, Vol. 20, nr 2Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Populus davidiana, native to Korea and central Asian countries, is a major contributor to the Korean forest cover. In the current study, using high-throughput RNA-seq mediated transcriptome analysis, we identified about 87 P. davidiana WRKY transcription factors (PopdaWRKY TFs) that showed differential expression to dehydration stress in both sensitive and tolerant cultivars. Our results suggested that, on average, most of the WRKY genes were upregulated in tolerant cultivars but downregulated in sensitive cultivars. Based on protein sequence alignment, P. davidiana WRKYs were classified into three major groups, I, II, III, and further subgroups. Phylogenetic analysis showed that WRKY TFs and their orthologs in Arabidopsis and rice were clustered together in the same subgroups, suggesting similar functions across species. Significant correlation was found among qRT-PCR and RNA-seq analysis. In vivo analysis using model plant Arabidopsis showed that atwrky62 (orthologous to Potri.016G137900) knockout mutants were significantly sensitive to dehydration possibly due to an inability to close their stomata under dehydration conditions. In addition, a concomitant decrease in expression of ABA biosynthetic genes was observed. The AtHK1 that regulates stomatal movement was also downregulated in atwrky62 compared to the wild type. Taken together, our findings suggest a regulatory role of PopdaWRKYs under dehydration stress.

  • 48. Imran, Qari Muhammad
    et al.
    Yun, Byung-Wook
    Pathogen-induced Defense Strategies in Plants2020Ingår i: Journal of Crop Science and Biotechnology, Vol. 23, nr 2, s. 97-105Artikel i tidskrift (Refereegranskat)
  • 49.
    Ishikawa, Yasuo
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Schröder, Wolfgang P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Functional analysis of the PsbP-like protein (sll1418) in Synechocystis sp PCC 68032005Ingår i: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 84, nr 1-3, s. 257-262Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A recent proteomic analysis of the thylakoid lumen of Arabidopsis thaliana revealed the presence of several PsbP-like proteins, and a homologue to this gene family was detected in the genome of the cyanobacterium Synechocystis sp. PCC 6803 (Schubert M, Petersson UA, Haas BJ, Funk C, Schroder WP, Kieselbach T (2002) J Biol Chem 277, 8354-8365). Using a peptide-directed antibody against this cyanobacterial PsbP-like protein (sll1418) we could show that it was localized in the thylakoid membrane and associated with Photosystem II. While salt washes did not remove the PsbP-like protein from the thylakoid membrane, it was partially lost during the detergent-based isolation of PSII membrane fractions. In total cell extracts this protein is present in the same amount as the extrinsic PsbO protein. We did not see any significant functional difference between the wild-type and a PsbP-like insertion mutant.

  • 50.
    Jiao, Xiang
    et al.
    College of Mechanical and Electronic Engineering, Nanjing Forestry University.
    Zhang, Huichun
    College of Mechanical and Electronic Engineering, Nanjing Forestry University.
    Zheng, Jiaqiang
    College of Mechanical and Electronic Engineering, Nanjing Forestry University.
    Yin, Yue
    College of Mechanical and Electronic Engineering, Nanjing Forestry University.
    Wang, Guosu
    College of Mechanical and Electronic Engineering, Nanjing Forestry University.
    Chen, Ying
    College of Forestry, Nanjing Forestry University.
    Ge, Yufeng
    Department of Biological Systems Engineering, University of Nebraska-Lincoln.
    Yu, Jun
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för matematik och matematisk statistik.
    Comparative analysis of nonlinear growth curve models for Arabidopsis thaliana rosette leaves2018Ingår i: Acta Physiologiae Plantarum, ISSN 0137-5881, E-ISSN 1861-1664, Vol. 40, nr 6, artikel-id 114Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    As a model organism, modeling and analysis of the phenotype of Arabidopsis thaliana (A. thaliana) leaves for a given genotype can help us better understand leaf growth regulation. A. thaliana leaves growth trajectories are to be nonlinear and the leaves contribute most to the above-ground biomass. Therefore, analysis of their change regulation and development of nonlinear growth models can better understand the phenotypic characteristics of leaves (e.g., leaf size) at different growth stages. In this study, every individual leaf size of A. thaliana rosette leaves was measured during their whole life cycle using non-destructive imaging measurement. And three growth models (Gompertz model, logistic model and Von Bertalanffy model) were analyzed to quantify the rosette leaves growth process of A. thaliana. Both graphical (plots of standardized residuals) and numerical measures (AIC, R2 and RMSE) were used to evaluate the fitted models. The results showed that the logistic model fitted better in describing the growth of A. thaliana leaves compared to Gompertz model and Von Bertalanffy model, as it gave higher R2 and lower AIC and RMSE for the leaves of A. thaliana at different growth stages (i.e., early leaf, mid-term leaf and late leaf).

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