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  • 51. Baena-González, Elena
    et al.
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Shaping plant development through the SnRK1–TOR metabolic regulators2017Inngår i: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 35, s. 152-157Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    SnRK1 (Snf1-related protein kinase 1) and TOR (target of rapamycin) are evolutionarily conserved protein kinases that lie at the heart of energy sensing, playing central and antagonistic roles in the regulation of metabolism and gene expression. Increasing evidence links these metabolic regulators to numerous aspects of plant development, from germination to flowering and senescence. This prompts the hypothesis that SnRK1 and TOR modify developmental programs according to the metabolic status to adjust plant growth to a specific environment. The aim of this review is to provide support to this hypothesis and to incentivize further studies on this topic by summarizing the work that establishes a genetic connection between SnRK1-TOR and plant development.

  • 52. Bai, Bing
    et al.
    Novák, Ondrej
    Ljung, Karin
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
    Bentsink, Leonie
    Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy2018Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, nr 3, s. 1077-1085Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The importance of translational regulation during Arabidopsis seed germination has been shown previously. Here the role of transcriptional and translational regulation during seed imbibition of the very dormant DELAY OF GERMINATION 1 (DOG1) near-isogenic line was investigated. Polysome profiling was performed on dormant and after-ripened seeds imbibed for 6 and 24 h in water and in the transcription inhibitor cordycepin. Transcriptome and translatome changes were investigated. Ribosomal profiles of after-ripened seeds imbibed in cordycepin mimic those of dormant seeds. The polysome occupancy of mRNA species is not affected by germination inhibition, either as a result of seed dormancy or as a result of cordycepin treatment, indicating the importance of the regulation of transcript abundance. The expression of auxin metabolism genes is discriminative during the imbibition of after-ripened and dormant seeds, which is confirmed by altered concentrations of indole-3-acetic acid conjugates and precursors.

  • 53.
    Bai, Bing
    et al.
    Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, the Netherlands; Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, the Netherlands.
    Peviani, Alessia
    van der Horst, Sjors
    Gamm, Magdalena
    Snel, Berend
    Bentsink, Leónie
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Molecular Plant Physiology, Utrecht University, 3584 CH Utrecht, the Netherlands.
    Extensive translational regulation during seed germination revealed by polysomal profiling2017Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, nr 1, s. 233-244Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed germination. The polysome occupancy of thousands of individual mRNAs changes to a large extent during the germination process. Intriguingly, these changes are restricted to two temporal phases (shifts) during germination, seed hydration and germination. Sequence features, such as upstream open reading frame number, transcript length, mRNA stability, secondary structures, and the presence and location of specific motifs correlated with this translational regulation. These features differed significantly between the two shifts, indicating that independent mechanisms regulate translation during seed germination. This study reveals substantial translational dynamics during seed germination and identifies development-dependent sequence features and cis elements that correlate with the translation control, uncovering a novel and important layer of gene regulation during seed germination.

  • 54. Bailey, S
    et al.
    Walters, R G
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Horton, P
    Acclimation of Arabidopsis thaliana to the light environment: the existence of separate low light and high light responses2001Inngår i: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 213, nr 5, s. 794-801Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The capacity for photosynthetic acclimation in Arabidopsis thaliana (L.) Heynh. cv. Landsberg erecta was assessed during growth over a broad range of irradiance. Discontinuities in the response to growth irradiance were revealed for the light- and CO2-saturated rate of photosynthesis (P-max) and the ratio of chlorophyll a to chlorophyll b (Chl a/b). Three separate phases in the response of P-max and Chl a/b to growth light were evident, with increases at low and high irradiance ranges and a plateau at intermediate irradiance. By measuring all chlorophyll-containing components of the thylakoid membrane that contribute to Chl alb we reveal that distinct strategies for growth at low and high irradiance underlie the discontinuous response. These strategies include, in addition to changes in the major light-harvesting complexes of photosystem II (LHCII) , large shifts in the amounts of both reaction centres as well as significant changes in the levels of minor LHCII and LHCI components.

  • 55.
    Bajhaiya, Amit K.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Univ Manchester, Fac Life Sci, Manchester, Lancs, England.
    Dean, Andrew P.
    Zeef, Leo A. H.
    Webster, Rachel E.
    Pittman, Jon K.
    PSR1 Is a Global Transcriptional Regulator of Phosphorus Deficiency Responses and Carbon Storage Metabolism in Chlamydomonas reinhardtii2016Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 170, nr 3, s. 1216-1234Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many eukaryotic microalgae modify their metabolism in response to nutrient stresses such as phosphorus (P) starvation, which substantially induces storage metabolite biosynthesis, but the genetic mechanisms regulating this response are poorly understood. Here, we show that P starvation-induced lipid and starch accumulation is inhibited in a Chlamydomonas reinhardtii mutant lacking the transcription factor Pi Starvation Response1 (PSR1). Transcriptomic analysis identified specific metabolism transcripts that are induced by P starvation but misregulated in the psr1 mutant. These include transcripts for starch and triacylglycerol synthesis but also transcripts for photosynthesis-, redox-, and stress signaling-related proteins. To further examine the role of PSR1 in regulating lipid and starch metabolism, PSR1 complementation lines in the psr1 strain and PSR1 overexpression lines in a cell wall-deficient strain were generated. PSR1 expression in the psr1 lines was shown to be functional due to rescue of the psr1 phenotype. PSR1 overexpression lines exhibited increased starch content and number of starch granules per cell, which correlated with a higher expression of specific starch metabolism genes but reduced neutral lipid content. Furthermore, this phenotype was consistent in the presence and absence of acetate. Together, these results identify a key transcriptional regulator in global metabolism and demonstrate transcriptional engineering in microalgae to modulate starch biosynthesis.

  • 56.
    Bajhaiya, Amit K.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Univ Manchester, Fac Life Sci, Michael Smith Bldg,Oxford Rd, Manchester M13 9PT, Lancs, England.
    Moreira, Javiera Ziehe
    Pittman, Jon K.
    Transcriptional Engineering of Microalgae: Prospects for High-Value Chemicals2017Inngår i: Trends in Biotechnology, ISSN 0167-7799, E-ISSN 1879-3096, Vol. 35, nr 2, s. 95-99Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Microalgae are diverse microorganisms that are of interest as novel sources of metabolites for various industrial, nutritional, and pharmaceutical applications. Recent studies have demonstrated transcriptional engineering of some metabolic pathways. We propose here that transcriptional engineering could be a viable means to manipulate the biosynthesis of specific high-value metabolic products.

  • 57.
    Bandau, Franziska
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Importance of tannins for responses of aspen to anthropogenic nitrogen enrichment2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Boreal forests are often strongly nitrogen (N) limited. However, human activities are leading to increased N inputs into these ecosystems, through atmospheric N deposition and forest fertilization. N input into boreal forests can promote net primary productivity, increase herbivore and pathogen damage, and shift plant species composition and community structure. Genetic diversity has been suggested as a key mechanism to promote a plant species’ stability within communities in response to environmental change. Within any plant population, specific traits (e.g. growth and defense traits) can vary substantially among individuals, and a greater variation in traits may increase chances for the persistence of at least some individuals of a population, when environmental conditions change. One aspect of plant chemistry that can greatly vary among different genotypes (GTs) are condensed tannin (CTs). These secondary metabolites have been suggested to affect plant performance in many ways, e.g. through influencing plant growth, the interactions of plants with herbivores and pathogens, and through affecting litter decomposition, and hence the return of nutrients to plants. To investigate how genotypic variation in foliar CT production may mediate the effects that anthropogenic N enrichment can have on plant performance and litter decomposition, I performed a series of experiments. For these experiments, aspen (Populus tremula) GTs with contrasting abilities to produce foliar CTs (i.e. low- vs. high-tannin producers) were grown under 3 N conditions, representing ambient N (+0 kg ha-1), upper level atmospheric N deposition (+15 kg ha-1), and forest fertilization rates (+150 kg ha-1). This general experimental set-up was once established in a field-like environment, from which natural enemies were excluded, and once in a field, in which enemies were present. In my first two studies, I investigated tissue chemistry and plant performance in both environments. I observed that foliar CT levels decreased in response to N in the enemy‑free environment (study I), but increased with added N when enemies were present (study II). These opposing responses to N may be explained by differences in soil N availability in the two environments, or by induction of CTs after enemy attack. Enemy damage generally increased in response to N, and was higher in low-tannin than in high-tannin plants across all N levels. Plant growth of high‑tannin plants was restricted under ambient and low N conditions, probably due to a trade-off between growth and defense. This growth constraint for high‑tannin plants was weakened, when high amounts of N were added (study I and II), and when enemy levels were sufficiently high, so that benefits gained through defense could outweigh the costs of defense production (study II). Despite those general responses of low- and high‑tannin producers to added N, I also observed a number of individual responses of GTs to N addition, which in some case were not connected to the intrinsic ability of the GTs to produce foliar CTs. In study III, gene expression levels in young leaves and phenolic pools of the plants that were grown in the enemy‑free environment were studied. This study revealed that gene control over the regulation of the phenylpropanoid pathway (PPP) was distributed across the entire pathway. Moreover, PPP gene expression was higher in high-tannin GTs than in low‑tannin GTs, particularly under ambient N. At the low N level, gene expressions declined for both low- and high-tannin producers, whereas at the high N level expression at the beginning and the end of the PPP was upregulated and difference between tannin groups disappeared. Furthermore, this study showed that phenolic pools were frequently uncorrelated, and that phenolic pools were only to some extent related to tannin production and gene expression. In study IV, I investigated the decomposability of litter from the field plants. I found that N enrichment generally decreased mass loss, but there was substantial genetic variation in decomposition rates, and GTs were differentially responsive to added N. Study IV further showed that CTs only had a weak effect on decomposition, and other traits, such as specific leaf area and the lignin:N ratio, could better explain genotypic difference in mass loss. Furthermore, N addition caused a shift in which traits most strongly influenced decomposition rates. Collectively, the result of these studies highlight the importance of genetic diversity to promote the stability of species in environments that experience anthropogenic change.

  • 58.
    Bandau, Franziska
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Albrectsen, Benedicte Riber
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Gundale, Michael J.
    Differences in constitutive tannin-level influence Populus tremula genotypes’ responses to anthropogenic N-enrichmentManuskript (preprint) (Annet vitenskapelig)
  • 59.
    Bandau, Franziska
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Albrectsen, Benedicte Riber
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Julkunen-Tiitto, Riitta
    Gundale, Michael J.
    Genotypic variability in Populus tremula L. affects how anthropogenic nitrogen enrichment influences litter decomposition2017Inngår i: Plant and Soil, ISSN 0032-079X, E-ISSN 1573-5036, Vol. 410, nr 1-2, s. 467-481Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Boreal forests can receive substantial nitrogen (N) enrichment via atmospheric N deposition and industrial forest fertilization. While it is known that N enrichment can impact ecosystem properties, such as litter decomposition, it remains poorly understood how genetic variability within plant species modifies these impacts. We grew replicates of ten Populus tremula L. genotypes (GTs) under 3 N conditions; ambient, and levels representing atmospheric N deposition and industrial forest fertilization. We measured leaf and litter physical and chemical traits, and conducted a litter decomposition assay. Leaf traits varied due to N treatment, GT, and constitutive tannin levels. Leaf traits were in some cases correlated with litter traits, and decomposition was influenced by single and interactive effects of N and GT. Nitrogen addition unexpectedly decelerated decomposition, potentially due to changes in specific leaf area (SLA). Variation in decomposition rates among the GTs was best explained by their differences in SLA, and lignin:N ratio. Nitrogen addition also caused a shift in which traits most strongly influenced decomposition. Our findings highlight that the considerable diversity present in tree species can have a strong influence on ecosystem processes, such as decomposition, and how these processes respond to environmental change.

  • 60.
    Bandau, Franziska
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Albrectsen, Benedicte Riber
    Julkunen-Tiitto, Riitta
    Gundale, Michael J.
    The effect of anthropogenic nitrogen enrichment on litter decomposition differs among contrasting Populus tremula L. genotypesArtikkel i tidsskrift (Annet vitenskapelig)
  • 61.
    Bandau, Franziska
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Decker, Vicki Huizu Guo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Gundale, Michael J.
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE 90183 Umeå, Sweden.
    Albrectsen, Benedicte Riber
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK 1871 Frederiksberg C, Denmark.
    Genotypic tannin levels in Populus tremula impact the way nitrogen enrichment affects growth and allocation responses for some traits and not for others2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 10, artikkel-id e0140971Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plant intraspecific variability has been proposed as a key mechanism by which plants adapt to environmental change. In boreal forests where nitrogen availability is strongly limited, nitrogen addition happens indirectly through atmospheric N deposition and directly through industrial forest fertilization. These anthropogenic inputs of N have numerous environmental consequences, including shifts in plant species composition and reductions in plant species diversity. However, we know less about how genetic differences within plant populations determine how species respond to eutrophication in boreal forests. According to plant defense theories, nitrogen addition will cause plants to shift carbon allocation more towards growth and less to chemical defense, potentially enhancing vulnerability to antagonists. Aspens are keystone species in boreal forests that produce condensed tannins to serve as chemical defense. We conducted an experiment using ten Populus tremula genotypes from the Swedish Aspen Collection that express extreme levels of baseline investment into foliar condensed tannins. We investigated whether investment into growth and phenolic defense compounds in young plants varied in response to two nitrogen addition levels, corresponding to atmospheric N deposition and industrial forest fertilization. Nitrogen addition generally caused growth to increase, and tannin levels to decrease; however, individualistic responses among genotypes were found for height growth, biomass of specific tissues, root: shoot ratios, and tissue lignin and N concentrations. A genotype's baseline ability to produce and store condensed tannins also influenced plant responses to N, although this effect was relatively minor. High-tannin genotypes tended to grow less biomass under low nitrogen levels and more at the highest fertilization level. Thus, the ability in aspen to produce foliar tannins is likely associated with a steeper reaction norm of growth responses, which suggests a higher plasticity to nitrogen addition, and potentially an advantage when adapting to higher concentrations of soil nitrogen.

  • 62. Barajas-Lopez, Juan de Dios
    et al.
    Blanco, Nicolas E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Plastid-to-nucleus communication, signals controlling the running of the plant cell2013Inngår i: Biochimica et Biophysica Acta. Molecular Cell Research, ISSN 0167-4889, E-ISSN 1879-2596, Vol. 1833, nr 2, s. 425-437Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids. 

  • 63.
    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 development2013Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 3, artikkel-id e60305Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 64. Barker-Åström, Kara
    et al.
    Schelin, Jenny
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Clarke, Adrian K
    Campbell, Douglas A
    Chlorosis during nitrogen starvation is altered by carbon dioxide and temperature status and is mediated by the ClpP1 protease in Synechococcus elongatus.2005Inngår i: Archives of Microbiology, ISSN 0302-8933, Vol. 183, nr 1, s. 66-9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The interactive effects of inorganic carbon status, temperature and light on chlorosis induced by nitrogen deficiency, and the roles of Clp proteases in this process were investigated. In wild-type cultures grown in high or ambient CO2, following transfer to media lacking combined nitrogen, phycocyanin per cell dropped primarily through dilution of the pigment through cell division, and also suffered variable degrees of net degradation. When grown at high CO2 (5%), chlorophyll (Chl) suffered net degradation to a greater extent than phycocyanin. In marked contrast, growth at ambient CO2 resulted in Chl per cell dropping through dilution. Conditions that drove net Chl degradation in the wild-type resulted in little or no net Chl degradation in a clpPI inactivation mutant, with Chl content dropping largely through growth dilution in the mutant. The chlorotic response of a clpPII inactivation strain was nearly the same as that of wild-type, although phycocyanin degradation may have been slightly accelerated in the former.

  • 65.
    Barros, Jaime
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Serk, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Granlund, Irene
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Pesquet, Edouard
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The cell biology of lignification in higher plants2015Inngår i: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 115, nr 7, s. 1053-1074Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Background Lignin is a polyphenolic polymer that strengthens and waterproofs the cell wall of specialized plant cell types. Lignification is part of the normal differentiation programme and functioning of specific cell types, but can also be triggered as a response to various biotic and abiotic stresses in cells that would not otherwise be lignifying.

    Scope Cell wall lignification exhibits specific characteristics depending on the cell type being considered. These characteristics include the timing of lignification during cell differentiation, the palette of associated enzymes and substrates, the sub-cellular deposition sites, the monomeric composition and the cellular autonomy for lignin monomer production. This review provides an overview of the current understanding of lignin biosynthesis and polymerization at the cell biology level.

    Conclusions The lignification process ranges from full autonomy to complete co-operation depending on the cell type. The different roles of lignin for the function of each specific plant cell type are clearly illustrated by the multiple phenotypic defects exhibited by knock-out mutants in lignin synthesis, which may explain why no general mechanism for lignification has yet been defined. The range of phenotypic effects observed include altered xylem sap transport, loss of mechanical support, reduced seed protection and dispersion, and/or increased pest and disease susceptibility.

  • 66.
    Barros-Rios, Jaime
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Malvar, Rosa A.
    Jung, Hans-Joachim G.
    Bunzel, Mirko
    Santiago, Rogelio
    Divergent selection for ester-linked diferulates in maize pith stalk tissues. Effects on cell wall composition and degradability2012Inngår i: Phytochemistry, ISSN 0031-9422, E-ISSN 1873-3700, Vol. 83, s. 43-50Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cross-linking of grass cell wall components through diferulates (DFAs) has a marked impact on cell wall properties. However, results of genetic selection for DFA concentration have not been reported for any grass species. We report here the results of direct selection for ester-linked DFA concentration in maize stalk pith tissues and the associated changes in cell wall composition and biodegradability. After two cycles of divergent selection, maize populations selected for higher total DFA (DFAT) content (CHs) had 16% higher DFAT concentrations than populations selected for lower DFAT content (as). These significant DFA concentration gains suggest that DFA deposition in maize pith parenchyma cell walls is a highly heritable trait that is genetically regulated and can be modified trough conventional breeding. Maize populations selected for higher DFAT had 13% less glucose and 10% lower total cell wall concentration than CLs, suggesting that increased cross-linking of feruloylated arabinoxylans results in repacking of the matrix and possibly in thinner and firmer cell walls. Divergent selection affected esterified DFAT and monomeric ferulate ether cross link concentrations differently, supporting the hypothesis that the biosynthesis of these cell wall components are separately regulated. As expected, a more higher DFA ester cross-coupled arabinoxylan network had an effect on rumen cell wall degradability (CLs showed 12% higher 24-h total polysaccharide degradability than CHs). Interestingly, 8-8-coupled DFAs, previously associated with cell wall strength, were the best predictors of pith cell wall degradability (negative impact). Thus, further research on the involvement of these specific DFA regioisomers in limiting cell wall biodegradability is encouraged. (C) 2012 Elsevier Ltd. All rights reserved.

  • 67.
    Bashar Shafiul, Shamrat
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Characterization of cell wall in transgenic aspen with modified xylan acetylation2015Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    ABSTRACT

    Mature plant cells are enclosed by inflexible wall made up of cellulose microfibrils, pectins, hemicelluloses and in some cases lignin. This cell wall provides the structure and the defense for plant cells. In secondary cell walls of dicotyledons, major hemicellulose is xylan consisting of β-(1, 4)-linked xylose units. Xylan is synthesized in Golgi apparatus by several enzymes activities. REDUCED WALL ACETYLATION (RWA) genes are involved in xylan acetylation. These genes were downregulated in hybrid aspen in order to reduce xylan acetylation activity during its biosynthesis. In addition, acetyl xylan esterase (FC2) from the fungus Aspergillus niger was expressed in hybrid aspen to modify xylan acetylation post-synthetically. In this work, I have studied effects of these modifications on wood cell wall composition.

    The cell wall components were sequentially extracted by using the small scale method and the weight of extractives, lignin, hemicelluloses and celluloses per weight of dry wood were determined. In addition, the Updegraff cellulose, Klason lignin contents per weight of extractive free wood were determined and monosugar compositions of non-cellulosic components were analyzed by methanolysis and Trimethylsilyl derivatisation (TMS). 

    I have found that content of cellulose determined by sequential extraction method was significantly increased in all constructs as compared to the wild type. Reduction of lignin (as determined by sequential extraction) was found in DFC2 construct and RWA RNAi 35S-AB and CD constructs. Furthermore, RWA RNAi 35S-CD and RWA RNAi WP-ABCD constructs showed decreased hemicellulose as compared to the wild type. Moreover, DFC2 constructs exhibited decrease in non-cellulosic sugars hydrolyzed during TMS. FC2 expressing lines showed a reduction in xylose which is the main building block of xylan. In contrast, glucose and galactose contents were increased. Inhibition of expression of all RWA genes (WP-ABCD) caused similar changes.

    Considering all the data I conclude that, reduced acetylation of xylan can affect extractability, biosynthesis or modification of polysaccharides and lignin in cell wall.

    Keywords: Cellulose microfibrils; pectins; hemicellulose; lignin, xylan; secondary wall; aspen; xylan biosynthesis; biosynthesis of polysaccharides. 

  • 68.
    Bañares de Dios, Guillermo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Elucidating the role of CSK during early light response and chloroplast development2014Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Elucidating the role of CSK during early light response and chloroplast development

    Chloroplasts of higher plants have evolved from endosymbiotic, ancestor of modern prokaryotic cyanobacteria. During evolution most of the genes from the genome of the endosymbiont have moved to the nucleus of it host. As a consequence the components of the photosynthetic machinery are encoded both in the chloroplastic and in the nuclear genomes. Therefore, expression of both genomes must be tightly coordinated to ensure a simultaneous and stoichiometric biosynthesis of the chloroplast components at different developmental stages and under environmental or metabolic changes. This is achieved by a mechanism referred to as retrograde signalling. During retrograde signalling, signals are emitted from the chloroplast consisting on intracellular pathways emitted by the chloroplast communicating the status of the chloroplast and regulating the expression of nuclear genes encoding plastid components. The aim of this project was to elucidate the role of CSK (Chloroplast Sensor Kinase) in relation to previously described retrograde signalling components PRIN2 (Plastid Redox INsensitive 2) and GUN1 (Genomes UNcoupled 1). CSK is a plastid kinase involved in the long- term, acclimation response to balance the ratio between PSII and PSI by regulating the expression of psaA. The activity of CSK is regulated by the redox state of the plastoquinone pool. My work revealed that CSK is up- regulated upon light exposure. In addition, similarly to the prin2 and gun1 mutants, the csk mutant exhibited lower chlorophyll content, a striking yellow cotyledon tip phenotype, impaired chloroplast development and a down- regulation of PEP dependent genes psaA and psbA during a de- etiolation development and for the establishment of PEP activity in light. Furthermore, the similarity in the mutant phenotypes suggests that CSK is involved in the same signalling pathway as PRIN2 and GUN1.

  • 69.
    Bellini, C
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Adventious roots2014Inngår i: eLSArtikkel, forskningsoversikt (Annet (populærvitenskap, debatt, mm))
  • 70.
    Bellini, Catherine
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Institut Jean-Pierre Bourgin, UMR 1318 INRA-AgroParisTech, Versailles, France.
    Pacurar, Daniel I
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Perrone, Irene
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Adventitious roots and lateral roots: similarities and differences2014Inngår i: Annual Review of Plant Biology, ISSN 1543-5008, E-ISSN 1545-2123, Vol. 65, s. 639-666Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    In addition to its role in water and nutrient uptake, the root system is fundamentally important because it anchors a plant to its substrate. Although a wide variety of root systems exist across different species, all plants have a primary root (derived from an embryonic radicle) and different types of lateral roots. Adventitious roots, by comparison, display the same functions as lateral roots but develop from aerial tissues. In addition, they not only develop as an adaptive response to various stresses, such as wounding or flooding, but also are a key limiting component of vegetative propagation. Lateral and adventitious roots share key elements of the genetic and hormonal regulatory networks but are subject to different regulatory mechanisms. In this review, we discuss the developmental processes that give rise to lateral and adventitious roots and highlight knowledge acquired over the past few years about the mechanisms that regulate adventitious root formation.

  • 71.
    Benedict, Catherine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Cold Acclimation: Dissecting the plant low temperature signaling pathway using functional genomics2006Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The physiological process of cold acclimation protects plants native to the temperate regions of the world from the deleterious effects of low and freezing temperatures. This is achieved by a series of transcriptional, regulatory, and metabolic changes that enable continued growth and survival. Within minutes of exposure to temperatures below ca. 10°C, a complex cascade of transcriptional events is initiated to accomplish these changes. The initial alarm phase favors the rapid induction of a library of stress proteins with protective functions (e.g. COR proteins). This is followed by a cold hardened phase, characterized by maximal freezing tolerance, which continues until either the stress is removed, or the plant's metabolic and/or developmental state can no longer support maximal resistance.

    We have studied some of the important transcription factors and transcriptional changes associated with the initial alarm and later hardened phases of cold acclimation in the herbaceous annual Arabidopsis thaliana and the woody perennial Populus spp. We confirmed the functionality of the CBF-mediated signaling cascade in Poplar overexpressing AtCBF1, but noted that regulon composition and endogenous poplar CBF ortholog induction appeared to be tissue-specific. The lack of statistically significant DRE enrichment in the Poplar AtCBF1 regulons led us to investige cis-element abundance in the cold-associated transcription factor regulons of publicly available microarray data from Arabidopsis, leading to the development of a gene voting method of microarray analysis that we used to test for regulatory associations between transcription factors and their downstream cis-elements and gene targets. This analysis resulted in a new transcriptional model of the ICE1-mediated signaling cascade and implicated a role for phytochrome A. Application of this same method to microarray data from arabidopsis leaves developed at low temperature allowed us to identify a new cis-element, called DDT, which possessed enhancer-blocking function during the alarm stage of cold stress, but was enriched in the promoters of genes upregulated during the later cold hardened stages. As leaf growth and development at low temperature correlated with the enhancement freeze tolerance in Arabidopsis, we compared the transcriptomes of rapidly growing and fully grown poplar leaves at night (when both low temperatures and PhyA status might play important roles in nature), in the hopes of comparing this data with that of cold-treated leaves in the future. We identified the nocturnal mode of leaf growth in Populus deltoides as predominantly proliferative as opposed to expansive, and potentially linked to cellular carbohydrate status.

  • 72.
    Benedict, Catherine
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Geisler, Matt
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Huner, Norman
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis.2006Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 141, nr 4, s. 1219-1232Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (–1), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 (induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.

  • 73.
    Benedict, Catherine
    et al.
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysiologisk botanik.
    Lundmark, Maria
    Druart, Nathalie
    Strand, Åsa
    Gardeström, Per
    Bako, Lazlo
    Hurry, Vaughan
    The novel enhancer-blocking cis-element DDT is enriched in genes associated with long-term acclimation in Arabidopsis thalianaManuskript (Annet vitenskapelig)
  • 74.
    Benedict, Catherine
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Skinner, J. S.
    Meng, R.
    Chang, Y.
    Bhalerao, R.
    Finn, C.
    Chen, T. H. H.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten.
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    The Role of the CBF-dependent Signalling Pathway in Woody Perennials2006Inngår i: Cold Hardiness in Plants: Molecular Genetics, Cell Biology and Physiology / [ed] T Chen, M Uemura, S Fujikawa, Wallingford: CABI Publishing, 2006, s. 167-180Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 75.
    Benedict, Catherine
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Skinner, Jeffrey S
    Meng, Rengong
    Chang, Yongjian
    Bhalerao, Rishikesh
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Huner, Norman P A
    Finn, Chad E
    Chen, Tony H H
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The CBF1-dependent low temperature signalling pathway, regulon and increase in freeze tolerance are conserved in Populus spp2006Inngår i: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 29, nr 7, s. 1259-1272Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The meristematic tissues of temperate woody perennials must acclimate to freezing temperatures to survive the winter and resume growth the following year. To determine whether the C-repeat binding factor (CBF) family of transcription factors contributing to this process in annual herbaceous species also functions in woody perennials, we investigated the changes in phenotype and transcript profile of transgenic Populus constitutively expressing CBF1 from Arabidopsis (AtCBF1). Ectopic expression of AtCBF1 was sufficient to significantly increase the freezing tolerance of non-acclimated leaves and stems relative to wild-type plants. cDNA microarray experiments identified genes up-regulated by ectopic AtCBF1 expression in Populus, demonstrated a strong conservation of the CBF regulon between Populus and Arabidopsis and identified differences between leaf and stem regulons. We studied the induction kinetics and tissue specificity of four CBF paralogues identified from the Populus balsamifera subsp. trichocarpa genome sequence (PtCBFs). All four PtCBFs are cold-inducible in leaves, but only PtCBF1 and PtCBF3 show significant induction in stems. Our results suggest that the central role played by the CBF family of transcriptional activators in cold acclimation of Arabidopsis has been maintained in Populus. However, the differential expression of the PtCBFs and differing clusters of CBF-responsive genes in annual (leaf) and perennial (stem) tissues suggest that the perennial-driven evolution of winter dormancy may have given rise to specific roles for these 'master-switches' in the different annual and perennial tissues of woody species.

  • 76.
    Benlloch, Reyes
    et al.
    Department of Forest Genetics and Plant Physiology, SLU.
    Shevela, Dmitriy
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hainzl, Tobias
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Grundström, Christin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Shutova, Tatyana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sauer-Eriksson, Elisabeth
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Crystal structure and functional characterization of Photosystem II-associated carbonic anhydrase CAH3 in Chlamydomonas reinhardtii2015Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 167, nr 3, s. 950-962Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In oxygenic photosynthesis, light energy is stored in the form of chemical energy by converting CO2 and water into carbohydrates.The light-driven oxidation of water that provides the electrons and protons for the subsequent CO2 fixation takes place inphotosystem II (PSII). Recent studies show that in higher plants, HCO3– increases PSII activity by acting as a mobile acceptor ofthe protons produced by PSII. In the green alga Chlamydomonas reinhardtii, a luminal carbonic anhydrase, CrCAH3, was suggested toimprove proton removal from PSII, possibly by rapid reformation of HCO3– from CO2. In this study, we investigated the interplaybetween PSII and CrCAH3 by membrane inlet mass spectrometry and x-ray crystallography. Membrane inlet mass spectrometrymeasurements showed that CrCAH3 was most active at the slightly acidic pH values prevalent in the thylakoid lumen underillumination. Two crystal structures of CrCAH3 in complex with either acetazolamide or phosphate ions were determined at 2.6- and2.7-Å resolution, respectively. CrCAH3 is a dimer at pH 4.1 that is stabilized by swapping of the N-terminal arms, a feature notpreviously observed in a-type carbonic anhydrases. The structure contains a disulfide bond, and redox titration of CrCAH3 functionwith dithiothreitol suggested a possible redox regulation of the enzyme. The stimulating effect of CrCAH3 and CO2/HCO3– on PSIIactivity was demonstrated by comparing the flash-induced oxygen evolution pattern of wild-type and CrCAH3-less PSIIpreparations. We showed that CrCAH3 has unique structural features that allow this enzyme to maximize PSII activity at lowpH and CO2 concentration.

  • 77. 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 Arabidopsis2015Inngår i: Nature plants, ISSN 2055-026X, Vol. 1, nr 12, artikkel-id 15176Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 78. Bergman, Anders
    et al.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ericson, Ingemar
    Method to Obtain a Chlorophyll-free Preparation of Intact Mitochondria from Spinach Leaves.1980Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 66, nr 3, s. 442-445Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mitochondria from green leaves of spinach have been prepared using a three-step procedure involving differential centrifugation, partition in an aqueous dextran polyethylene glycol two-phase system and Percoll gradient centrifugation. The mitochondrial fractions after the different steps of purification were compared. The final mitochondrial preparation was totally free from chloroplast material measured as chlorophyll content. The enrichment of mitochondria in relation to peroxisomes and microsomes was approximately 12 and 33 times, respectively, based on NAD:isocitrate dehydrogenase activity, glycolate oxidase activity, and NADPH:cytochrome c oxidoreductase activity. The apparent intactness of the inner and the outer mitochondrial membranes was higher than 90% as measured by latency of enzyme activities. The mitochondria showed high respiratory rates with respiratory control and the ADP/O ratios approached the theoretical limits.

  • 79. Bergman, Birgitta
    et al.
    Huss-Danell, Kerstin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    ULTRASTRUCTURE OF STIGONEMA IN THE CEPHALODIA OF STEREOCAULON-PASCHALE1983Inngår i: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 15, s. 181-190Artikkel i tidsskrift (Fagfellevurdert)
  • 80.
    Bernhardsson, Carolina
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Robinson, Kathryn M.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Abreu, Ilka N.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Univ Copenhagen, Sect Plant Biochem, Dept Plant & Environm Sci, DK-1871 Frederiksberg, Denmark.
    Ingvarsson, Pär K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes2013Inngår i: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 16, nr 6, s. 791-798Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plantherbivore interactions vary across the landscape and have been hypothesised to promote local adaption in plants to the prevailing herbivore regime. Herbivores that feed on European aspen (Populus tremula) change across regional scales and selection on host defence genes may thus change at comparable scales. We have previously observed strong population differentiation in a set of inducible defence genes in Swedish P. tremula. Here, we study the geographic patterns of abundance and diversity of herbivorous insects, the untargeted metabolome of the foliage and genetic variation in a set of wound-induced genes and show that the geographic structure co-occurs in all three data sets. In response to this structure, we observe local maladaptation of herbivores, with fewer herbivores on local trees than on trees originated from more distant localities. Finally, we also identify 28 significant associations between single nucleotide polymorphisms SNPs from defence genes and a number of the herbivore traits and metabolic profiles.

  • 81.
    Bernhardsson, Carolina
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Robinson, Kathryn M.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Abreu, Ilka N.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Ingvarsson, Pär K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Population differentiation in arthropod community structure and phenotypic association with inducible defense genes in European Aspen (Populus tremula L., salicaceae)Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Plant-herbivore interactions are known to vary across a landscape due to both variation in abiotic and biotic factors. Such spatial variation tends to promoting local adaption of plants to the prevailing herbivore regime. Here we use data from a common garden to look for patterns across populations in the abundance and diversity of herbivorous insects. We also screen for variation in the untargeted metabolome of the foliage of a subset of the same trees. We also search for phenotypic associations between genetic variation in a number of wound-induced genes and phenotypic variation in herbivore abundance, diversity and in metabolomes. We observe significant genetic variation in a number of herbivore-related traits but low correlations between traits. We do observe substantial genetic structure in both herbivore community structure and in metabolic profiles and this structure is aligned with genetic structure we have previously documented for a set of defense genes. We also identify a number of significant associations between SNPs from wound-induced defense genes and a number of the herbivore traits and metabolic profiles. However, these associations are likely not causal, but are rather caused by the underlying population structure we observe. These results highlight to the importance of historical processes and the need to better understand both the current-day geographic distribution of different herbivore species as well as the post-glacial colonization history of both plants and herbivores.

  • 82.
    Bernhardsson, Carolina
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
    Vidalis, Amaryllis
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München.
    Wang, Xi
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
    Scofield, Douglas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Uppsala Multidisciplinary Center for Advanced Computational Science; Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala, Sweden.
    Schiffthaler, Bastian
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Baison, John
    Street, Nathaniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Garcia-Gil, M. Rosario
    Ingvarsson, Pär K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
    An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)2019Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, nr 5, s. 1623-1632Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

  • 83.
    Besya, Azim-Berdy
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Grönlund, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Intrinsic phenotypic stability of a bi-stable auto regulatory gene2016Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikkel-id 22951Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Even under homogenous conditions clonal cells can assume different distinct states for generations to follow, also known as epigenetic inheritance. Such long periods of different phenotypic states can be formed due to the existence of more than one stable state in the molecule concentration, where the different states are explored through molecular fluctuations. By formulating a single reaction variable representing the birth and death of molecules, including transcription, translation and decay, we calculate the escape time from the phenotypic states attained from autocatalytic synthesis through a Fokker-Planck formulation and integration of an effective pseudo-potential. We calculate the stability of the phenotypic states both for cooperative binding feedback and dimer binding feedback, resulting in non-linear decay.

  • 84.
    Betson, Tatiana R
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Augusti, Angela
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Schleucher, Jürgen
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Quantification of deuterium isotopomers of tree-ring cellulose using nuclear magnetic resonance.2006Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 78, nr 24, s. 8406-8411Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Stable isotopes in tree rings are important tools for reconstruction of past climate. Deuterium (D) is of particular interest since it may contain climate signals and report on tree physiology. Measurements of the D/H ratio of tree-ring cellulose have proven difficult to interpret, presumably because the D/H ratio of the whole molecule blends the abundances of the seven D isotopomers of cellulose. Here we present a method to measure the abundance of the D isotopomers of tree-ring cellulose by nuclear magnetic resonance spectroscopy (NMR). The method transforms tree-ring cellulose into a glucose derivative that gives highly resolved, quantifiable deuterium NMR spectra. General guidelines for measurement of D isotopomers by NMR are described. The transformation was optimized for yield and did not alter the original D isotopomer abundances, thus, conserving the original signals recorded in wood cellulose. In the tree-ring samples tested, the abundances of D isotopomers varied by approximately ±10% (2% standard error). This large variability can only be caused by biochemistry processes and shows that more information is present in D isotopomer abundances, compared to the D/H ratio. Therefore, measurements of the D isotopomer distribution of tree rings may be used to obtain information on long-term adaptations to environmental changes and past climate change.

  • 85. Betson, Tatiana R.
    et al.
    Augusti, Angela
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Schleucher, Jürgen
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Quantifying deuterium isotopomers of cellulose using Nuclear Magnetic Resonance2006Inngår i: Analytical Chemistry, Vol. 78, nr 24, s. 8406-8411Artikkel i tidsskrift (Fagfellevurdert)
  • 86. Betti, Marco
    et al.
    Bauwe, Hermann
    Busch, Florian A.
    Fernie, Alisdair R.
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Levey, Myles
    Ort, Donald R.
    Parry, Martin A. J.
    Sage, Rowan
    Timm, Stefan
    Walker, Berkley
    Weber, Andreas P. M.
    Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement2016Inngår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 67, nr 10, s. 2977-2988Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Recycling of the 2-phosphoglycolate generated by the oxygenase reaction of Rubisco requires a complex and energy-consuming set of reactions collectively known as the photorespiratory cycle. Several approaches aimed at reducing the rates of photorespiratory energy or carbon loss have been proposed, based either on screening for natural variation or by means of genetic engineering. Recent work indicates that plant yield can be substantially improved by the alteration of photorespiratory fluxes or by engineering artificial bypasses to photorespiration. However, there is also evidence indicating that, under certain environmental and/or nutritional conditions, reduced photorespiratory capacity may be detrimental to plant performance. Here we summarize recent advances obtained in photorespiratory engineering and discuss prospects for these advances to be transferred to major crops to help address the globally increasing demand for food and biomass production.

  • 87. Bhalerao, RP
    et al.
    Collier, JL
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Grossman, AR
    The structure of phycobilisomes in mutants of synechococcus sp strain pcc-7942 devoid of specific linker polypeptides1995Inngår i: Photochemistry and Photobiology, ISSN 0031-8655, E-ISSN 1751-1097, Vol. 61, nr 3, s. 298-302Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effect of elimination of the 30, 33 and 9 kDa phycobilisome rod-linker polypeptides on rod length was examined by electron microscopy of phycobilisomes isolated from wild-type Synechococcus sp. strain PCC 7942 and from genetically engineered mutants with lesions in the genes encoding the rod-linker polypeptides. The maximum rod length in the absence of the 33 kDa linker polypeptide was two phycocyanin hexamers, whereas rods with up to five hexamers were found in the mutant strain lacking the 30 kDa linker polypeptide. Elimination of the 9 kDa linker polypeptide did not have a significant effect on rod length. Finally, mutants lacking either the 30 or 33 kDa rod-associated linker polypeptides had an increased number of rods that terminated with a phycocyanin trimer. These observations are discussed with respect to the role of the linker polypeptides in the biosynthesis of the rod substructure.

  • 88. Bhalerao, RP
    et al.
    Gillbro, T
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Structure and energy-transfer of the phycobilisome in a linker protein replacement mutant of cyanobacterium synechococcus-79421991Inngår i: Biochimica et Biophysica Acta, ISSN 0006-3002, E-ISSN 1878-2434, Vol. 1060, nr 1, s. 59-66Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The role of the linker proteins in the biogenesis and energy transfer of the phycobilisome rod was monitored by making insertional inactivation in the cpcI gene coding for the core-proximal 33 kilodalton (kDa) protein in the cyanobacterium Synechococcus 7942. The insertion leaves the cpcH gene coding for the core-distal 30 kDa protein intact and functional. Analysis of the phycobilisome protein composition of the cpcI mutant shows that the 30 kDa protein is present in normal amounts in the rod, indicating that the 30 kDa linker protein can replace the 33 kDa protein in the biogenesis and structural integrity of the rod. The absorption and fluorescence characteristics of the mutated phycobilisome is almost indistinguishable from that of the wild-type of the same rod length. The fluorescence kinetics from the cpcI mutant show that the dominating decay component has a lifetime from phycocyanin of 69 ps as compared to 72 ps found for the wild-type phycobilisome with the same rod length. The results show that replacing the 33 kDa for the 30 kDa linker in the rod does not alter the energy harvesting or the energy transfer characteristics of the rod in contrast to what has been concluded from data obtained from in vitro experiments. We conclude that the linker polypeptides have only a minor influence on the energy transfer characteristics of the rod but are mainly involved in determining the length of the rod in response to changing environmental light conditions.

  • 89. Bhalerao, RP
    et al.
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Factors influencing the phycobilisome rod composition of the cyanobacterium synechococcus sp pcc-7942: effects of reduced phycocyanin content, lack of rod-linkers, and over-expression of the rod-terminating linker1994Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 90, nr 1, s. 187-197Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Four novel mutants with altered phycobilisomes were constructed in the cyanobacterium Synechococcus 7942 to study factors influencing the rod length and composition. These mutants show (1) reduced phycocyanin content, (2) reduced phycocyanin content combined with loss of the 33 kDa linker, (3) loss of the 30 kDa rod-linker and (4) overexpression of the 9 kDa rod terminating linker. For these mutants we determined the 33 to 27 kDa and 30 to 27 kDa linker ratios in the isolated phycobilisomes and compared these ratios with those in the wild type. The 30 kDa linker can be incorporated into the rods in absence of the 33 kDa linker. The incorporation of the 30 kDa linker is lower in absence of the 33 kDa linker. When the 30 kDa linker is missing, an increase in the level of the 33 kDa linker is seen, indicating that there could be an excess of the 33 kDa linker in the cells. Our results also show that a reduction in the phycocyanin content causes a decrease in the rod length simultaneously with a reduction of the 30/27 linker ratio, without altering the 33/27 ratio. Reduced phycocyanin content and absence of the 33 kDa linker cause a dramatic reduction in the incorporation of the 30 kDa linker into the rods in the mutant B2SMIKM. Over-expression of the 9 kDa linker results in a decreased incorporation of both the 33 and 30 kDa linkers into the rods, the effect being more pronounced for the 30 kDa linker. This result indicates that the level of the 9 kDa linker relative to those of the 33 and the 30 kDa linkers may be an important determinant of the phycobilisome rod length.

  • 90. Bhalerao, RP
    et al.
    Lind, LK
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Cloning of the cpce and cpcf genes from synechococcus sp pcc-6301 and their inactivation in synechococcus sp pcc-79421994Inngår i: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 26, nr 1, s. 313-326Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Two open reading frames denoted as cpcE and cpcF were cloned and sequenced from Synechococcus sp. PCC 6301. The cpcE and cpcF genes are located downstream of the cpcB2A2 gene cluster in the phycobilisome rod operon and can be transcribed independently of the upstream cpcB2A2 gene cluster. The cpcE and cpcF genes were separately inactivated by insertion of a kanamycin resistance cassette in Synechococcus sp. PCC 7942 to generate mutants R2EKM and R2FKM, respectively, both of which display a substantial reduction in spectroscopically detectable phycocyanin. The levels of beta- and alpha-phycocyanin polypeptides were reduced in the R2EKM and R2FKM mutants although the phycocyanin and linker genes are transcribed at normal levels in the mutants as in the wild type indicating the requirement of the functional cpcE and cpcF genes for normal accumulation of phycocyanin. Two biliprotein fractions were isolated on sucrose density gradient from the R2EKM/R2FKM mutants. The faster sedimenting fraction consisted of intact phycobilisomes. The slower sedimenting biliprotein fraction was found to lack phycocyanin polypeptides, thus no free phycocyanin was detected in the mutants. Characterization of the phycocyanin from the mutants revealed that it was chromophorylated, had a lambda(max) similar to that from the wild type and could be assembled into the phycobilisome rods. Thus, although phycocyanin levels are reduced in the R2EKM and R2FKM mutants, the remaining phycocyanin seems to be chromophorylated and similar to that in the wild type with respect to phycobilisome rod assembly and energy transfer to the core.

  • 91. Bhalerao, RP
    et al.
    Lind, LK
    Persson, CE
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Cloning of the phycobilisome rod linker genes from the cyanobacterium synechococcus sp pcc-6301 och their inactivation in synechococcus sp pcc-79421993Inngår i: Molecular General Genetics, ISSN 0026-8925, E-ISSN 1432-1874, Vol. 237, nr 1-2, s. 89-96Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The phycobilisome rod linker genes in the two closely related cyanobacteria Synechococcus sp. PCC 6301 and Synechococcus sp. PCC 7942 were studied. Southern blot analysis showed that the genetic organization of the phycobilisome rod operon is very similar in the two strains. The phycocyanin gene pair is duplicated and separated by a region of about 2.5 kb. The intervening region between the duplicated phycocyanin gene pair was cloned from Synechococcus sp. PCC 6301 and sequenced. Analysis of this DNA sequence revealed the presence of three open reading frames corresponding to 273, 289 and 81 amino acids, respectively. Insertion of a kanamycin resistance cassette into these open reading frames indicated that they corresponded to the genes encoding the 30, 33 and 9 kDa rod linkers, respectively, as judged by the loss of specific linkers from the phycobilisomes of the insertional mutants. Amino acid compositions of the 30 and 33 kDa linkers derived from the DNA sequence were found to deviate from those of purified 33 and 30 kDa linkers in the amounts of glutamic acid/glutamine residues. On the basis of similarity of the amino acid sequence of the rod linkers between Synechococcus sp. PCC 6301 and Calothrix sp. PCC 7601 we name the genes encoding the 30, 33 and 9 kDa linkers cpcH, cpcI and cpcD, respectively. The three linker genes were found to be co-transcribed on an mRNA of 3700 nucleotides. However, we also detected a smaller species of mRNA, of 3400 nucleotides, which would encode only the cpcH and cpcI genes. The 30 kDa linker was still found in phycobilisome rods lacking the 33 kDa linker and the 9 kDa linker was detected in mutants lacking the 33 or the 30 kDa linkers. Free phycocyanin was found in the mutants lacking the 33 or the 30 kDa linkers, whereas no free phycocyanin could be found in the mutant lacking the 9 kDa linker.

  • 92.
    Bhalerao, Rupali
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Keskitalo, Johanna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sterky, Fredrik
    Erlandsson, Rikard
    Björkbacka, Harry
    Birve, Simon Jonsson
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Karlsson, Jan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Lundeberg, Joakim
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gene expression in autumn leaves2003Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 131, nr 2, s. 430-442Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Two cDNA libraries were prepared, one from leaves of a field-grown aspen (Populus tremula) tree, harvested just before any visible sign of leaf senescence in the autumn, and one from young but fully expanded leaves of greenhouse-grown aspen (Populus tremula x tremuloides). Expressed sequence tags (ESTs; 5,128 and 4,841, respectively) were obtained from the two libraries. A semiautomatic method of annotation and functional classification of the ESTs, according to a modified Munich Institute of Protein Sequences classification scheme, was developed, utilizing information from three different databases. The patterns of gene expression in the two libraries were strikingly different. In the autumn leaf library, ESTs encoding metallothionein, early light-inducible proteins, and cysteine proteases were most abundant. Clones encoding other proteases and proteins involved in respiration and breakdown of lipids and pigments, as well as stress-related genes, were also well represented. We identified homologs to many known senescence-associated genes, as well as seven different genes encoding cysteine proteases, two encoding aspartic proteases, five encoding metallothioneins, and 35 additional genes that were up-regulated in autumn leaves. We also indirectly estimated the rate of plastid protein synthesis in the autumn leaves to be less that 10% of that in young leaves.

  • 93.
    Birve, Simon
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Selstam, Eva
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Johansson, L B A
    Secondary structure of NADPH: protochlorophyllide oxidoreductase examined by circular dichroism and prediction methods1996Inngår i: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 317, nr 2, s. 549-555Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To study the secondary structure of the enzyme NADPH:protochlorophyllide oxidoreductase (PCOR), a novel method of enzyme isolation was developed. The detergent isotridecyl poly(ethylene glycol) ether (Genapol X-080) selectively solubilizes the enzyme from a prolamellar-body fraction isolated from wheat (Triticum aestivum L.). The solubilized fraction was further purified by ion-exchange chromatography. The isolated enzyme was studied by fluorescence spectroscopy at 77 K, and by CD spectroscopy. The fluorescence-emission spectra revealed that the binding properties of the substrate and co-substrate were preserved and that photo-reduction occurred. The CD spectra of PCOR were analysed for the relative amounts of the secondary structures, alpha-helix, beta-sheet, turn and random coil. The secondary structure composition was estimated to be 33% alpha-helix, 19% beta-sheet, 20% turn and 28% random coil. These values are in agreement with those predicted by the Predict Heidelberg Deutschland and self-optimized prediction method from alignments methods. The enzyme has some amino acid identity with other NADPH-binding enzymes containing the Rossmann fold. The Rossmann-fold fingerprint motif is localized in the N-terminal region and at the expected positions in the predicted secondary structure. It is suggested that PCOR is anchored to the interfacial region of the membrane by either a beta-sheet or an alpha-helical region containing tryptophan residues. A hydrophobic loop-region could also be involved in membrane anchoring.

  • 94. Bishop, NI
    et al.
    Öquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    CORRELATION OF THE PHOTOSYSTEM-I AND PHOTOSYSTEM-II REACTION CENTER CHLOROPHYLL-PROTEIN COMPLEXES, CP-AI AND CP-AII, WITH PHOTOSYSTEM ACTIVITY AND LOW-TEMPERATURE FLUORESCENCE EMISSION PROPERTIES IN MUTANTS OF SCENEDESMUS1980Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 49, nr 4, s. 477-486Artikkel i tidsskrift (Fagfellevurdert)
  • 95.
    Björken, Lars
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysiologisk botanik.
    Detection of endophytic fungi in aspen2007Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    Endophytes are mutualistic fungi living in green tissue of all plants examined so far.Some of these fungi can produce compounds that are beneficial to the host plant, and it isalso known that some pathogenic fungi live parts of their lives as endophytes. Endophyticinteractions have been well characterized in various grasses, but much is unknown abouttheir interactions with trees. One reason for this is that the fungal biodiversity is muchlarger among endophytes in trees than in grasses, another is that screening for endophytestakes a lot of work. The goal of this thesis work was to develop a polymerase chainreaction (PCR) based method that is simple, fast and reliable for detection of endophytesin aspens. Eleven primer pairs were designed, each pair specific for one fungus. Afteroptimization and evaluation four of the primer pairs were found to be both specific andsensitive, and could detect fungus in DNA preparations from leaf samples.

  • 96.
    Björkholm, Patrik
    et al.
    The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala.
    Daniluk, Pawel
    Department of Biophysics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
    Kryshtafovych, Andriy
    UC Davis Genome Centre, UC Davis, USA.
    Fidelis, Krzysztof
    UC Davis Genome Centre, UC Davis, USA.
    Andersson, Robin
    The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala.
    Hvidsten, Torgeir
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts.2009Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 25, nr 10, s. 1264-1270Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    MOTIVATION: Correct prediction of residue-residue contacts in proteins that lack good templates with known structure would take ab initio protein structure prediction a large step forward. The lack of correct contacts, and in particular long-range contacts, is considered the main reason why these methods often fail. RESULTS: We propose a novel hidden Markov model (HMM)-based method for predicting residue-residue contacts from protein sequences using as training data homologous sequences, predicted secondary structure and a library of local neighborhoods (local descriptors of protein structure). The library consists of recurring structural entities incorporating short-, medium- and long-range interactions and is general enough to reassemble the cores of nearly all proteins in the PDB. The method is tested on an external test set of 606 domains with no significant sequence similarity to the training set as well as 151 domains with SCOP folds not present in the training set. Considering the top 0.2 x L predictions (L = sequence length), our HMMs obtained an accuracy of 22.8% for long-range interactions in new fold targets, and an average accuracy of 28.6% for long-, medium- and short-range contacts. This is a significant performance increase over currently available methods when comparing against results published in the literature.

  • 97. Björn, Lars Olof
    et al.
    Sundqvist, Christer
    Öquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysiologisk botanik. Umeå Plant Science Centre.
    A tribute to Per Halldal (1922-1986), a Norwegian photobiologist in Sweden.2007Inngår i: Photosynthesis Research, ISSN 0166-8595, Vol. 92, nr 1, s. 7-11Artikkel i tidsskrift (Annet vitenskapelig)
  • 98.
    Blanco, Nicolas E.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ceccoli, Romina D.
    Dalla Via, Maria V.
    Voss, Ingo
    Segretin, Maria E.
    Bravo-Almonacid, Fernando F.
    Melzer, Michael
    Hajirezaei, Mohammad-Reza
    Scheibe, Renate
    Hanke, Guy T.
    Expression of the Minor Isoform Pea Ferredoxin in Tobacco Alters Photosynthetic Electron Partitioning and Enhances Cyclic Electron Flow2013Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 161, nr 2, s. 866-879Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ferredoxins (Fds) are ferrosulfoproteins that function as low-potential electron carriers in plants. The Fd family is composed of several isoforms that share high sequence homology but differ in functional characteristics. In leaves, at least two isoforms conduct linear and cyclic photosynthetic electron transport around photosystem I, and mounting evidence suggests the existence of at least partial division of duties between these isoforms. To evaluate the contribution of different kinds of Fds to the control of electron fluxes along the photosynthetic electron transport chain, we overexpressed a minor pea (Pisum sativum) Fd isoform (PsFd1) in tobacco (Nicotiana tabacum) plants. The transplastomic OeFd1 plants exhibited variegated leaves and retarded growth and developmental rates. Photosynthetic studies of these plants indicated a reduction in carbon dioxide assimilation rates, photosystem II photochemistry, and linear electron flow. However, the plants showed an increase in nonphotochemical quenching, better control of excitation pressure at photosystem II, and no evidence of photoinhibition, implying a better dynamic regulation to remove excess energy from the photosynthetic electron transport chain. Finally, analysis of P700 redox status during illumination confirmed that the minor pea Fd isoform promotes enhanced cyclic flow around photosystem I. The two novel features of this work are: (1) that Fd levels achieved in transplastomic plants promote an alternative electron partitioning even under greenhouse light growth conditions, a situation that is exacerbated at higher light intensity measurements; and (2) that an alternative, minor Fd isoform has been overexpressed in plants, giving new evidence of labor division among Fd isoforms.

  • 99.
    Blanco, Nicolas E.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Guinea-Diaz, Manuel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Whelan, James
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Interaction between plastid and mitochondrial retrograde signalling pathways during changes to plastid redox status2014Inngår i: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 369, nr 1640, artikkel-id 20130231Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mitochondria and chloroplasts depend upon each other; photosynthesis provides substrates for mitochondrial respiration and mitochondrial metabolism is essential for sustaining photosynthetic carbon assimilation. In addition, mitochondrial respiration protects photosynthesis against photoinhibition by dissipating excess redox equivalents from the chloroplasts. Genetic defects in mitochondrial function result in an excessive reduction and energization of the chloroplast. Thus, it is clear that the activities of mitochondria and plastids need to be coordinated, but the manner by which the organelles communicate to coordinate their activities is unknown. The regulator of alternative oxidase (rao1) mutant was isolated as a mutant unable to induce AOX1a expression in response to the inhibitor of the mitochondrial cytochrome c reductase (complex III), antimycin A. RAO1 encodes the nuclear localized cyclin-dependent kinase E1 (CDKE1). Interestingly, the rao1 mutant demonstrates a genome uncoupled phenotype also in response to redox changes in the photosynthetic electron transport chain. Thus, CDKE1 was shown to regulate both LIGHT HARVESTING COMPLEX B (LHCB) and ALTERNATIVE OXIDASE 1 (AOX1a) expression in response to retrograde signals. Our results suggest that CDKE1 is a central nuclear component integrating mitochondrial and plastid retrograde signals and plays a role in regulating energy metabolism during the response to stress.

  • 100.
    Blanco, Nicolas E.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Centro de Estudios Fotosintéticos y Bioquímicos, Universidad Nacional de Rosario (CEFOBI-CONICET/UNR), Rosario, Argentina.
    Liebsch, Daniela
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina.
    Guinea Diaz, Manuel
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Whelan, James
    Dual and dynamic intracellular localization of Arabidopsis thaliana SnRK1.12019Inngår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, nr 8, s. 2325-2338Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sucrose non-fermenting 1 (SNF1)-related protein kinase 1.1 (SnRK1.1; also known as KIN10 or SnRK1 alpha) has been identified as the catalytic subunit of the complex SnRK1, the Arabidopsis thaliana homologue of a central integrator of energy and stress signalling in eukaryotes dubbed AMPK/Snf1/SnRK1. A nuclear localization of SnRK1.1 has been previously described and is in line with its function as an integrator of energy and stress signals. Here, using two biological models (Nicotiana benthamiana and Arabidopsis thaliana), native regulatory sequences, different microscopy techniques, and manipulations of cellular energy status, it was found that SnRK1.1 is localized dynamically between the nucleus and endoplasmic reticulum (ER). This distribution was confirmed at a spatial and temporal level by co-localization studies with two different fluorescent ER markers, one of them being the SnRK1.1 phosphorylation target HMGR. The ER and nuclear localization displayed a dynamic behaviour in response to perturbations of the plastidic electron transport chain. These results suggest that an ER-associated SnRK1.1 fraction might be sensing the cellular energy status, being a point of crosstalk with other ER stress regulatory pathways.

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