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  • 1.
    Albrectsen, Benedicte
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    From micro towards the macro scale2006In: New Phytologist, Vol. 172, p. 7-10Article in journal (Refereed)
  • 2.
    Albrectsen, Benedicte R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Björkén, Lars
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Varad, Akkamahadevi
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hagner, Åsa
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wedin, Mats
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Endophytic fungi in European aspen (Populus tremula) leaves - diversity, detection, and a suggested correlation with herbivory resistance2010In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 41, no 1, p. 17-28Article in journal (Refereed)
    Abstract [en]

    According to the geographic mosaic theory of coevolution (GMTC), clines of traits reflecting local co-adaptation (including resistance genes) should be common between a host and its parasite and should persist across time. To test the GMTC-assumption of persistent clinal patterns we compared the natural prevalence of two parasites on aspen Populus tremula trees: mining moths of the genus Phyllocnistis and leaf rust Melampsora spp. Damage data were collated from the Swedish National Forest Damage Inventory (2004–2006). In addition, occurrence of the parasites was scored in field conditions in two common gardens in the north and south of Sweden over five growing seasons (2004–2008), then related to biomass (stem height and diameter) and to concentrations of eleven leaf phenolics. Phyllocnistis mainly occurred in the northern garden, a distribution range which was confirmed by the countrywide inventory, although Phyllocnistis was more abundant on southern clones, providing evidence for possible local maladaptation. Melampsora occurred all over the country and in both gardens, but built up more quickly on northern clones, which suggests a centre of local clone maladaptation in the north. Stem growth also followed a clinal pattern as did the concentration of three phenolic compounds: benzoic acid, catechin and cinnamic acid. However, only benzoic acid was related to parasite presence: negatively to Phyllocnistis and positively to Melampsora and it could thus be a potential trait under selection.

    In conclusion, clines of Phyllocnistis were stronger and more persistent compared to Melampsora, which showed contrasting clines of varying strength. Our data thus support the assumption of the GMTC model that clines exist in the border between hot and cold spots and that they may be less persistent for parasites with an elevated gene flow, and/or for parasites which cover relatively larger hot spots surrounded by fewer cold spots.

  • 3.
    Albrectsen, Benedicte R
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Witzell, Johanna
    Robinson, Kathryn M
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wulff, Sören
    Luquez, Virginia MC
    Ågren, Rickard
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Large scale geographic clines of parasite damage to Populus tremula L2010In: Ecography, ISSN 0906-7590, E-ISSN 1600-0587, Vol. 33, no 3, p. 483-493Article in journal (Refereed)
    Abstract [en]

    In conclusion, clines of Phyllocnistis were stronger and more persistent compared to Melampsora, which showed contrasting clines of varying strength. Our data thus support the assumption of the GMTC model that clines exist in the border between hot and cold spots and that they may be less persistent for parasites with an elevated gene flow, and/or for parasites which cover relatively larger hot spots surrounded by fewer cold spots.

  • 4. Andersson, Anders
    et al.
    Keskitalo, Johanna
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Bhalerao, Rupali
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Sterky, Fredrik
    Wissel, Kirsten
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tandre, Karolina
    Aspeborg, Henrik
    Moyle, Richard
    Ohmiya, Yasunori
    Bhalerao, Rishikesh
    Brunner, Amy
    Gustafsson, Petter
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lundeberg, Joakim
    Nilsson, Ove
    Sandberg, Göran
    Strauss, Steven
    Sundberg, Björn
    Uhlen, Mathias
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nilsson, Peter
    A transcriptional timetable of autumn senescence2004In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 5, no 4, p. R24-Article in journal (Refereed)
    Abstract [en]

    Background We have developed genomic tools to allow the genus Populus (aspens and cottonwoods) to be exploited as a full-featured model for investigating fundamental aspects of tree biology. We have undertaken large-scale expressed sequence tag (EST) sequencing programs and created Populus microarrays with significant gene coverage. One of the important aspects of plant biology that cannot be studied in annual plants is the gene activity involved in the induction of autumn leaf senescence. Results On the basis of 36,354 Populus ESTs, obtained from seven cDNA libraries, we have created a DNA microarray consisting of 13,490 clones, spotted in duplicate. Of these clones, 12,376 (92%) were confirmed by resequencing and all sequences were annotated and functionally classified. Here we have used the microarray to study transcript abundance in leaves of a free-growing aspen tree (Populus tremula) in northern Sweden during natural autumn senescence. Of the 13,490 spotted clones, 3,792 represented genes with significant expression in all leaf samples from the seven studied dates. Conclusions We observed a major shift in gene expression, coinciding with massive chlorophyll degradation, that reflected a shift from photosynthetic competence to energy generation by mitochondrial respiration, oxidation of fatty acids and nutrient mobilization. Autumn senescence had much in common with senescence in annual plants; for example many proteases were induced. We also found evidence for increased transcriptional activity before the appearance of visible signs of senescence, presumably preparing the leaf for degradation of its components.

  • 5.
    Andersson, Jenny
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Walters, Robin G
    Horton, Peter
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antisense inhibition of the photosynthetic antenna proteins CP29 and CP26: implications for the mechanism of protective energy dissipation2001In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 13, no 5, p. 1193-1204Article in journal (Refereed)
    Abstract [en]

    The specific roles of the chlorophyll a/b binding proteins CP29 and CP26 in light harvesting and energy dissipation within the photosynthetic apparatus have been investigated. Arabidopsis was transformed with antisense constructs against the genes encoding the CP29 or CP26 apoprotein, which gave rise to several transgenic lines with remarkably low amounts of the antisense target proteins. The decrease in the level of CP24 protein in the CP29 antisense lines indicates a physical interaction between these complexes. Analysis of chlorophyll fluorescence showed that removal of the proteins affected photosystem II function, probably as a result of changes in the organization of the light-harvesting antenna. However, whole plant measurements showed that overall photosynthetic rates were similar to those in the wild type. Both antisense lines were capable of the qE type of nonphotochemical fluorescence quenching, although there were minor changes in the capacity for quenching and in its induction kinetics. High-light-induced violaxanthin deepoxidation to zeaxanthin was not affected, although the pool size of these pigments was decreased slightly. We conclude that CP29 and CP26 are unlikely to be sites for nonphotochemical quenching.

  • 6.
    Andersson, Jenny
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wentworth, Mark
    Walters, Robin G
    Howard, Caroline A
    Ruban, Alexander V
    Horton, Peter
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Absence of the Lhcb1 and Lhcb2 proteins of the light-harvesting complex of photosystem II - effects on photosynthesis, grana stacking and fitness2003In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 35, no 3, p. 350-361Article in journal (Refereed)
    Abstract [en]

    We have constructed Arabidopsis thaliana plants that are virtually devoid of the major light-harvesting complex, LHC II. This was accomplished by introducing the Lhcb2.1 coding region in the antisense orientation into the genome by Agrobacterium-mediated transformation. Lhcb1 and Lhcb2 were absent, while Lhcb3, a protein present in LHC II associated with photosystem (PS) II, was retained. Plants had a pale green appearance and showed reduced chlorophyll content and an elevated chlorophyll a/b ratio. The content of PS II reaction centres was unchanged on a leaf area basis, but there was evidence for increases in the relative levels of other light harvesting proteins, notably CP26, associated with PS II, and Lhca4, associated with PS I. Electron microscopy showed the presence of grana. Photosynthetic rates at saturating irradiance were the same in wild-type and antisense plants, but there was a 10-15% reduction in quantum yield that reflected the decrease in light absorption by the leaf. The antisense plants were not able to perform state transitions, and their capacity for non-photochemical quenching was reduced. There was no difference in growth between wild-type and antisense plants under controlled climate conditions, but the antisense plants performed worse compared to the wild type in the field, with decreases in seed production of up to 70%.

  • 7. Apuli, Rami-Petteri
    et al.
    Bernhardsson, Carolina
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Schiffthaler, Bastian
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Robinson, Kathryn M
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ingvarsson, Pär K.
    Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)2020In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 10, no 1, p. 299-309Article in journal (Refereed)
    Abstract [en]

    The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

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  • 8.
    Arshad, Rameez
    et al.
    Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic; Electron microscopy group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
    Saccon, Francesco
    Queen Mary University of London, School of Biological and Behavioural Sciences, London, UK.
    Bag, Pushan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Biswas, Avratanu
    Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
    Calvaruso, Claudio
    Institute for Molecular Biosciences,Goethe University of Frankfurt, Frankfurt, Germany.
    Bhatti, Ahmad Farhan
    Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands.
    Grebe, Steffen
    Department of Life Technologies, MolecularPlant Biology, University of Turku, Turku, Finland.
    Mascoli, Vincenzo
    Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
    Mahbub, Moontaha
    Queen Mary University of London, School of Biological and Behavioural Sciences, London, UK; Department of Botany, Jagannath University, Dhaka, Bangladesh.
    Muzzopappa, Fernando
    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, France.
    Polyzois, Alexandros
    Université de Paris, Faculté de pharmacie de Paris, CiTCoM UMR 8038 CNRS, Paris, France.
    Schiphorst, Christo
    Dipartimento di Biotecnologie, Università di Verona, Verona, Italy.
    Sorrentino, Mirella
    Photon Systems Instruments, spol. s.r.o., Drásov, Czechia; Department of Agricultural Sciences, University of Naples Federico II, Napoli, Italy.
    Streckaité, Simona
    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, France.
    van Amerongen, Herbert
    Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands.
    Aro, Eva-Mari
    Department of Life Technologies, MolecularPlant Biology, University of Turku, Turku, Finland.
    Bassi, Roberto
    Dipartimento di Biotecnologie, Università di Verona, Verona, Italy.
    Boekema, Egbert J.
    Electron microscopy group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
    Croce, Roberta
    Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
    Dekker, Jan
    Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
    van Grondelle, Rienk
    Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Kirilovsky, Diana
    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, France.
    Kouřil, Roman
    Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic.
    Michel, Sylvie
    Université de Paris, Faculté de pharmacie de Paris, CiTCoM UMR 8038 CNRS, Paris, France.
    Mullineaux, Conrad W.
    Queen Mary University of London, School of Biological and Behavioural Sciences, London, UK.
    Panzarová, Klára
    Photon Systems Instruments, spol. s.r.o., Drásov, Czechia.
    Robert, Bruno
    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, France.
    Ruban, Alexander V.
    Queen Mary University of London, School of Biological and Behavioural Sciences, London, UK.
    van Stokkum, Ivo
    Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
    Wientjes, Emilie
    Laboratory of Biophysics, Wageningen University, Wageningen, the Netherlands.
    Büchel, Claudia
    Institute for Molecular Biosciences,Goethe University of Frankfurt, Frankfurt, Germany.
    A kaleidoscope of photosynthetic antenna proteins and their emerging roles2022In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 189, no 3, p. 1204-1219Article in journal (Refereed)
    Abstract [en]

    Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

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  • 9.
    Babst, Benjamin A
    et al.
    Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA 30602, USA.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Orians, Colin M
    Department of Biology, Tufts University, Medford, MA 02155, USA.
    Local and systemic transcriptome responses to herbivory and jasmonic acid in Populus2009In: The Genetics & Genomes, Vol. 5, no 3, p. 459-474Article in journal (Refereed)
    Abstract [en]

    We used DNA microarrays to examine local and systemic transcriptional responses to herbivory by gypsy moth larvae (GM) and exogenous jasmonic acid (JAtrt) in leaves of Populus nigra L. to identify candidate signaling and defense genes and also to examine primary metabolism, as might relate to tolerance of damage. GM and JAtrt altered expression of over 800 genes, most of which have putative roles in defense signaling, secondary metabolism, and primary metabolism. Additionally, numerous uncharacterized genes responded to herbivory, providing a rich resource for future studies. There was limited overlap (14%) between the responses to GM and JAtrt. GM did, however, result in strong upregulation of genes involved not only in JA biosynthesis but also abscisic acid biosynthesis and other signaling pathways. GM induced known resistance transcripts, including polyphenolic biosynthetic genes, proteinase inhibitors, and amino acid deaminases. According to GOStats pathway level analysis, GM altered primary metabolism, including aromatic amino acid biosynthesis, fatty acid β-oxidation, and carbohydrate and organic acid metabolism. These alterations may be related to increased demands for substrate for secondary metabolites or may serve a tolerance-related role. Responses were more intense locally in treated leaves than in untreated (systemic) leaves and systemic responses were mostly a subset of the genes induced locally. A stronger local response might be needed to cope with localized stresses and wound healing. Since Populus in general and this clone in particular are known for their systemic induced resistance, genes induced both locally and systemically may be the highest quality candidates for resistance.

  • 10. BADER, P
    et al.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    JONSSON, BG
    WOOD-INHABITING FUNGI AND SUBSTRATUM DECLINE IN SELECTIVELY LOGGED BOREAL SPRUCE FORESTS1995In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 72, no 3, p. 355-362Article in journal (Refereed)
    Abstract [en]

    Eleven Norway spruce Picea abies (L.) Karst. forests in the boreal zone of Sweden were studied to investigate the effects of selective cuttings on wood-inhabiting fungi from the families Polyporaceae, Hymenochaetaceae and Corticiaceae (Basidiomycota). The II sites constitute a gradient from extensively logged to semi-natural forests. Old selective leggings that occurred about 100 years ago have significantly decreased the availability of large and highly decayed logs. Based on fruit bodies, both the total species number as well as the number of threatened species decreased with increasing degree of cutting. Some of the occurring wood-inhabiting fungi are commonly accepted as indicator species of forests with old-growth conditions. These species showed pronounced preferences for well decayed and large logs. They were also more frequent in the less affected sites and became rarer with increasing degree of cutting; they therefore seem to be good indicators of forests less affected by logging.

  • 11.
    Bag, Pushan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Chukhutsina, Volha
    Zhang, Zishan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Present address: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Shandong, China.
    Paul, Suman
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Present address: Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
    Ivanov, Alexander G.
    Shutova, Tatiana
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Croce, Roberta
    Holzwarth, Alfred R.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Direct energy transfer from photosystem II to photosystem I confers winter sustainability in Scots Pine2020In: Nature Communications, E-ISSN 2041-1723, Vol. 11, no 1, article id 6388Article in journal (Refereed)
    Abstract [en]

    Evergreen conifers in boreal forests can survive extremely cold (freezing) temperatures during long dark winter and fully recover during summer. A phenomenon called "sustained quenching" putatively provides photoprotection and enables their survival, but its precise molecular and physiological mechanisms are not understood. To unveil them, here we have analyzed seasonal adjustment of the photosynthetic machinery of Scots pine (Pinus sylvestris) trees by monitoring multi-year changes in weather, chlorophyll fluorescence, chloroplast ultrastructure, and changes in pigment-protein composition. Analysis of Photosystem II and Photosystem I performance parameters indicate that highly dynamic structural and functional seasonal rearrangements of the photosynthetic apparatus occur. Although several mechanisms might contribute to 'sustained quenching' of winter/early spring pine needles, time-resolved fluorescence analysis shows that extreme down-regulation of photosystem II activity along with direct energy transfer from photosystem II to photosystem I play a major role. This mechanism is enabled by extensive thylakoid destacking allowing for the mixing of PSII with PSI complexes. These two linked phenomena play crucial roles in winter acclimation and protection. Evergreen conifers rely on 'sustained quenching' to protect their photosynthetic machinery during long, cold winters. Here, Bag et al. show that direct energy transfer (spillover) from photosystem II to photosystem I triggered by loss of grana stacking in chloroplast is the major component of sustained quenching in Scots pine.

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  • 12.
    Bag, Pushan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lihavainen, Jenna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Delhomme, Nicolas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Riquelme, Thomas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Robinson, Kathryn M.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    An atlas of the Norway spruce needle seasonal transcriptome2021In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 108, no 6, p. 1815-1829Article in journal (Refereed)
    Abstract [en]

    Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

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  • 13.
    Bag, Pushan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Farci, Domenica
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Solubilization method for isolation of photosynthetic mega- And super-complexes from conifer thylakoids2021In: Bio-protocol, E-ISSN 2331-8325, Vol. 11, no 17, article id e4144Article in journal (Refereed)
    Abstract [en]

    Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with “fragile” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.

  • 14.
    Bag, Pushan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Shutova, Tatiana
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Shevela, Dmitriy
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lihavainen, Jenna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nanda, Sanchali
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ivanov, Alexander G.
    Department of Biology, University of Western Ontario, ON, London, Canada; Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria.
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry, Ångström laboratory, Uppsala University, Uppsala, Sweden.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Flavodiiron-mediated O2 photoreduction at photosystem I acceptor-side provides photoprotection to conifer thylakoids in early spring2023In: Nature Communications, E-ISSN 2041-1723, Vol. 14, no 1, article id 3210Article in journal (Refereed)
    Abstract [en]

    Green organisms evolve oxygen (O2) via photosynthesis and consume it by respiration. Generally, net O2 consumption only becomes dominant when photosynthesis is suppressed at night. Here, we show that green thylakoid membranes of Scots pine (Pinus sylvestris L) and Norway spruce (Picea abies) needles display strong O2 consumption even in the presence of light when extremely low temperatures coincide with high solar irradiation during early spring (ES). By employing different electron transport chain inhibitors, we show that this unusual light-induced O2 consumption occurs around photosystem (PS) I and correlates with higher abundance of flavodiiron (Flv) A protein in ES thylakoids. With P700 absorption changes, we demonstrate that electron scavenging from the acceptor-side of PSI via O2 photoreduction is a major alternative pathway in ES. This photoprotection mechanism in vascular plants indicates that conifers have developed an adaptative evolution trajectory for growing in harsh environments.

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  • 15. Bailey, S
    et al.
    Walters, R G
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Horton, P
    Acclimation of Arabidopsis thaliana to the light environment: the existence of separate low light and high light responses2001In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 213, no 5, p. 794-801Article in journal (Refereed)
    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.

  • 16. Benson, Samuel L
    et al.
    Maheswaran, Pratheesh
    Ware, Maxwell A
    Hunter, C Neil
    Horton, Peter
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, 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 Arabidopsis2015In: Nature plants, ISSN 2055-026X, Vol. 1, no 12, article id 15176Article in journal (Refereed)
    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.

  • 17.
    Bernhardsson, Carolina
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Robinson, Kathryn M.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Abreu, Ilka N.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Univ Copenhagen, Sect Plant Biochem, Dept Plant & Environm Sci, DK-1871 Frederiksberg, Denmark.
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Geographic structure in metabolome and herbivore community co-occurs with genetic structure in plant defence genes2013In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 16, no 6, p. 791-798Article in journal (Refereed)
    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.

  • 18.
    Bernhardsson, Carolina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Robinson, Kathryn M.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Abreu, Ilka N.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Population differentiation in arthropod community structure and phenotypic association with inducible defense genes in European Aspen (Populus tremula L., salicaceae)Manuscript (preprint) (Other academic)
    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.

  • 19.
    Bhalerao, Rupali
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Keskitalo, Johanna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sterky, Fredrik
    Erlandsson, Rikard
    Björkbacka, Harry
    Birve, Simon Jonsson
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gustafsson, Petter
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Lundeberg, Joakim
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gene expression in autumn leaves2003In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 131, no 2, p. 430-442Article in journal (Refereed)
    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.

  • 20. Bossmann, B
    et al.
    Knoetzel, J
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Screening of chlorina mutants of barley (Hordeum vulgare L.) with antibodies against light-harvesting proteins of PS I and PS II: Absence of specific antenna proteins1997In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 52, no 2, p. 127-136Article in journal (Refereed)
    Abstract [en]

    Twenty-three chlorina (clo) mutants from the barley mutant collection of the Carlsberg Laboratory, Copenhagen, were tested for the presence of the four light-harvesting chlorophyll (Chl) a/b-binding proteins (LHC) of Photosystem I (Lhcal-4) and the PS II antenna proteins Lhcb1-3 (LHC II), Lhcb4-6 (CP29, CP26, CP24) and PsbS (CP22) using monospecific and monoclonal antibodies. Mutants allelic to barley mutant clo-f2, impaired in Chi b synthesis, provided evidence that Lhca4, Lhcb1 and Lhcb6 are unstable in the absence of Chi b, and the accumulation of Lhcb2, Lhcb3 and Lhcb4 is also impaired. Mutants at the locus chlorina-a (clo-a(117), clo-a(126) and clo-a(134)) lack or have only trace amounts of Lhca1, Lhca4, Lhcb1 and Lhcb3, whereas a mutant at the locus chlorina-b (clo-b(125)) had reduced amounts of all Lhca proteins. These two mutations could have an effect in protein import or assembly. Evidence is presented that Lhcb5 is the innermost LHC protein of PS II, and that Lhca1 and Lhca4, which have been supposed to be intimately associated in the LHCI-730 complex, can accumulate independently of each other. 77 K fluorescence emission spectra taken from leaves of clo-f2(101), clo-a(126) and clo-b(125) indicate that chlorophyll(s) emitting at 742 nm are coupled to the presence of Lhca4 that is bound to the reaction centre, and those emitting around 730 nm are located on Lhca1.

  • 21.
    Boussardon, Clément
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bag, Pushan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Juvany, Marta
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Šimura, Jan
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Ljung, Karin
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Keech, Olivier
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence2022In: Communications Biology, E-ISSN 2399-3642, Vol. 5, no 1, article id 1043Article in journal (Refereed)
    Abstract [en]

    The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

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  • 22.
    Bylesjö, Max
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Eriksson, Daniel
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Moritz, Thomas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Orthogonal projections to latent structures as a strategy for microarray data normalization2007In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 8, no 207Article in journal (Refereed)
    Abstract [en]

    Background

    During generation of microarray data, various forms of systematic biases are frequently introduced which limits accuracy and precision of the results. In order to properly estimate biological effects, these biases must be identified and discarded.

    Results

    We introduce a normalization strategy for multi-channel microarray data based on orthogonal projections to latent structures (OPLS); a multivariate regression method. The effect of applying the normalization methodology on single-channel Affymetrix data as well as dual-channel cDNA data is illustrated. We provide a parallel comparison to a wide range of commonly employed normalization methods with diverse properties and strengths based on sensitivity and specificity from external (spike-in) controls. On the illustrated data sets, the OPLS normalization strategy exhibits leading average true negative and true positive rates in comparison to other evaluated methods.

    Conclusions

    The OPLS methodology identifies joint variation within biological samples to enable the removal of sources of variation that are non-correlated (orthogonal) to the within-sample variation. This ensures that structured variation related to the underlying biological samples is separated from the remaining, bias-related sources of systematic variation. As a consequence, the methodology does not require any explicit knowledge regarding the presence or characteristics of certain biases. Furthermore, there is no underlying assumption that the majority of elements should be non-differentially expressed, making it applicable to specialized boutique arrays.

  • 23.
    Bylesjö, Max
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Eriksson, Daniel
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sjöström, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    MASQOT: a method for cDNA microarray spot quality control.2005In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 6, p. 250-Article in journal (Refereed)
    Abstract [en]

    Background

    cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.

    Results

    A novel methodology for cDNA microarray spot quality control is outlined. Multivariate discriminant analysis was used to assess spot quality based on existing and novel descriptors. The presented methodology displays high reproducibility and was found superior in identifying unreliable data compared to other evaluated methodologies.

    Conclusion

    The proposed methodology for cDNA microarray spot quality control generates non-discrete values of spot quality which can be utilized as weights in subsequent analysis procedures as well as to discard spots of undesired quality using the suggested threshold values. The MASQOT approach provides a consistent assessment of spot quality and can be considered an alternative to the labor-intensive manual quality assessment process.

  • 24.
    Bylesjö, Max
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Nilsson, Robert
    Umeå University, Faculty of Medicine, Umeå Life Science Centre (ULSC).
    Srivastava, Vaibhav
    Grönlund, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Johansson, Annika I
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Moritz, Thomas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Wingsle, Gunnar
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen2009In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 8, no 1, p. 199-210Article in journal (Refereed)
    Abstract [en]

    Tree biotechnology will soon reach a mature state where it will influence the overall supply of fiber, energy and wood products. We are now ready to make the transition from identifying candidate genes, controlling important biological processes, to discovering the detailed molecular function of these genes on a broader, more holistic, systems biology level. In this paper, a strategy is outlined for informative data generation and integrated modeling of systematic changes in transcript, protein and metabolite profiles measured from hybrid aspen samples. The aim is to study characteristics of common changes in relation to genotype-specific perturbations affecting the lignin biosynthesis and growth. We show that a considerable part of the systematic effects in the system can be tracked across all platforms and that the approach has a high potential value in functional characterization of candidate genes.

  • 25.
    Bylesjö, Max
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Segura, Vincent
    Soolanayakanahally, Raju Y
    Rae, Anne M
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Gustafsson, Petter
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Street, Nathaniel R
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    LAMINA: a tool for rapid quantification of leaf size and shape parameters2008In: BMC Plant Biology, E-ISSN 1471-2229, Vol. 8, article id 82Article in journal (Refereed)
    Abstract [en]

    Background: An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.

    Results: We have developed LAMINA (Leaf shApe deterMINAtion), a new tool for the automated analysis of images of leaves. LAMINA has been designed to provide classical indicators of leaf shape (blade dimensions) and size (area), which are typically required for correlation analysis to biomass productivity, as well as measures that indicate asymmetry in leaf shape, leaf serration traits, and measures of herbivory damage (missing leaf area). In order to allow Principal Component Analysis (PCA) to be performed, the location of a chosen number of equally spaced boundary coordinates can optionally be returned.

    Conclusion: We demonstrate the use of the software on a set of 500 scanned images, each containing multiple leaves, collected from a common garden experiment containing 116 clones of Populus tremula (European trembling aspen) that are being used for association mapping, as well as examples of leaves from other species. We show that the software provides an efficient and accurate means of analysing leaf area in large datasets in an automated or semi-automated work flow.

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  • 26.
    Bylesjö, Max
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Eriksson, Daniel
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Moritz, Thomas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    MASQOT-GUI: spot quality assessment for the two-channel microarray platform2006In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 22, no 20, p. 2554-2555Article in journal (Refereed)
    Abstract [en]

    MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated. AVAILABILITY: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at http://masqot-gui.sourceforge.net/

  • 27.
    Böhlenius, Henrik
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Huang, Tao
    Charbonnel-Campaa, Laurence
    Brunner, Amy M
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strauss, Steven H
    Nilsson, Ove
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees.2006In: Science, ISSN 1095-9203, Vol. 312, no 5776, p. 1040-3Article in journal (Refereed)
    Abstract [en]

    Forest trees display a perennial growth behavior characterized by a multiple-year delay in flowering and, in temperate regions, an annual cycling between growth and dormancy. We show here that the CO/FT regulatory module, which controls flowering time in response to variations in daylength in annual plants, controls flowering in aspen trees. Unexpectedly, however, it also controls the short-day–induced growth cessation and bud set occurring in the fall. This regulatory mechanism can explain the ecogenetic variation in a highly adaptive trait: the critical daylength for growth cessation displayed by aspen trees sampled across a latitudinal gradient spanning northern Europe.

  • 28.
    Courtois-Moreau, Charleen L
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Muñiz, Luis
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Bollhöner, Benjamin
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kaneda, Minako
    Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
    Samuels, Lacey
    Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    A unique program for cell death in xylem fibers of Populus stem2009In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 58, no 2, p. 260-274Article in journal (Refereed)
    Abstract [en]

    Maturation of the xylem elements involves extensive deposition of secondary cell-wall material and autolytic processes resulting in cell death. We describe here a unique type of cell-death program in xylem fibers of hybrid aspen (Populus tremula x P. tremuloides) stems, including gradual degradative processes in both the nucleus and cytoplasm concurrently with the phase of active cell-wall deposition. Nuclear DNA integrity, as determined by TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling) and Comet (single-cell gel electrophoresis) assays, was compromised early during fiber maturation. In addition, degradation of the cytoplasmic contents, as detected by electron microscopy of samples fixed by high-pressure freezing/freeze substitution (HPF-FS), was gradual and resulted in complete loss of the cytoplasmic contents well before the loss of vacuolar integrity, which is considered to be the moment of death. This type of cell death differs significantly from that seen in xylem vessels. The loss of vacuolar integrity, which is thought to initiate cell degradative processes in the xylem vessels, is one of the last processes to occur before the final autolysis of the remaining cell contents in xylem fibers. High-resolution microarray analysis in the vascular tissues of Populus stem, combined with in silico analysis of publicly available data repositories, suggests the involvement of several previously uncharacterized transcription factors, ethylene, sphingolipids and light signaling as well as autophagy in the control of fiber cell death.

  • 29.
    Damkjær, Jakob T
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kereïche, Sami
    Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.
    Johnson, Matthew P
    School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom.
    Kovacs, Laszlo
    Institute of Plant Biology, Biological Research Center, Hungarian Academy of Sciences, H-6726 Szeged, Hungary.
    Kiss, Anett Z
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Boekema, Egbert J
    Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.
    Ruban, Alexander V
    School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, United Kingdom.
    Horton, Peter
    Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The photosystem II light-harvesting protein Lhcb3 affects the macrostructure of photosystem II and the rate of state transitions in Arabidopsis2009In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 21, p. 3245-3256Article in journal (Refereed)
    Abstract [en]

    The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.

  • 30.
    de La Torre, Amanda R
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Birol, Inanc
    Bousquet, Jean
    Ingvarsson, Pär K
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jones, Steven J. M
    Keeling, Christopher I
    MacKay, John
    Nilsson, Ove
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Ritland, Kermit
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Yanchuk, Alvin
    Zerbe, Philipp
    Bohlmann, Jörg
    Insights into conifer giga-genomes2014In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 166, no 4, p. 1724-1732Article in journal (Refereed)
    Abstract [en]

    Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world's forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20-30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes.

  • 31. Demmig-Adams, Barbara
    et al.
    Ebbert, Volker
    Mellman, David L
    Mueh, Kristine E
    Schaffer, Lisa
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zarter, C Ryan
    Adamska, Iwona
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Adams III, William W
    Modulation of PsbS and flexible vs sustained energy dissipation by light environment in different species2006In: Physiologia Plantarum, Vol. 127, p. 670-80Article in journal (Refereed)
    Abstract [en]

    Contrasting acclimation strategies of photosynthesis and photoprotection were identified for annual mesophytes (spinach, pumpkin, and Arabidopsis) vs the tropical evergreen Monstera deliciosa. The annual species utilized full sunlight for photosynthesis to a much greater extent than the evergreen species. Conversely, the evergreen species exhibited a greater capacity for photoprotective thermal energy dissipation as well as a greater expression of the PsbS protein in full sun than the annual species. In all species, the majority of thermal energy dissipation [assessed as non-photochemical fluorescence quenching (NPQ)] was the flexible, ΔpH-dependent form of NPQ over the entire range of growth light environments. However, in response to a transfer of shade-grown plants to high light, the evergreen species exhibited a high level of sustained thermal dissipation (qI), but the annual species did not. This sustained energy dissipation in the evergreen species was not ΔpH-dependent nor did the low level of PsbS in shade leaves increase upon transfer to high light for several days. Sustained ΔpH-independent NPQ was correlated (a) initially, with sustained D1 protein phosphorylation and xanthophyll cycle arrest and (b) subsequently, with an accumulation over several days of PsbS-related one-helix proteins and newly synthesized zeaxanthin and lutein.

  • 32.
    Edlund, Erik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Novak, Ondrej
    Karady, Michael
    Ljung, Karin
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Contrasting patterns of cytokinins between years in senescing aspen leaves2017In: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 40, p. 622-634Article in journal (Refereed)
    Abstract [en]

    Cytokinins are plant hormones that typically block or delay leaf senescence. We profiled 34 different cytokinins/cytokinin metabolites (including precursors, conjugates and degradation products) in leaves of a free-growing mature aspen (Populus tremula) before and after the initiation of autumnal senescence over three consecutive years. The levels and profiles of individual cytokinin species, or classes/groups, varied greatly between years, despite the fact that the onset of autumn senescence was at the same time each year, and senescence was not associated with depletion of either active or total cytokinin levels. Levels of aromatic cytokinins (topolins) were low and changed little over the autumn period. Diurnal variations and weather-dependent variations in cytokinin content were relatively limited. We also followed the expression patterns of all aspen genes implicated as having roles in cytokinin metabolism or signaling, but neither the pattern of regulation of any group of genes nor the expression of any particular gene supported the notion that decreased cytokinin signaling could explain the onset of senescence. Based on the results from this tree, we therefore suggest that cytokinin depletion is unlikely to explain the onset of autumn leaf senescence in aspen.

  • 33. Ensminger, Ingo
    et al.
    Sveshnikov, Dmitry
    Campbell, Douglas A.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lloyd, Jon
    Shibistova, Olga
    Öquist, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Intermittent low temperatures constrain spring recovery of photosynthesis in boreal Scots pine forests2004In: Global Change Biology, ISSN 1354-1013, Vol. 10, no 6, p. 995-1008Article in journal (Refereed)
    Abstract [en]

    During winter and early spring, evergreen boreal conifers are severely stressed because light energy cannot be used when photosynthesis is pre-empted by low ambient temperatures. To study photosynthetic performance dynamics in a severe boreal climate, seasonal changes in photosynthetic pigments, chloroplast proteins and photochemical efficiency were studied in a Scots pine forest near Zotino, Central Siberia. In winter, downregulation of photosynthesis involved loss of chlorophylls, a twofold increase in xanthophyll cycle pigments and sustained high levels of the light stress-induced zeaxanthin pigment. The highest levels of xanthophylls and zeaxanthin did not occur during the coldest winter period, but rather in April when light was increasing, indicating an increased capacity for thermal dissipation of excitation energy at that time. Concomitantly, in early spring the D1 protein of the photosystem II (PSII) reaction centre and the light-harvesting complex of PSII dropped to their lowest annual levels. In April and May, recovery of PSII activity, chloroplast protein synthesis and rearrangements of pigments were observed as air temperatures increased above 0°C. Nevertheless, severe intermittent low-temperature episodes during this period not only halted but actually reversed the physiological recovery. During these spring low-temperature episodes, protective processes involved a complementary function of the PsbS and early light-induced protein thylakoid proteins. Full recovery of photosynthesis did not occur until the end of May. Our results show that even after winter cold hardening, photosynthetic activity in evergreens responds opportunistically to environmental change throughout the cold season. Therefore, climate change effects potentially improve the sink capacity of boreal forests for atmospheric carbon. However, earlier photosynthesis in spring in response to warmer temperatures is strongly constrained by environmental variation, counteracting the positive effects of an early recovery process.

  • 34.
    Escamez, Sacha
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Robinson, Kathryn M.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Luomaranta, Mikko
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gandla, Madhavi Latha
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mähler, Niklas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Yassin, Zakiya
    RISE AB, Stockholm, Sweden.
    Grahn, Thomas
    RISE AB, Stockholm, Sweden.
    Scheepers, Gerhard
    RISE AB, Stockholm, Sweden.
    Stener, Lars-Göran
    The Forestry Research Institute of Sweden, Ekebo, Svalöv, Sweden.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jönsson, Leif J.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock2023In: Biotechnology for Biofuels and Bioproducts, E-ISSN 2731-3654, Vol. 16, no 1, article id 65Article in journal (Refereed)
    Abstract [en]

    Background: Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

    Results: We recorded 65 wood-related and growth traits in a population of 113 natural aspen genotypes from Sweden (https://doi.org/10.5061/dryad.gtht76hrd). These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy and structure, and 25 wood saccharification traits as indicators of bioconversion potential. Glucose release after saccharification with acidic pretreatment correlated positively with tree stem height and diameter and the carbohydrate content of the wood, and negatively with the content of lignin and the hemicellulose sugar units. Most of these traits displayed extensive natural variation within the aspen population and high broad-sense heritability, supporting their potential in genetic improvement of feedstocks towards improved bioconversion. Finally, a genome-wide association study (GWAS) revealed 13 genetic loci for saccharification yield (on a whole-tree-biomass basis), with six of them intersecting with associations for either height or stem diameter of the trees.

    Conclusions: The simple growth traits of stem height and diameter were identified as good predictors of wood saccharification yield in aspen trees. GWAS elucidated the underlying genetics, revealing putative genetic markers for bioconversion of bioenergy tree feedstocks.

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  • 35.
    Fataftah, Nazeer
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bag, Pushan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    André, Domenique
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Lihavainen, Jenna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Zhang, Bo
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Ingvarsson, Pär K.
    Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Nilsson, Ove
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    GIGANTEA influences leaf senescence in trees in two different ways2021In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 187, no 4, p. 2435-2450Article in journal (Refereed)
    Abstract [en]

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

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  • 36.
    Fataftah, Nazeer
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Edlund, Erik
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden.
    Lihavainen, Jenna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bag, Pushan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Björkén, Lars
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Näsholm, Torgny
    Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not2022In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 174, no 3, article id e13690Article in journal (Refereed)
    Abstract [en]

    Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N ((Formula presented.)) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

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  • 37. Fracheboud, Yvan
    et al.
    Luquez, Virginia
    Björkén, Lars
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The control of autumn senescence in European aspen2009In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 149, no 4, p. 1982-1991Article in journal (Refereed)
    Abstract [en]

    The initiation, progression, and natural variation of autumn senescence in European aspen (Populus tremula) was investigated by monitoring chlorophyll degradation in (1) trees growing in natural stands and (2) cloned trees growing in a greenhouse under various light regimes. The main trigger for the initiation of autumn senescence in aspen is the shortening photoperiod, but there was a large degree of variation in the onset of senescence, both within local populations and among trees originating from different populations, where it correlated with the latitude of their respective origins. The variation for onset of senescence with a population was much larger than the variation of bud set. Once started, autumn senescence was accelerated by low temperature and longer nights, and clones that started to senescence late had a faster senescence. Bud set and autumn senescence appeared to be under the control of two independent critical photoperiods, but senescence could not be initiated until a certain time after bud set, suggesting that bud set and growth arrest are important for the trees to acquire competence to respond to the photoperiodic trigger to undergo autumn senescence. A timetable of events related to bud set and autumn senescence is presented.

  • 38.
    Frenkel, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bellafiore, Stephane
    Rochaix, Jean-David
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hierarchy amongst photosynthetic acclimation responses for plant fitness2007In: Physiologia Plantarum, Vol. 129, no 2, p. 455-459Article in journal (Refereed)
    Abstract [en]

    We have compared the seed production of Arabidopsis wild-type and mutant plants impaired in the regulation of the photosynthetic light reactions grown under natural conditions in the field. Mutant plants (npq4) lacking feedback de-excitation were, as previously demonstrated, severely affected in seed production. Seed sets of plants deficient in state transitions (stn7) were 19% smaller than those of wild-type plants, whereas plants missing the STN8 kinase required for the phosphorylation of the core photosystem II reaction centre polypeptides (stn8) had a normal seed production. Plants lacking both STN7 and STN8 kinases were strongly affected, indicating that these mutations act synergistically. In contrast, npq4×stn7 double mutants had the same seed set as npq4 mutants.

  • 39.
    Frenkel, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Johansson Jänkänpää, Hanna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Moen, Jon
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Plant photoprotection influences herbivore preferencesManuscript (preprint) (Other (popular science, discussion, etc.))
  • 40.
    Frenkel, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Johansson Jänkänpää, Hanna
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Moen, Jon
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    An illustrated gardener's guide to transgenic Arabidopsis field experiments2008In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 180, no 2, p. 545-555Article in journal (Refereed)
    Abstract [en]

    Field studies with transgenic Arabidopsislines have been performed over 8 yr, to better understand the influence that certain genes have on plant performance. Many (if not most) plant phenotypes cannot be observed under the near constant, low-stress conditions in growth chambers, making field experiments necessary. However, there are challenges in performing such experiments: permission must be obtained and regulations obeyed, the profound influence of uncontrollable biotic and abiotic factors has to be considered, and experimental design has to be strictly controlled.

    The aim here is to provide inspiration and guidelines for researchers who are not used to setting up such experiments, allowing others to learn from our mistakes. This is believed to be the first example of a ‘manual’ for field experiments with transgenic Arabidopsisplants. Many of the challenges encountered are common for all field experiments, and many researchers from ecological backgrounds are skilled in such methods. There is huge potential in combining the detailed mechanistic understanding of molecular biologists with ecologists’ expertise in examining plant performance under field conditions, and it is suggested that more interdisciplinary collaborations will open up new scientific avenues to aid analyses of the roles of genetic and physiological variation in natural systems.

  • 41.
    Frenkel, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Külheim, Carsten
    Johansson Jänkänpää, Hanna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Skogström, Oskar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Dall Osto, Luca
    Ågren, Jon
    Bassi, Roberto
    Moritz, Thomas
    Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences.
    Moen, Jon
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Improper excess light energy dissipation in Arabidopsis results in a metabolic reprogramming2009In: BMC Plant Biology, E-ISSN 1471-2229, Vol. 9, no 12, p. 1-16Article in journal (Refereed)
    Abstract [en]

    Background: Plant performance is affected by the level of expression of PsbS, a key photoprotective protein involved in the process of feedback de-excitation (FDE), or the qE component of non-photochemical quenching, NPQ.

    Results: In studies presented here, under constant laboratory conditions the metabolite profiles of leaves of wild-type Arabidopsis thaliana and plants lacking or overexpressing PsbS were very similar, but under natural conditions their differences in levels of PsbS expression were associated with major changes in metabolite profiles. Some carbohydrates and amino acids differed ten-fold in abundance between PsbS-lacking mutants and over-expressers, with wild-type plants having intermediate amounts, showing that a metabolic shift had occurred. The transcriptomes of the genotypes also varied under field conditions, and the genes induced in plants lacking PsbS were similar to those reportedly induced in plants exposed to ozone stress or treated with methyl jasmonate (MeJA). Genes involved in the biosynthesis of JA were up-regulated, and enzymes involved in this pathway accumulated. JA levels in the undamaged leaves of field-grown plants did not differ between wild-type and PsbS-lacking mutants, but they were higher in the mutants when they were exposed to herbivory.

    Conclusion: These findings suggest that lack of FDE results in increased photooxidative stress in the chloroplasts of Arabidopsis plants grown in the field, which elicits a response at the transcriptome level, causing a redirection of metabolism from growth towards defence that resembles a MeJA/JA response.

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  • 42.
    Frenkel, Martin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Külheim, Carsten
    Johansson Jänkänpää, Hanna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Skogström, Oskar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Frigerio, Sara
    Ågren, Jon
    Bassi, Roberto
    Moritz, Thomas
    Moen, Jon
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Improper regulation of light harvesting in Arabidopsis results in a metabolic reprogrammingManuscript (preprint) (Other (popular science, discussion, etc.))
  • 43.
    Ganeteg, Ulrika
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Klimmek, Frank
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Ihalainen, J.
    Ruban, A.
    Benson, S.
    van Roon, H.
    Scheller, H.V.
    Horton, P.
    Dekker, J.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Structure and function of the lightharvesting complex of higher plant photosystem IManuscript (preprint) (Other academic)
  • 44.
    Ganeteg, Ulrika
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Klimmek, Frank
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Lhca5 - an LHC-type protein associated with photosystem I2004In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 54, no 5, p. 641-651Article in journal (Refereed)
    Abstract [en]

    The light-harvesting antenna of higher plant photosystem (PS) I is known to be composed of four different types of light-harvesting complex (LHC) proteins (Lhca1–4). However, the genomic sequence of Arabidopsis thaliana contains open reading frames coding for two additional LHC type proteins (Lhca5–6) that are presumably associated with PSI. While Lhca6 might not be expressed at all, ESTs have been detected for the Lhca5 gene in Arabidopsis and a number of other plant species. Here we demonstrate the presence of the Lhca5 gene product in the thylakoid membrane of Arabidopsis as an additional type of Lhca-protein associated with PSI. Lhca5 seems to be regulated differently from the other LHC proteins since Lhca5 mRNA levels increase under high light conditions. Analyses reported here of Lhca5 in plants lacking individual Lhca1–4 proteins show that it is more abundant in plants lacking Lhca1/4, and suggest that it interacts in a direct physical fashion with Lhca2 or Lhca3. We propose that Lhca5 binds chlorophylls in a similar fashion to the other Lhca proteins and is associated with PSI only in sub-stoichiometric amounts. 

  • 45.
    Ganeteg, Ulrika
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Külheim, Carsten
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Andersson, Jenny
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Is each light-harvesting complex protein important for plant fitness?2004In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 134, no 1, p. 502-509Article in journal (Refereed)
    Abstract [en]

    Many of the photosynthetic genes are conserved among all higher plants, indicating that there is strong selective pressure to maintain the genes of each protein. However, mutants of these genes often lack visible growth phenotypes, suggesting that they are important only under certain conditions or have overlapping functions. To assess the importance of specific genes encoding the light-harvesting complex (LHC) proteins for the survival of the plant in the natural environment, we have combined two different scientific traditions by using an ecological fitness assay on a set of genetically modified Arabidopsis plants with differing LHC protein contents. The fitness of all of the LHC-deficient plants was reduced in some of the growth environments, supporting the hypothesis that each of the genes has been conserved because they provide ecological flexibility, which is of great adaptive value given the highly variable conditions encountered in nature.

  • 46.
    Garcia Cerdan, Jose Gines
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sveshnikov, Dmitry
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dewez, David
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antisense inhibition of the PsbX protein affects PSII integrity in the higher plant Arabidopsis Thaliana2009In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, no 2, p. 191-202Article in journal (Refereed)
    Abstract [en]

    PSII, the oxygen-evolving complex of photosynthetic organisms, contains an intriguingly large number of low molecular weight proteins. PsbX, one of these proteins, is ubiquitous in PSII complexes of cyanobacteria and plants. In previous studies, deletion of the PsbX protein in cyanobacteria has not resulted in clear phenotypic changes. Here we report the construction of an antisense (AS-PsbX) line in Arabidopsis thaliana with <10% of wild-type PsbX levels. AS-PsbX plants are capable of photoautotrophic growth, but biochemical, biophysical and immunological evidence demonstrates that reduction of PsbX contents leads to reduced levels of functional assembled PSII core complexes, while the light-harvesting antennae are not affected. In addition, levels of phosphorylation of the core proteins D1, D2 and CP43 are severely reduced in the antisense plants relative to their wild-type counterparts. We conclude that PsbX is important for accumulation of functional PSII.

  • 47.
    Garci­a-Lorenzo, Maribel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjödin, Andreas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Protease gene families in Populus and Arabidopsis2006In: BMC Plant Biology, E-ISSN 1471-2229, Vol. 6, no 30, p. 1-24Article in journal (Refereed)
    Abstract [en]

    Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution. RESULTS: We have performed a comparative analysis of protease genes in the two sequenced dicot genomes, Arabidopsis thaliana and Populus trichocarpa by using genes coding for proteases in the MEROPS database 1 for Arabidopsis to identify homologous sequences in Populus. A multigene-based phylogenetic analysis was performed. Most protease families were found to be larger in Populus than in Arabidopsis, reflecting recent genome duplication. Detailed studies on e.g. the DegP, Clp, FtsH, Lon, rhomboid and papain-Like protease families showed the pattern of gene family expansion and gene loss was complex. We finally show that different Populus tissues express unique suites of protease genes and that the mRNA levels of different classes of proteases change along a developmental gradient. CONCLUSION: Recent gene family expansion and contractions have made the Arabidopsis and Populus complements of proteases different and this, together with expression patterns, gives indications about the roles of the individual gene products or groups of proteases.

  • 48. Grebe, Steffen
    et al.
    Trotta, Andrea
    Bajwa, Azfar A.
    Suorsa, Marjaana
    Gollan, Peter J.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tikkanen, Mikko
    Aro, Eva-Mari
    The unique photosynthetic apparatus of Pinaceae: analysis of photosynthetic complexes in Picea abies2019In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 70, no 12, p. 3211-3225Article in journal (Refereed)
    Abstract [en]

    Pinaceae are the predominant photosynthetic species in boreal forests, but so far no detailed description of the protein components of the photosynthetic apparatus of these gymnosperms has been available. In this study we report a detailed characterization of the thylakoid photosynthetic machinery of Norway spruce (Picea abies (L.) Karst). We first customized a spruce thylakoid protein database from translated transcript sequences combined with existing protein sequences derived from gene models, which enabled reliable tandem mass spectrometry identification of P. abies thylakoid proteins from two-dimensional large pore blue-native/SDS-PAGE. This allowed a direct comparison of the two-dimensional protein map of thylakoid protein complexes from P. abies with the model angiosperm Arabidopsis thaliana. Although the subunit composition of P. abies core PSI and PSII complexes is largely similar to that of Arabidopsis, there was a high abundance of a smaller PSI subcomplex, closely resembling the assembly intermediate PSI* complex. In addition, the evolutionary distribution of light-harvesting complex (LHC) family members of Pinaceae was compared in silico with other land plants, revealing that P. abies and other Pinaceae (also Gnetaceae and Welwitschiaceae) have lost LHCB4, but retained LHCB8 (formerly called LHCB4.3). The findings reported here show the composition of the photosynthetic apparatus of P. abies and other Pinaceae members to be unique among land plants.

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  • 49. Grebe, Steffen
    et al.
    Trotta, Andrea
    Bajwa, Azfar Ali
    Mancini, Ilaria
    Bag, Pushan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Tikkanen, Mikko
    Aro, Eva-Mari
    Specific thylakoid protein phosphorylations are prerequisites for overwintering of Norway spruce (Picea abies) photosynthesis2020In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 117, no 30, p. 17499-17509Article in journal (Refereed)
    Abstract [en]

    Coping of evergreen conifers in boreal forests with freezing temperatures on bright winter days puts the photosynthetic machinery in great risk of oxidative damage. To survive harsh winter conditions, conifers have evolved a unique but poorly characterized photoprotection mechanism, a sustained form of nonphotochemical quenching (sustained NPQ). Here we focused on functional properties and underlying molecular mechanisms related to the development of sustained NPQ in Norway spruce (Picea abies). Data were collected during 4 consecutive years (2016 to 2019) from trees growing in sun and shade habitats. When day temperatures dropped below -4 degrees C, the specific N-terminally triply phosphorylated LHCB1 isoform (3p-LHCII) and phosphorylated PSBS (p-PSBS) could be detected in the thylakoid membrane. Development of sustained NPQ coincided with the highest level of 3p-LHCII and p-PSBS, occurring after prolonged coincidence of bright winter days and temperatures close to -10 degrees C. Artificial induction of both the sustained NPQ and recovery from naturally induced sustained NPQ provided information on differential dynamics and light-dependence of 3p-LHCII and p-PSBS accumulation as prerequisites for sustained NPQ. Data obtained collectively suggest three components related to sustained NPQ in spruce: 1) Freezing temperatures induce 3p-LHCII accumulation independently of light, which is suggested to initiate destacking of appressed thylakoid membranes due to increased electrostatic repulsion of adjacent membranes; 2) p-PSBS accumulation is both light -and temperature-dependent and closely linked to the initiation of sustained NPQ, which 3) in concert with PSII photoinhibition, is suggested to trigger sustained NPQ in spruce.

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  • 50.
    Gustafsson, Petter
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    LIDHOLM, J
    LUNDBERG, AK
    STRUCTURE AND REGULATION OF PHOTOSYNTHESIS GENES IN PINUS-SYLVESTRIS (SCOTS PINE) AND PINUS-CONTORTA (LODGEPOLE PINE)1991In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 43, no 3-4, p. 287-300Article in journal (Refereed)
    Abstract [en]

    The structure and regulation of one nuclear and one chloroplast gene was studied in Pinus sylvestris (Scots pine) and Pinus contorta (lodgepole pine). cDNA copies of the nuclear located cab genes of Pinus sylvestris, coding for the light-harvesting chlorophyll a/b-binding proteins of photosystem II (LHC-II), were cloned. cab-II genes coding for both types of LHC-II polypeptides, Types 1 and 2, were found. An analysis of the DNA sequences of several different cab-II cDNAs shows that they have a high bias for the nucleotides G and C at the third base positions of the codons, making them more similar to monocot than to dicot genes. Two of the three genes were found to be located within CpG islands. The cab-II genes were found to be expressed in dark-grown seedlings in contrast to what has been found for most angiosperms. The chloroplast genomes of conifers were shown to lack the inverted repeat organization normally found in higher plants, mosses and green algae. The psbA gene, located in the chloroplast genome and coding for the D1 polypeptide in the reaction center of photosystem II, was found to be tandemly duplicated in P. contorta. Cloning and sequence analysis of the two psbA genes and the surrounding regions showed that the duplicated segment is 1.97 kb long and that it ends 19 bp downstream from the psbA stop codon. The corresponding locus of P. sylvestris, which lacks the duplication, was cloned and characterized. A comparison with P. contorta indicates how the duplication/insertion event has occurred. A comparison of third codon position between P. contorta psbA and that of other plants indicated an almost equidistant evolutionary relationship between P. contorta, spinach (or barley) and Marchantia polymorpha.

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