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  • 251. Fülöp, Katalin
    et al.
    Tarayre, Sylvie
    Kelemen, Zsolt
    Horváth, Gábor
    Kevei, Zoltán
    Nikovics, Krisztina
    Bakó, László
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Biological Research Center; Hungarian Academy of Sciences; Szeged, Hungary.
    Brown, Spencer
    Kondorosi, Adam
    Kondorosi, Eva
    Arabidopsis anaphase-promoting complexes: multiple activators and wide range of substrates might keep APC perpetually busy2005Inngår i: Cell Cycle, ISSN 1538-4101, E-ISSN 1551-4005, Vol. 4, nr 8, s. 1084-1092Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The anaphase-promoting complex (APC), a multisubunit E3 ubiquitin ligase, is an essential regulator of the cell cycle from metaphase until S phase in yeast and metazoans. APC mediates degradation of numerous cell cycle-related proteins, including mitotic cyclins and its activation and substrate-specificity are determined by two adaptor proteins, Cdc20 and Cdh1. Plants have multiple APC activators and the Cdh1-type proteins, in addition, are represented by two subclasses, known as Ccs52A and Ccs52B. The Arabidopsis genome contains five cdc20 genes as well as ccs52A1, ccs52A2 and ccs52B.In Schizosaccharomyces pombe, expression of the three Atccs52 genes elicited distinct phenotypes supporting nonredundant function of the AtCcs52 proteins. Consistent with these activities, the AtCcs52 proteins were able to bind both to the yeast and the Arabidopsis APCs. In synchronized Arabidopsis cell cultures the cdc20 transcripts were present from early G2 until the M-phase exit, ccs52B from G2/M to M while ccs52A1 and ccs52A2 were from late M until early G2, suggesting consecutive action of these APC activators in the plant cell cycle. The AtCcs52 proteins interacted with different subsets of mitotic cyclins, in accordance with their expression profiles, either in free- or CDK-bound forms. Expression of most APC subunits was constitutive, whereas cdc27a and cdc27b, corresponding to two forms of apc3, and ubc19 and ubc20 encoding E2-C type ubiquitin-conjugating enzymes displayed differences in their cell cycle regulation. These data indicate the existence of numerous APC(Cdc20/Ccs52/Cdc27) forms in Arabidopsis, which in conjunction with different E2 enzymes might have distinct or complementary functions at distinct stages of the cell cycle.

  • 252. Galvao, Vinicius Costa
    et al.
    Collani, Silvio
    Horrer, Daniel
    Schmid, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana2015Inngår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 84, nr 5, s. 949-962Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process.

  • 253. Gama, Filipe
    et al.
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Eymery, Francoise
    Finkemeier, Iris
    Gelhaye, Eric
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Dietz, Karl Josef
    Rey, Pascal
    Jacquot, Jean-Pierre
    Rouhier, Nicolas
    The mitochondrial type II peroxiredoxin from poplar2007Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 129, nr 1, s. 196-206Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mitochondria are a major site of reactive oxygen species production and controlling the peroxide levels in this compartment is essential. Peroxiredoxins (Prx) are heme-free peroxidases, which use reactive cysteines for their catalysis and reducing systems for their regeneration. One of the two Prxs present in poplar mitochondria, Prx IIF, expressed as a recombinant protein, was found to reduce a broad range of peroxides with electrons provided preferentially by glutaredoxin and to a lesser extent by glutathione, all the thioredoxins tested being inefficient. This protein is constitutively expressed because it is found in all tissues analyzed. Its expression is modified during a biotic interaction between poplar and the rust fungus Melampsora laricii populina. On the other hand, Prx IIF expression does not substantially vary under abiotic stress conditions. Nevertheless, water deficit or chilling and probably induced senescence, but not photooxidative conditions or heavy metal treatment, also led to a small increase in PrxIIF abundance in Arabidopsis thaliana plants.

  • 254. Gamm, Magdalena
    et al.
    Peviani, Alessia
    Honsel, Anne
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Snel, Berend
    Smeekens, Sjef
    Hanson, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Increased sucrose levels mediate selective mRNA translation in Arabidopsis2014Inngår i: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 14, artikkel-id 306Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Protein synthesis is a highly energy demanding process and is regulated according to cellular energy levels. Light and sugar availability affect mRNA translation in plant cells but the specific roles of these factors remain unclear. In this study, sucrose was applied to Arabidopsis seedlings kept in the light or in the dark, in order to distinguish sucrose and light effects on transcription and translation. These were studied using microarray analysis of steady-state mRNA and mRNA bound to translating ribosomes. Results: Steady-state mRNA levels were affected differently by sucrose in the light and in the dark but general translation increased to a similar extent in both conditions. For a majority of the transcripts changes of the transcript levels were followed by changes in polysomal mRNA levels. However, for 243 mRNAs, a change in polysomal occupancy (defined as polysomal levels related to steady-state levels of the mRNA) was observed after sucrose treatment in the light, but not in the dark condition. Many of these mRNAs are annotated as encoding ribosomal proteins, supporting specific translational regulation of this group of transcripts. Unexpectedly, the numbers of ribosomes bound to each mRNA decreased for mRNAs with increased polysomal occupancy. Conclusions: Our results suggest that sucrose regulate translation of these 243 mRNAs specifically in the light, through a novel regulatory mechanism. Our data shows that increased polysomal occupancy is not necessarily leading to more ribosomes per transcript, suggesting a mechanism of translational induction not solely dependent on increased translation initiation rates.

  • 255.
    Ganeteg, U.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gustafsson, P.
    Jansson, S.
    The properties of the chlorophyll a/b-binding proteins Lhca2 and Lhca3 studied in vivo using antisense inhibition2001Inngår i: Plant Physiol, Vol. 127, s. 150-158Artikkel i tidsskrift (Fagfellevurdert)
  • 256.
    Ganeteg, Ulrika
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Klimmek, Frank
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Ihalainen, J.
    Ruban, A.
    Benson, S.
    van Roon, H.
    Scheller, H.V.
    Horton, P.
    Dekker, J.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Structure and function of the lightharvesting complex of higher plant photosystem IManuskript (preprint) (Annet vitenskapelig)
  • 257.
    Ganeteg, Ulrika
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Klimmek, Frank
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Lhca5--an LHC-type protein associated with photosystem I.2004Inngår i: Plant Molecular Biology, ISSN 0167-4412, Vol. 54, nr 5, s. 641-51Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 258.
    Ganeteg, Ulrika
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Külheim, Carsten
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Andersson, Jenny
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Is each light-harvesting complex protein important for plant fitness?2004Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 134, nr 1, s. 502-509Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 259.
    Gao, Jie
    et al.
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Wang, Baosheng
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Mao, Ian-Feng
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Ingvarsson, Pär
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Zeng, Qing-Yin
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Wang, Xiao-Ru
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
    Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau2012Inngår i: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, nr 19, s. 4811-4827Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.

  • 260.
    Garcia Cerdan, Jose Gines
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    PsbW knock out plants reveals changes in the stabilization of the PSII-LHCII supercomplexes macro-organization of ArabidopsisManuskript (Annet (populærvitenskap, debatt, mm))
  • 261.
    Garcia Cerdan, Jose Gines
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sveshnikov, Dmitry
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Dewez, David
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Antisense inhibition of the PsbX protein affects PSII integrity in the higher plant Arabidopsis Thaliana2009Inngår i: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, nr 2, s. 191-202Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 262.
    Garci­a-Lorenzo, Maribel
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Protease gene families in Populus and Arabidopsis2006Inngår i: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 6, nr 30, s. 1-24Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 263.
    García-Cerdán, José G
    et al.
    Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
    Kovács, Laszlo
    Tóth, Tünde
    Kereïche, Sami
    Aseeva, Elena
    Boekema, Egbert J
    Mamedov, Fikret
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants2011Inngår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 65, nr 3, s. 368-381Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    PsbW, a 6.1-kDa low-molecular-weight protein, is exclusive to photosynthetic eukaryotes, and associates with the photosystem II (PSII) protein complex. In vivo and in vitro comparison of Arabidopsis thaliana wild-type plants with T-DNA insertion knock-out mutants completely lacking the PsbW protein, or with antisense inhibition plants exhibiting decreased levels of PsbW, demonstrated that the loss of PsbW destabilizes the supramolecular organization of PSII. No PSII-LHCII supercomplexes could be detected or isolated in the absence of the PsbW protein. These changes in macro-organization were accompanied by a minor decrease in the chlorophyll fluorescence parameter FV/FM, a strongly decreased PSII core protein phosphorylation and a modification of the redox state of the plastoquinone (PQ) pool in dark-adapted leaves. In addition, the absence of PsbW protein led to faster redox changes in the PQ pool, i.e. transitions from state 1 to state 2, as measured by changes in stationary fluorescence (FS) kinetics, compared with the wild type. Despite these dramatic effects on macromolecular structure, the transgenic plants exhibited no significant phenotype under normal growth conditions. We suggest that the PsbW protein is located close to the minor antenna of the PSII complex, and is important for the contact and stability between several PSII-LHCII supercomplexes.

  • 264.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    ADENYLATE RATIOS IN THE CYTOSOL, CHLOROPLASTS AND MITOCHONDRIA OF BARLEY LEAF PROTOPLASTS DURING PHOTOSYNTHESIS AT DIFFERENT CARBON-DIOXIDE CONCENTRATIONS1987Inngår i: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 212, nr 1, s. 114-118Artikkel i tidsskrift (Fagfellevurdert)
  • 265.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    METABOLITE LEVELS IN THE CHLOROPLAST AND EXTRACHLOROPLAST COMPARTMENTS OF BARLEY LEAF PROTOPLASTS DURING THE INITIAL PHASE OF PHOTOSYNTHETIC INDUCTION1993Inngår i: Biochimica et Biophysica Acta, ISSN 0006-3002, E-ISSN 1878-2434, Vol. 1183, nr 2, s. 327-332Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Metabolite levels were determined in the chloroplast and extrachloroplast compartments of barley protoplasts during photosynthetic induction using rapid fractionation by membrane filtration. This method allowed studies with a high time resolution the first determination of subcellular metabolite content bring made after only 0.3 s. Upon illumination, dark-adapted protoplasts exhibited a 1 min lag phase prior to commencement of oxygen evolution, and the maximum rate was reached after 4 to 5 min. In contrast to oxygen evolution, the ATP/ADP ratio in the chloroplasts increased from 1 to 2 within 0.5 s and reached a maximum of about 5 after 2 s. There was a dramatic increase in the extrachloroplastic ATP/ADP ratio within a few seconds, reaching a maximum after about 15 s. During the initial phase of photosynthetic induction, the subcellular ATP/ADP ratios were very similar in photorespiratory (low CO,) and non-photorespiratory (high CO,) conditions. The ATP/ADP ratios in both the chloroplast and extrachloroplast compartments remained high until photosynthetic oxygen evolution started and then decreased when the photosynthetic rate reached its maximum. In steady-state photosynthesis the subcellular ATP/ADP ratios were considerably higher under photorespiratory conditions as compared to non-photorespiratory conditions. During the initial phase of photosynthetic induction, 3-phosphoglycerate decreased and triose phosphates increased both in the chloroplast and extrachloroplast compartments. The changes in these metabolites are consistent with a 3-phosphoglycerate/triose phosphate shuttle using the phosphate translocator as the means to supply ATP to the cytosol during photosynthetic induction.

  • 266.
    Gardeström, Per
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bergman, A
    Ericson, I
    Oxidation of Glycine via the Respiratory Chain in Mitochondria Prepared from Different Parts of Spinach.1980Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 65, nr 2, s. 389-91Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mitochondria were prepared from roots, stalks, leaves, and leaf veins of spinach. The mitochondrial preparations were examined for their ability to oxidize glycine via the respiratory chain. It is shown that the glycine-oxidizing capacity is restricted to photosynthetically active tissue. The activity is present in mitochondria from the green parts of the leaves, but not in mitochondria from roots, stalks, or leaf veins.

  • 267.
    Gardeström, Per
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Edwards, G E
    Isolation of Mitochondria from Leaf Tissue of Panicum miliaceum, a NAD-Malic Enzyme Type C(4) Plant.1983Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 71, nr 1, s. 24-9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A mechanical isolation procedure was developed to study the respiratory properties of mitochondria from the mesophyll and bundle sheath tissue of Panicum miliaceum, a NAD-malic enzyme C(4) plant. A mesophyll fraction and a bundle sheath fraction were obtained from young leaves by differential mechanical treatment. The purity of both fractions was about 80%, based on analysis of the cross-contamination of ribulose bisphosphate carboxylase activity and phosphoenolpyruvate carboxylase activity.Mitochondria were isolated from the two fractions by differential centrifugation and Percoll density gradient centrifugation. The enrichment of mitochondria relative to chloroplast material was about 75-fold in both preparations.Both types of mitochondria oxidized NADH and succinate with respiratory control. Malate oxidation in mesophyll mitochondria was sensitive to KCN and showed good respiratory control. In bundle sheath mitochondria, malate oxidation was largely insensitive to KCN and showed no respiratory control. The oxidation was strongly inhibited by salicylhydroxamic acid, showing that the alternative oxidase was involved. The bundle sheath mitochondria of this type of C(4) species contribute to C(4) photosynthesis through decarboxylation of malate. Malate oxidation linked to an uncoupled, alternative pathway may allow decarboxylation to proceed without the restraints which might occur via coupled electron flow through the cytochrome chain.

  • 268.
    Gardeström, Per
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    EDWARDS, GE
    HENRICSON, D
    ERICSON, I
    THE LOCALIZATION OF SERINE HYDROXYMETHYLTRANSFERASE IN LEAVES OF C-3 AND C-4 SPECIES1985Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 64, nr 1, s. 29-33Artikkel i tidsskrift (Fagfellevurdert)
  • 269.
    Gardeström, Per
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    ERICSON, I
    SEPARATION OF SPINACH LEAF MITOCHONDRIA ACCORDING TO SURFACE-PROPERTIES - PARTITION IN AQUEOUS POLYMER 2-PHASE SYSTEMS1987Inngår i: Methods in Enzymology, ISSN 0076-6879, E-ISSN 1557-7988, Vol. 148, s. 434-442Artikkel i tidsskrift (Fagfellevurdert)
  • 270.
    Gardeström, Per
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Lernmark, U
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    The contribution of mitochondria to energetic metabolism in photosynthetic cells1995Inngår i: Journal of Bioenergetics and Biomembranes, ISSN 0145-479X, E-ISSN 1573-6881, Vol. 27, nr 4, s. 415-421Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mitochondria fulfill important functions in photosynthetic cells not only in darkness but also in light. Mitochondrial oxidative phosphorylation is probably the main mechanism to supply ATP for extrachloroplastic functions in both conditions. Furthermore, during photosynthesis mitochondrial electron transport is important for regulation of the redox balance in the cell. This makes mitochondrial function an integral part of a flexible metabolic system in the photosynthetic cell. This flexibility is probably very important in order to allow the metabolism to override disturbances caused by the changing environment which plants are adapted to.

  • 271.
    Gardeström, Per
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    WIGGE, B
    INFLUENCE OF PHOTORESPIRATION ON ATP/ADP RATIOS IN THE CHLOROPLASTS, MITOCHONDRIA, AND CYTOSOL, STUDIES BY RAPID FRACTIONATION OF BARLEY (HORDEUM-VULGARE) PROTOPLASTS1988Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 88, nr 1, s. 69-76Artikkel i tidsskrift (Fagfellevurdert)
  • 272. Geisler, Matt
    et al.
    Kleczkowski, Leszek
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Karpinski, Stanislaw
    A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements; identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis.2006Inngår i: Plant Journal, ISSN 0960-7412, Vol. 45, nr 3, s. 384-98Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Short motifs of many cis-regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.

  • 273. Geisler, Matt
    et al.
    Wilczynska, Malgorzata
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Karpinski, Stanislaw
    Kleczkowski, Leszek
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Toward a blueprint for UDP-glucose pyrophosphorylase structure/function properties: homology-modeling analyses.2004Inngår i: Plant Molecular Biology, ISSN 0167-4412, Vol. 56, nr 5, s. 783-94Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.

  • 274. Geisler-Lee, Jane
    et al.
    Geisler, Matt
    Coutinho, Pedro M
    Segerman, Bo
    Nishikubo, Nobuyuki
    Takahashi, Junko
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Aspeborg, Henrik
    Djerbi, Soraya
    Master, Emma
    Andersson-Gunnerås, Sara
    Sundberg, Björn
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Karpinski, Stanislaw
    Teeri, Tuula T
    Kleczkowski, Leszek
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Henrissat, Bernard
    Mellerowicz, Ewa J
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Poplar carbohydrate-active enzymes. Gene identification and expression analyses.2006Inngår i: Plant Physiology, ISSN 0032-0889, Vol. 140, nr 3, s. 946-62Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr. & Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar (Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis (Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.

  • 275.
    Gendre, Delphine
    et al.
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences.
    Oh, Jaesung
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences.
    Boutté, Yohann
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences.
    Best, Jacob G
    Samuels, Lacey
    Nilsson, Robert
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences.
    Uemura, Tomohiro
    Marchant, Alan
    Bennett, Malcolm J
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bhalerao, Rishikesh P
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences.
    Conserved Arabidopsis ECHIDNA protein mediates trans-Golgi-network trafficking and cell elongation2011Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, nr 19, s. 8048-8053Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Multiple steps of plant growth and development rely on rapid cell elongation during which secretory and endocytic trafficking via the trans-Golgi network (TGN) plays a central role. Here, we identify the ECHIDNA (ECH) protein from Arabidopsis thaliana as a TGN-localized component crucial for TGN function. ECH partially complements loss of budding yeast TVP23 function and a Populus ECH complements the Arabidopsis ech mutant, suggesting functional conservation of the genes. Compared with wild-type, the Arabidopsis ech mutant exhibits severely perturbed cell elongation as well as defects in TGN structure and function, manifested by the reduced association between Golgi bodies and TGN as well as mislocalization of several TGN-localized proteins including vacuolar H(+)-ATPase subunit a1 (VHA-a1). Strikingly, ech is defective in secretory trafficking, whereas endocytosis appears unaffected in the mutant. Some aspects of the ech mutant phenotype can be phenocopied by treatment with a specific inhibitor of vacuolar H(+)-ATPases, concanamycin A, indicating that mislocalization of VHA-a1 may account for part of the defects in ech. Hence, ECH is an evolutionarily conserved component of the TGN with a central role in TGN structure and function.

  • 276. Gendre, Delphine
    et al.
    Baral, Anirban
    Dang, Xie
    Esnay, Nicolas
    Boutté, Yohann
    Stanislas, Thomas
    Vain, Thomas
    Claverol, Stéphane
    Gustavsson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Lin, Deshu
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Institute of Biochemistry and Biology, Plant Physiology, Universityof Potsdam, Germany.
    Bhalerao, Rishikesh P.
    Rho-of-plant activated root hair formation requires Arabidopsis YIP4a/b gene function2019Inngår i: Development, ISSN 0950-1991, E-ISSN 1477-9129, Vol. 146, nr 5, artikkel-id dev168559Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Root hairs are protrusions from root epidermal cells with crucial roles in plant soil interactions. Although much is known about patterning, polarity and tip growth of root hairs, contributions of membrane trafficking to hair initiation remain poorly understood. Here, we demonstrate that the trans-Golgi network-localized YPT-INTERACTING PROTEIN 4a and YPT-INTERACTING PROTEIN 4b (YIP4a/b) contribute to activation and plasma membrane accumulation of Rho-of-plant (ROP) small GTPases during hair initiation, identifying YIP4a/b as central trafficking components in ROP-dependent root hair formation.

  • 277. Geng, Xiaoyu
    et al.
    Horst, Walter J.
    Golz, John F.
    Lee, Joanne E.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ding, Zhaojun
    Yang, Zhong-Bao
    LEUNIG_HOMOLOG transcriptional co-repressor mediates aluminium sensitivity through PECTIN METHYLESTERASE46-modulated root cell wall pectin methylesterification in Arabidopsis2017Inngår i: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 90, nr 3, s. 491-504Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A major factor determining aluminium (Al) sensitivity in higher plants is the binding of Al to root cell walls. The Al binding capacity of cell walls is closely linked to the extent of pectin methylesterification, as the presence of methyl groups attached to the pectin backbone reduces the net negative charge of this polymer and hence limits Al binding. Despite recent progress in understanding the molecular basis of Al resistance in a wide range of plants, it is not well understood how the methylation status of pectin is mediated in response to Al stress. Here we show in Arabidopsis that mutants lacking the gene LEUNIG_HOMOLOG (LUH), a member of the Groucho-like family of transcriptional co-repressor, are less sensitive to Al-mediated repression of root growth. This phenotype is correlated with increased levels of methylated pectin in the cell walls of luh roots as well as altered expression of cell wall-related genes. Among the LUH-repressed genes, PECTIN METHYLESTERASE46 (PME46) was identified as reducing Al binding to cell walls and hence alleviating Al-induced root growth inhibition by decreasing PME enzyme activity. seuss-like2 (slk2) mutants responded to Al in a similar way as luh mutants suggesting that a LUH-SLK2 complex represses the expression of PME46. The data are integrated into a model in which it is proposed that PME46 is a major inhibitor of pectin methylesterase activity within root cell walls.

  • 278.
    Gentili, Francesco
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Phosphorus, nitrogen and their interactions affect N-2 fixation, N isotope fractionation and N partitioning in Hippophae rhamnoides2006Inngår i: Symbiosis, ISSN 0334-5114, E-ISSN 1878-7665, Vol. 41, nr 1, s. 39-45Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The interactive effects of varying phosphorus and nitrogen supplies on N-2 fixation, N isotope fractionation during N uptake, and N partitioning among plant parts were studied in the actinorhizal plant Hippophae rhamnoides L. (sea buckthorn). Plants were grown for six weeks after inoculation with the N-2-fixing actinomycete Frankia and differences in N accumulation were used to quantify N-2 fixation. N-15 natural abundance was analysed to study N isotope fractionation in specific plant parts in plants receiving different levels of N and P. Furthermore, the root system was split to study N isotope fractionation in roots supplied with different levels of N and P. Phosphorus stimulated N-2 fixation by direct effects on nodule dry matter and nodule function, rather than indirectly via plant growth. Phosphorus also stimulated N uptake from solution and influenced N isotope fractionation during N uptake. The inclusion of N-15 natural abundance analyses made it possible to detect P effects on N uptake, fractionation and N-2 fixation even though the plants used both N-2 fixation and combined N as N sources.

  • 279.
    Gentili, Francesco
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Nilsson, Marie-Charlotte
    Zackrisson, Olle
    DeLuca, Thomas H
    Sellstedt, Anita
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Physiological and molecular diversity of feather moss associative N2-fixing cyanobacteria.2005Inngår i: Journal of Experimental Botany, ISSN 0022-0957, Vol. 56, nr 422, s. 3121-7Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cyanobacteria colonizing the feather moss Pleurozium schreberi were isolated from moss samples collected in northern Sweden and subjected to physiological and molecular characterization. Morphological studies of isolated and moss-associated cyanobacteria were carried out by light microscopy. Molecular tools were used for cyanobacteria identification, and a reconstitution experiment of the association between non-associative mosses and cyanobacteria was conducted. The influence of temperature on N2 fixation in the different cyanobacterial isolates and the influence of light and temperature on N2-fixation rates in the moss were studied using the acetylene reduction assay. Two different cyanobacteria were effectively isolated from P. schreberi: Nostoc sp. and Calothrix sp. A third genus, Stigonema sp. was identified by microscopy, but could not be isolated. The Nostoc sp. was found to fix N2 at lower temperatures than Calothrix sp. Nostoc sp. and Stigonema sp. were the predominant cyanobacteria colonizing the moss. The attempt to reconstitute the association between the moss and cyanobacteria was successful. The two isolated genera of cyanobacteria in feather moss samples collected in northern Sweden differ in their temperature optima, which may have important ecological implications.

  • 280. Giacomello, Stefania
    et al.
    Salmen, Fredrik
    Terebieniec, Barbara K.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Vickovic, Sanja
    Navarro, José Fernandez
    Alexeyenko, Andrey
    Reimegard, Johan
    McKee, Lauren S.
    Mannapperuma, Chanaka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Bulone, Vincent
    Ståhl, Patrik L.
    Sundström, Jens F.
    Street, Nathaniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Lundeberg, Joakim
    Spatially resolved transcriptome profiling in model plant species2017Inngår i: Nature Plants, ISSN 2055-026X, Vol. 3, nr 6, artikkel-id 17061Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study highresolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes highthroughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.

  • 281.
    Goretti, Daniela
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy.
    Martignago, Damiano
    Landini, Martina
    Brambilla, Vittoria
    Gomez-Ariza, Jorge
    Gnesutta, Nerina
    Galbiati, Francesca
    Collani, Silvio
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Takagi, Hiroki
    Terauchi, Ryohei
    Mantovani, Roberto
    Fornara, Fabio
    Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes2017Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, nr 1, artikkel-id e1006530Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes.

  • 282. Gough, Simon P
    et al.
    Rzeznicka, Kamila
    Peterson Wulff, Ragna
    Francisco, Jose da Cruz
    Hansson, Andreas
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysiologisk botanik. Umeå Plant Science Centre.
    Jensen, Poul Erik
    Hansson, Mats
    A new method for isolating physiologically active Mg-protoporphyrin monomethyl ester, the substrate of the cyclase enzyme of the chlorophyll biosynthetic pathway.2007Inngår i: Plant Physiology and Biochemistry, ISSN 0981-9428, Vol. 45, nr 12, s. 932-6Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mg-protoporphyrin monomethyl ester (MPE) is a biosynthetic intermediate of chlorophyll and converted by MPE cyclase to protochlorophyllide. Limited availability of MPE has so far hampered cyclase research. In a new, simplified, method MPE was prepared from freeze dried bchE mutant Rhodobacter capsulatus DB575 cells by extraction with acetone/H2O/25% NH3. Isolated MPE was identified by absorption and fluorescence spectroscopy, and its purity was analyzed by HPLC. The extracted MPE was dried and redissolved in buffered DMSO and its substrate activity is shown by enzymatic cyclase assays. A linear time course was observed for MPE conversion to protochlorophyllide by enzymes from barley etioplasts. Our innovation of freeze drying the R. capsulatus cells before extraction provides a high yield method for MPE, which is significantly faster and more reproducible than previous extraction methods.

  • 283. Goulas, Estelle
    et al.
    Schubert, Maria
    Kieselbach, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kleczkowski, Leszek
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature.2006Inngår i: Plant Journal, ISSN 0960-7412, Vol. 47, nr 5, s. 720-34Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cold acclimation and over-wintering by herbaceous plants are energetically expensive and are dependent on functional plastid metabolism. To understand how the stroma and the lumen proteomes adapt to low temperatures, we have taken a proteomic approach (difference gel electrophoresis) to identify proteins that changed in abundance in Arabidopsis chloroplasts during cold shock (1 day), and short- (10 days) and long-term (40 days) acclimation to 5°C. We show that cold shock (1 day) results in minimal change in the plastid proteomes, while short-term (10 days) acclimation results in major changes in the stromal but few changes in the lumen proteome. Long-term acclimation (40 days) results in modulation of the proteomes of both compartments, with new proteins appearing in the lumen and further modulations in protein abundance occurring in the stroma. We identify 43 differentially displayed proteins that participate in photosynthesis, other plastid metabolic functions, hormone biosynthesis and stress sensing and signal transduction. These findings not only provide new insights into the cold response and acclimation of Arabidopsis, but also demonstrate the importance of studying changes in protein abundance within the relevant cellular compartment.

  • 284. Granado-Yela, C
    et al.
    García-Verdugo, C
    Carrillo, K
    Rubio DE Casas, R
    Kleczkowski, Leszek A
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Balaguer, L
    Temporal matching among diurnal photosynthetic patterns within the crown of the evergreen sclerophyll Olea europaea L2011Inngår i: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 34, nr 5, s. 800-810Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 285.
    Granlund, Irene
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Hall, Michael
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Kieselbach, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Schröder, Wolfgang P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Light induced changes in protein expression and uniform regulation of transcription in the thylakoid lumen of Arabidopsis thaliana2009Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 4, nr 5, s. e5649-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In plants oxygenic photosynthesis is performed by large protein complexes found in the thylakoid membranes of chloroplasts. The soluble thylakoid lumen space is a narrow and compressed region within the thylakoid membrane which contains 80-200 proteins. Because the thylakoid lumen proteins are in close proximity to the protein complexes of photosynthesis, it is reasonable to assume that the lumen proteins are highly influenced by the presence of light. To identify light regulated proteins in the thylakoid lumen of Arabidopsis thaliana we developed a faster thylakoid preparation and combined this with difference gel electrophoresis (DIGE) of dark-adapted and light-adapted lumen proteomes. The DIGE experiments revealed that 19 lumen proteins exhibit increased relative protein levels after eight hour light exposure. Among the proteins showing increased abundance were the PsbP and PsbQ subunits of Photosystem II, major plastocyanin and several other proteins of known or unknown function. In addition, co-expression analysis of publicly available transcriptomic data showed that the co-regulation of lumen protein expression is not limited to light but rather that lumen protein genes exhibit a high uniformity of expression. The large proportion of thylakoid lumen proteins displaying increased abundance in light-adapted plants, taken together with the observed uniform regulation of transcription, implies that the majority of thylakoid lumen proteins have functions that are related to photosynthetic activity. This is the first time that an analysis of the differences in protein level during a normal day/night cycle has been performed and it shows that even a normal cycle of light significantly influences the thylakoid lumen proteome. In this study we also show for the first time, using co-expression analysis, that the prevalent lumenal chloroplast proteins are very similarly regulated at the level of transcription.

  • 286.
    Granlund, Irene
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Storm, Patrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Schubert, Maria
    Department of Life Sciences, Södertörns University College, SE-141 89 Huddinge, Sweden.
    García-Cerdán, José G
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Funk, Christiane
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The TL29 protein is lumen located, associated with PSII and not an ascorbate peroxidase2009Inngår i: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, nr 11, s. 1898-1910Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The TL29 protein is one of the more abundant proteins in the thylakoid lumen of plant chloroplasts. Based on its sequence homology to ascorbate peroxidases, but without any supporting biochemical evidence, TL29 was suggested to be involved in the plant defense system against reactive oxygen species and consequently renamed to APX4. Our in vivo and in vitro analyses failed to show any peroxidase activity associated with TL29; it bound neither heme nor ascorbate. Recombinant overexpressed TL29 had no ascorbate-dependent peroxidase activity, and various mutational analyses aiming to convert TL29 into an ascorbate peroxidase failed. Furthermore, in the thylakoid lumen no such activity could be associated with TL29 and, additionally, TL29 knock-out mutants did not show any decreased peroxidase activity or increased content of radical oxygen species when grown under light stress. Instead we could show that TL29 is a lumen-located component associated with PSII.

  • 287.
    Gratz, Regina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Expression Studies of AminoAcid Transporters belonging to the Lysine and Hisitidine Transporter (LHT) Family in Hybrid Aspen Populus tremula L. x tremuloides Michx.2013Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    The human based input of fixed nitrogen, e.g. due to nitrogenous fertilizers, is the second most important driver of global change. The active input was, however, necessary due to a fast growing demand for agricultural products in order to feed an expanding world population in the last decades. Severe environmental damages are visible now, which is why it is crucial to find alternative ways to increase plant growth and biomass production without applying massive amounts of fertilizers. One way is to identify genes, which are able to improve nitrogen use efficiency (NUE) in plants when manipulated. Especially genes involved in nitrogen uptake, assimilation and remobilization, such as amino acid transporters are of great interest. Therefore a detailed knowledge about molecular processes regarding nitrogen transport in the respective plant species is crucial. So far, there is not much known about amino acid uptake mechanisms in tree species, which is why this work focuses on hybrid aspen. It was aimed to investigate the tissue expression patterns of genes encoding putative amino acid transporters in order to find potential target genes for improving NUE in the long term.

    It was shown that eight homologs of a main Arabidopsis amino acid transporter, AtLHT1, are expressed in poplar. The eight amino acid transporters displayed different expression patterns, with expression in roots, stem and leaves of young hybrid aspen. To analyze the impacts of an increased amino acid uptake phenotype in a tree model system, PtLHT1.2 was cloned into an expression vector for Agrobacterium-mediated transformation into hybrid aspen. These results will be of great value for further studies regarding NUE in tree models.

  • 288.
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Cell polarity: lateral perspectives2010Inngår i: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 20, nr 10, s. R446-R448Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The outer and inner (lateral) plasma membranes of the outermost cell layer in plants provide selective barriers to the environment. Recent studies provide perspectives on how asymmetric protein localization is established at lateral membranes.

  • 289.
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Out of the shade and into the light2011Inngår i: Nature Cell Biology, ISSN 1465-7392, E-ISSN 1476-4679, Vol. 13, nr 4, s. 347-349Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plants reach for the sun by avoiding the shade and by directly growing towards the light. Two studies now suggest that the polar relocation of PIN3, a transporter directing the flow of the plant hormone auxin, drives both growth processes. PIN3 repolarization occurs downstream of shade perception through phytochrome photoreceptors, whereas blue light perceived by phototropin initiates polar recycling of PIN3 and growth towards the light.

  • 290.
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Plant biology: Unveiling the Casparian strip.2011Inngår i: Nature, ISSN 1476-4687, Vol. 473, nr 7347, s. 294-5Artikkel i tidsskrift (Fagfellevurdert)
  • 291. Greer, DH
    et al.
    Ottander, Christina
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för naturvetenskapernas och matematikens didaktik.
    Öquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Photoinhibition and recovery of photosynthesis in intact barley leaves at 5 and 20°C1991Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 81, nr 2, s. 203-210Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Photoinhibition of photosynthesis and its recovery were studied in intact barley (Hordeum vulgare L. cv. Gunilla) leaves grown in a controlled environment by exposing them to two temperatures, 5 and 20-degrees-C, and a range of photon flux densities in excess of that during growth. Additionally, photoinhibition was examined in the presence of chloramphenicol (CAP, an inhibitor of chloroplast protein synthesis) and of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU). Susceptibility to photoinhibition was much higher at 5 than at 20-degrees-C. Furthermore, at 20-degrees-C CAP exacerbated photoinhibition strongly, whereas CAP had little additional effect (10%) at 5-degrees-C. These results support the model that net photoinhibition is the difference between the inactivation and repair of photosystem II (PSII); i.e. the degradation and synthesis of the reaction centre protein, D1. Furthermore, the steady-state extent of photoinhibition was strongly dependent on temperature and the results indicated this was manifested through the effects of temperature on the repair process of PSII. We propose that the continuous repair of PSII at 20-degrees-C conferred at least some protection from photoinhibition. At 5-degrees-C the repair process was largely inhibited, with increased photoinhibition as a consequence. However, we suggest where repair is inhibited by low temperature, some protection is alternatively conferred by the photoinhibited reaction centres. Providing they are not degraded, such centres could still dissipate excitation energy non-radiatively, thereby conferring protection of remaining photochemically active centres under steady-state conditions. A fraction of PS II centres were capable of resisting photoinhibition when the repair process was inhibited by CAP. This is discussed in relation to PS II heterogeneity. Furthermore, the repair process was not apparently activated within 3 h when barley leaves were transferred to photoinhibitory light conditions at 20-degrees-C.

  • 292. Grimberg, Åsa
    et al.
    Lager, Ida
    Street, Nathaniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Robinson, Kathryn M
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Marttila, Salla
    Mähler, Niklas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Ingvarsson, Pär K.
    Bhalerao, Rishikesh P.
    Storage lipid accumulation is controlled by photoperiodic signal acting via regulators of growth cessation and dormancy in hybrid aspen2018Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 219, nr 2, s. 619-630Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The signalling pathways that control seasonal modulation of carbon metabolism in perennial plants are poorly understood. Using genetic, metabolic and natural variation approaches, we identify factors mediating photoperiodic control of storage lipid accumulation in the model tree hybrid aspen (Populus tremula x tremuloides). We characterized lipid accumulation in transgenic hybrid aspen with impaired photoperiodic and hormonal responses. Genome-wide association mapping was performed in Swedish aspen (P.tremula) genotypes to determine genetic loci associated with genotype variation in lipid content. Our data show that the storage lipid triacylglycerol (TAG) accumulates in cambial meristem and pith rays of aspen in response to photoperiodic signal controlling growth cessation and dormancy induction. We show that photoperiodic control of TAG accumulation is mediated by the FLOWERING LOCUS T/CONSTANS module, which also controls the induction of growth cessation. Hormonal and chromatin remodelling pathways also contribute to TAG accumulation by photoperiodic signal. Natural variation exists in lipid accumulation that is controlled by input from multiple loci. Our data shed light on how the control of storage metabolism is temporally coordinated with growth cessation and dormancy by photoperiodic signal, and reveals that storage lipid accumulation between seeds and perennating organs of trees may involve distinct regulatory circuits.

  • 293.
    Grönlund, Andreas
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Bhalerao, Rishikesh P
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Karlsson, Jan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Modular gene expression in Poplar: a multilayer network approach2009Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 181, nr 2, s. 315-322Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    * By applying a multilayer network approach to an extensive set of Poplar microarray data, a genome-wide coexpression network has been detected and explored.

    * Multilayer networks were generated from minimum spanning trees (MSTs) using Kruskal's algorithm from random jack-knife resamplings of half of the full data set. The final network is obtained from the union of all the generated MSTs.

    * The gene expression correlations display a highly clustered topology, which is more pronounced when introducing links appearing in relatively few of the generated MSTs. The network also reveals a modular architecture, reflecting functional groups with relatively frequent gene-to-gene communication. Furthermore, the observed modular structure overlaps with different gene activities in different tissues, and closely related tissues show similar over- and/or under-expression patterns at the modular scale.

    * It is shown that including links that appear in a few of the generated MSTs increases the information quality of the network. In other words, a link may be 'weak' because it reflects rare signaling events rather than merely a signal weakened by noise. The method allows, from comparisons of random 'null networks', tuning to maximize the information obtainable.

  • 294.
    Grönlund, Andreas
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Holme, Petter
    Minnhagen, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Dynamic scaling regimes of collective decision making2008Inngår i: EPL - Europhysics Letters, Vol. 81, nr 2, s. 28003-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We investigate a social system of agents faced with a binary choice. We assume there is a correct, or beneficial, outcome of this choice. Furthermore, we assume agents are influenced by others in making their decision, and that the agents can obtain information that may guide them towards making a correct decision. The dynamic model we propose is of nonequilibrium type, converging to a final decision. We run it on random graphs and scale-free networks. On random graphs, we find two distinct regions in terms of the finalizing time —the time until all agents have finalized their decisions. On scale-free networks, on the other hand, there do not seem to be such distinct scaling regions.

  • 295.
    Grönlund, Andreas
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Lötstedt, Per
    Elf, Johan
    Transcription factor binding kinetics constrain noise suppression via negative feedback2013Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, s. 1864-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Negative autoregulation, where a transcription factor regulates its own expression by preventing transcription, is commonly used to suppress fluctuations in gene expression. Recent single molecule in vivo imaging has shown that it takes significant time for a transcription factor molecule to bind its chromosomal binding site. Given the slow association kinetics, transcription factor mediated feedback cannot at the same time be fast and strong. Here we show that with a limited association rate follows an optimal transcription factor binding strength where noise is maximally suppressed. At the optimal binding strength the binding site is free a fixed fraction of the time independent of the transcription factor concentration. One consequence is that high-copy number transcription factors should bind weakly to their operators, which is observed for transcription factors in Escherichia coli. The results demonstrate that a binding site's strength may be uncorrelated to its functional importance.

  • 296.
    Guinea Diaz, Manuel
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Hernandez-Verdeja, Tamara
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Kremnev, Dmitry
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Crawford, Tim
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Dubreuil, Carole
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Redox regulation of PEP activity during seedling establishment in Arabidopsis thaliana2018Inngår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, artikkel-id 50Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Activation of the plastid-encoded RNA polymerase is tightly controlled and involves a network of phosphorylation and, as yet unidentified, thiol-mediated events. Here, we characterize PLASTID REDOX INSENSITIVE2, a redox-regulated protein required for full PEP-driven transcription. PRIN2 dimers can be reduced into the active monomeric form by thioredoxins through reduction of a disulfide bond. Exposure to light increases the ratio between the monomeric and dimeric forms of PRIN2. Complementation of prin2-2 with different PRIN2 protein variants demonstrates that the monomer is required for light-activated PEP-dependent transcription and that expression of the nuclear-encoded photosynthesis genes is linked to the activity of PEP. Activation of PEP during chloroplast development likely is the source of a retrograde signal that promotes nuclear LHCB expression. Thus, regulation of PRIN2 is the thiol-mediated mechanism required for full PEP activity, with PRIN2 monomerization via reduction by TRXs providing a mechanistic link between photosynthetic electron transport and activation of photosynthetic gene expression.

  • 297.
    Gullberg, Jonas
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jonsson, Pär
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Nordström, Anders
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjöström, Michael
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Moritz, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry2004Inngår i: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 331, nr 2, s. 283-295Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The usual aim in metabolomic studies is to quantify the entire metabolome of each of a series of biological samples. To do this for complex biological matrices, e.g., plant tissues, efficient and reproducible extraction protocols must be developed. However, derivatization protocols must also be developed if GC/MS (one of the mostly widely used analytical methods for metabolomics) is involved. The aim of this study was to investigate how different chemical and physical factors (extraction solvent, derivatization reagents, and temperature) affect the extraction and derivatization of the metabolome from leaves of the plant Arabidopsis thaliana. Using design of experiment procedures, variation was systematically introduced, and the effects of this variation were analyzed using regression models. The results show that this approach allows a reliable protocol for metabolomic analysis of Arabidopsis to be determined with a relatively limited number of experiments. Following two different investigations an extraction and derivatization protocol was chosen. Further, the reproducibility of the analysis of 66 endogenous compounds was investigated, and it was shown that both hydrophilic and lipophilic compounds were detected with high reproducibility.

  • 298. Gundale, Michael J.
    et al.
    Sverker, Jennie
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Nilsson, Marie-Charlotte
    Wardle, David A.
    Variation in protein complexation capacity among and within six plant species across a boreal forest chronosequence2010Inngår i: Plant Ecology, ISSN 1385-0237, E-ISSN 1573-5052, Vol. 211, nr 2, s. 253-266Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We investigated among and within species variation in several litter chemical properties, including protein complexation capacity (PCC), for six plant species across a boreal forest chronosequence in northern Sweden across which stand fertility declines sharply with stand age. We hypothesized (1) that evergreen species which dominate in late-successional stands would exhibit higher PCCs than deciduous species that dominate in young stands, (2) that individual species would increase their PCCs in response to nutrient limitation as succession proceeds, and (3) that differences in PCC among litter types would determine their interactive effects with proteins on soil N and C mineralization. The data demonstrated a high PCC, but a low PCC per unit of soluble phenol, for two deciduous species that dominate in early-successional high fertility stands, providing mixed support for our first hypothesis. No species demonstrated a significant correlation between their PCC and stand age, which did not support our second hypothesis. Finally, a soil incubation assay revealed that litter extracts for three of the six species had negative interactive effects with added proteins on N mineralization rates, and that all six species demonstrated positive interactive effects with protein on C mineralization. This pattern did not provide strong support for our third hypothesis, and suggests that N immobilization was likely a more important factor regulating N mineralization than stabilization of proteins into tannin complexes. These data suggest that multiple interactive mechanisms between litter extracts and proteins likely occur simultaneously to influence the availability of N in soils.

  • 299. GUSTAFSSON, L
    et al.
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    LOW GENETIC-VARIATION IN SWEDISH POPULATIONS OF THE RARE SPECIES VICIA-PISIFORMIS (FABACEAE) REVEALED WITH RFLP (RDNA) AND RAPD1994Inngår i: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 189, nr 3-4, s. 133-148Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Nine Swedish populations, 1-5 individuals/population, and one cultivated individual of the rare species Vicia pisiformis were investigated for genetic variation. In hybridizations with two rDNA probes using 8 restriction enzymes, only two individuals belonging to one population were polymorphic. A map of the rDNA gene cluster was constructed for four of the restriction enzymes used. Two of the polymorphic sites were mapped and were found to be located outside regions coding for rRNA, presumably caused by single point mutations or small deletions. The repeat length of the rDNA region was c. 10,000 bp, which corresponds well with the size found for other species belonging to Fabaceae. No length polymorphism was found in the intergenic spacer, contrary to the situation found for most other plant species investigated for rDNA variation. The haplotype diversity for the species (Hsp Shannon) was very low (0.055). Within-population values (Hpop) was 0 for all populations except the variable one, which had 0.301. PCR amplification with 6 random primers also revealed very low levels of genetic diversity. A polymorphism was observed in a limited number of individuals for four populations. Hsp was 0.065 and HpopBAR was 0.050. The average D value (Wetton) for the PCR haplotypes was 0.99.

  • 300.
    Gustafsson, Petter
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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)1991Inngår i: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 43, nr 3-4, s. 287-300Artikkel i tidsskrift (Fagfellevurdert)
    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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