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  • 101.
    Blanco-Rivero, Amaya
    et al.
    Madrid, Spain.
    Shutova, Tatiana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    José Román, María
    Madrid, Spain.
    Villarejo, Arsenio
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain.
    Martinez, Flor
    Madrid, Spain.
    Phosphorylation Controls the Localization and Activation of the Lumenal Carbonic Anhydrase in Chlamydomonas reinhardtii2012Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, nr 11, artikkel-id e49063Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Cah3 is the only carbonic anhydrase (CA) isoform located in the thylakoid lumen of Chlamydomonas reinhardtii. Previous studies demonstrated its association with the donor side of the photosystem II (PSII) where it is required for the optimal function of the water oxidizing complex. However this enzyme has also been frequently proposed to perform a critical function in inorganic carbon acquisition and CO2 fixation and all mutants lacking Cah3 exhibit very poor growth after transfer to low CO2 conditions. Results/Conclusions: In the present work we demonstrate that after transfer to low CO2, Cah3 is phosphorylated and that phosphorylation is correlated to changes in its localization and its increase in activity. When C. reinhardtii wild-type cells were acclimated to limiting CO2 conditions, the Cah3 activity increased about 5-6 fold. Under these conditions, there were no detectable changes in the level of the Cah3 polypeptide. The increase in activity was specifically inhibited in the presence of Staurosporine, a protein kinase inhibitor, suggesting that the Cah3 protein was post-translationally regulated via phosphorylation. Immunoprecipitation and in vitro dephosphorylation experiments confirm this hypothesis. In vivo phosphorylation analysis of thylakoid polypeptides indicates that there was a 3-fold increase in the phosphorylation signal of the Cah3 polypeptide within the first two hours after transfer to low CO2 conditions. The increase in the phosphorylation signal was correlated with changes in the intracellular localization of the Cah3 protein. Under high CO2 conditions, the Cah3 protein was only associated with the donor side of PSII in the stroma thylakoids. In contrast, in cells grown at limiting CO2 the protein was partly concentrated in the thylakoids crossing the pyrenoid, which did not contain PSII and were surrounded by Rubisco molecules. Significance: This is the first report of a CA being post-translationally regulated and describing phosphorylation events in the thylakoid lumen.

  • 102. Blumenstein, Kathrin
    et al.
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Martin, Juan A.
    Hultberg, Malin
    Sieber, Thomas N.
    Helander, Marjo
    Witzell, Johanna
    Nutritional niche overlap potentiates the use of endophytes in biocontrol of a tree disease2015Inngår i: BioControl (Dordrecht), ISSN 1386-6141, E-ISSN 1573-8248, Vol. 60, nr 5, s. 655-667Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Asymptomatic endophytic fungi are often regarded as potent biocontrol agents in plants, but the competitive interactions between endophytes and other microbes within the same host plant are poorly understood. We tested a hypothesis that as compared to asymptomatic endophytes, an aggressive pathogen inhabiting the same host is able to utilize carbon substrates more efficiently. Using phenotype microarray, we determined the carbon utilization profiles of the highly virulent Dutch elm disease (DED) pathogen Ophiostoma novo-ulmi, and four asymptomatic elm (Ulmus spp.) endophyte isolates that were selected based on their differential association to the DED-susceptibility pattern of the host elms. The competitive interactions between isolates were evaluated using a niche overlap index. In contrast to our hypothesis, the studied endophytes exhibited extensive niche overlap with the pathogen, suggesting that some endophyte strains might protect elms against DED-pathogen through competition for substrates and provide new tools for biocontrol of DED.

  • 103.
    Blumenstein, Kathrin
    et al.
    Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Macaya-Sanz, David
    Madrid, Spain.
    Martin, Juana A.
    Madrid, Spain.
    Albrectsen, Benedicte R.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark.
    Witzell, Johanna
    Joensuu, Finland.
    Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes2015Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, artikkel-id 1033Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    There is an increasing need to calibrate microbial community profiles obtained through next generation sequencing (NGS) with relevant taxonomic identities of the microbes, and to further associate these identities with phenotypic attributes. Phenotype MicroArray (PM) techniques provide a semi-high throughput assay for characterization and monitoring the microbial cellular phenotypes. Here, we present detailed descriptions of two different PM protocols used in our recent studies on fungal endophytes of forest trees, and highlight the benefits and limitations of this technique. We found that the PM approach enables effective screening of substrate utilization by endophytes. However, the technical limitations are multifaceted and the interpretation of the PM data challenging. For the best result, we recommend that the growth conditions for the fungi are carefully standardized. In addition, rigorous replication and control strategies should be employed whether using pre-configured, commercial microwell-plates or in-house designed PM plates for targeted substrate analyses. With these precautions, the PM technique is a valuable tool to characterize the metabolic capabilities of individual endophyte isolates, or successional endophyte communities identified by NGS, allowing a functional interpretation of the taxonomic data. Thus, PM approaches can provide valuable complementary information for NGS studies of fungal endophytes in forest trees.

  • 104.
    Bollhöner, Benjamin
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Significance of hydrolytic enzymes expressed during xylem cell death2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Xylem is an inherent feature of all vascular plants and functions in water transport and mechanical support. In order to efficiently transport water, xylem cells are reinforced by secondary walls before they undergo programmed cell death and their cell contents are removed by autolysis to create a hollow tube. During their differentiation, xylem cells express various hydrolytic enzymes, such as proteases, nucleases and lipases, but only in a few examples has their role in xylem cell death been characterized. This thesis focuses on the regulatory aspects of xylem cell death and the autolytic cell clearance in vessel elements and fibers of hybrid aspen (Populus tremula L. x tremuloides Michx.) and in vessel elements of Arabidopsis thaliana. Using comparative transcriptomic analysis, candidate genes for fiber-specific cell death processes were identified. Further, a hypothesis is presented on the regulation of thermospermine levels in the vasculature by a negative feedback-loop involving auxin and the class III Homeodomain-Leucine Zipper (HD-ZIP III) transcription factor HOMEOBOX8 (PtHB8). The role of the Arabidopsis METACASPASE9 (AtMC9) in xylem cell death was characterized using molecular tools, such as reporter lines and fluorescent fusion proteins, and electron microscopy (TEM). This showed that cell death initiation is not controlled by AtMC9. Instead, evidence is presented for the involvement of AtMC9 in the post mortem autolysis of vessel elements that follows tonoplast rupture and leads to the formation of the hollow conduit. Cell death-associated genes were further observed to be expressed during the emergence of lateral roots in Arabidopsis thaliana. This led to the discovery that cells overlying a lateral root primordium undergo cell death, which was demonstrated by detection of DNA degradation and TEM analysis. It is concluded that cell death facilitates emergence of lateral roots through the overlying tissues in a concerted manner with cell wall remodelling. Together, these findings show that although individual hydrolytic enzymes may be dispensable for plant growth and development, their common regulators are the tool for understanding their function and importance.

  • 105.
    Bollhöner, Benjamin
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Jokipii-Lukkari, Soile
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bygdell, Joakim
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Stael, Simon
    Adriasola, Mathilda
    Muñiz, Luis
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Van Breusegem, Frank
    Ezcurra, Inés
    Wingsle, Gunnar
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    The function of two type II metacaspases in woody tissues of Populus trees2018Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, nr 4, s. 1551-1565Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 106.
    Bollhöner, Benjamin
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Voss, Ute
    Prestele, Jakob
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Wilson, Michael
    Kenobi, Kim
    Viotti, Corrado
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    André, Domenique
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Lers, Amnon
    Bennett, Malcolm
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Programmed cell death in overlying tissues facilitates lateral root emergenceManuskript (preprint) (Annet vitenskapelig)
  • 107.
    Bollhöner, Benjamin
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Zhang, Bo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Stael, Simon
    Denancé, Nicolas
    Overmyer, Kirk
    Goffner, Deborah
    Van Breusegem, Frank
    Tuominen, Hannele
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Post mortem function of AtMC9 in xylem vessel elements2013Inngår i: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 200, nr 2, s. 498-510Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cell death of xylem elements is manifested by rupture of the tonoplast and subsequent autolysis of the cellular contents. Metacaspases have been implicated in various forms of plant cell death but regulation and execution of xylem cell death by metacaspases remains unknown. Analysis of the type II metacaspase gene family in Arabidopsis thaliana supported the function of METACASPASE 9 (AtMC9) in xylem cell death. Progression of xylem cell death was analysed in protoxylem vessel elements of 3-d-old atmc9 mutant roots using reporter gene analysis and electron microscopy. Protoxylem cell death was normally initiated in atmc9 mutant lines, but detailed electron microscopic analyses revealed a role for AtMC9 in clearance of the cell contents post mortem, that is after tonoplast rupture. Subcellular localization of fluorescent AtMC9 reporter fusions supported a post mortem role for AtMC9. Further, probe-based activity profiling suggested a function of AtMC9 on activities of papain-like cysteine proteases. Our data demonstrate that the function of AtMC9 in xylem cell death is to degrade vessel cell contents after vacuolar rupture. We further provide evidence on a proteolytic cascade in post mortem autolysis of xylem vessel elements and suggest that AtMC9 is part of this cascade.

  • 108. Boone, Celia K
    et al.
    Keefover-Ring, Ken
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Mapes, Abigail C
    Adams, Aaron S
    Bohlmann, Jörg
    Raffa, Kenneth F
    Bacteria associated with a tree-killing insect reduce concentrations of plant defense compounds2013Inngår i: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 39, nr 7, s. 1003-1006Artikkel i tidsskrift (Fagfellevurdert)
  • 109. Borodich, A
    et al.
    Rojdestvenski, I
    Cottam, M
    Anderson, J
    Oquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Segregation of the photosystems in higher plant thylakoids and short- and long-term regulation by a mesoscopic approach2003Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 225, nr 4, s. 431-441Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper we consider the relationship between the lateral segregation of photosystems I and II in the grana and characteristics of the short- and long-term regulation in thylakoids following the mesoscopic approach. Our study is thermodynamic; it is based on the Flory-Huggins theory for binary mixtures and the McMillan-Mayer theory of heterogeneous solutions. We demonstrate that state transitions promote rearrangement of photosystems by either favoring their mixing after LHCII phosphorylation or enhancing their segregation after LHCII dephosphorylation. This regulation influences the entire system properties locally. We also demonstrate that the variations of the photosystem ratio promote rearrangement of the photosystems preserving their segregation. This regulation influences the entire system properties globally. The studies presented are another indication of the importance of the segregation of the photosystems in the grana thylakoids of higher plants. Segregation of PSIs and PSIIs is a signature of the spinodal decomposition, which is a fine regulatory mechanism, related to both the short- and long-term adaptations of the photosynthetic apparatus in higher plant thylakoids. (C) 2003 Elsevier Ltd. All rights reserved.

  • 110. Borodich, A
    et al.
    Rojdestvenski, I
    Cottam, M
    Oquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Segregation of the photosystems in thylakoids depends on their size2003Inngår i: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1606, nr 1-3, s. 73-82Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Lateral segregation of two types of photosystems in thylakoid membranes of green plants is one of the key factors that provide the stability and fine-tuning of the light quanta supply by pigment proteins and non-cyclic electron transport. Due to this specific feature of the membrane structural organization, the photosynthetic units function in the green plants with optimal performance. In this report a mesoscopic theory is outlined to address the physical aspects of segregation phenomenon. Results of theoretical studies and computer simulations suggest that charge mismatch and the size difference between two photosystems in grana are most responsible for their lateral segregation, which is driven by the screened electrostatic and lipid-induced interactions. Comparative simulations of photosystems of different sizes show the crucial dependence of their ordering on a geometrical parameter. It seems that the size effect alone may prevent photosystems from segregated arrangement in cyanobacterial thylakoids. (C) 2003 Elsevier B.V. All rights reserved.

  • 111. BORODIN, V
    et al.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    THE EFFECT OF LIGHT QUALITY ON THE INDUCTION OF EFFICIENT PHOTOSYNTHESIS UNDER LOW CO2 CONDITIONS IN CHLAMYDOMONAS-REINHARDTII AND CHLORELLA-PYRENOIDOSA1994Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 92, nr 2, s. 254-260Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The effect of blue and red light on the adaptation to low CO2 conditions was studied in high-CO2 grown cultures of Chlorella pyrenoidosa (82T) and Chlamydomonas reinhardtii (137(+)) by measuring O-2 exchange under various inorganic carbon (C-i) concentrations. At equal photosynthetic photon flux density (PPFD), blue light was more favourable for adaptation in both species, compared to red light. The difference in photosynthetic oxygen evolution between cells adapted to low C-i under blue and red light was more pronounced when oxygen evolution was measured under low C-i compared to high C-i conditions. The effect of light quality on adaptation remained for several hours. The different effects caused by blue and red light was observed in C. pyrenoidosa over a wide range of PPFD with increasing differences at increasing PPFD. The maximal difference was obtained at a PPFD above 1 500 mu mol m(-2) s(-1). We found no difference in the extracellular carbonic anhydrase activity between blue- and red light adapted cells. The light quality effect recorded under C-i-limiting conditions in C. reinhardtii cells adapted to air, was only 37% less when instead of pure blue light red light containing 12.5% of blue light (similar PPFD as blue light) was used during adaptation to low carbon. This indicates that in addition to affecting photosynthesis, blue light affected a sensory system involved in algal adaptation to low C-i conditions. Since the affinity for C-i of C. pyrenoidosa and C. reinhardtii cells adapted to air under blue light was higher than that of cells adapted under red light, we suggest that induction of some component(s) of the C-i accumulating mechanism is regulated by the light quality.

  • 112. Bossmann, B
    et al.
    Knoetzel, J
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, 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 proteins1997Inngår i: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 52, nr 2, s. 127-136Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 113. Bourque, S.
    et al.
    Jeandroz, S.
    Grandperret, V.
    Lehotai, Nora
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, Dijon, France.
    Aime, S.
    Soltis, D. E.
    Miles, N. W.
    Melkonian, M.
    Deyholos, M. K.
    Leebens-Mack, J. H.
    Chase, M. W.
    Rothfels, C. J.
    Stevenson, D. W.
    Graham, S. W.
    Wang, X.
    Wu, S.
    Pires, J. C.
    Edger, P. P.
    Yan, Z.
    Xie, Y.
    Carpenter, E. J.
    Wong, G. K. S.
    Wendehenne, D.
    Nicolas-Frances, V.
    The Evolution of HD2 Proteins in Green Plants2016Inngår i: Trends in Plant Science, ISSN 1360-1385, E-ISSN 1878-4372, Vol. 21, nr 12, s. 1008-1016Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    In eukaryotes, protein deacetylation is carried out by two well-conserved his tone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.

  • 114. Boutte, Yohann
    et al.
    Jonsson, Kristoffer
    McFarlane, Heather E.
    Johnson, Errin
    Gendre, Delphine
    Swarup, Ranjan
    Friml, Jiri
    Samuels, Lacey
    Robert, Stephanie
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Bhalerao, Rishikesh P.
    ECHIDNA-mediated post-Golgi trafficking of auxin carriers for differential cell elongation2013Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, nr 40, s. 16259-16264Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development.

  • 115.
    Boutté, Yohann
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Frescatada-Rosa, Márcia
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Men, Shuzhen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Chow, Cheung-Ming
    Ebine, Kazuo
    Gustavsson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Johansson, Lenore
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ueda, Takashi
    Moore, Ian
    Jürgens, Gerd
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Endocytosis restricts Arabidopsis KNOLLE syntaxin to the cell division plane during late cytokinesis2010Inngår i: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 29, nr 3, s. 546-58Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 116.
    Boutté, Yohann
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Cellular processes relying on sterol function in plants2009Inngår i: Current opinion in plant biology, ISSN 1369-5266, E-ISSN 1879-0356, Vol. 12, nr 6, s. 705-713Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sterols are lipophilic membrane components essential for diverse cellular functions. The plant sterol biosynthesis pathway has largely been defined by biochemical approaches. Sterol function has been investigated by the pharmacological and genetic manipulation of sterol biosynthesis. However, mechanisms by which sterols influence cellular processes and targets of sterol function remain largely unknown. During the last two years, new Arabidopsis sterol biosynthesis mutants have been characterized. Their analysis has revealed the contributions of known and alternative routes of sterol biosynthesis to various cellular processes. Subcellular localization and trafficking of a sterol-binding protein have been investigated and first steps towards in vivo characterization of sterol-enriched membrane domains have been taken. Finally, mechanistic insight into the role of plant sterols during endocytosis and the establishment of cell polarity has been obtained.

  • 117.
    Boutté, Yohann
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Men, Shuzhen
    Grebe, Markus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Fluorescent in situ visualization of sterols in Arabidopsis roots2011Inngår i: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 6, nr 4, s. 446-456Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sterols are eukaryotic membrane components with crucial roles in diverse cellular processes. Elucidation of sterol function relies on development of tools for in situ sterol visualization. Here we describe protocols for in situ sterol localization in Arabidopsis thaliana root cells, using filipin as a specific probe for detection of fluorescent filipin-sterol complexes. Currently, filipin is the only established tool for sterol visualization in plants. Filipin labeling can be performed on aldehyde-fixed samples, largely preserving fluorescent proteins and being compatible with immunocytochemistry. Filipin can also be applied for probing live cells, taking into account the fact that it inhibits sterol-dependent endocytosis. The experimental procedures described are designed for fluorescence detection by confocal laser-scanning microscopy with excitation of filipin-sterol complexes at 364 nm. The protocols require 1 d for sterol covisualization with fluorescent proteins in fixed or live roots and 2 d for immunocytochemistry on whole-mount roots.

  • 118.
    Brackmann, Klaus
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Contribution of endocytic trafficking and epidermal morphology genes to planar polarity formation in the Arabidopsis root epidermis2010Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
  • 119. BRENTEL, I
    et al.
    Selstam, Eva
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    LINDBLOM, G
    PHASE-EQUILIBRIA OF MIXTURES OF PLANT GALACTOLIPIDS - THE FORMATION OF A BICONTINUOUS CUBIC PHASE1985Inngår i: Biochimica et Biophysica Acta, ISSN 0006-3002, E-ISSN 1878-2434, Vol. 812, nr 3, s. 816-826Artikkel i tidsskrift (Fagfellevurdert)
  • 120.
    Brouwer, Bastiaan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Shedding Light on Shade- and Dark-Induced Leaf Senescence2012Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Leaf senescence is the final stage of leaf development, during which the leaf relocates most of itsvaluable nutrients to developing or storing parts of the plant. As this process progresses, leaves losetheir green color and their capacity to perform photosynthesis. Shade and darkness are well-knownas factors inducing leaf senescence and it has been proposed that senescence can be initiated byreductions in photosynthesis, photomorphogenesis and transpiration. However, despite the fact thatthe signaling mechanisms regulating each of these processes have been extensively described,particularly in seedlings, their contribution to the initiation of senescence in mature leaves stillremains unclear. Furthermore, the use of different experimental systems to study shade-inducedleaf senescence has yielded several divergent results, which altogether complicate the overallunderstanding of leaf senescence.

    To address this, darkened plants and individually darkened leaves, which show different rates of leafsenescence, were studied. Comparing the transcriptome and metabolome of these two darktreatmentsrevealed that they differed distinctly with regard to their metabolic strategies. Wholedarkened plants were severely carbohydrate-starved, accumulated amino acids and slowed downtheir metabolism. In contrast, individually darkened leaves showed continued active metabolismcoupled to senescence-associated degradation and relocation of amino acids.

    This knowledge was used to set up a new system to study how shade affects leaf senescence in themodel plant Arabidopsis thaliana. Use of this system revealed that different senescence-associatedhallmarks appeared in response to different intensities of shade. Some of these hallmarks werefurther shown to be part of both leaf senescence and photosynthetic acclimation to low light.

    Finally, using this system on phytochrome mutants revealed that loss of phytochrome A increasedthe loss of chlorophyll under shade, without increasing the expression of senescence-associatedgenes.

    Together, these findings suggest that shade-induced leaf senescence, which is generally perceived asa single process, is actually an intricate network of different processes that work together tomaintain an optimal distribution of nutrients within the plant.

  • 121.
    Brouwer, Bastiaan
    et al.
    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).
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Far-red light reduces senescence-associated chlorophyll loss under low light via a Phytochrome A-mediated Far-red High Irradiance ResponseManuskript (preprint) (Annet vitenskapelig)
  • 122.
    Brouwer, Bastiaan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Keech, Olivier
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis2014Inngår i: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 65, nr 14, s. 4037-4049Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phytochrome is thought to control the induction of leaf senescence directly, however, the signalling and molecular mechanisms remain unclear. In the present study, an ecophysiological approach was used to establish a functional connection between phytochrome signalling and the physiological processes underlying the induction of leaf senescence in response to shade. With shade it is important to distinguish between complete and partial shading, during which either the whole or only a part of the plant is shaded, respectively. It is first shown here that, while PHYB is required to maintain chlorophyll content in a completely shaded plant, only PHYA is involved in maintaining the leaf chlorophyll content in response to partial plant shading. Second, it is shown that leaf yellowing associated with strong partial shading in phyA-mutant plants actually correlates to a decreased biosynthesis of chlorophyll rather than to an increase of its degradation. Third, it is shown that the physiological impact of this decreased biosynthesis of chlorophyll in strongly shaded phyA-mutant leaves is accompanied by a decreased capacity to adjust the Light Compensation Point. However, the increased leaf yellowing in phyA-mutant plants is not accompanied by an increase of senescence-specific molecular markers, which argues against a direct role of PHYA in inducing leaf senescence in response to partial shade. In conclusion, it is proposed that PHYA, but not PHYB, is essential for fine-tuning the chlorophyll biosynthetic pathway in response to partial shading. In turn, this mechanism allows the shaded leaf to adjust its photosynthetic machinery to very low irradiances, thus maintaining a positive carbon balance and repressing the induction of leaf senescence, which can occur under prolonged periods of shade.

  • 123.
    Brouwer, Bastiaan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ziolkowska, Agnieszka
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bagard, Matthieu
    Keech, Olivier
    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).
    The impact of light intensity on shade-induced leaf senescence2012Inngår i: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 35, nr 6, s. 1084-1098Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Plants often have to cope with altered light conditions, which in leaves induce various physiological responses ranging from photosynthetic acclimation to leaf senescence. However, our knowledge of the regulatory pathways by which shade and darkness induce leaf senescence remains incomplete. To determine to what extent reduced light intensities regulate the induction of leaf senescence, we performed a functional comparison between Arabidopsis leaves subjected to a range of shading treatments. Individually covered leaves, which remained attached to the plant, were compared with respect to chlorophyll, protein, histology, expression of senescence-associated genes, capacity for photosynthesis and respiration, and light compensation point (LCP). Mild shading induced photosynthetic acclimation and resource partitioning, which, together with a decreased respiration, lowered the LCP. Leaf senescence was induced only under strong shade, coinciding with a negative carbon balance and independent of the red/far-red ratio. Interestingly, while senescence was significantly delayed at very low light compared with darkness, phytochrome A mutant plants showed enhanced chlorophyll degradation under all shading treatments except complete darkness. Taken together, our results suggest that the induction of leaf senescence during shading depends on the efficiency of carbon fixation, which in turn appears to be modulated via light receptors such as phytochrome A.

  • 124. BRUNES, L
    et al.
    Öquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    ELIASSON, L
    ON THE REASON FOR THE DIFFERENT PHOTOSYNTHETIC RATES OF SEEDLINGS OF PINUS-SILVESTRIS AND BETULA-VERRUCOSA1980Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 66, nr 5, s. 940-944Artikkel i tidsskrift (Fagfellevurdert)
  • 125.
    Brunoni, Federica
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Ljung, Karin
    Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
    Bellini, Catherine
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Control of root meristem establishment in conifers2019Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 165, nr 1, s. 81-89Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The evolution of terrestrial plant life was made possible by the establishment of a root system, which enabled plants to migrate from aquatic to terrestrial habitats. During evolution, root organization has gradually progressed from a very simple to a highly hierarchical architecture. Roots are initiated during embryogenesis and branch afterward through lateral root formation. Additionally, adventitious roots can be formed post-embryonically from aerial organs. Induction of adventitious roots (ARs) forms the basis of the vegetative propagation via cuttings in horticulture, agriculture and forestry. This method, together with somatic embryogenesis, is routinely used to clonally multiply conifers. In addition to being utilized as propagation techniques, adventitious rooting and somatic embryogenesis have emerged as versatile models to study cellular and molecular mechanisms of embryo formation and organogenesis of coniferous species. Both formation of the embryonic root and the AR primordia require the establishment of auxin gradients within cells that coordinate the developmental response. These processes also share key elements of the genetic regulatory networks that, e.g. are triggering cell fate. This minireview gives an overview of the molecular control mechanisms associated with root development in conifers, from initiation in the embryo to post-embryonic formation in cuttings.

  • 126.
    Brännström, Kristoffer
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Gharibyan, Anna L.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Islam, Tohidul
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Iakovleva, Irina
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Nilsson, Lina
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Lee, Cheng Choo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Sandblad, Linda
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten).
    Pamrén, Annelie
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Olofsson, Anders
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips2018Inngår i: Data in Brief, E-ISSN 2352-3409, Vol. 19, s. 1166-1170Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We demonstrate the use of Scanning Electron microscopy (SEM) in combination with Surface Plasmon Resonance (SPR) to probe and verify the formation of amyloid and its morphology on an SPR chip. SPR is a technique that measures changes in the immobilized weight on the chip surface and is frequently used to probe the formation and biophysical properties of amyloid structures. In this context it is of interest to also monitor the morphology of the formed structures. The SPR chip surface is made of a layer of gold, which represent a suitable material for direct analysis of the surface using SEM. The standard SPR chip used here (CM5-chip, GE Healthcare, Uppsala, Sweden) can easily be disassembled and directly analyzed by SEM. In order to verify the formation of amyloid fibrils in our experimental conditions we analyzed also in-solution produced structures by using Transmission Electron Microscopy (TEM). For further details and experimental findings, please refer to the article published in Journal of Molecular Biology, (Brännström K. et al., 2018) [1].

  • 127.
    Burén, Stefan
    Umeå universitet, Teknisk-naturvetenskaplig fakultet, Fysiologisk botanik.
    Targeting and function of CAH1: Characterization of a novel protein pathway to the plant cell chloroplast2010Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The chloroplast is the organelle within a plant cell where photosynthesis takes place. This organelle originates from a cyanobacterium that was engulfed by a eukaryotic cell. During the transition from endosymbiont to organelle most of the cyanobacterial genes were transferred to the nuclear genome of the host cell, resulting in a chloroplast with a much reduced genome that requires massive import of gene products (proteins) back to the organelle. The majority of these proteins are translated in the cytosol as pre-proteins containing targeting information that directs them to a translocon complex in the chloroplast envelope, the Toc-Tic system, through which these proteins are transported.

    We have identified a protein in the model plant Arabidopsis thaliana, CAH1, that is trafficked via the endomembrane system (ER/Golgi apparatus) to the chloroplast instead of using the Toc-Tic machinery. This transport is partly mediated by canonical vesicle trafficking elements involved in ER to Golgi transport, such as Sar1 and RabD GTPases. Analysis of point mutated variants of CAH1 showed that both N-linked glycans and an intra-molecular disulphide bridge are required for correct folding, trafficking and function of the protein. Since chloroplasts lack N-glycosylation machinery, we propose that a route for chloroplast proteins that require endomembrane-specific post-translational modifications for their functionality exists as a complement to the Toc-Tic system.

    We also show that mutant plants with disrupted CAH1 gene expression have reduced rates of CO2 uptake and accumulate lower amounts of starch compared to wild-type plants, indicating an important function of the CAH1 protein for the photosynthetic capacity of Arabidopsis.

    Further study of CAH1 will not only be important to reveal its role in photosynthesis, but characterization of this novel protein pathway to the chloroplast can also shed light on how the plant cell evolved and clarify the purpose of keeping several chloroplast import pathways working in parallel. In addition, knowledge about this pathway could increase the opportunities for using plants as bio-factories for production of recombinant glycoproteins, which make up the vast majority of the bio-pharmaceutical molecules.

  • 128.
    Burén, Stefan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Blanco-Rivero, Amaya
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Ortega-Villasante, Cristina
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Samuelsson, Göran
    Villarejo, Arsenio
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Specific suppression of the chloroplast N-glycosylated carbonic anhydrase (CAH1) has major impact on the photosynthetic performance of Arabidopsis thalianaManuskript (preprint) (Annet vitenskapelig)
  • 129.
    Burén, Stefan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ortega-Villasante, Cristina
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Blanco-Rivero, Amaya
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Martínez-Bernardini, Andrea
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Shutova, Tatiana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bako, Laszlo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Villarejo, Arsenio
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    N-glycosylation is required for trafficking and activity of a chloroplast-localized carbonic anhydrase (CAH1) in Arabidopsis thalianaManuskript (preprint) (Annet vitenskapelig)
  • 130.
    Burén, Stefan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ortega-Villasante, Cristina
    Blanco-Rivero, Amaya
    Martínez-Bernardini, Andrea
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Shutova, Tatiana
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Shevela, Dmitriy
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Messinger, Johannes
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bako, Laszlo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Villarejo, Arsenio
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Importance of post-translational modifications for functionality of a chloroplast-localized carbonic anhydrase (CAH1) in Arabidopsis thaliana2011Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, nr 6, s. e21021-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background

    The Arabidopsis CAH1 alpha-type carbonic anhydrase is one of the few plant proteins known to be targeted to the chloroplast through the secretory pathway. CAH1 is post-translationally modified at several residues by the attachment of N-glycans, resulting in a mature protein harbouring complex-type glycans. The reason of why trafficking through this non-canonical pathway is beneficial for certain chloroplast resident proteins is not yet known. Therefore, to elucidate the significance of glycosylation in trafficking and the effect of glycosylation on the stability and function of the protein, epitope-labelled wild type and mutated versions of CAH1 were expressed in plant cells.

    Methodology/Principal Findings

    Transient expression of mutant CAH1 with disrupted glycosylation sites showed that the protein harbours four, or in certain cases five, N-glycans. While the wild type protein trafficked through the secretory pathway to the chloroplast, the non-glycosylated protein formed aggregates and associated with the ER chaperone BiP, indicating that glycosylation of CAH1 facilitates folding and ER-export. Using cysteine mutants we also assessed the role of disulphide bridge formation in the folding and stability of CAH1. We found that a disulphide bridge between cysteines at positions 27 and 191 in the mature protein was required for correct folding of the protein. Using a mass spectrometric approach we were able to measure the enzymatic activity of CAH1 protein. Under circumstances where protein N-glycosylation is blocked in vivo, the activity of CAH1 is completely inhibited.

    Conclusions/Significance

    We show for the first time the importance of post-translational modifications such as N-glycosylation and intramolecular disulphide bridge formation in folding and trafficking of a protein from the secretory pathway to the chloroplast in higher plants. Requirements for these post-translational modifications for a fully functional native protein explain the need for an alternative route to the chloroplast.

  • 131.
    Burén, Stefan
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Ortega-Villasante, Cristina
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Samuelsson, Göran
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Bako, Laszlo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Villarejo, Arsenio
    Department of Biology, Universidad Autónoma de Madrid, Spain.
    Optimization of the 2A peptide coexpression system to study trafficking of the plastid N-glycoprotein CAH1 in Arabidopsis thalianaManuskript (preprint) (Annet vitenskapelig)
  • 132. Bykova, Natalia V
    et al.
    Keerberg, Olav
    Pärnik, Tiit
    Bauwe, Hermann
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Interaction between photorespiration and respiration in transgenic potato plants with antisense reduction in glycine decarboxylase.2005Inngår i: Planta, ISSN 0032-0935, Vol. 222, nr 1, s. 130-40Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Abstract Potato (Solanum tuberosum L. cv. Désirée) plants with an antisense reduction in the P-protein of the glycine decarboxylase complex (GDC) were used to study the interaction between respiration and photorespiration. Mitochondria isolated from transgenic plants had a decreased capacity for glycine oxidation and glycine accumulated in the leaves. Malate consumption increased in leaves of GDC deficient plants and the capacity for malate and NADH oxidation increased in isolated mitochondria. A lower level of alternative oxidase protein and decreased partitioning of electrons to the alternative pathway was found in these plants. The adenylate status was altered in protoplasts from transgenic plants, most notably the chloroplastic ATP/ADP ratio increased. The lower capacity for photorespiration in leaves of GDC deficient plants was compensated for by increased respiratory decarboxylations in the light. This is interpreted as a decreased light suppression of the tricarboxylic acid cycle in GDC deficient plants in comparison to wild-type plants. The results support the view that respiratory decarboxylations in the light are restricted at the level of the pyruvate dehydrogenase complex and/or isocitrate dehydrogenase and that this effect is likely to be mediated by mitochondrial photorespiratory products.

  • 133. Bykova, Natalia V.
    et al.
    Møller, Ian M.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Igamberdiev, Abir U.
    The function of glycine decarboxylase complex is optimized to maintain high photorespiratory flux via buffering of its reaction products2014Inngår i: Mitochondrion (Amsterdam. Print), ISSN 1567-7249, E-ISSN 1872-8278, Vol. 19, s. 357-364Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oxidation of glycine in photorespiratory pathway is the major flux through mitochondria of C3 plants in the light. It sustains increased intramitochondrial concentrations of NADH and NADPH, which are required to engage the internal rotenone-insensitive NAD(P)H dehydrogenases and the alternative oxidase. We discuss here possible mechanisms of high photorespiratory flux maintenance in mitochondria and suggest that it is fulfilled under conditions where the concentrations of glycine decarboxylase reaction products NADH and CO2 achieve an equilibrium provided by malate dehydrogenase and carbonic anhydrase, respectively. This results in the removal of these products from the glycine decarboxylase multienzyme active sites and in the maintenance of their concentrations at levels sufficiently low to prevent substrate inhibition of the reaction. 

  • 134. Bykova, Natalia V
    et al.
    Rasmusson, Allan G.
    Igamberdiev, Abir U
    Department of Plant Science, Faculty Agriculture and Food Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
    Gardeström, Per
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Møller, Ian M.
    Two separate transhydrogenase activities are present in plant mitochondria1999Inngår i: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 265, nr 1, s. 106-111Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Inside-out submitochondrial particles from both potato tubers and pea leaves catalyze the transfer of hydride equivalents from NADPH to NAD(+) as monitored with a substrate-regenerating system. The NAD(+) analogue acetylpyridine adenine dinucleotide is also reduced by NADPH and incomplete inhibition by the complex I inhibitor diphenyleneiodonium (DPI) indicates that hive enzymes are involved in this reaction. Gel-filtration chromatography of solubilized mitochondrial membrane complexes confirms that the DPI-sensitive TH activity is due to NADH-ubiquinone oxidoreductase (EC 1,6,5,3, complex I), whereas the DPI-insensitive activity is due to a separate enzyme eluting around 220 kDa. The DPI-insensitive TH activity is specific for the 4B proton on NADH, whereas there is no indication of a 4A-specific activity characteristic of a mammalian-type energy-linked TH. The DPI-insensitive TH may be similar to the soluble type of transhydrogenase found in, e.g., Pseudomonas. The presence of non-energy-linked TR: activities directly coupling the matrix NAD(H) and NADP(H) pools will have important consequences for the regulation of NADP-linked processes in plant mitochondria. (C) 1999 Academic Press.

  • 135.
    Bylesjö, Max
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Eriksson, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    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).
    Moritz, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Orthogonal projections to latent structures as a strategy for microarray data normalization2007Inngår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 8, nr 207Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 136.
    Bylesjö, Max
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Eriksson, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjödin, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Sjöström, Michael
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    MASQOT: a method for cDNA microarray spot quality control.2005Inngår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 6, s. 250-Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 137.
    Bylesjö, Max
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Nilsson, Robert
    Umeå universitet, Medicinska fakulteten, Umeå Life Science Centre (ULSC).
    Srivastava, Vaibhav
    Grönlund, Andreas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Johansson, Annika I
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Karlsson, Jan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Moritz, Thomas
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Wingsle, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen2009Inngår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 8, nr 1, s. 199-210Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 138.
    Bylesjö, Max
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Segura, Vincent
    Soolanayakanahally, Raju Y
    Rae, Anne M
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Street, Nathaniel R
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    LAMINA: a tool for rapid quantification of leaf size and shape parameters2008Inngår i: BMC Plant Biology, ISSN 1471-2229, Vol. 8, nr 82, s. 1-9Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 139.
    Bylesjö, Max
    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).
    Eriksson, Daniel
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Moritz, Thomas
    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).
    Trygg, Johan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    MASQOT-GUI: spot quality assessment for the two-channel microarray platform2006Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 22, nr 20, s. 2554-2555Artikkel i tidsskrift (Fagfellevurdert)
    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/

  • 140.
    Bäck, Siri
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    No Lhcb1 or Lhcb2 isoforms alone has a significant effect on state transitions2012Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
  • 141.
    Böhlenius, Henrik
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Huang, Tao
    Charbonnel-Campaa, Laurence
    Brunner, Amy M
    Jansson, Stefan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Strauss, Steven H
    Nilsson, Ove
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees.2006Inngår i: Science, ISSN 1095-9203, Vol. 312, nr 5776, s. 1040-3Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 142. Caballero-Pérez, Juan
    et al.
    Espinal-Centeno, Annie
    Falcon, Francisco
    García-Ortega, Luis F.
    Curiel-Quesada, Everardo
    Cruz-Hernández, Andrés
    Bako, Laszlo
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Chen, Xuemei
    Martínez, Octavio
    Alberto Arteaga-Vázquez, Mario
    Herrera-Estrella, Luis
    Cruz-Ramírez, Alfredo
    Transcriptional landscapes of Axolotl (Ambystoma mexicanum)2018Inngår i: Developmental Biology, ISSN 0012-1606, E-ISSN 1095-564X, Vol. 433, nr 2, s. 227-239Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The axolotl (Ambystoma mexicanum) is the vertebrate model system with the highest regeneration capacity. Experimental tools established over the past 100 years have been fundamental to start unraveling the cellular and molecular basis of tissue and limb regeneration. In the absence of a reference genome for the Axolotl, transcriptomic analysis become fundamental to understand the genetic basis of regeneration.

    Here we present one of the most diverse transcriptomic data sets for Axolotl by profiling coding and non coding RNAs from diverse tissues. We reconstructed a population of 115,906 putative protein coding mRNAs as full ORFs (including isoforms). We also identified 352 conserved miRNAs and 297 novel putative mature miRNAs.

    Systematic enrichment analysis of gene expression allowed us to identify tissue-specific protein-coding transcripts. We also found putative novel and conserved microRNAs which potentially target mRNAs which are reported as important disease candidates in heart and liver.

  • 143. Campbell, Catherine
    et al.
    Atkinson, Lindsey
    Zaragoza-Castells, Joana
    Lundmark, Maria
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.
    Atkin, Owen
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Acclimation of photosynthesis and respiration in response to change in growth temperature is asynchronous across plant functional groups2007Inngår i: New Phytologist, ISSN 0028-646XArtikkel i tidsskrift (Fagfellevurdert)
  • 144. Campbell, Catherine
    et al.
    Atkinson, Lindsey
    Zaragoza-Castells, Joana
    Lundmark, Maria
    Atkin, Owen
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Acclimation of photosynthesis and respiration is asynchronous in response to changes in temperature regardless of plant functional group.2007Inngår i: New Phytologist, ISSN 0028-646X, Vol. 176, nr 2, s. 375-89Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    • Gas exchange, fluorescence, western blot and chemical composition analyses were combined to assess if three functional groups (forbs, grasses and evergreen trees/shrubs) differed in acclimation of leaf respiration (R) and photosynthesis (A) to a range of growth temperatures (7, 14, 21 and 28°C).

    • When measured at a common temperature, acclimation was greater for R than for A and differed between leaves experiencing a 10-d change in growth temperature (PE) and leaves newly developed at each temperature (ND). As a result, the R : A ratio was temperature dependent, increasing in cold-acclimated plants. The balance was largely restored in ND leaves. Acclimation responses were similar among functional groups.

    • Across the functional groups, cold acclimation was associated with increases in nonstructural carbohydrates and nitrogen. Cold acclimation of R was associated with an increase in abundance of alternative and/or cytochrome oxidases in a species-dependent manner. Cold acclimation of A was consistent with an initial decrease and subsequent recovery of thylakoid membrane proteins and increased abundance of proteins involved in the Calvin cycle.

    • Overall, the results point to striking similarities in the extent and the biochemical underpinning of acclimation of R and A among contrasting functional groups differing in overall rates of metabolism, chemical composition and leaf structure.

  • 145. Campbell, D
    et al.
    Bruce, D
    Carpenter, C
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Oquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Two forms of the photosystem II D1 protein alter energy dissipation and state transitions in the cyanobacterium Synechococcus sp PCC 79421996Inngår i: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 47, nr 2, s. 131-144Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Synechococcus sp. PCC 7942 (Anacystis nidulans R2) contains two forms of the Photosystem II reaction centre protein D1, which differ in 25 of 360 amino acids. D1:1 predominates under low light hut is transiently replaced by D1:2 upon shifts to higher light. Mutant cells containing only D1:1 have lower photochemical energy capture efficiency and decreased resistance to photoinhibition, compared to cells containing D1:2. We show that when dark-adapted or under low to moderate light, cells with D1:1 have higher non-photochemical quenching of PS II fluorescence (higher q(N)) than do cells with D1:2. This is reflected in the 77 K chlorophyll emission spectra, with lower Photosystem II fluorescence at 697-698 nm in cells containing D1:1 than in cells with D1:2. This difference in quenching of Photosystem II fluorescence occurs upon excitation of both chlorophyll at 435 nm and phycobilisomes at 570 nm. Measurement of time-resolved room temperature fluorescence shows that Photosystem II fluorescence related to charge stabilization is quenched more rapidly in cells containing D1:1 than in those with D1:2. Cells containing D1:1 appear generally shifted towards State II, with PS II down-regulated, while cells with D1:2 tend towards State I. In these cyanobacteria electron transport away from PS II remains non-saturated even under photoinhibitory levels of light. Therefore, the higher activity of D1:2 Photosystem II centres may allow more rapid photochemical dissipation of excess energy into the electron transport chain. D1:1 confers capacity for extreme State II which may be of benefit under low and variable light.

  • 146. Campbell, D
    et al.
    Clarke, A K
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Oquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Oxygen-dependent electron flow influences photosystem II function and psbA gene expression in the cyanobacterium Synechococcus sp PCC 79421999Inngår i: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 105, nr 4, s. 746-755Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    During acclimated growth in Synechococcus sp, PCC 7942 a substantial proportion of the electrons extracted from mater by photosystem II ultimately flow back to oxygen, This flow increases rapidly under high light, which allows Synechococcus to maintain photosystem II centers largely open, even under excessive excitation, The electron flow to oxygen with increasing light accounts for the progressive discrepancy between the light response curve of measured oxygen evolution, and the light response curve of photosystem II activity estimated from fluorescence measures. In cells under anoxia this flexible electron sink is lost and photosystem II centers suffer partial closure at the growth light intensity, with closure becoming more severe under excess light. As predicted from earlier work this PSII closure results in rapid loss of psbAI message, encoding the D1:1 protein of PSII, and induction of psbAII/AIII encoding the alternate D1:2 protein. The changes in the mRNA pool are not, however, reflected at the protein level, and D1:1 remains in the thylakoid membranes. There is no accumulation of D1:2, despite some continued synthesis of other proteins. PSII closure, therefore, results in repression of psbAI and induction psbAII/AIII expression, but D1:1/D1:2 exchange is blocked by anoxia, downstream from transcription. D1:1 protein and PSII activity are quite stable under anoxia and moderate illumination, Nevertheless, upon recovery under oxygenic conditions, the existing D1:1 is lost from the membranes, resulting in a transient drop in PSII activity. This suggests that under normal conditions the cells use oxygen to facilitate preemptive turnover of D1 proteins.

  • 147. Campbell, D
    et al.
    Eriksson, Mats-Jerry
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Oquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Clarke, A K
    A cyanobacterium resists UV-B by exchanging Photosystem II D1 proteins.1997Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 114, nr 3, s. 30004-30004Artikkel i tidsskrift (Fagfellevurdert)
  • 148. Campbell, D
    et al.
    Eriksson, Mats-Jerry
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Oquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Clarke, A K
    The cyanobacterium Synechococcus resists UV-B by exchanging photosystem II reaction-center D1 proteins1998Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 95, nr 1, s. 364-369Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Current ambient UV-B levels can significantly depress productivity in aquatic habitats, largely because UV-B inhibits several steps of photosynthesis, including the photooxidation of water catalyzed by photosystem II, We show that upon UV-B exposure the cyanobacterium Synechococcus sp, PCC 7942 rapidly changes the expression of a family of three psbA genes encoding photosystem II D1 proteins, In wild-type cells the psbAI gene is expressed constitutively, but strong accumulations of psbAII and psbAIII transcripts are induced within 15 min of moderate UV-B exposure (0.4 W/m(2)), This transcriptional response causes an exchange of two distinct photosystem II D1 proteins, D1:1 is encoded by psbAI, but on UV-B exposure, it is largely replaced by the alternate D1:2 form, encoded by both psbAII and psbAIII, The total content of D1 and other photosystem II reaction center protein, D2, remained unchanged throughout the UV exposure, as did the content and composition of the phycobilisome, Wild-type cells suffered only slight transient inhibition of photosystem II function under UV-B exposure, In marked contrast, under the same UV-B treatment, a mutant strain expressing only psbAI suffered severe (40%) and sustained inhibition of photosystem II function, Another mutant strain with constitutive expression of psbAII and psbAIII was almost completely resistant to the UV-B treatment, showing no inhibition of photosystem II function and only a slight drop in electron transport, In Synechococcus the rapid exchange of alternate D1 forms, therefore, accounts for much of the cellular resistance to UV-B inhibition of photosystem II activity and photosynthetic electron transport, This molecular plasticity may be an important element in community-level responses to UV-B, where susceptibility to UV-B inhibition of photosynthesis changes diurnally.

  • 149. Campbell, D
    et al.
    Hurry, Vaughan
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Clarke, A K
    Gustafsson, Petter
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Oquist, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Chlorophyll fluorescence analysis of cyanobacterial photosynthesis and acclimation1998Inngår i: Microbiology and molecular biology reviews, ISSN 1092-2172, E-ISSN 1098-5557, Vol. 62, nr 3, s. 667-+Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Cyanobacteria are ecologically important photosynthetic prokaryotes that also serve as popular model organisms for studies of photosynthesis and gene regulation. Both molecular and ecological studies of cyanobacteria benefit from real-time information on photosynthesis and acclimation. Monitoring in vivo chlorophyll fluorescence can provide noninvasive measures of photosynthetic physiology in a wide range of cyanobacteria and cyanolichens and requires only small samples. Cyanobacterial fluorescence patterns are distinct from those of plants, because of key structural and functional properties of cyanobacteria. These include significant fluorescence emission from the light-harvesting phycobiliproteins; large and rapid changes in fluorescence yield (state transitions) which depend on metabolic and environmental conditions; and flexible, overlapping respiratory and photosynthetic electron transport chains. The fluorescence parameters F-V/F-M. F-V'/F-M', q(p),q(N), NPQ, and phi PS II were originally developed to extract information from the fluorescence signals of higher plants. In this review, we consider how the special properties of cyanobacteria can be accommodated and used to extract biologically useful information from cyanobacterial in vivo chlorophyll fluorescence signals. We describe how the pattern of fluorescence yield versus light intensity can be used to predict the acclimated light level for a cyanobacterial population, giving information valuable for both laboratory and field studies of acclimation processes. The size of the change in fluorescence yield during dark-to-light transitions can provide information on respiration and the iron status of the cyanobacteria. Finally, fluorescence parameters cart be used to estimate the electron transport rate at the acclimated growth light intensity.

  • 150. Campbell, D
    et al.
    OQUIST, Gunnar
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).
    Predicting light acclimation in cyanobacteria from nonphotochemical quenching of photosystem II fluorescence, which reflects state transitions in these organisms1996Inngår i: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 111, nr 4, s. 1293-1298Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An important factor in photosynthetic ecophysiology is the light regime that a photobiont is acclimated to exploit. In a wide range of cyanobacteria and cyano-lichens, the easily measured fluorescence parameters, coefficient of nonphotochemical quenching of photosystem II variable fluorescence (q(N)) and nonphotochemical quenching, decline to a minimum near the acclimated growth light intensity. This characteristic pattern predicts the integrated light regime to which populations are acclimated, information that is particularly useful for cyanobacteria or cyano-lichens from habitats with highly variable light intensities. q(N) reflects processes that compete with photosystem II photochemistry for absorbed excitation energy. In cyanobacteria, we find no evidence for energy-dependent quenching mechanisms, which are the predominant components of q(N) in higher plants. Instead, in cyanobacteria, q(N) correlates closely with the excitation flow from the phycobilisome to photosystem I, indicating that q(N) reflects the state transition mechanism for equilibration of excitation from the phycobilisome to the two photosystems.

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