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  • 1.
    Angelcheva, Liudmila
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mishra, Yogesh
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kjellsen, Trygve D.
    Department of Biology, Norwegian University of Science and Technology.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strimbeck, Richard G.
    Department of Biology, Norwegian University of Science and Technology.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Metabolomic analysis of extreme freezing tolerance in Siberian spruce (Picea obovata)2014In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 204, no 3, p. 545-555Article in journal (Refereed)
    Abstract [en]

    Siberian spruce (Picea obovata) is one of several boreal conifer species that can survive at extremely low temperatures (ELTs). When fully acclimated, its tissues can survive immersion in liquid nitrogen. Relatively little is known about the biochemical and biophysical strategies of ELT survival. We profiled needle metabolites using gas chromatography coupled with mass spectrometry (GC-MS) to explore the metabolic changes that occur during cold acclimation caused by natural temperature fluctuations. In total, 223 metabolites accumulated and 52 were depleted in fully acclimated needles compared with pre-acclimation needles. The metabolite profiles were found to develop in four distinct phases, which are referred to as pre-acclimation, early acclimation, late acclimation and fully acclimated. Metabolite changes associated with carbohydrate and lipid metabolism were observed, including changes associated with increased raffinose family oligosaccharide synthesis and accumulation, accumulation of sugar acids and sugar alcohols, desaturation of fatty acids, and accumulation of digalactosylglycerol. We also observed the accumulation of protein and nonprotein amino acids and polyamines that may act as compatible solutes or cryoprotectants. These results provide new insight into the mechanisms of freezing tolerance development at the metabolite level and highlight their importance in rapid acclimation to ELT in P.obovata.

  • 2.
    Cain, Peter
    et al.
    Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK .
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Robinson, Colin
    Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK .
    A novel extended family of stromal thioredoxins2009In: Plant Molecular Biology, ISSN 0167-4412, E-ISSN 1573-5028, Vol. 70, no 3, p. 273-281Article in journal (Refereed)
    Abstract [en]

    Thioredoxins play key regulatory roles in chloroplasts by linking photosynthetic light reactions to a series of plastid functions. In addition to the established groups of thioredoxins, f, m, x, and y, novel plant thioredoxins were also considered to include WCRKC motif proteins, CDSP32, the APR proteins, the lilium proteins and HCF164. Despite their important roles, the subcellular locations of many novel thioredoxins has remained unknown. Here, we report a study of their subcellular location using the cDNA clone resources of TAIR. In addition to filling all gaps in the subcellular map of the established chloroplast thioredoxins f, m, x and y, we show that the members of the WCRKC family are targeted to the stroma and provide evidence for a stromal location of the lilium proteins. The combined data from this and related studies indicate a consistent stromal location of the known Arabidopsis chloroplast thioredoxins except for thylakoid-bound HCF164.

  • 3. Carlberg, Inger
    et al.
    Hansson, Maria
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Andersson, Bertil
    Vener, Alexander V
    A novel plant protein undergoing light-induced phosphorylation and release from the photosynthetic thylakoid membranes2003In: PNAS, Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, no 2, p. 757-62Article in journal (Refereed)
    Abstract [en]

    The characteristics of a phosphoprotein with a relative electrophoretic mobility of 12 kDa have been unknown during two decades of studies on redox-dependent protein phosphorylation in plant photosynthetic membranes. Digestion of this protein from spinach thylakoid membranes with trypsin and subsequent tandem nanospray-quadrupole-time-of-flight mass spectrometry of the peptides revealed a protein sequence that did not correspond to any previously known protein. Sequencing of the corresponding cDNA uncovered a gene for a precursor protein with a transit peptide followed by a strongly basic mature protein with a molecular mass of 8,640 Da. Genes encoding homologous proteins were found on chromosome 3 of Arabidopsis and rice as well as in ESTs from 20 different plant species, but not from any other organisms. The protein can be released from the membrane with high salt and is also partially released in response to light-induced phosphorylation of thylakoids, in contrast to all other known thylakoid phosphoproteins, which are integral to the membrane. On the basis of its properties, this plant-specific protein is named thylakoid soluble phosphoprotein of 9 kDa (TSP9). Mass spectrometric analyses revealed the existence of non-, mono-, di-, and triphosphorylated forms of TSP9 and phosphorylation of three distinct threonine residues in the central part of the protein. The phosphorylation and release of TSP9 from the photosynthetic membrane on illumination favor participation of this basic protein in cell signaling and regulation of plant gene expression in response to changing light conditions.

  • 4.
    Chen, Yang-Er
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. College of Life Sciences, Sichuan Agricultural University, Ya'an, China.
    Yuan, Shu
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Comparison of methods for extracting thylakoid membranes of Arabidopsis plants2016In: Physiologia Plantarum: An International Journal for Plant Biology, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 156, no 1, p. 3-12Article in journal (Refereed)
    Abstract [en]

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

  • 5.
    Cheregi, Otilia
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kotabová, Eva
    Prášil, Ondřej
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kaňa, Radek
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Presence of state transitions in the cryptophyte alga Guillardia theta2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 20, p. 6461-6470Article in journal (Refereed)
    Abstract [en]

    Plants and algae have developed various regulatory mechanisms for optimal delivery of excitation energy to the photosystems even during fluctuating light conditions; these include state transitions as well as non-photochemical quenching. The former process maintains the balance by redistributing antennae excitation between the photosys-tems, meanwhile the latter by dissipating excessive excitation inside the antennae. In the present study, these mecha-nisms have been analysed in the cryptophyte alga Guillardia theta. Photoprotective non-photochemical quenching was observed in cultures only after they had entered the stationary growth phase. These cells displayed a diminished overall photosynthetic efficiency, measured as CO2 assimilation rate and electron transport rate. However, in the logarithmic growth phase G. theta cells redistributed excitation energy via a mechanism similar to state transitions. These state transitions were triggered by blue light absorbed by the membrane integrated chlorophyll a/c antennae, and green light absorbed by the lumenal biliproteins was ineffective. It is proposed that state transitions in G. thetaare induced by small re-arrangements of the intrinsic antennae proteins, resulting in their coupling/uncoupling to the photosystems in state 1 or state 2, respectively. G. theta therefore represents a chromalveolate algae able to perform state transitions.

  • 6.
    Dubreuil, Carole
    et al.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Jin, Xu
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Barajas-López, Juan de Dios
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Hewitt, Timothy C.
    Tanz, Sandra K.
    Dobrenel, Thomas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hanson, Johannes
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Pesquet, Edouard
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Arrhenius Laboratory, Department of Ecology, Environment, and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
    Grönlund, Andreas
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Small, Ian
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Establishment of Photosynthesis through Chloroplast Development Is Controlled by Two Distinct Regulatory Phases2018In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 176, no 2, p. 1199-1214Article in journal (Refereed)
    Abstract [en]

    Chloroplasts develop from undifferentiated proplastids present in meristematic tissue. Thus, chloroplast biogenesis is closely connected to leaf development, which restricts our ability to study the process of chloroplast biogenesis per se. As a consequence, we know relatively little about the regulatory mechanisms behind the establishment of the photosynthetic reactions and how the activities of the two genomes involved are coordinated during chloroplast development. We developed a single cell-based experimental system from Arabidopsis (Arabidopsis thaliana) with high temporal resolution allowing for investigations of the transition from proplastids to functional chloroplasts. Using this unique cell line, we could show that the establishment of photosynthesis is dependent on a regulatory mechanism involving two distinct phases. The first phase is triggered by rapid light-induced changes in gene expression and the metabolome. The second phase is dependent on the activation of the chloroplast and generates massive changes in the nuclear gene expression required for the transition to photosynthetically functional chloroplasts. The second phase also is associated with a spatial transition of the chloroplasts from clusters around the nucleus to the final position at the cell cortex. Thus, the establishment of photosynthesis is a two-phase process with a clear checkpoint associated with the second regulatory phase allowing coordination of the activities of the nuclear and plastid genomes.

  • 7. Edvardsson, Anna
    et al.
    Shapiguzov, Alexey
    Petersson, Ulrika A
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry. Umeå Plant Science Centre.
    Vener, Alexander V
    Immunophilin AtFKBP13 Sustains All Peptidyl-Prolyl Isomerase Activity in the Thylakoid Lumen from Arabidopsis thaliana Deficient in AtCYP20-22007In: Biochemistry, Vol. 46, no 33, p. 9432-42Article in journal (Refereed)
    Abstract [en]

    The physiological roles of immunophilins are unclear, but many possess peptidyl-prolyl isomerase (PPIase) activity, and they have been found in all organisms examined to date, implying that they are involved in fundamental, protein-folding processes. The chloroplast thylakoid lumen of the higher plant Arabidopsis thaliana contains up to 16 immunophilins (five cyclophilins and 11 FKBPs), but only two of them, AtCYP20-2 and AtFKBP13, have been found to be active PPIases, indicating that the other immunophilins in this cellular compartment may have lost their putative PPIase activities. To assess this possibility, we characterized two independent Arabidopsis knockout lines lacking AtCYP20-2 in enzymological and quantitative proteomic analyses. The PPIase activity in thylakoid lumen preparations of both mutants was equal to that of corresponding wild-type preparations, and comparative two-dimensional difference gel electrophoresis analyses of the lumenal proteins of the mutants and wild type showed that none of the potential PPIases was more abundant in the AtCYP20-2 deficient plants. Enzymatic analyses established that all PPIase activity in the mutant thylakoid lumen was attributable to AtFKBP13, and oxidative activation of this enzyme compensated for the lack of AtCYP20-2. Accordingly, sequence analyses of the potential catalytic domains of lumenal cyclophilins and FKBPs demonstrated that only AtCYP20-2 and AtFKBP13 possess all of the amino acid residues found to be essential for PPIase activity in earlier studies of human cyclophilin A and FKBP12. Thus, none of the immunophilins in the chloroplast thylakoid lumen of Arabidopsis except AtCYP20-2 and AtFKBP13 appear to possess prolyl isomerase activity toward peptide substrates.

  • 8. Fey, Holger
    et al.
    Piano, Dario
    Horn, Ruth
    Fischer, David
    Schmidt, Matthias
    Ruf, Stephanie
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Bock, Ralph
    Büchel, Claudia
    Isolation of highly active photosystem II core complexes with a His-tagged Cyt b559 subunit from transplastomic tobacco plants2008In: Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1777, no 12, p. 1501-9Article in journal (Refereed)
    Abstract [en]

    Photosystem II (PSII) is a huge multi-protein-complex consisting, in higher plants and green algae, of the PS II core and the adjacent light harvesting proteins. In the study reported here, N-terminal His-tags were added to the plastome-encoded α-subunit of cytochrome b559, PsbE, in tobacco plants, thus facilitating rapid, mild purification of higher plant PSII. Biolistic chloroplast transformation was used to replace the wildtype psbE gene by His-tagged counterparts. Transgenic plants did not exhibit an obvious phenotype. However, the oxygen evolution capacity of thylakoids prepared from the mutants compared to the wildtype was reduced by 10–30% depending on the length of the His-tag, although Fv/Fm values differed only slightly. Homoplasmic F1 plants were used to isolate PSII cores complexes. The cores contained no detectable traces of LHC or PsaA/B polypeptides, but the main core subunits of PSII could be identified using immunodetection and mass spectroscopy. In addition, Psb27 and PsbS were detected. The presence of the former was presumably due to the preparation method, since PSII complexes located in the stroma are also isolated. In contrast to previous reports, PsbS was solely found as a monomer on SDS-PAGE in the PSII core complexes of tobacco.

  • 9.
    Funk, Christiane
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Wiklund, Ronney
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Jansson, Christer
    D1′ centers are less efficient than normal photosystem II centers2001In: FEBS Letters, Vol. 505, no 1, p. 113-7Article in journal (Refereed)
    Abstract [en]

    One prominent difference between the photosystem II (PSII) reaction center protein D1′ in Synechocystis 6803 and normal D1 is the replacement of Phe-186 in D1 with leucine in D1′. Mutants of Synechocystis 6803 producing only D1′, or containing engineered D1 proteins with Phe-186 substitutions, were analyzed by 77 K fluorescence emission spectra, chlorophyll a fluorescence induction yield and decay kinetics, and flash-induced oxygen evolution. Compared to D1-containing PSII centers, D1′ centers exhibited a 50% reduction in variable chlorophyll a fluorescence yield, while the flash-induced O2 evolution pattern was unaffected. In the F186 mutants, both the P680+/QA− recombination and O2 oscillation pattern were noticeably perturbed.

  • 10.
    Garcia Cerdan, Jose Gines
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sveshnikov, Dmitry
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Dewez, David
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Antisense inhibition of the PsbX protein affects PSII integrity in the higher plant Arabidopsis Thaliana2009In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, no 2, p. 191-202Article in journal (Refereed)
    Abstract [en]

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

  • 11.
    García-Cerdán, José G
    et al.
    Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
    Kovács, Laszlo
    Tóth, Tünde
    Kereïche, Sami
    Aseeva, Elena
    Boekema, Egbert J
    Mamedov, Fikret
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The PsbW protein stabilizes the supramolecular organization of photosystem II in higher plants2011In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 65, no 3, p. 368-381Article in journal (Refereed)
    Abstract [en]

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

  • 12. Goulas, Estelle
    et al.
    Schubert, Maria
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kleczkowski, Leszek
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gardeström, Per
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hurry, Vaughan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The chloroplast lumen and stromal proteomes of Arabidopsis thaliana show differential sensitivity to short- and long-term exposure to low temperature.2006In: Plant Journal, ISSN 0960-7412, Vol. 47, no 5, p. 720-34Article in journal (Refereed)
    Abstract [en]

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

  • 13.
    Granlund, Irene
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Light induced changes in protein expression and uniform regulation of transcription in the thylakoid lumen of Arabidopsis thaliana2009In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 4, no 5, p. e5649-Article in journal (Refereed)
    Abstract [en]

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

  • 14.
    Granlund, Irene
    et al.
    Swedish University of Agricultural Sciences, Umeå.
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Difference gel electrophoresis (DIGE)2010In: Encyclopedia of Life Sciences, Wiley , 2010Chapter in book (Other (popular science, discussion, etc.))
    Abstract [en]

    One of the largest challenges in proteomics today is to be able to quantify the composition and amount of proteins found in a specific cell or tissue at a defined time point. Difference gel electrophoresis (DIGE) is a gel electrophoresis-based technique for protein quantification in complex mixtures. In DIGE the high resolution of two-dimensional gel electrophoresis is combined with the excellent dynamic range obtained by fluorescent tag labelling of protein samples. The output of DIGE experiments provides information about how many proteins display changed expression levels on a specific treatment. In addition, proteins of interest can be excised and identified with conventional mass spectrometry techniques and further analysed by other biochemical methods.

  • 15.
    Granlund, Irene
    et al.
    Umeå University, Faculty of Science and Technology.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Physics.
    Alm, Rikard
    Schröder, Wolfgang P.
    Emanuelsson, Cecilia
    Clustering of MS spectra as a rationale to resolve protein variants by detecting modified peptides within clustersArticle in journal (Refereed)
  • 16.
    Granlund, Irene
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Alm, Rikard
    Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Emanuelsson, Cecilia
    Department of Biochemistry, Centre for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
    Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS2011In: Journal of proteomics, ISSN 1876-7737, Vol. 74, no 8, p. 1190-1200Article in journal (Refereed)
    Abstract [en]

    It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program (http://bioinfo.thep.lu.se/speclust.html). The tool can also be used to remove peaks of contaminating proteins and to improve protein identification, especially for species without a fully sequenced genome. Mutually exclusive peptide peaks within a cluster provide a good starting point for MS/MS investigation of modified peptides, here exemplified by the identification of an A to E substitution that accounts for the isoelectric heterogeneity in protein isoforms.

  • 17.
    Granlund, Irene
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Storm, Patrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schubert, Maria
    Department of Life Sciences, Södertörns University College, SE-141 89 Huddinge, Sweden.
    García-Cerdán, José G
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The TL29 protein is lumen located, associated with PSII and not an ascorbate peroxidase2009In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 50, no 11, p. 1898-1910Article in journal (Refereed)
    Abstract [en]

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

  • 18.
    Granlund, Irene
    et al.
    Umeå University, Faculty of Science and Technology.
    Storm, Patrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schubert, Maria
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The TL29 Protein is a Redox Regulated Extrinsic Protein of Photosystem II and not an Ascorbate PeroxidaseArticle in journal (Refereed)
  • 19.
    Hall, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sauer, Uwe
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Purification, crystallization and preliminary X-ray analysis of PPD6, a PsbP-domain protein from Arabidopsis thaliana2012In: Acta Crystallographica. Section F: Structural Biology and Crystallization Communications, ISSN 1744-3091, E-ISSN 1744-3091, Vol. 68, no 3, p. 278-280Article in journal (Refereed)
    Abstract [en]

    The PsbP protein is an extrinsic component of photosystem II that together with PsbO and PsbQ forms the thylakoid lumenal part of the oxygen-evolving complex in higher plants. In addition to PsbP, the thylakoid lumen contains two PsbP-like proteins (PPLs) and six PsbP-domain proteins (PPDs). While the functions of the PsbP-like proteins PPL1 and PPL2 are currently under investigation, the function of the PsbP-domain proteins still remains completely unknown. PPD6 is unique among the PsbP family of proteins in that it contains a conserved disulfide bond which can be reduced in vitro by thioredoxin. The crystal structure determination of the PPD6 protein has been initiated in order to elucidate its function and to gain deeper insights into redox-regulation pathways in the thylakoid lumen. PPD6 has been expressed, purified and crystallized and preliminary X-ray diffraction data have been collected. The crystals belonged to space group P2(1), with unit-cell parameters a = 47.0, b = 64.3, c = 62.0 Å, β = 94.2°, and diffracted to a maximum d-spacing of 2.1 Å.

  • 20.
    Hall, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mata-Cabana, Alejandro
    Instituto de Bioquimica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas – Universidad de Sevilla, Spain.
    Åkerlund, Hans-Erik
    Department of Biochemistry, Molecular Protein Science, Lund University, Lund, Sweden.
    Florencio, Francisco J
    Instituto de Bioquimica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas – Universidad de Sevilla, Spain.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lindahl, Marika
    Instituto de Bioquimica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas – Universidad de Sevilla, Spain.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Thioredoxin targets of the plant chloroplast lumen and their implications for plastid function2010In: Proteomics, ISSN 1615-9861, Vol. 10, no 5, p. 987-1001Article in journal (Refereed)
    Abstract [en]

    The light-dependent regulation of stromal enzymes by thioredoxin-catalysed disulphide/dithiol exchange is known as a classical mechanism for control of chloroplast metabolism. Recent proteome studies show that thioredoxin targets are present not only in the stroma but in all chloroplast compartments, from the envelope to the thylakoid lumen. Thioredoxin-mediated redox control appears to be a common feature of important pathways, such as the Calvin cycle, starch synthesis and tetrapyrrole biosynthesis. However, the extent of thiol-dependent redox regulation in the thylakoid lumen has not been previously systematically explored. In this study, we addressed thioredoxin-linked redox control in the chloroplast lumen of Arabidopsis thaliana.Using complementary proteomics approaches, we identified 19 thioredoxin target proteins, thus covering more than 40 percent of the currently known lumenal chloroplast proteome. We show that the redox state of thiols is decisive for degradation of the extrinsic PsbO1 and PsbO2 subunits of photosystem II. Moreover, disulphide reduction inhibits activity of the xanthophyll cycle enzyme violaxanthin de-epoxidase, which participates in thermal dissipation of excess absorbed light. Our results indicate that redox-controlled reactions in the chloroplast lumen play essential roles in the function of photosystem II and the regulation of adaptation to light intensity.

  • 21.
    Hall, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mishra, Yogesh
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Preparation of stroma, thylakoid membrane, and lumen fractions from arabidopsis thaliana chloroplasts for proteomic analysis2011In: In Chloroplast Research in Arabidopsis: Methods and Protocols, Volume II. R. / [ed] Paul Jarvis, Springer Science + Business Media, LLC 2011 , 2011, Vol. 775, no 3, p. 207-222Chapter in book (Refereed)
    Abstract [en]

    For many studies regarding important chloroplast processes such as oxygenic photosynthesis, fractionation of the total chloroplast proteome is a necessary first step. Here, we describe a method for isolating the stromal, the thylakoid membrane, and the thylakoid lumen subchloroplast fractions from Arabidopsis thaliana leaf material. All three fractions can be isolated sequentially from the same plant material in a single day preparation. The isolated fractions are suitable for various proteomic analyses such as simple mapping studies or for more complex experiments such as differential expression analysis using two-dimensional difference gel electrophoresis (2D-DIGE) or mass spectrometry (MS)-based techniques. Besides this, the obtained fractions can also be used for many other purposes such as immunological assays, enzymatic activity assays, and studies of protein complexes by native-polyacrylamide gel electrophoresis (native-PAGE).

  • 22.
    Hall, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Chemistry.
    Thioredoxin interactions of the chloroplast lumen of Arabidopsis thaliana indicate a redox regulation of the xanthophyll cycle, in Photosynthesis2008In: Energy from the Sun - 14th International Congress on Photosynthesis, 2008Conference paper (Other academic)
  • 23.
    Hall, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    von Sydow, Lotta
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Storm, Patrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sauer, Uwe
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The lumenal pentapeptide repeat proteins TL15 and TL20.3 are novel chaperone-like proteins in the chloroplast lumen of higher plantsManuscript (preprint) (Other academic)
    Abstract [en]

    In the thylakoid lumen of Arabidopsis thaliana, three pentapeptide repeat family proteins of unknown function are localized. Pentapeptide repeat proteins (PRP) are comprised of at least eight tandem repeats of five amino acids of the consensus sequence A(D/N)LXX, which fold into a quadrilateral beta helix structure. Here we have solved the crystal structure of the mature form of the lumenal PRP protein TL15 to 1.3 Å resolution. TL15 is comprised of a main pentapeptide domain, consisting of a total of 19 pentapeptide repeats which form five turns of a beta helix, and a C-terminal alpha helix domain consisting of two alpha helices. The alpha helices form a ‘cap’ at the C-terminal end of the beta helix and are connected by a disulphide bond between the conserved cysteine residues C122 and C142. Furthermore we show that the lumenal PRPs TL15 and TL20.3 can assist in refolding of a chemically denatured substrate in vitro, indicating foldase chaperone activity. The three lumenal PRPs have been previously identified as targets of thioredoxin, and interestingly we observed a greatly increased chaperone activity of TL15 and TL20.3 after reduction of their disulphide bonds. Our results provide the high resolution crystal structure of the TL15 protein and our analysis of chaperone activity suggests that TL15 and TL20.3 may constitute a novel type of redox-regulated molecular chaperones in the chloroplast lumen of higher plants.

  • 24. Haniewicz, Patrycja
    et al.
    De Sanctis, Daniele
    Büchel, Claudia
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Loi, Maria Cecilia
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Bochtler, Matthias
    Piano, Dario
    Isolation of monomeric photosystem II that retains the subunit PsbS.2013In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 118, no 3, p. 199-207Article in journal (Refereed)
    Abstract [en]

    Photosystem II has been purified from a transplastomic strain of Nicotiana tabacum according to two different protocols. Using the procedure described in Piano et al. (Photosynth Res 106:221-226, 2010) it was possible to isolate highly active PSII composed of monomers and dimers but depleted in their PsbS protein content. A "milder" procedure than the protocol reported by Fey et al. (Biochim Biophys Acta 1777:1501-1509, 2008) led to almost exclusively monomeric PSII complexes which in part still bind the PsbS protein. This finding might support a role for PSII monomers in higher plants.

  • 25. Huang, Fang
    et al.
    Hedman, Erik
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kieselbach, Thomas
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Norling, Birgitta
    Isolation of Outer Membrane of Synechocystis sp. PCC 6803 and Its Proteomic Characterization2004In: Molecular & Cellular Proteomics, ISSN 1535-9476, Vol. 3, no 6, p. 586-95Article in journal (Refereed)
    Abstract [en]

    In this report, we describe a newly developed method for isolating outer membranes from Synechocystis sp. PCC 6803 cells. The purity of the outer membrane fraction was verified by immunoblot analysis using antibodies against membrane-specific marker proteins. We investigated the protein composition of the outer membrane using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry followed by database identification. Forty-nine proteins were identified corresponding to 29 different gene products. All of the identified proteins have a putative N-terminal signal peptide. About 40% of the proteins identified represent hypothetical proteins with unknown function. Among the proteins identified are a Toc75 homologue, a protein that was initially found in the outer envelope of chloroplasts in pea, as well as TolC, putative porins, and a pilus protein. Other proteins identified include ABC transporters and GumB, which has a suggested function in carbohydrate export. A number of proteases such as HtrA were also found in the outer membrane of Synechocystis sp. PCC 6803.

  • 26. Huesgen, Pitter F.
    et al.
    Alami, Meriem
    Lange, Philipp F.
    Foster, Leonard J.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Overall, Christopher M.
    Green, Beverley R.
    Proteomic Amino-Termini Profiling Reveals Targeting Information for Protein Import into Complex Plastids2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 9, p. e74483-Article in journal (Refereed)
    Abstract [en]

    In organisms with complex plastids acquired by secondary endosymbiosis from a photosynthetic eukaryote, the majority of plastid proteins are nuclear-encoded, translated on cytoplasmic ribosomes, and guided across four membranes by a bipartite targeting sequence. In-depth understanding of this vital import process has been impeded by a lack of information about the transit peptide part of this sequence, which mediates transport across the inner three membranes. We determined the mature N-termini of hundreds of proteins from the model diatom Thalassiosira pseudonana, revealing extensive N-terminal modification by acetylation and proteolytic processing in both cytosol and plastid. We identified 63 mature N-termini of nucleus-encoded plastid proteins, deduced their complete transit peptide sequences, determined a consensus motif for their cleavage by the stromal processing peptidase, and found evidence for subsequent processing by a plastid methionine aminopeptidase. The cleavage motif differs from that of higher plants, but is shared with other eukaryotes with complex plastids.

  • 27.
    Ishikawa, Yasuo
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Functional analysis of the PsbP-like protein (sll1418) in Synechocystis sp PCC 68032005In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 84, no 1-3, p. 257-262Article in journal (Refereed)
    Abstract [en]

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

  • 28.
    Johansson Jänkänpää, Hanna
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Mishra, Yogesh
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Metabolic profiling reveals metabolic shifts in Arabidopsis plants grown under different light conditions2012In: Plant, Cell and Environment, ISSN 0140-7791, E-ISSN 1365-3040, Vol. 35, no 10, p. 1824-1836Article in journal (Refereed)
    Abstract [en]

    Plants have tremendous capacity to adjust their morphology, physiology and metabolism in response to changes in growing conditions. Thus, analysis solely of plants grown under constant conditions may give partial or misleading indications of their responses to the fluctuating natural conditions in which they evolved. To obtain data on growth-condition dependent differences in metabolite levels we compared leaf metabolite profiles of Arabidopsis thaliana growing under three constant laboratory light conditions: 30 (LL), 300 (NL) and 600 (HL) µmol photons m(-2) s(-1) . We also shifted plants to the field and followed their metabolite composition for three days. Numerous compounds showed light-intensity dependent accumulation, including: many sugars and sugar derivatives (fructose, sucrose, glucose, galactose and raffinose); tricarboxylic acid (TCA) cycle intermediates and amino acids (ca. 30% of which were more abundant under HL and 60% under LL). However, the patterns differed after shifting NL plants to field conditions. Levels of most identified metabolites (mainly amino acids, sugars and TCA cycle intermediates) rose after 2 h and peaked after 73 h, indicative of a "biphasic response" and "circadian" effects. The results provide new insight into metabolomic level mechanisms of plant acclimation, and highlight the role of known protectants under natural conditions.

  • 29.
    Kieselbach, Thomas
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Chloroplast (Part IV Organelle Proteomics)2008In: Plant Proteomics: Technologies, Strategies, and Applications, John Wiley & Sons, Inc., New Jersey , 2008Chapter in book (Refereed)
  • 30.
    Kieselbach, Thomas
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    The proteome of the chloroplast lumen of higher plants2003In: Photosynthesis Research, Vol. 78, no 3, p. 249-64Article in journal (Refereed)
    Abstract [en]

    Recent research in proteomics of the higher plant chloroplast has achieved considerable progress and added to our knowledge of lumenal chloroplast proteins. This work shows that chloroplast lumen has its own specific proteome and may comprise as many as 80 proteins. Although the new map of the lumenal proteome provides a great deal of information, it also raises numerous questions because the physiological functions of most of the novel lumenal proteins are unknown. In this Minireview, we summarize the latest discoveries regarding lumenal proteins and present the currently known facts about the lumenal chloroplast proteome of higher plants.

  • 31.
    Kjellsen, Trygve D
    et al.
    Department of Biology, Norwegian University of Science and Technology.
    Shiryaeva, Liudmila
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Strimbeck, G Richard
    Department of Biology, Norwegian University of Science and Technology.
    Proteomics of extreme freezing tolerance in Siberian spruce (Picea obovata)2010In: Journal of Proteomics, ISSN 1874-3919, Vol. 73, no 5, p. 965-975Article in journal (Refereed)
    Abstract [en]

    Differential expression of proteins in needles of the extreme freeze tolerant conifer Picea obovata during September, October and November was analyzed using DIGE technology and multivariate analysis. More than 1200 spots were detected, and the abundance of 252 of these spots was significantly altered during the course of acclimation. The 252 spots were clustered into five distinct expression profiles. Among the protein spots showing differential expression, 43 were identified by MALDI-TOF/TOF and twelve of them matched proteins associated with various biotic and abiotic stress responses in other plants. Dehydrins, Hsp70s, AAA+ ATPases, lipocalin, cyclophilins, glycine-rich protein (GNP) and several reactive oxygen intermediate scavenging proteins showed increased accumulation levels from September to November. The expression profiles and putative role of the identified proteins during acclimation and freezing tolerance are discussed.

  • 32.
    Lundberg, Erik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Storm, Patrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Crystal structure of the TL29 protein from Arabidopsis thaliana: An APX homolog without peroxidase activity2011In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 176, no 1, p. 24-31Article in journal (Refereed)
    Abstract [en]

    TL29 is a plant-specific protein found in the thylakoid lumen of chloroplasts. Despite the putative requirement in plants for a peroxidase close to the site of photosynthetic oxygen production, and the sequence homology of TL29 to ascorbate peroxidases, so far biochemical methods have not shown this enzyme to possess peroxidase activity. Here we report the three-dimensional X-ray crystal structure of recombinant TL29 from Arabidopsis thaliana at a resolution of 2.5 Å. The overall structure of TL29 is mainly alpha helical with six longer and six shorter helical segments. The TL29 structure resembles that of typical ascorbate peroxidases, however, crucial differences were found in regions that would be important for heme and ascorbate binding. Such differences suggest it to be highly unlikely that TL29 functions as a peroxidase.

  • 33.
    Marino, Giada
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Huesgen, Pitter F
    Eckhard, Ulrich
    Overall, Christopher M
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Family-wide characterization of Matrix Metallo-proteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity.2014In: Biochemical Journal, ISSN 0264-6021, E-ISSN 1470-8728, Vol. 457, no 2, p. 335-346Article in journal (Refereed)
    Abstract [en]

    Matrix metalloproteases (MMPs) are a family of zinc-dependent endopeptidases widely distributed throughout all kingdoms of life. In mammals, MMPs play key roles in many physiological and pathological processes including remodeling of the extracellular matrix. In the genome of the annual plant Arabidopsis thaliana five MMP-like proteins (At-MMPs) are encoded, but their function is unknown. Previous work on these enzymes was limited to gene expression analysis, and so far proteolytic activity has been shown only for At1-MMP. We expressed and purified the catalytic domains of all five At-MMPs as His-tagged proteins in E.coli to delineate the biochemical differences and similarities among the Arabidopsis MMP family members. We demonstrate that all five recombinant At-MMPs are active proteases with distinct preferences for different protease substrates. Furthermore, we performed a family-wide characterization of their biochemical properties and highlight similarities and differences in their cleavage site specificities as well as pH- and temperature dependent activities. Detailed analysis of their sequence specificity using Proteomic Identification of protease Cleavage Sites (PICS) revealed profiles similar to human MMPs with the exception of At5-MMP; homology models of the At-MMP catalytic domains supported these results. Our results suggest that each At-MMP may be involved in different proteolytic processes during plant growth and development.

  • 34.
    Mishra, Yogesh
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chaurasia, Neha
    Rai, Lal Chand
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Sauer, Uwe H
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Expression, purification, crystallization and preliminary X-ray crystallographic studies of alkyl hydroperoxide reductase (AhpC) from the cyanobacterium Anabaena sp. PCC 71202011In: Acta Crystallographica. Section F: Structural Biology and Crystallization Communications, ISSN 1744-3091, E-ISSN 1744-3091, Vol. 67, no 10, p. 1203-1206Article in journal (Refereed)
    Abstract [en]

    Alkyl hydroperoxide reductase (AhpC) is a key component of a large family of thiol-specific antioxidant (TSA) proteins distributed among prokaryotes and eukaryotes. AhpC is involved in the detoxification of reactive oxygen species (ROS) and reactive sulfur species (RSS). Sequence analysis of AhpC from the cyanobacterium Anabaena sp. PCC 7120 shows that this protein belongs to the 1-Cys class of peroxiredoxins (Prxs). It has recently been reported that enhanced expression of this protein in Escherichia coli offers tolerance to multiple stresses such as heat, salt, copper, cadmium, pesticides and UV-B. However, the structural features and the mechanism behind this process remain unclear. To provide insights into its biochemical function, AhpC was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. Diffraction data were collected to a maximum d-spacing of 2.5 Å using synchrotron radiation. The crystal belonged to space group P212121, with unit-cell parameters a = 80, b = 102, c = 109.6 Å. The structure of AhpC from Anabaena sp. PCC 7120 was determined by molecular-replacement methods using the human Prx enzyme hORF6 (PDB entry1prx) as the template.

     

  • 35.
    Mishra, Yogesh
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Locmelis, Roland
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Nam, Kwangho
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX, 76019-0065, USA.
    Söderberg, Christopher A. G.
    Storm, Patrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Chaurasia, Neha
    Rai, Lal Chand
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Sauer, Uwe H.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 71202017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 17151Article in journal (Refereed)
    Abstract [en]

    Peroxiredoxins (Prxs) are vital regulators of intracellular reactive oxygen species levels in all living organisms. Their activity depends on one or two catalytically active cysteine residues, the peroxidatic Cys (C-P) and, if present, the resolving Cys (C-R). A detailed catalytic cycle has been derived for typical 2-Cys Prxs, however, little is known about the catalytic cycle of 1-Cys Prxs. We have characterized Prx6 from the cyanobacterium Anabaena sp. strain PCC7120 (AnPrx6) and found that in addition to the expected peroxidase activity, AnPrx6 can act as a molecular chaperone in its dimeric state, contrary to other Prxs. The AnPrx6 crystal structure at 2.3 angstrom resolution reveals different active site conformations in each monomer of the asymmetric obligate homo-dimer. Molecular dynamic simulations support the observed structural plasticity. A FSH motif, conserved in 1-Cys Prxs, precedes the active site PxxxTxxCp signature and might contribute to the 1-Cys Prx reaction cycle.

  • 36.
    Mishra, Yogesh
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Johansson Jankanpää, Hanna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kiss, Anett Z
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components2012In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 12, p. 6-Article in journal (Refereed)
    Abstract [en]

    Background:Plants exhibit phenotypic plasticity and respond to differences in environmental conditions by acclimation. We have systematically compared leaves of Arabidopsis thaliana plants grown in the field and under controlled low, normal and high light conditions in the laboratory to determine their most prominent phenotypic differences.

    Results: Compared to plants grown under field conditions, the "indoor plants" had larger leaves, modified leaf shapes and longer petioles. Their pigment composition also significantly differed; indoor plants had reduced levels of xanthophyll pigments. In addition, Lhcb1 and Lhcb2 levels were up to three times higher in the indoor plants, but differences in the PSI antenna were much smaller, with only the low-abundance Lhca5 protein showing altered levels. Both isoforms of early-light-induced protein (ELIP) were absent in the indoor plants, and they had less non-photochemical quenching (NPQ). The field-grown plants had a high capacity to perform state transitions. Plants lacking ELIPs did not have reduced growth or seed set rates, but their mortality rates were sometimes higher. NPQ levels between natural accessions grown under different conditions were not correlated.

    Conclusion: Our results indicate that comparative analysis of field-grown plants with those grown under artificial conditions is important for a full understanding of plant plasticity and adaptation.

  • 37. Pesaresi, Paolo
    et al.
    Scharfenberg, Michael
    Weigel, Martin
    Granlund, Irene
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Finazzi, Giovanni
    Rappaport, Fabrice
    Masiero, Simona
    Furini, Antonella
    Jahns, Peter
    Leister, Dario
    Mutants, overexpressors, and interactors of Arabidopsis Plastocyanin Isoforms: Revised roles of Plastocyanin in photosynthetic electron flow and Thylakoid redox state2009In: Molecular Plant, ISSN 1674-2052, EISSN 1752-9867, Vol. 2, no 2, p. 236-248Article in journal (Refereed)
    Abstract [en]

    Two homologous plastocyanin isoforms are encoded by the genes PETE1 and PETE2 in the nuclear genome of Arabidopsis thaliana. The PETE2 transcript is expressed at considerably higher levels and the PETE2 protein is the more abundant isoform. Null mutations in the PETE genes resulted in plants, designated pete1 and pete2, with decreased plastocyanin contents. However, despite reducing plastocyanin levels by over 90%, a pete2 null mutation on its own affects rates of photosynthesis and growth only slightly, whereas pete1 knockout plants, with about 60-80% of the wild-type plastocyanin level, did not show any alteration. Hence, plastocyanin concentration is not limiting for photosynthetic electron flow under optimal growth conditions, perhaps implying other possible physiological roles for the protein. Indeed, plastocyanin has been proposed previously to cooperate with cytochrome c6A (Cyt c6A) in thylakoid redox reactions, but we find no evidence for a physical interaction between the two proteins, using interaction assays in yeast. We observed homodimerization of Cyt c6A in yeast interaction assays, but also Cyt c6A homodimers failed to interact with plastocyanin. Moreover, phenotypic analysis of atc6-1 pete1 and atc6-1 pete2 double mutants, each lacking Cyt c6A and one of the two plastocyanin-encoding genes, failed to reveal any genetic interaction. Overexpression of either PETE1 or PETE2 in the pete1 pete2 double knockout mutant background results in essentially wild-type photosynthetic performance, excluding the possibility that the two plastocyanin isoforms could have distinct functions in thylakoid electron flow.

  • 38. Plöchinger, Magdalena
    et al.
    Schwenkert, Serena
    von Sydow, Lotta
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Meurer, Jörg
    Functional Update of the Auxiliary Proteins PsbW, PsbY, HCF136, PsbN, TerC and ALB3 in Maintenance and Assembly of PSII2016In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, article id 423Article in journal (Refereed)
    Abstract [en]

    Assembly of Photosystem (PS) II in plants has turned out to be a highly complex process which, at least in part, occurs in a sequential order and requires many more auxiliary proteins than subunits present in the complex. Owing to the high evolutionary conservation of the subunit composition and the three-dimensional structure of the PSII complex, most plant factors involved in the biogenesis of PSII originated from cyanobacteria and only rarely evolved de novo. Furthermore, in chloroplasts the initial assembly steps occur in the non-appressed stroma lamellae, whereas the final assembly including the attachment of the major LHCII antenna proteins takes place in the grana regions. The stroma lamellae are also the place where part of PSII repair occurs, which very likely also involves assembly factors. In cyanobacteria initial PSII assembly also occurs in the thylakoid membrane, in so-called thylakoid centers, which are in contact with the plasma membrane. Here, we provide an update on the structures, localisations, topologies, functions, expression and interactions of the low molecular mass PSII subunits PsbY, PsbW and the auxiliary factors HCF136, PsbN, TerC and ALB3, assisting in PSII complex assembly and protein insertion into the thylakoid membrane.

  • 39.
    Schröder, Wolfgang
    et al.
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Chemistry.
    Update on chloroplast proteomics2003In: Photosynthesis Research, ISSN 0166-8595 (Print) 1573-5079 (Online), Vol. 78, no 3, p. 181-93Article in journal (Refereed)
    Abstract [en]

    Currently, relatively few proteomics studies of chloroplast have been published, but the field has just started emerging and is likely to develop more rapidly in the future. While the complex membrane structure of the chloroplast makes it difficult to study its entire proteome by global approaches, proteomics has considerably increased our knowledge of the proteins of single compartments such as, for instance, the envelope and the thylakoid lumen. Proteomics has also succeeded in the subunit characterisation of select protein complexes such as the ribosomes and the cytochrome b 6f complex. In addition, proteomics was successfully applied to find new potential target pathways for thioredoxin-mediated signal transduction. In this review, we present an overview of the latest developments in the field of chloroplast proteomics and discuss their impact on photosynthesis research. In addition, we summarise the current state of research in proteomics of the photosynthetic cyanobactrium Synechocystis sp. PCC 6803.

  • 40. Schubert, Maria
    et al.
    Petersson, Ulrika A
    Haas, Brian J
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Chemistry.
    Proteome map of the chloroplast lumen of Arabidopsis thaliana2003In: Journal of Biological Chemistry, Vol. 278, no 15, p. 13590-Article in journal (Refereed)
  • 41. Schubert, Maria
    et al.
    Petersson, Ulrika A
    Haas, Brian J
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Chemistry.
    Proteome Map of the Chloroplast Lumen of Arabidopsis thaliana2002In: Journal of Biological Chemistry, Vol. 277, no 10, p. 8354-65Article in journal (Refereed)
    Abstract [en]

    The thylakoid membrane of the chloroplast is the center of oxygenic photosynthesis. To better understand the function of the luminal compartment within the thylakoid network, we have carried out a systematic characterization of the luminal thylakoid proteins from the model organism Arabidopsis thaliana. Our data show that the thylakoid lumen has its own specific proteome, of which 36 proteins were identified. Besides a large group of peptidyl-prolyl cis-trans isomerases and proteases, a family of novel PsbP domain proteins was found. An analysis of the luminal signal peptides showed that 19 of 36 luminal precursors were marked by a twin-arginine motif for import via the Tat pathway. To compare the model organism Arabidopsis with another typical higher plant, we investigated the proteome from the thylakoid lumen of spinach and found that the luminal proteins from both plants corresponded well. As a complement to our experimental investigation, we made a theoretical prediction of the luminal proteins from the whole Arabidopsis genome and estimated that the thylakoid lumen of the chloroplast contains ~80 proteins.

  • 42.
    Shi, Lan-Xin
    et al.
    Department of Plant Biology, University of California-Davis, USA.
    Hall, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Photosystem II, a growing complex: Updates on newly discovered components and low molecular mass proteins2012In: Biochimica et Biophysica Acta, ISSN 0006-3002, E-ISSN 1878-2434, Vol. 1817, no 1, p. 13-25Article in journal (Refereed)
    Abstract [en]

    Photosystem II is a unique complex capable of absorbing light and splitting water. The complex has been thoroughly studied and to date there are more than 40 proteins identified, which bind to the complex either stably or transiently. Another special feature of this complex is the unusually high content of low molecular mass proteins that represent more than half of the proteins. In this review we summarize the recent findings on the low molecular mass proteins (<15 kDa) and present an overview of the newly identified components as well. We have also performed co-expression analysis of the genes encoding PSII proteins to see if the low molecular mass proteins form a specific sub-group within the Photosystem II complex. Interestingly we found that the chloroplast-localized genes encoding PSII proteins display a different response to environmental and stress conditions compared to the nuclear localized genes. This article is part of a Special Issue entitled: Photosystem II.

     

  • 43. Shia, Lan-Xin
    et al.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    The low molecular mass subunits of the photosynthetic supracomplex, photosystem II2004In: Biochimica et Biophysica Acta (BBA) - Bioenergetics, ISSN 0005-2728, Vol. 1608, no 2-3, p. 75-96Article in journal (Refereed)
    Abstract [en]

    The photosystem II (PSII) complex is located in the thylakoid membrane of higher plants, algae and cyanobacteria and drives the water oxidation process of photosynthesis, which splits water into reducing equivalents and molecular oxygen by solar energy. Electron and X-ray crystallography analyses have revealed that the PSII core complex contains between 34 and 36 transmembrane α-helices, depending on the organism. Of these helices at least 12–14 are attributed to low molecular mass proteins. However, to date, at least 18 low molecular mass (<10 kDa) subunits are putatively associated with the PSII complex. Most of them contain a single transmembrane span and their protein sequences are conserved among photosynthetic organisms. In addition, these proteins do not have any similarity to any known functional proteins in any type of organism, and only two of them bind a cofactor. These findings raise intriguing questions about why there are so many small protein subunits with single-transmembrane spans in the PSII complex, and their possible functions. This article reviews our current knowledge of this group of proteins. Deletion mutations of the low molecular mass subunits from both prokaryotic and eukaryotic model systems are compared in an attempt to understand the function of these proteins. From these comparisons it seems that the majority of them are involved in stabilization, assembly or dimerization of the PSII complex. The small proteins may facilitate fast dynamic conformational changes that the PSII complex needs to perform an optimal photosynthetic activity.

  • 44.
    Shiryaeva, Liudmila
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Strimbeck, G Richard
    Department of Biology, Norwegian University of Science and Technology.
    Shiryaev, Anton S
    Department of Engineering Cybernetics, Norwegian University of Science and Technology.
    Pair-wise multicomparison and OPLS analyses of cold-acclimation phases in Siberian spruce2012In: Metabolomics, ISSN 1573-3882, Vol. 8, no Suppl 1, p. 123-130Article in journal (Refereed)
    Abstract [en]

    Analysis of metabolomics data often goes beyond the task of discovering biomarkers and can be aimed at recovering other important characteristics of observed metabolomic changes. In this paper we explore different methods to detect the presence of distinctive phases in seasonal-responsive changes of metabolomic patterns of Siberian spruce (Picea obovata) during cold acclimation occurred in the period from mid-August to January. Multivariate analysis, specifically orthogonal projection to latent structures discriminant analysis (OPLSDA), identified time points where the metabolomic patterns underwent substantial modifications as a whole, revealing four distinctive phases during acclimation. This conclusion was re-examined by a univariate analysis consisting of multiple pair-wise comparisons to identify homogeneity intervals for each metabolite. These tests complemented OPLS-DA, clarifying biological interpretation of the classification: about 60% of metabolites found responsive to the cold stress indeed changed at one or more of the time points predicted by OPLS-DA. However, the univariate approach did not support the proposed division of the acclimation period into four phases: less than 10% of metabolites altered during the acclimation had homogeneous levels predicted by OPLS-DA. This demonstrates that coupling the classification found by OPLS-DA and the analysis of dynamics of individual metabolites obtained by pair-wise multicomparisons reveals a more correct characterization of biochemical processes in freezing tolerant trees and leads to interpretations that cannot be deduced by either method alone. The combined analysis can be used in other ‘omics’-studies, where response factors have a causal dependence (like the time in the present work) and pairwise multicomparisons are not conservative.

  • 45.
    Shiryaeva, Liudmila
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Antti, Henrik
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Stattin, Pär
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Urology and Andrology.
    Kieselbach, Thomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Wikström, Pernilla
    Umeå University, Faculty of Medicine, Department of Medical Biosciences, Pathology.
    Two-dimensional difference gel electrophoresis to reveal proteins in plasma associated with high risk prostate cancerManuscript (preprint) (Other academic)
    Abstract [en]

    Prostate cancer is a common but highly variable disease. Conventional methods for prognostication are limited and needed to be complemented by novel biomarkers which could identify clinically significant tumors at a curable timepoint. With the aim to find biomarkers in plasma for high risk prostate cancer, we combined the ProteoMiner technology for protein fractionation with 2-dimentional difference gel electrophoresis (2D-DIGE). Plasma samples from patients with high risk tumors, defined to have bone metastases (M1, N=7) or locally advanced or poorly differentiated prostate cancer (M0, N=14), or benign disease (N=15) were analyzed. As a result of combined univariate and multivariate analyses (orthogonal partial least-squares discriminant analysis, OPLS-DA), 338 protein spots were found to be significantly associated with high risk prostate cancer. Ninety-eight (98) of the spots were successfully identified by LC-MS/MS, and OPLS-DA of those resulted in a reliable method for class separation; M1 vs. M0 vs. B (R2Xcum: 31.1%, R2Y cum: 59.9%, Q2cum: 41.4%, P < 0.0001). The panel of identified potential protein markers for high risk prostate cancer included highly to intermediately abundant plasma proteins involved in key processes such as lipid transport, coagulation, inflammation, and immune responses. Their putative roles for prostate cancer progression are discussed.

  • 46. Strimbeck, G Richard
    et al.
    Schaberg, Paul G
    Fossdal, Carl G
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kjellsen, Trygve D
    Extreme low temperature tolerance in woody plants2015In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 6, article id 884Article, review/survey (Refereed)
    Abstract [en]

    Woody plants in boreal to arctic environments and high mountains survive prolonged exposure to temperatures below -40°C and minimum temperatures below -60°C, and laboratory tests show that many of these species can also survive immersion in liquid nitrogen at -196°C. Studies of biochemical changes that occur during acclimation, including recent proteomic and metabolomic studies, have identified changes in carbohydrate and compatible solute concentrations, membrane lipid composition, and proteins, notably dehydrins, that may have important roles in survival at extreme low temperature (ELT). Consideration of the biophysical mechanisms of membrane stress and strain lead to the following hypotheses for cellular and molecular mechanisms of survival at ELT: (1) Changes in lipid composition stabilize membranes at temperatures above the lipid phase transition temperature (-20 to -30°C), preventing phase changes that result in irreversible injury. (2) High concentrations of oligosaccharides promote vitrification or high viscosity in the cytoplasm in freeze-dehydrated cells, which would prevent deleterious interactions between membranes. (3) Dehydrins bind membranes and further promote vitrification or act stearically to prevent membrane–membrane interactions.

  • 47. Suorsa, Marjaana
    et al.
    Rantala, Marjaana
    Danielsson, Ravi
    Järvi, Sari
    Paakkarinen, Virpi
    Schröder, Wolfgang P
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Styring, Stenbjörn
    Mamedov, Fikret
    Aro, Eva-Mari
    Dark-adapted spinach thylakoid protein heterogeneity offers insights into the photosystem II repair cycle2014In: Biochimica et Biophysica Acta - Bioenergetics, ISSN 0005-2728, E-ISSN 1879-2650, Vol. 1837, no 9, p. 1463-1471Article in journal (Refereed)
    Abstract [en]

    In higher plants, thylakoid membrane protein complexes show lateral heterogeneity in their distribution: photosystem (PS) II complexes are mostly located in grana stacks, whereas PSI and adenosine triphosphate (ATP) synthase are mostly found in the stroma-exposed thylakoids. However, recent research has revealed strong dynamics in distribution of photosystems and their light harvesting antenna along the thylakoid membrane. Here, the dark-adapted spinach (Spinacia oleracea L.) thylakoid network was mechanically fragmented and the composition of distinct PSII-related proteins in various thylakoid subdomains was analyzed in order to get more insights into the composition and localization of various PSII subcomplexes and auxiliary proteins during the PSII repair cycle. Most of the PSII subunits followed rather equal distribution with roughly 70% of the proteins located collectively in the grana thylakoids and grana margins; however, the low molecular mass subunits PsbW and PsbX as well as the PsbS proteins were found to be more exclusively located in grana thylakoids. The auxiliary proteins assisting in repair cycle of PSII were mostly located in stroma-exposed thylakoids, with the exception of THYLAKOID LUMEN PROTEIN OF 18.3 (TLP18.3), which was more evenly distributed between the grana and stroma thylakoids. The TL29 protein was present exclusively in grana thylakoids. Intriguingly, PROTON GRADIENT REGULATIONS (PGR5) was found to be distributed quite evenly between grana and stroma thylakoids, whereas PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1 (PGRL1) was highly enriched in the stroma thylakoids and practically missing from the grana cores. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.

  • 48. Sveshnikov, Dmitry
    et al.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    The PsbP-like protein (sll1418) of Synechocystis sp. PCC 6803 stabilises the donor side of Photosystem II2007In: Photosynthesis Research, ISSN 0166-8595 (Print) 1573-5079 (Online), Vol. 93, no 1-3, p. 101-109Article in journal (Refereed)
    Abstract [en]

    The PsbP-like protein of the cyanobacterium Synechocystis sp. PCC 6803 is a peripheral component of Photosystem II, located at the lumenal side of the thylakoid membrane. Removal of this protein leads to decreased competitive potential of a PsbP-like deletion mutant when grown in a mixture with wild-type cells. Flash-induced oxygen evolution traces of the mutant show a higher probability of misses, correlated with increased amplitudes of the S-states decay in the dark. Thermoluminescence emission traces demonstrate a changed charge recombination pattern in the mutant, the S3QB− couple becoming the major species instead of the S2QB−. Our data suggest a possible role of the PsbP-like protein in stabilisation of the charge separation in Photosystem II of cyanobacteria through interaction with the Mn cluster.

  • 49. Thidholm, Ellinor
    et al.
    Lindström, Viktoria
    Tissier, Christophe
    Robinson, Colin
    Schröder, Wolfgang
    Umeå University, Faculty of Science and Technology, Chemistry.
    Funk, Christiane
    Umeå University, Faculty of Science and Technology, Chemistry.
    Novel approach reveals localisation and assembly pathway of the PsbS and PsbW proteins into the photosystem II dimer2002In: FEBS LETTERS, ISSN 0014-5793, Vol. 513, no 2-3, p. 217-22Article in journal (Refereed)
    Abstract [en]

    A blue-native gel electrophoresis system was combined with an in organello import assay to specifically analyse the location and assembly of two nuclear-encoded photosystem 11 (PSII) subunits. With this method we were able to show that initially the low molecular mass PsbW protein is not associated with the monomeric form of PSII. Instead a proportion of newly imported PsbW is directly assembled in dimeric PSH super-complexes with very fast kinetics; its negatively charged N-terminal domain is essential for this process. The chlorophyll-binding PsbS protein, which is involved in energy dissipation, is first detected in the monomeric PSII subcomplexes, and only at later time points in the dimeric form of PSII. It seems to be bound tighter to the PSII core complex than to light harvesting complex II. These data point to radically different assembly pathways for different PSII subunits. (C) 2002 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.

  • 50.
    Torabi, Salar
    et al.
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    Umate, Pavan
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    Manavski, Nikolay
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    Ploechinger, Magdalena
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    Kleinknecht, Laura
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    Bogireddi, Hanumakumar
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Herrmann, Reinhold G.
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    Wanner, Gerhard
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Meurer, Joerg
    Biozentrum der Ludwig-Maximilians-Universität München, Department Biologie I, Planegg-Martinsried, Germany .
    PsbN is required for assembly of the photosystem II reaction center in Nicotiana tabacum2014In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 26, no 3, p. 1183-1199Article in journal (Refereed)
    Abstract [en]

    The chloroplast-encoded low molecular weight protein PsbN is annotated as a photosystem II (PSII) subunit. To elucidate the localization and function of PsbN, encoded on the opposite strand to the psbB gene cluster, we raised antibodies and inserted a resistance cassette into PsbN in both directions. Both homoplastomic tobacco (Nicotiana tabacum) mutants Delta psbN-F and Delta psbN-R show essentially the same PSII deficiencies. The mutants are extremely light sensitive and failed to recover from photoinhibition. Although synthesis of PSII proteins was not altered significantly, both mutants accumulated only similar to 25% of PSII proteins compared with the wild type. Assembly of PSII precomplexes occurred at normal rates, but heterodimeric PSII reaction centers (RCs) and higher order PSII assemblies were not formed efficiently in the mutants. The Delta psbN-R mutant was complemented by allotopic expression of the PsbN gene fused to the sequence of a chloroplast transit peptide in the nuclear genome. PsbN represents a bitopic trans-membrane peptide localized in stroma lamellae with its highly conserved C terminus exposed to the stroma. Significant amounts of PsbN were already present in dark-grown seedling. Our data prove that PsbN is not a constituent subunit of PSII but is required for repair from photoinhibition and efficient assembly of the PSII RC.

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