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Schröder L, Hegermann J, Pille P, Braun HP. The photosynthesis apparatus of European mistletoe (Viscum album). PLANT PHYSIOLOGY 2022; 190:1896-1914. [PMID: 35976139 PMCID: PMC9614478 DOI: 10.1093/plphys/kiac377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
European mistletoe (Viscum album) is known for its special mode of cellular respiration. It lacks the mitochondrial NADH dehydrogenase complex (Complex I of the respiratory chain) and has restricted capacities to generate mitochondrial adenosine triphosphate (ATP). Here, we present an investigation of the V. album energy metabolism taking place in chloroplasts. Thylakoids were purified from young V. album leaves, and membrane-bound protein complexes were characterized by Blue native polyacrylamide gel electrophoresis as well as by the complexome profiling approach. Proteins were systematically identified by label-free quantitative shotgun proteomics. We identified >1,800 distinct proteins (accessible at https://complexomemap.de/va_leaves), including nearly 100 proteins forming part of the protein complexes involved in the light-dependent part of photosynthesis. The photosynthesis apparatus of V. album has distinct features: (1) comparatively low amounts of Photosystem I; (2) absence of the NDH complex (the chloroplast pendant of mitochondrial Complex I involved in cyclic electron transport (CET) around Photosystem I); (3) reduced levels of the proton gradient regulation 5 (PGR5) and proton gradient regulation 5-like 1 (PGRL1) proteins, which offer an alternative route for CET around Photosystem I; (4) comparable amounts of Photosystem II and the chloroplast ATP synthase complex to other seed plants. Our data suggest a restricted capacity for chloroplast ATP biosynthesis by the photophosphorylation process. This is in addition to the limited ATP supply by the mitochondria. We propose a view on mistletoe's mode of life, according to which its metabolism relies to a greater extent on energy-rich compounds provided by the host trees.
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Affiliation(s)
- Lucie Schröder
- Institut für Pflanzgenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Jan Hegermann
- Institut für Funktionelle und Angewandte Anatomie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Patrick Pille
- Institut für Pflanzgenetik, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
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Sárvári É, Gellén G, Sági-Kazár M, Schlosser G, Solymosi K, Solti Á. Qualitative and quantitative evaluation of thylakoid complexes separated by Blue Native PAGE. PLANT METHODS 2022; 18:23. [PMID: 35241118 PMCID: PMC8895881 DOI: 10.1186/s13007-022-00858-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/12/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Blue Native polyacrylamide gel electrophoresis (BN PAGE) followed by denaturing PAGE is a widely used, convenient and time efficient method to separate thylakoid complexes and study their composition, abundance, and interactions. Previous analyses unravelled multiple monomeric and dimeric/oligomeric thylakoid complexes but, in certain cases, the separation of complexes was not proper. Particularly, the resolution of super- and megacomplexes, which provides important information on functional interactions, still remained challenging. RESULTS Using a detergent mixture of 1% (w/V) n-dodecyl-β-D-maltoside plus 1% (w/V) digitonin for solubilisation and 4.3-8% gel gradients for separation as methodological improvements in BN PAGE, several large photosystem (PS) I containing bands were detected. According to BN(/BN)/SDS PAGE and mass spectrometry analyses, these PSI bands proved to be PSI-NADH dehydrogenase-like megacomplexes more discernible in maize bundle sheath thylakoids, and PSI complexes with different light-harvesting complex (LHC) complements (PSI-LHCII, PSI-LHCII*) more abundant in mesophyll thylakoids of lincomycin treated maize. For quantitative determination of the complexes and their comparison across taxa and physiological conditions, sample volumes applicable to the gel, correct baseline determination of the densitograms, evaluation methods to resolve complexes running together, calculation of their absolute/relative amounts and distribution among their different forms are proposed. CONCLUSIONS Here we report our experience in Blue/Clear-Native polyacrylamide gel electrophoretic separation of thylakoid complexes, their identification, quantitative determination and comparison in different samples. The applied conditions represent a powerful methodology for the analysis of thylakoid mega- and supercomplexes.
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Affiliation(s)
- Éva Sárvári
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary.
| | - Gabriella Gellén
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, 1117, Hungary
| | - Máté Sági-Kazár
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
- Doctoral School of Biology, Institute of Biology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, 1117, Hungary
| | - Katalin Solymosi
- Department of Plant Anatomy, Institute of Biology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Ádám Solti
- Department of Plant Physiology and Molecular Plant Biology, Institute of Biology, Faculty of Science, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
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Lundquist PK. Tracking subplastidic localization of carotenoid metabolic enzymes with proteomics. Methods Enzymol 2022; 671:327-350. [DOI: 10.1016/bs.mie.2022.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Farhat N, Kouas W, Braun HP, Debez A. Stability of thylakoid protein complexes and preserving photosynthetic efficiency are crucial for the successful recovery of the halophyte Cakile maritima from high salinity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 166:177-190. [PMID: 34116337 DOI: 10.1016/j.plaphy.2021.05.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
Plants native to extreme habitats often face changes in environmental conditions such as salinity level and water availability. In response, plants have evolved efficient mechanisms allowing them to survive or recover. In the present work, effects of high salinity and salt-stress release were studied on the halophyte Cakile maritima. Four week-old plants were either cultivated at 0 mM NaCl or 200 mM NaCl. After one month of treatment, plants were further irrigated at either 0 mM NaCl, 200 mM NaCl, or rewatered to 0 mM NaCl (stress release). Upon salt stress, C. maritima plants exhibited reduced biomass production and shoot hydration which were associated with a decrease in the amount of chlorophyll a and b. However, under the same stressful conditions a significant increase of anthocyanin and malonyldialdehyde concentrations was noticed. Salt-stressed plants were able to maintain stable protein complexes of thylakoid membranes. Measurement of chlorophyll fluorescence and P700 redox state showed that PSI was more susceptible for damage by salinity than PSII. PSII machinery was significantly enhanced under saline conditions. All measured parameters were partially restored under salt-stress release conditions. Photoinhibition of PSI was also reversible and C. maritima was able to successfully re-establish PSI machinery indicating the high contribution of chloroplasts in salt tolerance mechanisms of C. maritima. Overall, to overcome high salinity stress, C. maritima sets a cascade of physio-biochemical and molecular pathways. Chloroplasts seem to act as metabolic centers as part of this adaptive process enabling growth restoration in this halophyte following salt stress release.
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Affiliation(s)
- Nèjia Farhat
- Laboratory of Extremophile Plants, Center of Biotechnology of Borj Cedria, (CBBC), P. O. Box 901, 2050, Hammam-Lif, Tunisia; Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University of Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Wafa Kouas
- Laboratory of Extremophile Plants, Center of Biotechnology of Borj Cedria, (CBBC), P. O. Box 901, 2050, Hammam-Lif, Tunisia
| | - Hans-Peter Braun
- Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University of Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Ahmed Debez
- Laboratory of Extremophile Plants, Center of Biotechnology of Borj Cedria, (CBBC), P. O. Box 901, 2050, Hammam-Lif, Tunisia; Department of Plant Proteomics, Institute of Plant Genetics, Leibniz University of Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
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Navazio L, Formentin E, Cendron L, Szabò I. Chloroplast Calcium Signaling in the Spotlight. FRONTIERS IN PLANT SCIENCE 2020; 11:186. [PMID: 32226434 PMCID: PMC7081724 DOI: 10.3389/fpls.2020.00186] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/07/2020] [Indexed: 05/22/2023]
Abstract
Calcium has long been known to regulate the metabolism of chloroplasts, concerning both light and carbon reactions of photosynthesis, as well as additional non photosynthesis-related processes. In addition to undergo Ca2+ regulation, chloroplasts can also influence the overall Ca2+ signaling pathways of the plant cell. Compelling evidence indicate that chloroplasts can generate specific stromal Ca2+ signals and contribute to the fine tuning of cytoplasmic Ca2+ signaling in response to different environmental stimuli. The recent set up of a toolkit of genetically encoded Ca2+ indicators, targeted to different chloroplast subcompartments (envelope, stroma, thylakoids) has helped to unravel the participation of chloroplasts in intracellular Ca2+ handling in resting conditions and during signal transduction. Intra-chloroplast Ca2+ signals have been demonstrated to occur in response to specific environmental stimuli, suggesting a role for these plant-unique organelles in transducing Ca2+-mediated stress signals. In this mini-review we present current knowledge of stimulus-specific intra-chloroplast Ca2+ transients, as well as recent advances in the identification and characterization of Ca2+-permeable channels/transporters localized at chloroplast membranes. In particular, the potential role played by cMCU, a chloroplast-localized member of the mitochondrial calcium uniporter (MCU) family, as component of plant environmental sensing is discussed in detail, taking into account some specific structural features of cMCU. In summary, the recent molecular identification of some players of chloroplast Ca2+ signaling has opened new avenues in this rapidly developing field and will hopefully allow a deeper understanding of the role of chloroplasts in shaping physiological responses in plants.
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Affiliation(s)
- Lorella Navazio
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
| | - Elide Formentin
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Ildikò Szabò
- Department of Biology, University of Padova, Padova, Italy
- Botanical Garden, University of Padova, Padova, Italy
- *Correspondence: Ildikò Szabò,
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Lande NV, Barua P, Gayen D, Kumar S, Chakraborty S, Chakraborty N. Proteomic dissection of the chloroplast: Moving beyond photosynthesis. J Proteomics 2019; 212:103542. [PMID: 31704367 DOI: 10.1016/j.jprot.2019.103542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/15/2019] [Accepted: 10/03/2019] [Indexed: 01/28/2023]
Abstract
Chloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO2 and H2O. It also serves as a major production site of multivariate pro-defense molecules, and coordinate with other organelles for cell defense. Chloroplast harbors 30-50% of total cellular proteins, out of which 80% are membrane residents and are difficult to solubilize. While proteome profiling has illuminated vast areas of biological protein space, a great deal of effort must be invested to understand the proteomic landscape of the chloroplast, which plays central role in photosynthesis, energy metabolism and stress-adaptation. Therefore, characterization of chloroplast proteome would not only provide the foundation for future investigation of expression and function of chloroplast proteins, but would open up new avenues for modulation of plant productivity through synchronizing chloroplastic key components. In this review, we summarize the progress that has been made to build new understanding of the chloroplast proteome and implications of chloroplast dynamicsing generate metabolic energy and modulating stress adaptation.
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Affiliation(s)
- Nilesh Vikram Lande
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pragya Barua
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dipak Gayen
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi 110067, India.
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7
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Schäfer P, Helm S, Köhler D, Agne B, Baginsky S. Consequences of impaired 1-MDa TIC complex assembly for the abundance and composition of chloroplast high-molecular mass protein complexes. PLoS One 2019; 14:e0213364. [PMID: 30865669 PMCID: PMC6415892 DOI: 10.1371/journal.pone.0213364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/20/2019] [Indexed: 12/28/2022] Open
Abstract
We report a systematic analysis of chloroplast high-molecular mass protein complexes using a combination of native gel electrophoresis and absolute protein quantification by MSE. With this experimental setup, we characterized the effect of the tic56-3 mutation in the 1-MDa inner envelope translocase (TIC) on the assembly of the chloroplast proteome. We show that the tic56-3 mutation results in a reduction of the 1-MDa TIC complex to approximately 10% of wildtype levels. Hierarchical clustering confirmed the association of malate dehydrogenase (MDH) with an envelope-associated FtsH/FtsHi complex and suggested the association of a glycine-rich protein with the 1-MDa TIC complex. Depletion of this complex leads to a reduction of chloroplast ATPase to approx. 75% of wildtype levels, while the abundance of the FtsH/FtsHi complex is increased to approx. 140% of wildtype. The accumulation of the major photosynthetic complexes is not affected by the mutation, suggesting that tic56-3 plants can sustain a functional photosynthetic machinery despite a significant reduction of the 1-MDa TIC complex. Together our analysis expands recent efforts to catalogue the native molecular masses of chloroplast proteins and provides information on the consequences of impaired accumulation of the 1-MDa TIC translocase for chloroplast proteome assembly.
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Affiliation(s)
- Peter Schäfer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
- * E-mail:
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8
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De Smet B, Willems P, Fernandez-Fernandez AD, Alseekh S, Fernie AR, Messens J, Van Breusegem F. In vivo detection of protein cysteine sulfenylation in plastids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:765-778. [PMID: 30394608 DOI: 10.1111/tpj.14146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 05/04/2023]
Abstract
Protein cysteine thiols are post-translationally modified under oxidative stress conditions. Illuminated chloroplasts are one of the important sources of hydrogen peroxide (H2 O2 ) and are highly sensitive to environmental stimuli, yet a comprehensive view of the oxidation-sensitive chloroplast proteome is still missing. By targeting the sulfenic acid YAP1C-trapping technology to the plastids of light-grown Arabidopsis cells, we identified 132 putatively sulfenylated plastid proteins upon H2 O2 pulse treatment. Almost half of the sulfenylated proteins are enzymes of the amino acid metabolism. Using metabolomics, we observed a reversible decrease in the levels of the amino acids Ala, Asn, Cys, Gln, Glu, His, Ile, Leu, Lys, Phe, Ser, Thr and Val after H2 O2 treatment, which is in line with an anticipated decrease in the levels of the glycolysis and tricarboxylic acid metabolites. Through the identification of an organelle-tailored proteome, we demonstrated that the subcellular targeting of the YAP1C probe enables us to study in vivo cysteine sulfenylation at the organellar level. All in all, the identification of these oxidation events in plastids revealed that several enzymes of the amino acid metabolism rapidly undergo cysteine oxidation upon oxidative stress.
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Affiliation(s)
- Barbara De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- VIB-VUB Center for Structural Biology, VIB, 1050, Brussels, Belgium
- Brussels Center for Redox Biology, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biochemistry, Ghent University, 9000, Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
| | - Alvaro D Fernandez-Fernandez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Joris Messens
- VIB-VUB Center for Structural Biology, VIB, 1050, Brussels, Belgium
- Brussels Center for Redox Biology, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
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Dissecting the chloroplast proteome of chickpea ( Cicer arietinum L.) provides new insights into classical and non-classical functions. J Proteomics 2017. [DOI: 10.1016/j.jprot.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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10
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Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber APM. Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts. MOLECULAR PLANT 2017; 10:197-211. [PMID: 27794502 DOI: 10.1016/j.molp.2016.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 05/08/2023]
Abstract
Blue native-PAGE (BN-PAGE) resolves protein complexes in their native state. When combined with immunoblotting, it can be used to identify the presence of high molecular weight complexes at high resolution for any protein, given a suitable antibody. To identify proteins in high molecular weight complexes on a large scale and to bypass the requirement for specific antibodies, we applied a tandem mass spectrometry (MS/MS) approach to BN-PAGE-resolved chloroplasts. Fractionation of the gel into six bands allowed identification and label-free quantification of 1000 chloroplast proteins with native molecular weight separation. Significantly, this approach achieves a depth of identification comparable with traditional shotgun proteomic analyses of chloroplasts, indicating much of the known chloroplast proteome is amenable to MS/MS identification under our fractionation scheme. By limiting the number of fractionation bands to six, we facilitate scaled-up comparative analyses, as we demonstrate with the reticulata chloroplast mutant displaying a reticulated leaf phenotype. Our comparative proteomics approach identified a candidate interacting protein of RETICULATA as well as effects on lipid remodeling proteins, amino acid metabolic enzymes, and plastid division machinery. We additionally highlight selected proteins from each sub-compartment of the chloroplast that provide novel insight on known or hypothesized protein complexes to further illustrate the utility of this approach. Our results demonstrate the high sensitivity and reproducibility of this technique, which is anticipated to be widely adaptable to other sub-cellular compartments.
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Affiliation(s)
- Peter K Lundquist
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany.
| | - Otho Mantegazza
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, BMFZ, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
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11
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Takabayashi A, Takabayashi S, Takahashi K, Watanabe M, Uchida H, Murakami A, Fujita T, Ikeuchi M, Tanaka A. PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms. PLANT & CELL PHYSIOLOGY 2017; 58:e10. [PMID: 28011869 DOI: 10.1093/pcp/pcw219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/01/2016] [Indexed: 05/29/2023]
Abstract
The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandem mass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocyanobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage.
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Affiliation(s)
- Atsushi Takabayashi
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
- CREST, JST, Kita-ku, Sapporo, Japan
| | - Saeka Takabayashi
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
- Department of Public Health, Graduate School of Medicine Hokkaido University, Kita-ku, Sapporo, Japan
| | - Kaori Takahashi
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Mai Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroko Uchida
- Kobe University Research Center for Inland Seas, Awaji, Japan
| | - Akio Murakami
- Kobe University Research Center for Inland Seas, Awaji, Japan
| | - Tomomichi Fujita
- Faculty of Science, Hokkaido University, N10 W8 Kita-ku, Sapporo 060-0810, Japan Tokyo, Tokyo, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Ayumi Tanaka
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, Japan
- CREST, JST, Kita-ku, Sapporo, Japan
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12
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Comparative Proteomic and Physiological Analysis Reveals the Variation Mechanisms of Leaf Coloration and Carbon Fixation in a Xantha Mutant of Ginkgo biloba L. Int J Mol Sci 2016; 17:ijms17111794. [PMID: 27801782 PMCID: PMC5133795 DOI: 10.3390/ijms17111794] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 12/31/2022] Open
Abstract
Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development. A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study. The chlorophyll content of YL was remarkably lower than that in GL. The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL. Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching. To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS. In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes. Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves. The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL. These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants.
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Wang X, Komatsu S. Plant subcellular proteomics: Application for exploring optimal cell function in soybean. J Proteomics 2016; 143:45-56. [PMID: 26808589 DOI: 10.1016/j.jprot.2016.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 01/11/2023]
Abstract
UNLABELLED Plants have evolved complicated responses to developmental changes and stressful environmental conditions. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular compartments during plant development and in response to biotic and abiotic stresses. Soybean, which is a valuable legume crop rich in protein and vegetable oil, can grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. To date, numerous proteomic studies have been performed in soybean to examine the specific protein profiles of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum. In this review, methods for the purification and purity assessment of subcellular organelles from soybean are summarized. In addition, the findings from subcellular proteomic analyses of soybean during development and under stresses, particularly flooding stress, are presented and the proteins regulated among subcellular compartments are discussed. Continued advances in subcellular proteomics are expected to greatly contribute to the understanding of the responses and interactions that occur within and among subcellular compartments during development and under stressful environmental conditions. BIOLOGICAL SIGNIFICANCE Subcellular proteomics has the potential to investigate the cellular events and interactions among subcellular compartments in response to development and stresses in plants. Soybean could grow in several climatic zones; however, the growth and yield of soybean are markedly decreased under stresses. Numerous proteomics of cell wall, plasma membrane, nucleus, mitochondrion, chloroplast, and endoplasmic reticulum was carried out to investigate the respecting proteins and their functions in soybean during development or under stresses. In this review, methods of subcellular-organelle enrichment and purity assessment are summarized. In addition, previous findings of subcellular proteomics are presented, and functional proteins regulated among different subcellular are discussed. Subcellular proteomics contributes greatly to uncovering responses and interactions among subcellular compartments during development and under stressful environmental conditions in soybean.
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Affiliation(s)
- Xin Wang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
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Noshi M, Hatanaka R, Tanabe N, Terai Y, Maruta T, Shigeoka S. Redox regulation of ascorbate and glutathione by a chloroplastic dehydroascorbate reductase is required for high-light stress tolerance in Arabidopsis. Biosci Biotechnol Biochem 2016; 80:870-7. [PMID: 26927949 DOI: 10.1080/09168451.2015.1135042] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chloroplasts are a significant site for reactive oxygen species production under illumination and, thus, possess a well-organized antioxidant system involving ascorbate. Ascorbate recycling occurs in different manners in this system, including a dehydroascorbate reductase (DHAR) reaction. We herein investigated the physiological significance of DHAR3 in photo-oxidative stress tolerance in Arabidopsis. GFP-fused DHAR3 protein was targeted to chloroplasts in Arabidopsis leaves. A DHAR3 knockout mutant exhibited sensitivity to high light (HL). Under HL, the ascorbate redox states were similar in mutant and wild-type plants, while total ascorbate content was significantly lower in the mutant, suggesting that DHAR3 contributes, at least to some extent, to ascorbate recycling. Activation of monodehydroascorbate reductase occurred in dhar3 mutant, which might compensate for the lack of DHAR3. Interestingly, glutathione oxidation was consistently inhibited in dhar3 mutant. These findings indicate that DHAR3 regulates both ascorbate and glutathione redox states to acclimate to HL.
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Affiliation(s)
- Masahiro Noshi
- a Faculty of Agriculture, Department of Advanced Bioscience , Kinki University , Nara , Japan
| | - Risa Hatanaka
- a Faculty of Agriculture, Department of Advanced Bioscience , Kinki University , Nara , Japan
| | - Noriaki Tanabe
- a Faculty of Agriculture, Department of Advanced Bioscience , Kinki University , Nara , Japan
| | - Yusuke Terai
- b Faculty of Life and Environmental Science, Department of Life Science and Biotechnology , Shimane University , Matsue , Japan
| | - Takanori Maruta
- b Faculty of Life and Environmental Science, Department of Life Science and Biotechnology , Shimane University , Matsue , Japan
| | - Shigeru Shigeoka
- a Faculty of Agriculture, Department of Advanced Bioscience , Kinki University , Nara , Japan
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Müller CS, Bildl W, Haupt A, Ellenrieder L, Becker T, Hunte C, Fakler B, Schulte U. Cryo-slicing Blue Native-Mass Spectrometry (csBN-MS), a Novel Technology for High Resolution Complexome Profiling. Mol Cell Proteomics 2015; 15:669-81. [PMID: 26598645 DOI: 10.1074/mcp.m115.054080] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 11/06/2022] Open
Abstract
Blue native (BN) gel electrophoresis is a powerful method for protein separation. Combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), it enables large scale identification of protein complexes and their subunits. Current BN-MS approaches, however, are limited in size resolution, comprehensiveness, and quantification. Here, we present a new methodology combining defined sub-millimeter slicing of BN gels by a cryo-microtome with high performance LC-MS/MS and label-free quantification of protein amounts. Application of this cryo-slicing BN-MS approach to mitochondria from rat brain demonstrated a high degree of comprehensiveness, accuracy, and size resolution. The technique provided abundance-mass profiles for 774 mitochondrial proteins, including all canonical subunits of the oxidative respiratory chain assembled into 13 distinct (super-)complexes. Moreover, the data revealed COX7R as a constitutive subunit of distinct super-complexes and identified novel assemblies of voltage-dependent anion channels/porins and TOM proteins. Together, cryo-slicing BN-MS enables quantitative profiling of complexomes with resolution close to the limits of native gel electrophoresis.
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Affiliation(s)
- Catrin S Müller
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Wolfgang Bildl
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Alexander Haupt
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg
| | - Lars Ellenrieder
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg
| | - Thomas Becker
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Carola Hunte
- §Institute for Biochemistry and Molecular Biology, Stefan-Meier-Strasse 17, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Bernd Fakler
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg
| | - Uwe Schulte
- From the ‡Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg; ¶Center for Biological Signaling Studies (BIOSS), Schänzlestrasse 18, 79104 Freiburg; ‖Logopharm GmbH, Schlossstrasse 14, 79232 March-Buchheim, Germany
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16
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Suzuki M, Takahashi S, Kondo T, Dohra H, Ito Y, Kiriiwa Y, Hayashi M, Kamiya S, Kato M, Fujiwara M, Fukao Y, Kobayashi M, Nagata N, Motohashi R. Plastid Proteomic Analysis in Tomato Fruit Development. PLoS One 2015; 10:e0137266. [PMID: 26371478 PMCID: PMC4570674 DOI: 10.1371/journal.pone.0137266] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 08/15/2015] [Indexed: 02/01/2023] Open
Abstract
To better understand the mechanism of plastid differentiation from chloroplast to chromoplast, we examined proteome and plastid changes over four distinct developmental stages of 'Micro-Tom' fruit. Additionally, to discover more about the relationship between fruit color and plastid differentiation, we also analyzed and compared 'Micro-Tom' results with those from two other varieties, 'Black' and 'White Beauty'. We confirmed that proteins related to photosynthesis remain through the orange maturity stage of 'Micro-Tom', and also learned that thylakoids no longer exist at this stage. These results suggest that at a minimum there are changes in plastid morphology occurring before all related proteins change. We also compared 'Micro-Tom' fruits with 'Black' and 'White Beauty' using two-dimensional gel electrophoresis. We found a decrease of CHRC (plastid-lipid-associated protein) and HrBP1 (harpin binding protein-1) in the 'Black' and 'White Beauty' varieties. CHRC is involved in carotenoid accumulation and stabilization. HrBP1 in Arabidopsis has a sequence similar to proteins in the PAP/fibrillin family. These proteins have characteristics and functions similar to lipocalin, an example of which is the transport of hydrophobic molecules. We detected spots of TIL (temperature-induced lipocalin) in 2D-PAGE results, however the number of spots and their isoelectric points differed between 'Micro-Tom' and 'Black'/'White Beauty'. Lipocalin has various functions including those related to environmental stress response, apoptosis induction, membrane formation and fixation, regulation of immune response, cell growth, and metabolism adjustment. Lipocalin related proteins such as TIL and HrBP1 could be related to the accumulation of carotenoids, fruit color and the differentiation of chromoplast.
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Affiliation(s)
- Miho Suzuki
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Sachiko Takahashi
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Takanori Kondo
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Hideo Dohra
- Instrumental Research Support Office, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Yumihiko Ito
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Yoshikazu Kiriiwa
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Marina Hayashi
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Shiori Kamiya
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Masaya Kato
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
| | - Masayuki Fujiwara
- The Plant Science Education Unit, Nara Institute of Science and Technology, Ikoma city, Nara, Japan
| | - Yoichiro Fukao
- The Plant Science Education Unit, Nara Institute of Science and Technology, Ikoma city, Nara, Japan
| | - Megumi Kobayashi
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo, Japan
| | - Noriko Nagata
- Faculty of Science, Japan Woman’s University, Bunkyo-ku, Tokyo, Japan
| | - Reiko Motohashi
- Faculty of Agriculture, Shizuoka University, Shizuoka city, Shizuoka, Japan
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17
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Glew MD, Veith PD, Chen D, Seers CA, Chen YY, Reynolds EC. Blue native-PAGE analysis of membrane protein complexes in Porphyromonas gingivalis. J Proteomics 2014; 110:72-92. [DOI: 10.1016/j.jprot.2014.07.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/01/2014] [Accepted: 07/20/2014] [Indexed: 11/30/2022]
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18
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Joaquín-Ramos A, Huerta-Ocampo JÁ, Barrera-Pacheco A, De León-Rodríguez A, Baginsky S, Barba de la Rosa AP. Comparative proteomic analysis of amaranth mesophyll and bundle sheath chloroplasts and their adaptation to salt stress. JOURNAL OF PLANT PHYSIOLOGY 2014; 171:1423-1435. [PMID: 25046763 DOI: 10.1016/j.jplph.2014.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 06/03/2023]
Abstract
The effect of salt stress was analyzed in chloroplasts of Amaranthus cruentus var. Amaranteca, a plant NAD-malic enzyme (NAD-ME) type. Morphology of chloroplasts from bundle sheath (BSC) and mesophyll (MC) was observed by transmission electron microscopy (TEM). BSC and MC from control plants showed similar morphology, however under stress, changes in BSC were observed. The presence of ribulose bisphosphate carboxylase/oxygenase (RuBisCO) was confirmed by immunohistochemical staining in both types of chloroplasts. Proteomic profiles of thylakoid protein complexes from BSC and MC, and their changes induced by salt stress were analyzed by blue-native polyacrylamide gel electrophoresis followed by SDS-PAGE (2-D BN/SDS-PAGE). Differentially accumulated protein spots were analyzed by LC-MS/MS. Although A. cruentus photosynthetic tissue showed the Kranz anatomy, the thylakoid proteins showed some differences at photosystem structure level. Our results suggest that A. cruentus var. Amaranteca could be better classified as a C3-C4 photosynthetic plant.
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Affiliation(s)
- Ahuitzolt Joaquín-Ramos
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - José Á Huerta-Ocampo
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - Alberto Barrera-Pacheco
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - Antonio De León-Rodríguez
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico
| | - Sacha Baginsky
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biochemie, Abteilung Pflanzenbiochemie, Weinbergweg 22 (Biozentrum), 06120 Halle (Saale), Germany
| | - Ana P Barba de la Rosa
- IPICyT, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa San José No. 2055, Lomas 4a Sección, San Luis Potosí, S.L.P. 78216, Mexico.
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19
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Nelson CJ, Alexova R, Jacoby RP, Millar AH. Proteins with high turnover rate in barley leaves estimated by proteome analysis combined with in planta isotope labeling. PLANT PHYSIOLOGY 2014; 166:91-108. [PMID: 25082890 PMCID: PMC4149734 DOI: 10.1104/pp.114.243014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Protein turnover is a key component in cellular homeostasis; however, there is little quantitative information on degradation kinetics for individual plant proteins. We have used (15)N labeling of barley (Hordeum vulgare) plants and gas chromatography-mass spectrometry analysis of free amino acids and liquid chromatography-mass spectrometry analysis of proteins to track the enrichment of (15)N into the amino acid pools in barley leaves and then into tryptic peptides derived from newly synthesized proteins. Using information on the rate of growth of barley leaves combined with the rate of degradation of (14)N-labeled proteins, we calculate the turnover rates of 508 different proteins in barley and show that they vary by more than 100-fold. There was approximately a 9-h lag from label application until (15)N incorporation could be reliably quantified in extracted peptides. Using this information and assuming constant translation rates for proteins during the time course, we were able to quantify degradation rates for several proteins that exhibit half-lives on the order of hours. Our workflow, involving a stringent series of mass spectrometry filtering steps, demonstrates that (15)N labeling can be used for large-scale liquid chromatography-mass spectrometry studies of protein turnover in plants. We identify a series of abundant proteins in photosynthesis, photorespiration, and specific subunits of chlorophyll biosynthesis that turn over significantly more rapidly than the average protein involved in these processes. We also highlight a series of proteins that turn over as rapidly as the well-known D1 subunit of photosystem II. While these proteins need further verification for rapid degradation in vivo, they cluster in chlorophyll and thiamine biosynthesis.
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Affiliation(s)
- Clark J Nelson
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ralitza Alexova
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Richard P Jacoby
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
| | - A Harvey Millar
- Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, University of Western Australia, Perth, Western Australia 6009, Australia
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