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Caccamo A, Vega de Luna F, Misztak AE, Pyr dit Ruys S, Vertommen D, Cardol P, Messens J, Remacle C. APX2 Is an Ascorbate Peroxidase-Related Protein that Regulates the Levels of Plastocyanin in Chlamydomonas. PLANT & CELL PHYSIOLOGY 2024; 65:644-656. [PMID: 38591346 PMCID: PMC11094752 DOI: 10.1093/pcp/pcae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 04/10/2024]
Abstract
The function of ascorbate peroxidase-related (APX-R) proteins, present in all green photosynthetic eukaryotes, remains unclear. This study focuses on APX-R from Chlamydomonas reinhardtii, namely, ascorbate peroxidase 2 (APX2). We showed that apx2 mutants exhibited a faster oxidation of the photosystem I primary electron donor, P700, upon sudden light increase and a slower re-reduction rate compared to the wild type, pointing to a limitation of plastocyanin. Spectroscopic, proteomic and immunoblot analyses confirmed that the phenotype was a result of lower levels of plastocyanin in the apx2 mutants. The redox state of P700 did not differ between wild type and apx2 mutants when the loss of function in plastocyanin was nutritionally complemented by growing apx2 mutants under copper deficiency. In this case, cytochrome c6 functionally replaces plastocyanin, confirming that lower levels of plastocyanin were the primary defect caused by the absence of APX2. Overall, the results presented here shed light on an unexpected regulation of plastocyanin level under copper-replete conditions, induced by APX2 in Chlamydomonas.
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Affiliation(s)
- Anna Caccamo
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, Chemin de la vallée 4, Liège 4000, Belgium
- VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels 1050, Belgium
- Brussels Center for Redox Biology, Pleinlaan 2, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Félix Vega de Luna
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, Chemin de la vallée 4, Liège 4000, Belgium
| | - Agnieszka E Misztak
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, Chemin de la vallée 4, Liège 4000, Belgium
| | - Sébastien Pyr dit Ruys
- de Duve Institute and MASSPROT platform, UCLouvain, Avenue Hippocrate 74, Brussels 1200, Belgium
| | - Didier Vertommen
- de Duve Institute and MASSPROT platform, UCLouvain, Avenue Hippocrate 74, Brussels 1200, Belgium
| | - Pierre Cardol
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, Chemin de la vallée 4, Liège 4000, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, Pleinlaan 2, Brussels 1050, Belgium
- Brussels Center for Redox Biology, Pleinlaan 2, Brussels 1050, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium
| | - Claire Remacle
- Genetics and Physiology of Microalgae, InBios/Phytosystems Research Unit, University of Liège, Chemin de la vallée 4, Liège 4000, Belgium
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2
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Sandoval-Ibáñez O, Rolo D, Ghandour R, Hertle AP, Armarego-Marriott T, Sampathkumar A, Zoschke R, Bock R. De-etiolation-induced protein 1 (DEIP1) mediates assembly of the cytochrome b 6f complex in Arabidopsis. Nat Commun 2022; 13:4045. [PMID: 35831297 PMCID: PMC9279372 DOI: 10.1038/s41467-022-31758-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
The conversion of light energy to chemical energy by photosynthesis requires the concerted action of large protein complexes in the thylakoid membrane. Recent work has provided fundamental insights into the three-dimensional structure of these complexes, but how they are assembled from hundreds of parts remains poorly understood. Particularly little is known about the biogenesis of the cytochrome b6f complex (Cytb6f), the redox-coupling complex that interconnects the two photosystems. Here we report the identification of a factor that guides the assembly of Cytb6f in thylakoids of chloroplasts. The protein, DE-ETIOLATION-INDUCED PROTEIN 1 (DEIP1), resides in the thylakoid membrane and is essential for photoautotrophic growth. Knock-out mutants show a specific loss of Cytb6f, and are defective in complex assembly. We demonstrate that DEIP1 interacts with the two cytochrome subunits of the complex, PetA and PetB, and mediates the assembly of intermediates in Cytb6f biogenesis. The identification of DEIP1 provides an entry point into the study of the assembly pathway of a crucial complex in photosynthetic electron transfer. The Cytb6f complex is a multi-subunit enzyme that couples the two photosystems during the light reactions of photosynthesis. Here the authors show that the thylakoid-localized DEIP1 protein interacts with the PetA and PetB subunits, and is essential for Cytb6f complex assembly in Arabidopsis.
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Affiliation(s)
- Omar Sandoval-Ibáñez
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - David Rolo
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rabea Ghandour
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alexander P Hertle
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Tegan Armarego-Marriott
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arun Sampathkumar
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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3
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Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK. Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009725. [PMID: 34492001 PMCID: PMC8448359 DOI: 10.1371/journal.pgen.1009725] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/17/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
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Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Katharine Guan
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Wendy Schackwitz
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joshua Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Dhruv Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Robert M. Shih
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rachel M. Dent
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Mansi Chovatia
- Joint Genome Institute, Berkeley, California, United States of America
| | - Aditi Sharma
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joel Martin
- Joint Genome Institute, Berkeley, California, United States of America
| | - Chia-Lin Wei
- Joint Genome Institute, Berkeley, California, United States of America
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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4
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A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2019; 116:18445-18454. [PMID: 31455733 PMCID: PMC6744930 DOI: 10.1073/pnas.1904587116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A phase-separated, liquid-like organelle called the pyrenoid mediates CO2 fixation in the chloroplasts of nearly all eukaryotic algae. While most algae have 1 pyrenoid per chloroplast, here we describe a mutant in the model alga Chlamydomonas that has on average 10 pyrenoids per chloroplast. Characterization of the mutant leads us to propose a model where multiple pyrenoids are favored by an increase in the surface area of the starch sheath that surrounds and binds to the liquid-like pyrenoid matrix. We find that the mutant's phenotypes are due to disruption of a gene, which we call StArch Granules Abnormal 1 (SAGA1) because starch sheath granules, or plates, in mutants lacking SAGA1 are more elongated and thinner than those of wild type. SAGA1 contains a starch binding motif, suggesting that it may directly regulate starch sheath morphology. SAGA1 localizes to multiple puncta and streaks in the pyrenoid and physically interacts with the small and large subunits of the carbon-fixing enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), a major component of the liquid-like pyrenoid matrix. Our findings suggest a biophysical mechanism by which starch sheath morphology affects pyrenoid number and CO2-concentrating mechanism function, advancing our understanding of the structure and function of this biogeochemically important organelle. More broadly, we propose that the number of phase-separated organelles can be regulated by imposing constraints on their surface area.
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5
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Grossman A, Sanz-Luque E, Yi H, Yang W. Building the GreenCut2 suite of proteins to unmask photosynthetic function and regulation. Microbiology (Reading) 2019; 165:697-718. [DOI: 10.1099/mic.0.000788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Arthur Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Emanuel Sanz-Luque
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Heng Yi
- Key Laboratory of Photobiology, Institute of Botany (CAS), Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Wenqiang Yang
- Key Laboratory of Photobiology, Institute of Botany (CAS), Beijing, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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6
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Wittkopp TM, Saroussi S, Yang W, Johnson X, Kim RG, Heinnickel ML, Russell JJ, Phuthong W, Dent RM, Broeckling CD, Peers G, Lohr M, Wollman FA, Niyogi KK, Grossman AR. GreenCut protein CPLD49 of Chlamydomonas reinhardtii associates with thylakoid membranes and is required for cytochrome b 6 f complex accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:1023-1037. [PMID: 29602195 DOI: 10.1111/tpj.13915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/23/2018] [Accepted: 03/06/2018] [Indexed: 06/08/2023]
Abstract
The GreenCut encompasses a suite of nucleus-encoded proteins with orthologs among green lineage organisms (plants, green algae), but that are absent or poorly conserved in non-photosynthetic/heterotrophic organisms. In Chlamydomonas reinhardtii, CPLD49 (Conserved in Plant Lineage and Diatoms49) is an uncharacterized GreenCut protein that is critical for maintaining normal photosynthetic function. We demonstrate that a cpld49 mutant has impaired photoautotrophic growth under high-light conditions. The mutant exhibits a nearly 90% reduction in the level of the cytochrome b6 f complex (Cytb6 f), which impacts linear and cyclic electron transport, but does not compromise the ability of the strain to perform state transitions. Furthermore, CPLD49 strongly associates with thylakoid membranes where it may be part of a membrane protein complex with another GreenCut protein, CPLD38; a mutant null for CPLD38 also impacts Cytb6 f complex accumulation. We investigated several potential functions of CPLD49, with some suggested by protein homology. Our findings are congruent with the hypothesis that CPLD38 and CPLD49 are part of a novel thylakoid membrane complex that primarily modulates accumulation, but also impacts the activity of the Cytb6 f complex. Based on motifs of CPLD49 and the activities of other CPLD49-like proteins, we suggest a role for this putative dehydrogenase in the synthesis of a lipophilic thylakoid membrane molecule or cofactor that influences the assembly and activity of Cytb6 f.
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Affiliation(s)
- Tyler M Wittkopp
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Wenqiang Yang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Xenie Johnson
- Laboratoire de Bioénergétique et Biotechnologie des Bactéries et Microalgues, CEA Cadarache, Saint Paul lez Durance, France
| | - Rick G Kim
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Mark L Heinnickel
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - James J Russell
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Witchukorn Phuthong
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Rachel M Dent
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, 80523, USA
| | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Martin Lohr
- Institut für Molekulare Physiologie - Pflanzenbiochemie, Johannes Gutenberg-Universität, 55099, Mainz, Germany
| | | | - Krishna K Niyogi
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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7
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Wittkopp TM, Schmollinger S, Saroussi S, Hu W, Zhang W, Fan Q, Gallaher SD, Leonard MT, Soubeyrand E, Basset GJ, Merchant SS, Grossman AR, Duanmu D, Lagarias JC. Bilin-Dependent Photoacclimation in Chlamydomonas reinhardtii. THE PLANT CELL 2017; 29:2711-2726. [PMID: 29084873 PMCID: PMC5728120 DOI: 10.1105/tpc.17.00149] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/26/2017] [Accepted: 10/27/2017] [Indexed: 05/18/2023]
Abstract
In land plants, linear tetrapyrrole (bilin)-based phytochrome photosensors optimize photosynthetic light capture by mediating massive reprogramming of gene expression. But, surprisingly, many green algal genomes lack phytochrome genes. Studies of the heme oxygenase mutant (hmox1) of the green alga Chlamydomonas reinhardtii suggest that bilin biosynthesis in plastids is essential for proper regulation of a nuclear gene network implicated in oxygen detoxification during dark-to-light transitions. hmox1 cannot grow photoautotrophically and photoacclimates poorly to increased illumination. We show that these phenotypes are due to reduced accumulation of photosystem I (PSI) reaction centers, the PSI electron acceptors 5'-monohydroxyphylloquinone and phylloquinone, and the loss of PSI and photosystem II antennae complexes during photoacclimation. The hmox1 mutant resembles chlorophyll biosynthesis mutants phenotypically, but can be rescued by exogenous biliverdin IXα, the bilin produced by HMOX1. This rescue is independent of photosynthesis and is strongly dependent on blue light. RNA-seq comparisons of hmox1, genetically complemented hmox1, and chemically rescued hmox1 reveal that tetrapyrrole biosynthesis and known photoreceptor and photosynthesis-related genes are not impacted in the hmox1 mutant at the transcript level. We propose that a bilin-based, blue-light-sensing system within plastids evolved together with a bilin-based retrograde signaling pathway to ensure that a robust photosynthetic apparatus is sustained in light-grown Chlamydomonas.
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Affiliation(s)
- Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
- Department of Biology, Stanford University, Stanford, California 94305
| | - Stefan Schmollinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Wei Hu
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Weiqing Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuling Fan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Michael T Leonard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Eric Soubeyrand
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Gilles J Basset
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Deqiang Duanmu
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
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Shi J, Huang T, Chai S, Guo Y, Wei J, Dou S, Li L, Liu G. Identification of Reference and Biomarker Proteins in Chlamydomonas reinhardtii Cultured under Different Stress Conditions. Int J Mol Sci 2017; 18:ijms18081822. [PMID: 28829403 PMCID: PMC5578208 DOI: 10.3390/ijms18081822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/25/2022] Open
Abstract
Reference proteins and biomarkers are important for the quantitative evaluation of protein abundance. Chlamydomonasreinhardtii was grown under five stress conditions (dark, cold, heat, salt, and glucose supplementation), and the OD750 and total protein contents were evaluated on days 0, 1, 2, 4, and 6 of culture. Antibodies for 20 candidate proteins were generated, and the protein expression patterns were examined by western blotting. Reference protein(s) for each treatment were identified by calculating the Pearson’s correlation coefficient (PCC) between target protein abundance and total protein content. Histone H3, beta tubulin 1 (TUB-1), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL), and mitochondrial F1F0 ATP synthase subunit 6 (ATPs-6) were the top reference proteins, because they were expressed stably under multiple stress conditions. The average relative-fold change (ARF) value of each protein was calculated to identify biomarkers. Heat shock protein 90B (HSP90B), flagellar associated protein (FAP127) and ATP synthase CF0 A subunit (ATPs-A) were suitable biomarkers for multiple treatments, while receptor of activated protein kinase C1 (RCK1), biotin carboxylase (BCR1), mitochondrial phosphate carrier protein (MPC1), and rubisco large subunit N-methyltransferase (RMT1) were suitable biomarkers for the dark, cold, heat, and glucose treatments, respectively.
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Affiliation(s)
- Jianan Shi
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Teng Huang
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Shuaijie Chai
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Yalu Guo
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Jian Wei
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Shijuan Dou
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Liyun Li
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Guozhen Liu
- Institute of Bioenergy, College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China.
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9
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A repeat protein links Rubisco to form the eukaryotic carbon-concentrating organelle. Proc Natl Acad Sci U S A 2016; 113:5958-63. [PMID: 27166422 DOI: 10.1073/pnas.1522866113] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biological carbon fixation is a key step in the global carbon cycle that regulates the atmosphere's composition while producing the food we eat and the fuels we burn. Approximately one-third of global carbon fixation occurs in an overlooked algal organelle called the pyrenoid. The pyrenoid contains the CO2-fixing enzyme Rubisco and enhances carbon fixation by supplying Rubisco with a high concentration of CO2 Since the discovery of the pyrenoid more that 130 y ago, the molecular structure and biogenesis of this ecologically fundamental organelle have remained enigmatic. Here we use the model green alga Chlamydomonas reinhardtii to discover that a low-complexity repeat protein, Essential Pyrenoid Component 1 (EPYC1), links Rubisco to form the pyrenoid. We find that EPYC1 is of comparable abundance to Rubisco and colocalizes with Rubisco throughout the pyrenoid. We show that EPYC1 is essential for normal pyrenoid size, number, morphology, Rubisco content, and efficient carbon fixation at low CO2 We explain the central role of EPYC1 in pyrenoid biogenesis by the finding that EPYC1 binds Rubisco to form the pyrenoid matrix. We propose two models in which EPYC1's four repeats could produce the observed lattice arrangement of Rubisco in the Chlamydomonas pyrenoid. Our results suggest a surprisingly simple molecular mechanism for how Rubisco can be packaged to form the pyrenoid matrix, potentially explaining how Rubisco packaging into a pyrenoid could have evolved across a broad range of photosynthetic eukaryotes through convergent evolution. In addition, our findings represent a key step toward engineering a pyrenoid into crops to enhance their carbon fixation efficiency.
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10
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Tetratricopeptide repeat protein protects photosystem I from oxidative disruption during assembly. Proc Natl Acad Sci U S A 2016; 113:2774-9. [PMID: 26903622 DOI: 10.1073/pnas.1524040113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A Chlamydomonas reinhardtii mutant lacking CGL71, a thylakoid membrane protein previously shown to be involved in photosystem I (PSI) accumulation, exhibited photosensitivity and highly reduced abundance of PSI under photoheterotrophic conditions. Remarkably, the PSI content of this mutant declined to nearly undetectable levels under dark, oxic conditions, demonstrating that reduced PSI accumulation in the mutant is not strictly the result of photodamage. Furthermore, PSI returns to nearly wild-type levels when the O2 concentration in the medium is lowered. Overall, our results suggest that the accumulation of PSI in the mutant correlates with the redox state of the stroma rather than photodamage and that CGL71 functions under atmospheric O2 conditions to allow stable assembly of PSI. These findings may reflect the history of the Earth's atmosphere as it transitioned from anoxic to highly oxic (1-2 billion years ago), a change that required organisms to evolve mechanisms to assist in the assembly and stability of proteins or complexes with O2-sensitive cofactors.
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11
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Li X, Zhang R, Patena W, Gang SS, Blum SR, Ivanova N, Yue R, Robertson JM, Lefebvre PA, Fitz-Gibbon ST, Grossman AR, Jonikas MC. An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. THE PLANT CELL 2016; 28:367-87. [PMID: 26764374 PMCID: PMC4790863 DOI: 10.1105/tpc.15.00465] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/30/2015] [Accepted: 01/11/2016] [Indexed: 05/18/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a leading unicellular model for dissecting biological processes in photosynthetic eukaryotes. However, its usefulness has been limited by difficulties in obtaining mutants in specific genes of interest. To allow generation of large numbers of mapped mutants, we developed high-throughput methods that (1) enable easy maintenance of tens of thousands of Chlamydomonas strains by propagation on agar media and by cryogenic storage, (2) identify mutagenic insertion sites and physical coordinates in these collections, and (3) validate the insertion sites in pools of mutants by obtaining >500 bp of flanking genomic sequences. We used these approaches to construct a stably maintained library of 1935 mapped mutants, representing disruptions in 1562 genes. We further characterized randomly selected mutants and found that 33 out of 44 insertion sites (75%) could be confirmed by PCR, and 17 out of 23 mutants (74%) contained a single insertion. To demonstrate the power of this library for elucidating biological processes, we analyzed the lipid content of mutants disrupted in genes encoding proteins of the algal lipid droplet proteome. This study revealed a central role of the long-chain acyl-CoA synthetase LCS2 in the production of triacylglycerol from de novo-synthesized fatty acids.
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Affiliation(s)
- Xiaobo Li
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Ru Zhang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Weronika Patena
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Spencer S Gang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Sean R Blum
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Nina Ivanova
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Rebecca Yue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Jacob M Robertson
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Paul A Lefebvre
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Sorel T Fitz-Gibbon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Martin C Jonikas
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
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12
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Critical role of Chlamydomonas reinhardtii ferredoxin-5 in maintaining membrane structure and dark metabolism. Proc Natl Acad Sci U S A 2015; 112:14978-83. [PMID: 26627249 DOI: 10.1073/pnas.1515240112] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Photosynthetic microorganisms typically have multiple isoforms of the electron transfer protein ferredoxin, although we know little about their exact functions. Surprisingly, a Chlamydomonas reinhardtii mutant null for the ferredoxin-5 gene (FDX5) completely ceased growth in the dark, with both photosynthetic and respiratory functions severely compromised; growth in the light was unaffected. Thylakoid membranes in dark-maintained fdx5 mutant cells became severely disorganized concomitant with a marked decrease in the ratio of monogalactosyldiacylglycerol to digalactosyldiacylglycerol, major lipids in photosynthetic membranes, and the accumulation of triacylglycerol. Furthermore, FDX5 was shown to physically interact with the fatty acid desaturases CrΔ4FAD and CrFAD6, likely donating electrons for the desaturation of fatty acids that stabilize monogalactosyldiacylglycerol. Our results suggest that in photosynthetic organisms, specific redox reactions sustain dark metabolism, with little impact on daytime growth, likely reflecting the tailoring of electron carriers to unique intracellular metabolic circuits under these two very distinct redox conditions.
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13
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Phuthong W, Huang Z, Wittkopp TM, Sznee K, Heinnickel ML, Dekker JP, Frese RN, Prinz FB, Grossman AR. The Use of Contact Mode Atomic Force Microscopy in Aqueous Medium for Structural Analysis of Spinach Photosynthetic Complexes. PLANT PHYSIOLOGY 2015; 169:1318-32. [PMID: 26220954 PMCID: PMC4587457 DOI: 10.1104/pp.15.00706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 07/24/2015] [Indexed: 05/02/2023]
Abstract
To investigate the dynamics of photosynthetic pigment-protein complexes in vascular plants at high resolution in an aqueous environment, membrane-protruding oxygen-evolving complexes (OECs) associated with photosystem II (PSII) on spinach (Spinacia oleracea) grana membranes were examined using contact mode atomic force microscopy. This study represents, to our knowledge, the first use of atomic force microscopy to distinguish the putative large extrinsic loop of Photosystem II CP47 reaction center protein (CP47) from the putative oxygen-evolving enhancer proteins 1, 2, and 3 (PsbO, PsbP, and PsbQ) and large extrinsic loop of Photosystem II CP43 reaction center protein (CP43) in the PSII-OEC extrinsic domains of grana membranes under conditions resulting in the disordered arrangement of PSII-OEC particles. Moreover, we observed uncharacterized membrane particles that, based on their physical characteristics and electrophoretic analysis of the polypeptides associated with the grana samples, are hypothesized to be a domain of photosystem I that protrudes from the stromal face of single thylakoid bilayers. Our results are interpreted in the context of the results of others that were obtained using cryo-electron microscopy (and single particle analysis), negative staining and freeze-fracture electron microscopy, as well as previous atomic force microscopy studies.
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Affiliation(s)
- Witchukorn Phuthong
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Zubin Huang
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Tyler M Wittkopp
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Kinga Sznee
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Mark L Heinnickel
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Jan P Dekker
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Raoul N Frese
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Fritz B Prinz
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
| | - Arthur R Grossman
- Department of Materials Science and Engineering (W.P., F.B.P.), Department of Mechanical Engineering (Z.H., F.B.P.), and Department of Biology (T.M.W.), Stanford University, Stanford, California 94305;Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (T.M.W., M.L.H., A.R.G.); andDepartment of Physics and Astronomy, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands (K.S., J.P.D., R.N.F.)
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14
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Schöttler MA, Tóth SZ, Boulouis A, Kahlau S. Photosynthetic complex stoichiometry dynamics in higher plants: biogenesis, function, and turnover of ATP synthase and the cytochrome b6f complex. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2373-400. [PMID: 25540437 DOI: 10.1093/jxb/eru495] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
During plant development and in response to fluctuating environmental conditions, large changes in leaf assimilation capacity and in the metabolic consumption of ATP and NADPH produced by the photosynthetic apparatus can occur. To minimize cytotoxic side reactions, such as the production of reactive oxygen species, photosynthetic electron transport needs to be adjusted to the metabolic demand. The cytochrome b6f complex and chloroplast ATP synthase form the predominant sites of photosynthetic flux control. Accordingly, both respond strongly to changing environmental conditions and metabolic states. Usually, their contents are strictly co-regulated. Thereby, the capacity for proton influx into the lumen, which is controlled by electron flux through the cytochrome b6f complex, is balanced with proton efflux through ATP synthase, which drives ATP synthesis. We discuss the environmental, systemic, and metabolic signals triggering the stoichiometry adjustments of ATP synthase and the cytochrome b6f complex. The contribution of transcriptional and post-transcriptional regulation of subunit synthesis, and the importance of auxiliary proteins required for complex assembly in achieving the stoichiometry adjustments is described. Finally, current knowledge on the stability and turnover of both complexes is summarized.
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Affiliation(s)
- Mark Aurel Schöttler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Szilvia Z Tóth
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alix Boulouis
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Sabine Kahlau
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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15
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Yang W, Catalanotti C, Wittkopp TM, Posewitz MC, Grossman AR. Algae after dark: mechanisms to cope with anoxic/hypoxic conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:481-503. [PMID: 25752440 DOI: 10.1111/tpj.12823] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular, soil-dwelling (and aquatic) green alga that has significant metabolic flexibility for balancing redox equivalents and generating ATP when it experiences hypoxic/anoxic conditions. The diversity of pathways available to ferment sugars is often revealed in mutants in which the activities of specific branches of fermentative metabolism have been eliminated; compensatory pathways that have little activity in parental strains under standard laboratory fermentative conditions are often activated. The ways in which these pathways are regulated and integrated have not been extensively explored. In this review, we primarily discuss the intricacies of dark anoxic metabolism in Chlamydomonas, but also discuss aspects of dark oxic metabolism, the utilization of acetate, and the relatively uncharacterized but critical interactions that link chloroplastic and mitochondrial metabolic networks.
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Affiliation(s)
- Wenqiang Yang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Claudia Catalanotti
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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16
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Dent RM, Sharifi MN, Malnoë A, Haglund C, Calderon RH, Wakao S, Niyogi KK. Large-scale insertional mutagenesis of Chlamydomonas supports phylogenomic functional prediction of photosynthetic genes and analysis of classical acetate-requiring mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:337-51. [PMID: 25711437 DOI: 10.1111/tpj.12806] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/11/2015] [Accepted: 02/18/2015] [Indexed: 05/21/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular green alga that is a key model organism in the study of photosynthesis and oxidative stress. Here we describe the large-scale generation of a population of insertional mutants that have been screened for phenotypes related to photosynthesis and the isolation of 459 flanking sequence tags from 439 mutants. Recent phylogenomic analysis has identified a core set of genes, named GreenCut2, that are conserved in green algae and plants. Many of these genes are likely to be central to the process of photosynthesis, and they are over-represented by sixfold among the screened insertional mutants, with insertion events isolated in or adjacent to 68 of 597 GreenCut2 genes. This enrichment thus provides experimental support for functional assignments based on previous bioinformatic analysis. To illustrate one of the uses of the population, a candidate gene approach based on genome position of the flanking sequence of the insertional mutant CAL027_01_20 was used to identify the molecular basis of the classical C. reinhardtii mutation ac17. These mutations were shown to affect the gene PDH2, which encodes a subunit of the plastid pyruvate dehydrogenase complex. The mutants and associated flanking sequence data described here are publicly available to the research community, and they represent one of the largest phenotyped collections of algal insertional mutants to date.
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Affiliation(s)
- Rachel M Dent
- Department of Plant and Microbial Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720-3102, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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17
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Yang W, Catalanotti C, D'Adamo S, Wittkopp TM, Ingram-Smith CJ, Mackinder L, Miller TE, Heuberger AL, Peers G, Smith KS, Jonikas MC, Grossman AR, Posewitz MC. Alternative acetate production pathways in Chlamydomonas reinhardtii during dark anoxia and the dominant role of chloroplasts in fermentative acetate production. THE PLANT CELL 2014; 26:4499-518. [PMID: 25381350 PMCID: PMC4277214 DOI: 10.1105/tpc.114.129965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 07/15/2014] [Accepted: 10/15/2014] [Indexed: 05/18/2023]
Abstract
Chlamydomonas reinhardtii insertion mutants disrupted for genes encoding acetate kinases (EC 2.7.2.1) (ACK1 and ACK2) and a phosphate acetyltransferase (EC 2.3.1.8) (PAT2, but not PAT1) were isolated to characterize fermentative acetate production. ACK1 and PAT2 were localized to chloroplasts, while ACK2 and PAT1 were shown to be in mitochondria. Characterization of the mutants showed that PAT2 and ACK1 activity in chloroplasts plays a dominant role (relative to ACK2 and PAT1 in mitochondria) in producing acetate under dark, anoxic conditions and, surprisingly, also suggested that Chlamydomonas has other pathways that generate acetate in the absence of ACK activity. We identified a number of proteins associated with alternative pathways for acetate production that are encoded on the Chlamydomonas genome. Furthermore, we observed that only modest alterations in the accumulation of fermentative products occurred in the ack1, ack2, and ack1 ack2 mutants, which contrasts with the substantial metabolite alterations described in strains devoid of other key fermentation enzymes.
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Affiliation(s)
- Wenqiang Yang
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Claudia Catalanotti
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Sarah D'Adamo
- Colorado School of Mines, Department of Chemistry and Geochemistry, Golden, Colorado 80401
| | - Tyler M Wittkopp
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305 Stanford University, Department of Biology, Stanford, California 94305
| | - Cheryl J Ingram-Smith
- Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina 29634
| | - Luke Mackinder
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Tarryn E Miller
- Colorado School of Mines, Department of Chemistry and Geochemistry, Golden, Colorado 80401
| | - Adam L Heuberger
- Colorado State University, Proteomics and Metabolomics Facility, Fort Collins, Colorado 80523
| | - Graham Peers
- Colorado State University, Department of Biology, Fort Collins, Colorado 80523
| | - Kerry S Smith
- Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina 29634
| | - Martin C Jonikas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Arthur R Grossman
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Matthew C Posewitz
- Colorado School of Mines, Department of Chemistry and Geochemistry, Golden, Colorado 80401
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18
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Hojka M, Thiele W, Tóth SZ, Lein W, Bock R, Schöttler MA. Inducible Repression of Nuclear-Encoded Subunits of the Cytochrome b6f Complex in Tobacco Reveals an Extraordinarily Long Lifetime of the Complex. PLANT PHYSIOLOGY 2014; 165:1632-1646. [PMID: 24963068 PMCID: PMC4119044 DOI: 10.1104/pp.114.243741] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/24/2014] [Indexed: 05/18/2023]
Abstract
The biogenesis of the cytochrome b6f complex in tobacco (Nicotiana tabacum) seems to be restricted to young leaves, suggesting a high lifetime of the complex. To directly determine its lifetime, we employed an ethanol-inducible RNA interference (RNAi) approach targeted against the essential nuclear-encoded Rieske protein (PetC) and the small M subunit (PetM), whose function in higher plants is unknown. Young expanding leaves of both PetM and PetC RNAi transformants bleached rapidly and developed necroses, while mature leaves, whose photosynthetic apparatus was fully assembled before RNAi induction, stayed green. In line with these phenotypes, cytochrome b6f complex accumulation and linear electron transport capacity were strongly repressed in young leaves of both RNAi transformants, showing that the M subunit is as essential for cytochrome b6f complex accumulation as the Rieske protein. In mature leaves, all photosynthetic parameters were indistinguishable from the wild type even after 14 d of induction. As RNAi repression of PetM and PetC was highly efficient in both young and mature leaves, these data indicate a lifetime of the cytochrome b6f complex of at least 1 week. The switch-off of cytochrome b6f complex biogenesis in mature leaves may represent part of the first dedicated step of the leaf senescence program.
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Affiliation(s)
- Marta Hojka
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wolfram Thiele
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Szilvia Z Tóth
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Wolfgang Lein
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mark Aurel Schöttler
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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19
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Johnson X, Steinbeck J, Dent RM, Takahashi H, Richaud P, Ozawa SI, Houille-Vernes L, Petroutsos D, Rappaport F, Grossman AR, Niyogi KK, Hippler M, Alric J. Proton gradient regulation 5-mediated cyclic electron flow under ATP- or redox-limited conditions: a study of ΔATpase pgr5 and ΔrbcL pgr5 mutants in the green alga Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2014; 165:438-52. [PMID: 24623849 PMCID: PMC4012601 DOI: 10.1104/pp.113.233593] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 03/07/2014] [Indexed: 05/18/2023]
Abstract
The Chlamydomonas reinhardtii proton gradient regulation5 (Crpgr5) mutant shows phenotypic and functional traits similar to mutants in the Arabidopsis (Arabidopsis thaliana) ortholog, Atpgr5, providing strong evidence for conservation of PGR5-mediated cyclic electron flow (CEF). Comparing the Crpgr5 mutant with the wild type, we discriminate two pathways for CEF and determine their maximum electron flow rates. The PGR5/proton gradient regulation-like1 (PGRL1) ferredoxin (Fd) pathway, involved in recycling excess reductant to increase ATP synthesis, may be controlled by extreme photosystem I acceptor side limitation or ATP depletion. Here, we show that PGR5/PGRL1-Fd CEF functions in accordance with an ATP/redox control model. In the absence of Rubisco and PGR5, a sustained electron flow is maintained with molecular oxygen instead of carbon dioxide serving as the terminal electron acceptor. When photosynthetic control is decreased, compensatory alternative pathways can take the full load of linear electron flow. In the case of the ATP synthase pgr5 double mutant, a decrease in photosensitivity is observed compared with the single ATPase-less mutant that we assign to a decreased proton motive force. Altogether, our results suggest that PGR5/PGRL1-Fd CEF is most required under conditions when Fd becomes overreduced and photosystem I is subjected to photoinhibition. CEF is not a valve; it only recycles electrons, but in doing so, it generates a proton motive force that controls the rate of photosynthesis. The conditions where the PGR5 pathway is most required may vary in photosynthetic organisms like C. reinhardtii from anoxia to high light to limitations imposed at the level of carbon dioxide fixation.
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20
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Heinnickel ML, Grossman AR. The GreenCut: re-evaluation of physiological role of previously studied proteins and potential novel protein functions. PHOTOSYNTHESIS RESEARCH 2013; 116:427-36. [PMID: 23873414 DOI: 10.1007/s11120-013-9882-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/01/2013] [Indexed: 05/06/2023]
Abstract
Based on comparative genomics, a list of proteins present in the green algal, flowering and nonflowering plant lineages, but not detected in nonphotosynthetic organisms, was assembled (Merchant et al., Science 318:245-250, 2007; Karpowicz et al., J Biol Chem 286:21427-21439, 2011). This protein grouping, previously designated the GreenCut, was established using stringent comparative genomic criteria; they are those Chlamydomonas reinhardtii proteins with orthologs in Arabidopsis thaliana, Physcomitrella patens, Oryza sativa, Populus tricocarpa and at least one of the three Ostreococcus species with fully sequenced genomes, but not in bacteria, yeast, fungi or mammals. Many GreenCut proteins are also present in red algae and diatoms and a subset of 189 have been identified as encoded on nearly all cyanobacterial genomes. Of the current GreenCut proteins (597 in total), approximately half have been studied previously. The functions or activities of a number of these proteins have been deduced from phenotypic analyses of mutants (defective for genes encoding specific GreenCut proteins) of A. thaliana, and in many cases the assigned functions do not exist in C. reinhardtii. Therefore, precise physiological functions of several previously studied GreenCut proteins are still not clear. The GreenCut also contains a number of proteins with certain conserved domains. Three of the most highly conserved domains are the FK506 binding, cyclophilin and PAP fibrillin domains; most members of these gene families are not well characterized. In general, our analysis of the GreenCut indicates that many processes critical to green lineage organisms remain unstudied or poorly characterized. We have begun to examine the functions of some GreenCut proteins in detail. For example, our work on the CPLD38 protein has demonstrated that it has an essential role in photosynthetic function and the stability of the cytochrome b 6 f complex.
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Affiliation(s)
- Mark L Heinnickel
- Department of Plant Biology, Carnegie Institute for Science, 260 Panama St, Stanford, CA, USA,
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