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Pancheri T, Baur T, Roach T. Singlet-Oxygen-Mediated Regulation of Photosynthesis-Specific Genes: A Role for Reactive Electrophiles in Signal Transduction. Int J Mol Sci 2024; 25:8458. [PMID: 39126029 DOI: 10.3390/ijms25158458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
During photosynthesis, reactive oxygen species (ROS) are formed, including hydrogen peroxide (H2O2) and singlet oxygen (1O2), which have putative roles in signalling, but their involvement in photosynthetic acclimation is unclear. Due to extreme reactivity and a short lifetime, 1O2 signalling occurs via its reaction products, such as oxidised poly-unsaturated fatty acids in thylakoid membranes. The resulting lipid peroxides decay to various aldehydes and reactive electrophile species (RES). Here, we investigated the role of ROS in the signal transduction of high light (HL), focusing on GreenCut2 genes unique to photosynthetic organisms. Using RNA seq. data, the transcriptional responses of Chlamydomonas reinhardtii to 2 h HL were compared with responses under low light to exogenous RES (acrolein; 4-hydroxynonenal), β-cyclocitral, a β-carotene oxidation product, as well as Rose Bengal, a 1O2-producing photosensitiser, and H2O2. HL induced significant (p < 0.05) up- and down-regulation of 108 and 23 GreenCut2 genes, respectively. Of all HL up-regulated genes, over half were also up-regulated by RES, including RBCS1 (ribulose bisphosphate carboxylase small subunit), NPQ-related PSBS1 and LHCSR1. Furthermore, 96% of the genes down-regulated by HL were also down-regulated by 1O2 or RES, including CAO1 (chlorophyllide-a oxygnease), MDH2 (NADP-malate dehydrogenase) and PGM4 (phosphoglycerate mutase) for glycolysis. In comparison, only 0-4% of HL-affected GreenCut2 genes were similarly affected by H2O2 or β-cyclocitral. Overall, 1O2 plays a significant role in signalling during the initial acclimation of C. reinhardtii to HL by up-regulating photo-protection and carbon assimilation and down-regulating specific primary metabolic pathways. Our data support that this pathway involves RES.
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Affiliation(s)
- Tina Pancheri
- Department of Botany, Faculty of Biology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Theresa Baur
- Department of Botany, Faculty of Biology, University of Innsbruck, 6020 Innsbruck, Austria
| | - Thomas Roach
- Department of Botany, Faculty of Biology, University of Innsbruck, 6020 Innsbruck, Austria
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2
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Jeffers TL, Purvine SO, Nicora CD, McCombs R, Upadhyaya S, Stroumza A, Whang K, Gallaher SD, Dohnalkova A, Merchant SS, Lipton M, Niyogi KK, Roth MS. Iron rescues glucose-mediated photosynthesis repression during lipid accumulation in the green alga Chromochloris zofingiensis. Nat Commun 2024; 15:6046. [PMID: 39025848 PMCID: PMC11258321 DOI: 10.1038/s41467-024-50170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 07/02/2024] [Indexed: 07/20/2024] Open
Abstract
Energy status and nutrients regulate photosynthetic protein expression. The unicellular green alga Chromochloris zofingiensis switches off photosynthesis in the presence of exogenous glucose (+Glc) in a process that depends on hexokinase (HXK1). Here, we show that this response requires that cells lack sufficient iron (-Fe). Cells grown in -Fe+Glc accumulate triacylglycerol (TAG) while losing photosynthesis and thylakoid membranes. However, cells with an iron supplement (+Fe+Glc) maintain photosynthesis and thylakoids while still accumulating TAG. Proteomic analysis shows that known photosynthetic proteins are most depleted in heterotrophy, alongside hundreds of uncharacterized, conserved proteins. Photosynthesis repression is associated with enzyme and transporter regulation that redirects iron resources to (a) respiratory instead of photosynthetic complexes and (b) a ferredoxin-dependent desaturase pathway supporting TAG accumulation rather than thylakoid lipid synthesis. Combining insights from diverse organisms from green algae to vascular plants, we show how iron and trophic constraints on metabolism aid gene discovery for photosynthesis and biofuel production.
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Affiliation(s)
- Tim L Jeffers
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ryan McCombs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Shivani Upadhyaya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Adrien Stroumza
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ken Whang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Sean D Gallaher
- UCLA DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
- Quantitative Biosciences Institute, University of California, Berkeley, CA, 94720, USA
| | - Alice Dohnalkova
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Quantitative Biosciences Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mary Lipton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
- 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.
| | - Melissa S Roth
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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3
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Kim RG, Huang W, Findinier J, Bunbury F, Redekop P, Shrestha R, Grismer TS, Vilarrasa-Blasi J, Jinkerson RE, Fakhimi N, Fauser F, Jonikas MC, Onishi M, Xu SL, Grossman AR. Chloroplast Methyltransferase Homolog RMT2 is Involved in Photosystem I Biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572672. [PMID: 38187728 PMCID: PMC10769443 DOI: 10.1101/2023.12.21.572672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Oxygen (O2), a dominant element in the atmosphere and essential for most life on Earth, is produced by the photosynthetic oxidation of water. However, metabolic activity can cause accumulation of reactive O2 species (ROS) and severe cell damage. To identify and characterize mechanisms enabling cells to cope with ROS, we performed a high-throughput O2 sensitivity screen on a genome-wide insertional mutant library of the unicellular alga Chlamydomonas reinhardtii. This screen led to identification of a gene encoding a protein designated Rubisco methyltransferase 2 (RMT2). Although homologous to methyltransferases, RMT2 has not been experimentally demonstrated to have methyltransferase activity. Furthermore, the rmt2 mutant was not compromised for Rubisco (first enzyme of Calvin-Benson Cycle) levels but did exhibit a marked decrease in accumulation/activity of photosystem I (PSI), which causes light sensitivity, with much less of an impact on other photosynthetic complexes. This mutant also shows increased accumulation of Ycf3 and Ycf4, proteins critical for PSI assembly. Rescue of the mutant phenotype with a wild-type (WT) copy of RMT2 fused to the mNeonGreen fluorophore indicates that the protein localizes to the chloroplast and appears to be enriched in/around the pyrenoid, an intrachloroplast compartment present in many algae that is packed with Rubisco and potentially hypoxic. These results indicate that RMT2 serves an important role in PSI biogenesis which, although still speculative, may be enriched around or within the pyrenoid.
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Affiliation(s)
- Rick G. Kim
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Weichao Huang
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Justin Findinier
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Freddy Bunbury
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Petra Redekop
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Ruben Shrestha
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - TaraBryn S Grismer
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | | | - Robert E. Jinkerson
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Neda Fakhimi
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Friedrich Fauser
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Martin C. Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Shou-Ling Xu
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Arthur R. Grossman
- Department of Biosphere Science and Engineering, Carnegie Institution for Science, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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4
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Zhang N, Venn B, Bailey CE, Xia M, Mattoon EM, Mühlhaus T, Zhang R. Moderate high temperature is beneficial or detrimental depending on carbon availability in the green alga Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:979-1003. [PMID: 37877811 DOI: 10.1093/jxb/erad405] [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: 05/21/2023] [Accepted: 10/21/2023] [Indexed: 10/26/2023]
Abstract
High temperatures impair plant growth and reduce agricultural yields, but the underlying mechanisms remain elusive. The unicellular green alga Chlamydomonas reinhardtii is an excellent model to study heat responses in photosynthetic cells due to its fast growth rate, many similarities in cellular processes to land plants, simple and sequenced genome, and ample genetic and genomics resources. Chlamydomonas grows in light by photosynthesis and with externally supplied acetate as an organic carbon source. Understanding how organic carbon sources affect heat responses is important for the algal industry but remains understudied. We cultivated wild-type Chlamydomonas under highly controlled conditions in photobioreactors at 25 °C (control), 35 °C (moderate high temperature), or 40 °C (acute high temperature) with or without constant acetate supply for 1 or 4 day. Treatment at 35 °C increased algal growth with constant acetate supply but reduced algal growth without sufficient acetate. The overlooked and dynamic effects of 35 °C could be explained by induced acetate uptake and metabolism. Heat treatment at 40 °C for more than 2 day was lethal to algal cultures with or without constant acetate supply. Our findings provide insights to understand algal heat responses and help improve thermotolerance in photosynthetic cells.
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Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Benedikt Venn
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | | | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Erin M Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Timo Mühlhaus
- Computational Systems Biology, RPTU Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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5
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Kafri M, Patena W, Martin L, Wang L, Gomer G, Ergun SL, Sirkejyan AK, Goh A, Wilson AT, Gavrilenko SE, Breker M, Roichman A, McWhite CD, Rabinowitz JD, Cross FR, Wühr M, Jonikas MC. Systematic identification and characterization of genes in the regulation and biogenesis of photosynthetic machinery. Cell 2023; 186:5638-5655.e25. [PMID: 38065083 PMCID: PMC10760936 DOI: 10.1016/j.cell.2023.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 08/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Photosynthesis is central to food production and the Earth's biogeochemistry, yet the molecular basis for its regulation remains poorly understood. Here, using high-throughput genetics in the model eukaryotic alga Chlamydomonas reinhardtii, we identify with high confidence (false discovery rate [FDR] < 0.11) 70 poorly characterized genes required for photosynthesis. We then enable the functional characterization of these genes by providing a resource of proteomes of mutant strains, each lacking one of these genes. The data allow assignment of 34 genes to the biogenesis or regulation of one or more specific photosynthetic complexes. Further analysis uncovers biogenesis/regulatory roles for at least seven proteins, including five photosystem I mRNA maturation factors, the chloroplast translation factor MTF1, and the master regulator PMR1, which regulates chloroplast genes via nuclear-expressed factors. Our work provides a rich resource identifying regulatory and functional genes and placing them into pathways, thereby opening the door to a system-level understanding of photosynthesis.
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Affiliation(s)
- Moshe Kafri
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Lance Martin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gillian Gomer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sabrina L Ergun
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - Arthur K Sirkejyan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia E Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michal Breker
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Asael Roichman
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Claire D McWhite
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Frederick R Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10021, USA
| | - Martin Wühr
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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6
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Knoshaug EP, Sun P, Nag A, Nguyen H, Mattoon EM, Zhang N, Liu J, Chen C, Cheng J, Zhang R, St. John P, Umen J. Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis. PLANT DIRECT 2023; 7:e527. [PMID: 38044962 PMCID: PMC10690477 DOI: 10.1002/pld3.527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 12/05/2023]
Abstract
The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome-wide protein-coding gene annotation. A substantial fraction of protein-coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): Arabidopsis thaliana (eudicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high-value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.
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Affiliation(s)
- Eric P. Knoshaug
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Peipei Sun
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Ambarish Nag
- Computational Sciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - Huong Nguyen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil ScienceTexas Tech UniversityLubbockTexasUSA
| | - Erin M. Mattoon
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical SciencesWashington University in Saint LouisSt. LouisMissouriUSA
| | | | - Jian Liu
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Chen Chen
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouriUSA
| | - Ru Zhang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Peter St. John
- Biosciences CenterNational Renewable Energy LaboratoryGoldenColoradoUSA
| | - James Umen
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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7
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Palande S, Kaste JAM, Roberts MD, Segura Abá K, Claucherty C, Dacon J, Doko R, Jayakody TB, Jeffery HR, Kelly N, Manousidaki A, Parks HM, Roggenkamp EM, Schumacher AM, Yang J, Percival S, Pardo J, Husbands AY, Krishnan A, Montgomery BL, Munch E, Thompson AM, Rougon-Cardoso A, Chitwood DH, VanBuren R. Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants. PLoS Biol 2023; 21:e3002397. [PMID: 38051702 PMCID: PMC10723737 DOI: 10.1371/journal.pbio.3002397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 12/15/2023] [Accepted: 10/20/2023] [Indexed: 12/07/2023] Open
Abstract
Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests that there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.
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Affiliation(s)
- Sourabh Palande
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Joshua A. M. Kaste
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Miles D. Roberts
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Kenia Segura Abá
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Carly Claucherty
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Jamell Dacon
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Rei Doko
- Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Thilani B. Jayakody
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Hannah R. Jeffery
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Nathan Kelly
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Andriana Manousidaki
- Department of Statistics and Probability, Michigan State University, East Lansing, Michigan, United States of America
| | - Hannah M. Parks
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Emily M. Roggenkamp
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Ally M. Schumacher
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jiaxin Yang
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Sarah Percival
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeremy Pardo
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Aman Y. Husbands
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Arjun Krishnan
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Beronda L Montgomery
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Elizabeth Munch
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Mathematics, Michigan State University, East Lansing, Michigan, United States of America
| | - Addie M. Thompson
- Department of Plant, Soil & Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America
| | - Alejandra Rougon-Cardoso
- Laboratory of Agrigenomic Sciences, Universidad Nacional Autónoma de México, ENES-León, León, Mexico
- Laboratorio Nacional Plantecc, ENES-León, León, Mexico
| | - Daniel H. Chitwood
- Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan, United States of America
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan, United States of America
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8
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Fernie AR, Skirycz A. Plant metabolism: A protein map of the photosynthetic organelle. Curr Biol 2023; 33:R1147-R1150. [PMID: 37935127 DOI: 10.1016/j.cub.2023.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
While chloroplasts are commonly recognized as a hub in photosynthetic metabolism, our understanding of the protein functionality and spatial organization remains fragmentary. A recent study provides insights into a number of poorly characterized proteins, including unexpected spatial distributions of enzymes.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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9
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Keller JM, Frieboes MJ, Jödecke L, Kappel S, Wulff N, Rindfleisch T, Sandoval-Ibanez O, Gerlach I, Thiele W, Bock R, Eirich J, Finkemeier I, Schünemann D, Zoschke R, Schöttler MA, Armbruster U. Eukaryote-specific assembly factor DEAP2 mediates an early step of photosystem II assembly in Arabidopsis. PLANT PHYSIOLOGY 2023; 193:1970-1986. [PMID: 37555435 PMCID: PMC10602607 DOI: 10.1093/plphys/kiad446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023]
Abstract
The initial step of oxygenic photosynthesis is the thermodynamically challenging extraction of electrons from water and the release of molecular oxygen. This light-driven process, which is the basis for most life on Earth, is catalyzed by photosystem II (PSII) within the thylakoid membrane of photosynthetic organisms. The biogenesis of PSII requires a controlled step-wise assembly process of which the early steps are considered to be highly conserved between plants and their cyanobacterial progenitors. This assembly process involves auxiliary proteins, which are likewise conserved. In the present work, we used Arabidopsis (Arabidopsis thaliana) as a model to show that in plants, a eukaryote-exclusive assembly factor facilitates the early assembly step, during which the intrinsic antenna protein CP47 becomes associated with the PSII reaction center (RC) to form the RC47 intermediate. This factor, which we named DECREASED ELECTRON TRANSPORT AT PSII (DEAP2), works in concert with the conserved PHOTOSYNTHESIS AFFECTED MUTANT 68 (PAM68) assembly factor. The deap2 and pam68 mutants showed similar defects in PSII accumulation and assembly of the RC47 intermediate. The combined lack of both proteins resulted in a loss of functional PSII and the inability of plants to grow photoautotrophically on the soil. While overexpression of DEAP2 partially rescued the pam68 PSII accumulation phenotype, this effect was not reciprocal. DEAP2 accumulated at 20-fold higher levels than PAM68, together suggesting that both proteins have distinct functions. In summary, our results uncover eukaryotic adjustments to the PSII assembly process, which involve the addition of DEAP2 for the rapid progression from RC to RC47.
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Affiliation(s)
- Jakob-Maximilian Keller
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Maureen Julia Frieboes
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ludwig Jödecke
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Sandrine Kappel
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Natalia Wulff
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Tobias Rindfleisch
- Computational Biology Unit, Department of Chemistry, University of Bergen, 5008 Bergen, Norway
| | - Omar Sandoval-Ibanez
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ines Gerlach
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Jürgen Eirich
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Iris Finkemeier
- Plant Physiology, Institute of Plant Biology and Biotechnology, University of Münster, 48143 Münster, Germany
| | - Danja Schünemann
- Molecular Biology of Plant Organelles, Ruhr University Bochum, 44780 Bochum, Germany
| | - Reimo Zoschke
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Mark Aurel Schöttler
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
| | - Ute Armbruster
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, 14476 Potsdam, Germany
- Institute of Molecular Photosynthesis, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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10
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Wang L, Patena W, Van Baalen KA, Xie Y, Singer ER, Gavrilenko S, Warren-Williams M, Han L, Harrigan HR, Hartz LD, Chen V, Ton VTNP, Kyin S, Shwe HH, Cahn MH, Wilson AT, Onishi M, Hu J, Schnell DJ, McWhite CD, Jonikas MC. A chloroplast protein atlas reveals punctate structures and spatial organization of biosynthetic pathways. Cell 2023; 186:3499-3518.e14. [PMID: 37437571 DOI: 10.1016/j.cell.2023.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/14/2023]
Abstract
Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,034 candidate chloroplast proteins using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of poorly characterized proteins; identify novel components of nucleoids, plastoglobules, and the pyrenoid; and reveal widespread protein targeting to multiple compartments. We discovered and further characterized cellular organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and unexpected spatial distributions of enzymes within the chloroplast. We also used machine learning to predict the localizations of other nuclear-encoded Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to accelerate studies of chloroplast architecture and functions.
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Affiliation(s)
- Lianyong Wang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Kelly A Van Baalen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yihua Xie
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Emily R Singer
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sophia Gavrilenko
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Linqu Han
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Henry R Harrigan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Linnea D Hartz
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vivian Chen
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Vinh T N P Ton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Saw Kyin
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Henry H Shwe
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Matthew H Cahn
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jianping Hu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA
| | - Danny J Schnell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Claire D McWhite
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.
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11
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Lv Y, Han F, Liu M, Zhang T, Cui G, Wang J, Yang Y, Yang YG, Yang W. Characteristics of N 6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:756-768. [PMID: 35550876 PMCID: PMC10787120 DOI: 10.1016/j.gpb.2022.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/12/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as photosynthesis, sexual reproduction, and life cycle. N6-methyladenosine (m6A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m6A modification during the sexual reproduction of Chlamydomonas remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle. The results show that m6A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in Chlamydomonas mRNAs. Moreover, m6A peaks in Chlamydomonas mRNAs are mainly enriched in the 3' untranslated regions (3'UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m6A levels of genes involved in the microtubule-associated pathway, indicating that m6A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m6A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m6A modification in the process of sexual reproduction in other plant organisms.
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Affiliation(s)
- Ying Lv
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Han
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengxia Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Guanshen Cui
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Jiaojiao Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenqiang Yang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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12
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Findinier J, Grossman AR. Chlamydomonas: Fast tracking from genomics. JOURNAL OF PHYCOLOGY 2023; 59:644-652. [PMID: 37417760 DOI: 10.1111/jpy.13356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Elucidating biological processes has relied on the establishment of model organisms, many of which offer advantageous features such as rapid axenic growth, extensive knowledge of their physiological features and gene content, and the ease with which they can be genetically manipulated. The unicellular green alga Chlamydomonas reinhardtii has been an exemplary model that has enabled many scientific breakthroughs over the decades, especially in the fields of photosynthesis, cilia function and biogenesis, and the acclimation of photosynthetic organisms to their environment. Here, we discuss recent molecular/technological advances that have been applied to C. reinhardtii and how they have further fostered its development as a "flagship" algal system. We also explore the future promise of this alga in leveraging advances in the fields of genomics, proteomics, imaging, and synthetic biology for addressing critical future biological issues.
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Affiliation(s)
- Justin Findinier
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
| | - Arthur R Grossman
- The Carnegie Institution for Science, Biosphere Science and Engineering, Stanford, California, USA
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13
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Leister D, Sharma A, Kerber N, Nägele T, Reiter B, Pasch V, Beeh S, Jahns P, Barbato R, Pribil M, Rühle T. An ancient metabolite damage-repair system sustains photosynthesis in plants. Nat Commun 2023; 14:3023. [PMID: 37230969 DOI: 10.1038/s41467-023-38804-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023] Open
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major catalyst in the conversion of carbon dioxide into organic compounds in photosynthetic organisms. However, its activity is impaired by binding of inhibitory sugars such as xylulose-1,5-bisphosphate (XuBP), which must be detached from the active sites by Rubisco activase. Here, we show that loss of two phosphatases in Arabidopsis thaliana has detrimental effects on plant growth and photosynthesis and that this effect could be reversed by introducing the XuBP phosphatase from Rhodobacter sphaeroides. Biochemical analyses revealed that the plant enzymes specifically dephosphorylate XuBP, thus allowing xylulose-5-phosphate to enter the Calvin-Benson-Bassham cycle. Our findings demonstrate the physiological importance of an ancient metabolite damage-repair system in degradation of by-products of Rubisco, and will impact efforts to optimize carbon fixation in photosynthetic organisms.
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Affiliation(s)
- Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152, Planegg-Martinsried, Germany
| | - Anurag Sharma
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY, USA
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Natalia Kerber
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152, Planegg-Martinsried, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152, Planegg-Martinsried, Germany
| | - Bennet Reiter
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152, Planegg-Martinsried, Germany
| | - Viviana Pasch
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152, Planegg-Martinsried, Germany
| | - Simon Beeh
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152, Planegg-Martinsried, Germany
- Department of Plant Physiology, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Peter Jahns
- Plant Biochemistry, Heinrich-Heine-University Düsseldorf, D-40225, Düsseldorf, Germany
| | - Roberto Barbato
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 15121, Alessandria, Italy
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Thilo Rühle
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152, Planegg-Martinsried, Germany.
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14
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Mattoon EM, McHargue W, Bailey CE, Zhang N, Chen C, Eckhardt J, Daum CG, Zane M, Pennacchio C, Schmutz J, O'Malley RC, Cheng J, Zhang R. High-throughput identification of novel heat tolerance genes via genome-wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii. PLANT, CELL & ENVIRONMENT 2023; 46:865-888. [PMID: 36479703 PMCID: PMC9898210 DOI: 10.1111/pce.14507] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35°C) or acute (40°C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we presented a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops.
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Affiliation(s)
- Erin M. Mattoon
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri 63130, USA
| | - William McHargue
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - James Eckhardt
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Chris G. Daum
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matt Zane
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christa Pennacchio
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan C. O'Malley
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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15
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Orr DJ, Robijns AKJ, Baker CR, Niyogi KK, Carmo-Silva E. Dynamics of Rubisco regulation by sugar phosphate derivatives and their phosphatases. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:581-590. [PMID: 36173669 PMCID: PMC9833046 DOI: 10.1093/jxb/erac386] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/28/2022] [Indexed: 05/31/2023]
Abstract
Regulating the central CO2-fixing enzyme Rubisco is as complex as its ancient reaction mechanism and involves interaction with a series of cofactors and auxiliary proteins that activate catalytic sites and maintain activity. A key component among the regulatory mechanisms is the binding of sugar phosphate derivatives that inhibit activity. Removal of inhibitors via the action of Rubisco activase is required to restore catalytic competency. In addition, specific phosphatases dephosphorylate newly released inhibitors, rendering them incapable of binding to Rubisco catalytic sites. The best studied inhibitor is 2-carboxy-d-arabinitol 1-phosphate (CA1P), a naturally occurring nocturnal inhibitor that accumulates in most species during darkness and low light, progressively binding to Rubisco. As light increases, Rubisco activase removes CA1P from Rubisco, and the specific phosphatase CA1Pase dephosphorylates CA1P to CA, which cannot bind Rubisco. Misfire products of Rubisco's complex reaction chemistry can also act as inhibitors. One example is xylulose-1,5-bisphosphate (XuBP), which is dephosphorylated by XuBPase. Here we revisit key findings related to sugar phosphate derivatives and their specific phosphatases, highlighting outstanding questions and how further consideration of these inhibitors and their role is important for better understanding the regulation of carbon assimilation.
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Affiliation(s)
| | - Alice K J Robijns
- Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Christopher R Baker
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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16
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Reiter B, Rosenhammer L, Marino G, Geimer S, Leister D, Rühle T. CGL160-mediated recruitment of the coupling factor CF1 is required for efficient thylakoid ATP synthase assembly, photosynthesis, and chloroplast development in Arabidopsis. THE PLANT CELL 2023; 35:488-509. [PMID: 36250886 PMCID: PMC9806626 DOI: 10.1093/plcell/koac306] [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: 03/30/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Chloroplast ATP synthases consist of a membrane-spanning coupling factor (CFO) and a soluble coupling factor (CF1). It was previously demonstrated that CONSERVED ONLY IN THE GREEN LINEAGE160 (CGL160) promotes the formation of plant CFO and performs a similar function in the assembly of its c-ring to that of the distantly related bacterial Atp1/UncI protein. Here, we show that in Arabidopsis (Arabidopsis thaliana) the N-terminal portion of CGL160 (AtCGL160N) is required for late steps in CF1-CFO assembly. In plants that lacked AtCGL160N, CF1-CFO content, photosynthesis, and chloroplast development were impaired. Loss of AtCGL160N did not perturb c-ring formation, but led to a 10-fold increase in the numbers of stromal CF1 subcomplexes relative to that in the wild type. Co-immunoprecipitation and protein crosslinking assays revealed an association of AtCGL160 with CF1 subunits. Yeast two-hybrid assays localized the interaction to a stretch of AtCGL160N that binds to the DELSEED-containing CF1-β subdomain. Since Atp1 of Synechocystis (Synechocystis sp. PCC 6803) could functionally replace the membrane domain of AtCGL160 in Arabidopsis, we propose that CGL160 evolved from a cyanobacterial ancestor and acquired an additional function in the recruitment of a soluble CF1 subcomplex, which is critical for the modulation of CF1-CFO activity and photosynthesis.
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Affiliation(s)
- Bennet Reiter
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität Munich, D-82152 Planegg-Martinsried, Germany
| | - Lea Rosenhammer
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität Munich, D-82152 Planegg-Martinsried, Germany
| | - Giada Marino
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität Munich, D-82152 Planegg-Martinsried, Germany
| | - Stefan Geimer
- Zellbiologie/Elektronenmikroskopie NW I/B1, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Dario Leister
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität Munich, D-82152 Planegg-Martinsried, Germany
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17
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Abstract
Economical production of photosynthetic organisms requires the use of natural day/night cycles. These induce strong circadian rhythms that lead to transient changes in the cells, requiring complex modeling to capture. In this study, we coupled times series transcriptomic data from the model green alga Chlamydomonas reinhardtii to a metabolic model of the same organism in order to develop the first transient metabolic model for diurnal growth of algae capable of predicting phenotype from genotype. We first transformed a set of discrete transcriptomic measurements (D. Strenkert, S. Schmollinger, S. D. Gallaher, P. A. Salomé, et al., Proc Natl Acad Sci U S A 116:2374–2383, 2019, https://doi.org/10.1073/pnas.1815238116) into continuous curves, producing a complete database of the cell’s transcriptome that can be interrogated at any time point. We also decoupled the standard biomass formation equation to allow different components of biomass to be synthesized at different times of the day. The resulting model was able to predict qualitative phenotypical outcomes of a starchless mutant. We also extended this approach to simulate all single-knockout mutants and identified potential targets for rational engineering efforts to increase productivity. This model enables us to evaluate the impact of genetic and environmental changes on the growth, biomass composition, and intracellular fluxes for diurnal growth. IMPORTANCE We have developed the first transient metabolic model for diurnal growth of algae based on experimental data and capable of predicting phenotype from genotype. This model enables us to evaluate the impact of genetic and environmental changes on the growth, biomass composition and intracellular fluxes of the model green alga, Chlamydomonas reinhardtii. The availability of this model will enable faster and more efficient design of cells for production of fuels, chemicals, and pharmaceuticals.
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18
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Zhang N, Pazouki L, Nguyen H, Jacobshagen S, Bigge BM, Xia M, Mattoon EM, Klebanovych A, Sorkin M, Nusinow DA, Avasthi P, Czymmek KJ, Zhang R. Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background). PLANTS (BASEL, SWITZERLAND) 2022; 11:585. [PMID: 35270055 PMCID: PMC8912731 DOI: 10.3390/plants11050585] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 05/02/2023]
Abstract
The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more heat-sensitive than CC-1690. Furthermore, CC-5325 had an intact cell wall which had comparable integrity to that in CC-1690 but appeared to have reduced thickness. Additionally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC1690 did. Finally, in comparison to CC-1690, CC-5325 had longer cilia in the medium with acetate but slower swimming speed in the medium without nitrogen and acetate. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms.
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Affiliation(s)
- Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Leila Pazouki
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Huong Nguyen
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Sigrid Jacobshagen
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA;
| | - Brae M. Bigge
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Ming Xia
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Erin M. Mattoon
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Anastasiya Klebanovych
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Maria Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Dmitri A. Nusinow
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Prachee Avasthi
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (B.M.B.); (P.A.)
| | - Kirk J. Czymmek
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; (N.Z.); (L.P.); (H.N.); (M.X.); (E.M.M.); (A.K.); (M.S.); (D.A.N.); (K.J.C.)
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19
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Wakao S, Niyogi KK. Chlamydomonas as a model for reactive oxygen species signaling and thiol redox regulation in the green lineage. PLANT PHYSIOLOGY 2021; 187:687-698. [PMID: 35237823 PMCID: PMC8491031 DOI: 10.1093/plphys/kiab355] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/13/2021] [Indexed: 05/15/2023]
Abstract
One-sentence summary: Advances in proteomic and transcriptomic studies have made Chlamydomonas a powerful research model in redox and reactive oxygen species regulation with unique and overlapping mechanisms with plants.
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Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Author for communication: Senior author
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
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20
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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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21
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Stuart D, Sandström M, Youssef HM, Zakhrabekova S, Jensen PE, Bollivar D, Hansson M. Barley Viridis-k links an evolutionarily conserved C-type ferredoxin to chlorophyll biosynthesis. THE PLANT CELL 2021; 33:2834-2849. [PMID: 34051099 PMCID: PMC8408499 DOI: 10.1093/plcell/koab150] [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: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
Ferredoxins are single-electron carrier proteins involved in various cellular reactions. In chloroplasts, the most abundant ferredoxin accepts electrons from photosystem I and shuttles electrons via ferredoxin NADP+ oxidoreductase to generate NADPH or directly to ferredoxin dependent enzymes. In addition, plants contain other isoforms of ferredoxins. Two of these, named FdC1 and FdC2 in Arabidopsis thaliana, have C-terminal extensions and functions that are poorly understood. Here we identified disruption of the orthologous FdC2 gene in barley (Hordeum vulgare L.) mutants at the Viridis-k locus; these mutants are deficient in the aerobic cyclase reaction of chlorophyll biosynthesis. The magnesium-protoporphyrin IX monomethyl ester cyclase is one of the least characterized enzymes of the chlorophyll biosynthetic pathway and its electron donor has long been sought. Agroinfiltrations showed that the viridis-k phenotype could be complemented in vivo by Viridis-k but not by canonical ferredoxin. VirK could drive the cyclase reaction in vitro and analysis of cyclase mutants showed that in vivo accumulation of VirK is dependent on cyclase enzyme levels. The chlorophyll deficient phenotype of viridis-k mutants suggests that VirK plays an essential role in chlorophyll biosynthesis that cannot be replaced by other ferredoxins, thus assigning a specific function to this isoform of C-type ferredoxins.
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Affiliation(s)
- David Stuart
- Department of Biology, Lund University, Lund 22362, Sweden
| | | | - Helmy M. Youssef
- Department of Biology, Lund University, Lund 22362, Sweden
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | | | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Frederiksberg DK-1958, Denmark
| | - David Bollivar
- Department of Biology, Illinois Wesleyan University, Bloomington, IL 61702-2900, USA
| | - Mats Hansson
- Department of Biology, Lund University, Lund 22362, Sweden
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22
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Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
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23
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Bakuła Z, Siedlecki P, Gromadka R, Gawor J, Gromadka A, Pomorski JJ, Panagiotopoulou H, Jagielski T. A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis. BMC Genomics 2021; 22:168. [PMID: 33750287 PMCID: PMC7941945 DOI: 10.1186/s12864-021-07491-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca algae are emerging pathogens, whose incidence has increased importantly over the past two decades. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. Although the algae are receiving more attention nowadays, there is still a substantial knowledge gap regarding their biology, and pathogenicity in particular. Here we report, for the first time, the complete nuclear genome, organelle genomes, and transcriptome of the P. wickerhamii type strain ATCC 16529. RESULTS The assembled genome size was of 16.7 Mbp, making it the smallest and most compact genome sequenced so far among the protothecans. Key features of the genome included a high overall GC content (64.5%), a high number (6081) and proportion (45.9%) of protein-coding genes, and a low repetitive sequence content (2.2%). The vast majority (90.6%) of the predicted genes were confirmed with the corresponding transcripts upon RNA-sequencing analysis. Most (93.2%) of the genes had their putative function assigned when searched against the InterProScan database. A fourth (23.3%) of the genes were annotated with an enzymatic activity possibly associated with the adaptation to the human host environment. The P. wickerhamii genome encoded a wide array of possible virulence factors, including those already identified in two model opportunistic fungal pathogens, i.e. Candida albicans and Trichophyton rubrum, and thought to be involved in invasion of the host or elicitation of the adaptive stress response. Approximately 6% of the P. wickerhamii genes matched a Pathogen-Host Interaction Database entry and had a previously experimentally proven role in the disease development. Furthermore, genes coding for proteins (e.g. ATPase, malate dehydrogenase) hitherto considered as potential virulence factors of Prototheca spp. were demonstrated in the P. wickerhamii genome. CONCLUSIONS Overall, this study is the first to describe the genetic make-up of P. wickerhamii and discovers proteins possibly involved in the development of protothecosis.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland
| | - Paweł Siedlecki
- Department of Systems Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland.,Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Robert Gromadka
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Agnieszka Gromadka
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jan J Pomorski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Hanna Panagiotopoulou
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096, Warsaw, Poland.
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24
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Fuentes-Ramírez EO, Vázquez-Acevedo M, Cabrera-Orefice A, Guerrero-Castillo S, González-Halphen D. The plastid proteome of the nonphotosynthetic chlorophycean alga Polytomella parva. Microbiol Res 2020; 243:126649. [PMID: 33285428 DOI: 10.1016/j.micres.2020.126649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 11/19/2022]
Abstract
The unicellular, free-living, nonphotosynthetic chlorophycean alga Polytomella parva, closely related to Chlamydomonas reinhardtii and Volvox carteri, contains colorless, starch-storing plastids. The P. parva plastids lack all light-dependent processes but maintain crucial metabolic pathways. The colorless alga also lacks a plastid genome, meaning no transcription or translation should occur inside the organelle. Here, using an algal fraction enriched in plastids as well as publicly available transcriptome data, we provide a morphological and proteomic characterization of the P. parva plastid, ultimately identifying several plastid proteins, both by mass spectrometry and bioinformatic analyses. Data are available via ProteomeXchange with identifier PXD022051. Altogether these results led us to propose a plastid proteome for P. parva, i.e., a set of proteins that participate in carbohydrate metabolism; in the synthesis and degradation of starch, amino acids and lipids; in the biosynthesis of terpenoids and tetrapyrroles; in solute transport and protein translocation; and in redox homeostasis. This is the first detailed plastid proteome from a unicellular, free-living colorless alga.
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Affiliation(s)
- Emma O Fuentes-Ramírez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX, Mexico.
| | - Miriam Vázquez-Acevedo
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX, Mexico.
| | - Alfredo Cabrera-Orefice
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| | - Sergio Guerrero-Castillo
- Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, the Netherlands; University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
| | - Diego González-Halphen
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX, Mexico.
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25
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Labella JI, Llop A, Contreras A. The default cyanobacterial linked genome: an interactive platform based on cyanobacterial linkage networks to assist functional genomics. FEBS Lett 2020; 594:1661-1674. [PMID: 32233038 DOI: 10.1002/1873-3468.13775] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/14/2020] [Accepted: 03/12/2020] [Indexed: 01/01/2023]
Abstract
A database of cyanobacterial linked genomes that can be accessed through an interactive platform (https://dfgm.ua.es/genetica/investigacion/cyanobacterial_genetics/Resources.html) was generated on the bases of conservation of gene neighborhood across 124 cyanobacterial species. It allows flexible generation of gene networks at different threshold values. The default cyanobacterial linked genome, whose global properties are analyzed here, connects most of the cyanobacterial core genes. The potential of the web tool is discussed in relation to other bioinformatics approaches based on guilty-by-association principles, with selected examples of networks illustrating its usefulness for genes found exclusively in cyanobacteria or in cyanobacteria and chloroplasts. We believe that this tool will provide useful predictions that are readily testable in Synechococcus elongatus PCC7942 and other model organisms performing oxygenic photosynthesis.
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Affiliation(s)
- Jose I Labella
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Antonio Llop
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
| | - Asuncion Contreras
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Spain
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26
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Reiter B, Vamvaka E, Marino G, Kleine T, Jahns P, Bolle C, Leister D, Rühle T. The Arabidopsis Protein CGL20 Is Required for Plastid 50S Ribosome Biogenesis. PLANT PHYSIOLOGY 2020; 182:1222-1238. [PMID: 31937683 PMCID: PMC7054867 DOI: 10.1104/pp.19.01502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 12/22/2019] [Indexed: 05/29/2023]
Abstract
Biogenesis of plastid ribosomes is facilitated by auxiliary factors that process and modify ribosomal RNAs (rRNAs) or are involved in ribosome assembly. In comparison with their bacterial and mitochondrial counterparts, the biogenesis of plastid ribosomes is less well understood, and few auxiliary factors have been described so far. In this study, we report the functional characterization of CONSERVED ONLY IN THE GREEN LINEAGE20 (CGL20) in Arabidopsis (Arabidopsis thaliana; AtCGL20), which is a Pro-rich, ∼10-kD protein that is targeted to mitochondria and chloroplasts. In Arabidopsis, CGL20 is encoded by segmentally duplicated genes of high sequence similarity (AtCGL20A and AtCGL20B). Inactivation of these genes in the atcgl20ab mutant led to a visible virescent phenotype and growth arrest at low temperature. The chloroplast proteome, pigment composition, and photosynthetic performance were significantly affected in atcgl20ab mutants. Loss of AtCGL20 impaired plastid translation, perturbing the formation of a hidden break in the 23S rRNA and causing abnormal accumulation of 50S ribosomal subunits in the high-molecular-mass fraction of chloroplast stromal extracts. Moreover, AtCGL20A-eGFP fusion proteins comigrated with 50S ribosomal subunits in Suc density gradients, even after RNase treatment of stromal extracts. Therefore, we propose that AtCGL20 participates in the late stages of the biogenesis of 50S ribosomal subunits in plastids, a role that presumably evolved in the green lineage as a consequence of structural divergence of plastid ribosomes.
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Affiliation(s)
- Bennet Reiter
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität, D-82152 Planegg-Martinsried, Germany
| | - Evgenia Vamvaka
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität, D-82152 Planegg-Martinsried, Germany
| | - Giada Marino
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität, D-82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität, D-82152 Planegg-Martinsried, Germany
| | - Peter Jahns
- Institute of Plant Biochemistry, Heinrich-Heine University, 40225 Duesseldorf, Germany
| | - Cordelia Bolle
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität, D-82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität, D-82152 Planegg-Martinsried, Germany
| | - Thilo Rühle
- Plant Molecular Biology Faculty of Biology I, Ludwig-Maximilians-Universität, D-82152 Planegg-Martinsried, Germany
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27
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Amstutz CL, Fristedt R, Schultink A, Merchant SS, Niyogi KK, Malnoë A. An atypical short-chain dehydrogenase-reductase functions in the relaxation of photoprotective qH in Arabidopsis. NATURE PLANTS 2020; 6:154-166. [PMID: 32055052 PMCID: PMC7288749 DOI: 10.1038/s41477-020-0591-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/28/2019] [Indexed: 05/20/2023]
Abstract
Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase-reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.
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Affiliation(s)
- Cynthia L Amstutz
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Rikard Fristedt
- Department of Physics and Astronomy, Vrije University of Amsterdam, Amsterdam, The Netherlands
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Alex Schultink
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Sabeeha S Merchant
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Alizée Malnoë
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden.
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28
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Nguyen ND, Blaby IK, Wang D. ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks. BMC Genomics 2019; 20:1003. [PMID: 31888454 PMCID: PMC6936142 DOI: 10.1186/s12864-019-6329-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster.
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Affiliation(s)
- Nam D Nguyen
- Deparment of Computer Science, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ian K Blaby
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA. .,US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, 4720, CA, USA.
| | - Daifeng Wang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, 53726, WI, USA. .,Waisman Center, University of Wisconsin-Madison, Madison, 53705, WI, USA.
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29
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Schober AF, R�o B�rtulos C, Bischoff A, Lepetit B, Gruber A, Kroth PG. Organelle Studies and Proteome Analyses of Mitochondria and Plastids Fractions from the Diatom Thalassiosira pseudonana. PLANT & CELL PHYSIOLOGY 2019; 60:1811-1828. [PMID: 31179502 PMCID: PMC6683858 DOI: 10.1093/pcp/pcz097] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 05/19/2023]
Abstract
Diatoms are unicellular algae and evolved by secondary endosymbiosis, a process in which a red alga-like eukaryote was engulfed by a heterotrophic eukaryotic cell. This gave rise to plastids of remarkable complex architecture and ultrastructure that require elaborate protein importing, trafficking, signaling and intracellular cross-talk pathways. Studying both plastids and mitochondria and their distinctive physiological pathways in organello may greatly contribute to our understanding of photosynthesis, mitochondrial respiration and diatom evolution. The isolation of such complex organelles, however, is still demanding, and existing protocols are either limited to a few species (for plastids) or have not been reported for diatoms so far (for mitochondria). In this work, we present the first isolation protocol for mitochondria from the model diatom Thalassiosira pseudonana. Apart from that, we extended the protocol so that it is also applicable for the purification of a high-quality plastids fraction, and provide detailed structural and physiological characterizations of the resulting organelles. Isolated mitochondria were structurally intact, showed clear evidence of mitochondrial respiration, but the fractions still contained residual cell fragments. In contrast, plastid isolates were virtually free of cellular contaminants, featured structurally preserved thylakoids performing electron transport, but lost most of their stromal components as concluded from Western blots and mass spectrometry. Liquid chromatography electrospray-ionization mass spectrometry studies on mitochondria and thylakoids, moreover, allowed detailed proteome analyses which resulted in extensive proteome maps for both plastids and mitochondria thus helping us to broaden our understanding of organelle metabolism and functionality in diatoms.
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Affiliation(s)
- Alexander F Schober
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
- Corresponding author: E-mail, ; Fax, +49(0)7531-88-4047
| | - Carolina R�o B�rtulos
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Annsophie Bischoff
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ansgar Gruber
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovsk� 1160/31, Česk� Budějovice, Czech Republic
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, Konstanz, Germany
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30
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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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31
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Armarego-Marriott T, Kowalewska Ł, Burgos A, Fischer A, Thiele W, Erban A, Strand D, Kahlau S, Hertle A, Kopka J, Walther D, Reich Z, Schöttler MA, Bock R. Highly Resolved Systems Biology to Dissect the Etioplast-to-Chloroplast Transition in Tobacco Leaves. PLANT PHYSIOLOGY 2019; 180:654-681. [PMID: 30862726 PMCID: PMC6501100 DOI: 10.1104/pp.18.01432] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/19/2019] [Indexed: 05/17/2023]
Abstract
Upon exposure to light, plant cells quickly acquire photosynthetic competence by converting pale etioplasts into green chloroplasts. This developmental transition involves the de novo biogenesis of the thylakoid system and requires reprogramming of metabolism and gene expression. Etioplast-to-chloroplast differentiation involves massive changes in plastid ultrastructure, but how these changes are connected to specific changes in physiology, metabolism, and expression of the plastid and nuclear genomes is poorly understood. Here, we describe a new experimental system in the dicotyledonous model plant tobacco (Nicotiana tabacum) that allows us to study the leaf deetiolation process at the systems level. We have determined the accumulation kinetics of photosynthetic complexes, pigments, lipids, and soluble metabolites and recorded the dynamic changes in plastid ultrastructure and in the nuclear and plastid transcriptomes. Our data describe the greening process at high temporal resolution, resolve distinct genetic and metabolic phases during deetiolation, and reveal numerous candidate genes that may be involved in light-induced chloroplast development and thylakoid biogenesis.
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Affiliation(s)
| | - Łucja Kowalewska
- Faculty of Biology, Department of Plant Anatomy and Cytology, University of Warsaw, 02-096 Warszawa, Poland
| | - Asdrubal Burgos
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- Laboratorio de Biotecnología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, CP 45200 Zapopan, Jalisco, Mexico
| | - Axel Fischer
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Wolfram Thiele
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Deserah Strand
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Sabine Kahlau
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- targenomix GmbH, 14476 Potsdam, Germany
| | - Alexander Hertle
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Dirk Walther
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Ziv Reich
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
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32
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Abstract
Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.
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Affiliation(s)
| | - Sabeeha S Merchant
- Departments of Plant and Microbial Biology and Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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33
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Li X, Patena W, Fauser F, Jinkerson RE, Saroussi S, Meyer MT, Ivanova N, Robertson JM, Yue R, Zhang R, Vilarrasa-Blasi J, Wittkopp TM, Ramundo S, Blum SR, Goh A, Laudon M, Srikumar T, Lefebvre PA, Grossman AR, Jonikas MC. A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat Genet 2019. [PMID: 30886426 DOI: 10.1038/s41588-019-0370-376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed that it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 higher-confidence genes are novel, opening new opportunities for advances in understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants, and animals.
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Affiliation(s)
- Xiaobo Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- School of Life Sciences, Westlake Institute for Advanced Study, Westlake University, Hangzhou, China
| | - Weronika Patena
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Friedrich Fauser
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Robert E Jinkerson
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Shai Saroussi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Moritz T Meyer
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nina Ivanova
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Jacob M Robertson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Rebecca Yue
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Ru Zhang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Silvia Ramundo
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Sean R Blum
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Audrey Goh
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew Laudon
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Tharan Srikumar
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul A Lefebvre
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.
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34
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A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. Nat Genet 2019; 51:627-635. [PMID: 30886426 PMCID: PMC6636631 DOI: 10.1038/s41588-019-0370-6] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 02/08/2019] [Indexed: 12/22/2022]
Abstract
Photosynthetic organisms provide food and energy for nearly all life on Earth, yet half of their protein-coding genes remain uncharacterized1,2. Characterization of these genes could be greatly accelerated by new genetic resources for unicellular organisms. Here, we generated a genome-wide, indexed library of mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii. The 62,389 mutants in the library, covering 83% of nuclear, protein-coding genes, are available to the community. Each mutant contains unique DNA barcodes, allowing the collection to be screened as a pool. We performed a genome-wide survey of genes required for photosynthesis, which identified 303 candidate genes. Characterization of one of these genes, the conserved predicted phosphatase-encoding gene CPL3, showed it is important for accumulation of multiple photosynthetic protein complexes. Notably, 21 of the 43 highest-confidence genes are novel, opening new opportunities for advances in our understanding of this biogeochemically fundamental process. This library will accelerate the characterization of thousands of genes in algae, plants and animals. Generation of a library of 62,389 mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii enables screening for genes required for photosynthesis and the identification of 303 candidate genes.
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35
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Schorsch M, Kramer M, Goss T, Eisenhut M, Robinson N, Osman D, Wilde A, Sadaf S, Brückler H, Walder L, Scheibe R, Hase T, Hanke GT. A unique ferredoxin acts as a player in the low-iron response of photosynthetic organisms. Proc Natl Acad Sci U S A 2018; 115:E12111-E12120. [PMID: 30514818 PMCID: PMC6304933 DOI: 10.1073/pnas.1810379115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Iron chronically limits aquatic photosynthesis, especially in marine environments, and the correct perception and maintenance of iron homeostasis in photosynthetic bacteria, including cyanobacteria, is therefore of global significance. Multiple adaptive mechanisms, responsive promoters, and posttranscriptional regulators have been identified, which allow cyanobacteria to respond to changing iron concentrations. However, many factors remain unclear, in particular, how iron status is perceived within the cell. Here we describe a cyanobacterial ferredoxin (Fed2), with a unique C-terminal extension, that acts as a player in iron perception. Fed2 homologs are highly conserved in photosynthetic organisms from cyanobacteria to higher plants, and, although they belong to the plant type ferredoxin family of [2Fe-2S] photosynthetic electron carriers, they are not involved in photosynthetic electron transport. As deletion of fed2 appears lethal, we developed a C-terminal truncation system to attenuate protein function. Disturbed Fed2 function resulted in decreased chlorophyll accumulation, and this was exaggerated in iron-depleted medium, where different truncations led to either exaggerated or weaker responses to low iron. Despite this, iron concentrations remained the same, or were elevated in all truncation mutants. Further analysis established that, when Fed2 function was perturbed, the classical iron limitation marker IsiA failed to accumulate at transcript and protein levels. By contrast, abundance of IsiB, which shares an operon with isiA, was unaffected by loss of Fed2 function, pinpointing the site of Fed2 action in iron perception to the level of posttranscriptional regulation.
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Affiliation(s)
- Michael Schorsch
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, United Kingdom
| | - Manuela Kramer
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, United Kingdom
| | - Tatjana Goss
- Plant Biochemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Marion Eisenhut
- Plant Biochemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Nigel Robinson
- Department of Biosciences, Durham University, DH1 3LE Durham, United Kingdom
| | - Deenah Osman
- Department of Biosciences, Durham University, DH1 3LE Durham, United Kingdom
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, 79104 Freiburg, Germany
| | - Shamaila Sadaf
- Institute of Chemistry of New Materials, University of Osnabrück, 49069 Osnabrück, Germany
| | - Hendrik Brückler
- Institute of Chemistry of New Materials, University of Osnabrück, 49069 Osnabrück, Germany
| | - Lorenz Walder
- Institute of Chemistry of New Materials, University of Osnabrück, 49069 Osnabrück, Germany
| | - Renate Scheibe
- Plant Physiology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Toshiharu Hase
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Guy T Hanke
- School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, United Kingdom;
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36
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Ng SM, Lee XW, Mat-Isa MN, Aizat-Juhari MA, Adam JH, Mohamed R, Wan KL, Firdaus-Raih M. Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions. Sci Rep 2018; 8:17258. [PMID: 30467394 PMCID: PMC6250676 DOI: 10.1038/s41598-018-35173-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Parasitic plants are known to discard photosynthesis thus leading to the deletion or loss of the plastid genes. Despite plastid genome reduction in non-photosynthetic plants, some nucleus-encoded proteins are transported back to the plastid to carry out specific functions. In this work, we study such proteins in Rafflesia cantleyi, a member of the holoparasitic genus well-known for producing the largest single flower in the world. Our analyses of three transcriptome datasets, two holoparasites (R. cantleyi and Phelipanche aegyptiaca) and one photosynthetic plant (Arabidopsis thaliana), suggest that holoparasites, such as R. cantleyi, retain some common plastid associated processes such as biosynthesis of amino acids and lipids, but are missing photosynthesis components that can be extensions of these pathways. The reconstruction of two selected biosynthetic pathways involving plastids correlates the trend of plastid retention to pathway complexity - transcriptome evidence for R. cantleyi suggests alternate mechanisms in regulating the plastidial heme and terpenoid backbone biosynthesis pathways. The evolution to holoparasitism from autotrophy trends towards devolving the plastid genes to the nuclear genome despite the functional sites remaining in the plastid, or maintaining non-photosynthetic processes in the plastid, before the eventual loss of the plastid and any site dependent functions.
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Affiliation(s)
- Siuk-Mun Ng
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Codon Genomics SB, No 26, Jalan Dutamas 7, Taman Dutamas Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Xin-Wei Lee
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Mohd-Noor Mat-Isa
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Mohd Afiq Aizat-Juhari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Jumaat Haji Adam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Rahmah Mohamed
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Mohd Firdaus-Raih
- Centre for Frontier Sciences, Faculty of Science and Technology and Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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37
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Hovde BT, Hanschen ER, Steadman Tyler CR, Lo CC, Kunde Y, Davenport K, Daligault H, Msanne J, Canny S, Eyun SI, Riethoven JJM, Polle J, Starkenburg SR. Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae). ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Allen JW, Tevatia R, Demirel Y, DiRusso CC, Black PN. Induction of oil accumulation by heat stress is metabolically distinct from N stress in the green microalgae Coccomyxa subellipsoidea C169. PLoS One 2018; 13:e0204505. [PMID: 30261009 PMCID: PMC6160078 DOI: 10.1371/journal.pone.0204505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022] Open
Abstract
Algae are often promoted as feedstock organisms to produce a sustainable petroleum fossil fuel alternative. However, to induce lipid accumulation most often requires a severe stress that is difficult to induce in large batch cultures. The objective of this study is to analyze and mathematically model heat stress on growth, chlorophyll content, triacylglyceride, and starch synthesis in algae. We initially screened 30 algal species for the most pronounced induction of lipid droplets from heat stress using confocal microscopy and mass spectroscopy techniques. One species, Coccomyxa subellipsoidea C169, was selected and subjected to further biochemical analyses using a jacketed bioreactor amended with 1% CO2 at 25°C, 30°C, 32°C, 33°C, 34°C, 35°C, and 36°C. Lipid and starch accumulation was less extreme than N stress. Growth was reduced above 25°C, but heat stress induced lipid droplet synthesis was negatively correlated with growth only past a demonstrated threshold temperature above 32°C. The optimal temperature for lipid accumulation was 35°C, which led to 6% of dry weight triglyceride content and a 72% reduction from optimal growth after 5 days. Fatty acid influx rates into triglycerides and 15N labeling of amino acids and proteins indicate that heat stress is mechanistically distinct from N stress. Thus, this study lends support to a novel hypothesis that lipid droplet triglycerides result from a redistribution of carbon flux as fatty acids to neutral storage lipids over membrane or other lipids.
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Affiliation(s)
- James W. Allen
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Rahul Tevatia
- Department of Chemical and Biomolecular Engineering, Othmer Hall, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Yaşar Demirel
- Department of Chemical and Biomolecular Engineering, Othmer Hall, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Concetta C. DiRusso
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Paul N. Black
- Department of Biochemistry, Beadle Center, University of Nebraska-Lincoln, University of Nebraska-Lincoln, Lincoln, NE, United States of America
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39
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Nellaepalli S, Ozawa SI, Kuroda H, Takahashi Y. The photosystem I assembly apparatus consisting of Ycf3-Y3IP1 and Ycf4 modules. Nat Commun 2018; 9:2439. [PMID: 29934511 PMCID: PMC6015050 DOI: 10.1038/s41467-018-04823-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
In oxygenic photosynthesis, light energy is converted into redox energy by two photosystems (PSI and PSII). PSI forms one of the largest multiprotein complexes in thylakoid membranes consisting of a core complex, peripheral light-harvesting complexes (LHCIs) and cofactors. Although the high-resolution structure of the PSI–LHCI complex has been determined, the assembly process remains unclear due to the rapid nature of the assembly process. Here we show that two conserved chloroplast-encoded auxiliary factors, Ycf3 and Ycf4, form modules that mediate PSI assembly. The first module consists of the tetratricopeptide repeat protein Ycf3 and its interacting partner, Y3IP1, and mainly facilitates the assembly of reaction center subunits. The second module consists of oligomeric Ycf4 and facilitates the integration of peripheral PSI subunits and LHCIs into the PSI reaction center subcomplex. We reveal that these two modules are major mediators of the PSI–LHCI assembly process. Photosystem I is a large multiprotein complex embedded in the chloroplast thylakoid membrane. Here the authors provide evidence for a modular assembly process, whereby Ycf3 facilitates assembly of the reaction center, while Ycf4 incorporates peripheral core and light harvesting complex subunits to the reaction center.
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Affiliation(s)
- Sreedhar Nellaepalli
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.,JST-CREST, Tokyo, Japan
| | - Shin-Ichiro Ozawa
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.,JST-CREST, Tokyo, Japan
| | - Hiroshi Kuroda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.,JST-CREST, Tokyo, Japan
| | - Yuichiro Takahashi
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan. .,JST-CREST, Tokyo, Japan.
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40
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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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Nowack ECM, Weber APM. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:51-84. [PMID: 29489396 DOI: 10.1146/annurev-arplant-042817-040209] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
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Affiliation(s)
- Eva C M Nowack
- Microbial Symbiosis and Organelle Evolution Group, Biology Department, Heinrich Heine University, 40225 Düsseldorf, Germany;
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany;
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42
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Dann M, Leister D. Enhancing (crop) plant photosynthesis by introducing novel genetic diversity. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0380. [PMID: 28808099 DOI: 10.1098/rstb.2016.0380] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2017] [Indexed: 12/22/2022] Open
Abstract
Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'.
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Affiliation(s)
- Marcel Dann
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
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43
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Fristedt R, Hu C, Wheatley N, Roy LM, Wachter RM, Savage L, Harbinson J, Kramer DM, Merchant SS, Yeates T, Croce R. RAF2 is a RuBisCO assembly factor in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:146-156. [PMID: 29396988 DOI: 10.1111/tpj.13849] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 06/07/2023]
Abstract
Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the reaction between gaseous carbon dioxide (CO2 ) and ribulose-1,5-bisphosphate. Although it is one of the most studied enzymes, the assembly mechanisms of the large hexadecameric RuBisCO is still emerging. In bacteria and in the C4 plant Zea mays, a protein with distant homology to pterin-4α-carbinolamine dehydratase (PCD) has recently been shown to be involved in RuBisCO assembly. However, studies of the homologous PCD-like protein (RAF2, RuBisCO assembly factor 2) in the C3 plant Arabidopsis thaliana (A. thaliana) have so far focused on its role in hormone and stress signaling. We investigated whether A. thalianaRAF2 is also involved in RuBisCO assembly. We localized RAF2 to the soluble chloroplast stroma and demonstrated that raf2 A. thaliana mutant plants display a severe pale green phenotype with reduced levels of stromal RuBisCO. We concluded that the RAF2 protein is probably involved in RuBisCO assembly in the C3 plant A. thaliana.
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Affiliation(s)
- Rikard Fristedt
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Chen Hu
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nicole Wheatley
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Laura M Roy
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rebekka M Wachter
- School of Molecular Sciences and Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ, USA
| | - Linda Savage
- Department of Energy Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Jeremy Harbinson
- Horticulture and Product Physiology Group, Wageningen University, Wageningen, The Netherlands
| | - David M Kramer
- Department of Energy Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Todd Yeates
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, USA
| | - Roberta Croce
- Biophysics of Photosynthesis, VU University Amsterdam, Amsterdam, The Netherlands
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Gallaher SD, Fitz-Gibbon ST, Strenkert D, Purvine SO, Pellegrini M, Merchant SS. High-throughput sequencing of the chloroplast and mitochondrion of Chlamydomonas reinhardtii to generate improved de novo assemblies, analyze expression patterns and transcript speciation, and evaluate diversity among laboratory strains and wild isolates. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:545-565. [PMID: 29172250 PMCID: PMC5775909 DOI: 10.1111/tpj.13788] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 05/18/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular chlorophyte alga that is widely studied as a reference organism for understanding photosynthesis, sensory and motile cilia, and for development of an algal-based platform for producing biofuels and bio-products. Its highly repetitive, ~205-kbp circular chloroplast genome and ~15.8-kbp linear mitochondrial genome were sequenced prior to the advent of high-throughput sequencing technologies. Here, high coverage shotgun sequencing was used to assemble both organellar genomes de novo. These new genomes correct dozens of errors in the prior genome sequences and annotations. Genome sequencing coverage indicates that each cell contains on average 83 copies of the chloroplast genome and 130 copies of the mitochondrial genome. Using protocols and analyses optimized for organellar transcripts, RNA-Seq was used to quantify their relative abundances across 12 different growth conditions. Forty-six percent of total cellular mRNA is attributable to high expression from a few dozen chloroplast genes. RNA-Seq data were used to guide gene annotation, to demonstrate polycistronic gene expression, and to quantify splicing of psaA and psbA introns. In contrast to a conclusion from a recent study, we found that chloroplast transcripts are not edited. Unexpectedly, cytosine-rich polynucleotide tails were observed at the 3'-end of all mitochondrial transcripts. A comparative genomics analysis of eight laboratory strains and 11 wild isolates of C. reinhardtii identified 2658 variants in the organellar genomes, which is 1/10th as much genetic diversity as is found in the nucleus.
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Affiliation(s)
- Sean D. Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- Corresponding author:
| | - Sorel T. Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - Samuel O. Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Sabeeha S. Merchant
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
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45
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Koskela MM, Dahlström KM, Goñi G, Lehtimäki N, Nurmi M, Velazquez-Campoy A, Hanke G, Bölter B, Salminen TA, Medina M, Mulo P. Arabidopsis FNRL protein is an NADPH-dependent chloroplast oxidoreductase resembling bacterial ferredoxin-NADP + reductases. PHYSIOLOGIA PLANTARUM 2018; 162:177-190. [PMID: 28833218 DOI: 10.1111/ppl.12621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/15/2017] [Indexed: 05/06/2023]
Abstract
Plastidic ferredoxin-NADP+ oxidoreductases (FNRs; EC:1.18.1.2) together with bacterial type FNRs (FPRs) form the plant-type FNR family. Members of this group contain a two-domain scaffold that forms the basis of an extended superfamily of flavin adenine dinucleotide (FAD) dependent oxidoreductases. In this study, we show that the Arabidopsis thaliana At1g15140 [Ferredoxin-NADP+ oxidoreductase-like (FNRL)] is an FAD-containing NADPH dependent oxidoreductase present in the chloroplast stroma. Determination of the kinetic parameters using the DCPIP NADPH-dependent diaphorase assay revealed that the reaction catalysed by a recombinant FNRL protein followed a saturation Michaelis-Menten profile on the NADPH concentration with kcat = 3.2 ± 0.2 s-1 , KmNADPH = 1.6 ± 0.3 μM and kcat /KmNADPH = 2.0 ± 0.4 μM-1 s-1 . Biochemical assays suggested that FNRL is not likely to interact with Arabidopsis ferredoxin 1, which is supported by the sequence analysis implying that the known Fd-binding residues in plastidic FNRs differ from those of FNRL. In addition, based on structural modelling FNRL has an FAD-binding N-terminal domain built from a six-stranded β-sheet and one α-helix, and a C-terminal NADP+ -binding α/β domain with a five-stranded β-sheet with a pair of α-helices on each side. The FAD-binding site is highly hydrophobic and predicted to bind FAD in a bent conformation typically seen in bacterial FPRs.
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Affiliation(s)
- Minna M Koskela
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Käthe M Dahlström
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Guillermina Goñi
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and GBsC-CSIC Joint Units), University of Zaragoza, Zaragoza, Spain
| | - Nina Lehtimäki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Markus Nurmi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Adrian Velazquez-Campoy
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and GBsC-CSIC Joint Units), University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain
| | - Guy Hanke
- School of Biochemistry and Chemistry, Queen Mary University of London, London, United Kingdom
| | - Bettina Bölter
- Department of Biology I, Botany, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tiina A Salminen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences and Institute of Biocomputation and Physics of Complex Systems (BIFI-IQFR and GBsC-CSIC Joint Units), University of Zaragoza, Zaragoza, Spain
| | - Paula Mulo
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
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46
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Xing J, Liu P, Zhao L, Huang F. Deletion of CGLD1 Impairs PSII and Increases Singlet Oxygen Tolerance of Green Alga Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2017; 8:2154. [PMID: 29326747 PMCID: PMC5736878 DOI: 10.3389/fpls.2017.02154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/05/2017] [Indexed: 05/24/2023]
Abstract
The green alga Chlamydomonas reinhardtii is a key model organism for studying photosynthesis and oxidative stress in unicellular eukaryotes. Using a forward genetics approach, we have identified and characterized a mutant x32, which lacks a predicted protein named CGLD1 (Conserved in Green Lineage and Diatom 1) in GreenCut2, under normal and stress conditions. We show that loss of CGLD1 resulted in minimal photoautotrophic growth and PSII activity in the organism. We observed reduced amount of PSII complex and core subunits in the x32 mutant based on blue-native (BN)/PAGE and immunoblot analysis. Moreover, x32 exhibited increased sensitivity to high-light stress and altered tolerance to different reactive oxygenic species (ROS) stress treatments, i.e., decreased resistance to H2O2/or tert-Butyl hydroperoxide (t-BOOH) and increased tolerance to neutral red (NR) and rose bengal (RB) that induce the formation of singlet oxygen, respectively. Further analysis via quantitative real-time PCR (qRT-PCR) indicated that the increased singlet-oxygen tolerance of x32 was largely correlated with up-regulated gene expression of glutathione-S-transferases (GST). The phenotypical and physiological implications revealed from our experiments highlight the important roles of CGLD1 in maintaining structure and function of PSII as well as in protection of Chlamydomonas under photo-oxidative stress conditions.
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Affiliation(s)
- Jiale Xing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Zhao
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fang Huang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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47
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Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. The Algal Revolution. TRENDS IN PLANT SCIENCE 2017; 22:726-738. [PMID: 28610890 DOI: 10.1016/j.tplants.2017.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/04/2017] [Accepted: 05/16/2017] [Indexed: 05/28/2023]
Abstract
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.
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Affiliation(s)
- Juliet Brodie
- Natural History Museum, Department of Life Sciences, London SW7 5BD, UK
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Olivier De Clerck
- Research Group Phycology, Ghent University, Krijgslaan 281, S8, 9000 Ghent, Belgium
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Claire Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, UK
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John A Raven
- Permanent address: Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, UK; School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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48
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Bobik K, McCray TN, Ernest B, Fernandez JC, Howell KA, Lane T, Staton M, Burch-Smith TM. The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:114-131. [PMID: 28346704 DOI: 10.1111/tpj.13550] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 05/06/2023]
Abstract
INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing. Loss of ISE2 from Arabidopsis thaliana leaves resulted in defects in C-to-U RNA editing, altered accumulation of chloroplast transcripts and chloroplast-encoded proteins, and defective processing of chloroplast ribosomal RNAs. Potential ISE2 substrates were identified by RNA immunoprecipitation followed by next-generation sequencing (RIP-seq), and the diversity of RNA species identified supports ISE2's involvement in multiple aspects of chloroplast RNA metabolism. Comprehensive phylogenetic analyses revealed that ISE2 is a non-canonical Ski2-like RNA helicase that represents a separate sub-clade unique to green photosynthetic organisms, consistent with its function as an essential protein. Thus ISE2's evolutionary conservation may be explained by its numerous roles in regulating chloroplast gene expression.
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Affiliation(s)
- Krzysztof Bobik
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tyra N McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Ben Ernest
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jessica C Fernandez
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Katharine A Howell
- Plant Energy Biology, ARC Center of Excellence, University of Western Australia, Perth, Australia
| | - Thomas Lane
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Margaret Staton
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Tessa M Burch-Smith
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
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49
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Shen J, Williams-Carrier R, Barkan A. PSA3, a Protein on the Stromal Face of the Thylakoid Membrane, Promotes Photosystem I Accumulation in Cooperation with the Assembly Factor PYG7. PLANT PHYSIOLOGY 2017; 174:1850-1862. [PMID: 28522455 PMCID: PMC5490921 DOI: 10.1104/pp.17.00524] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/17/2017] [Indexed: 05/16/2023]
Abstract
PSI is a large protein-pigment complex located in the thylakoid membrane in cyanobacteria, plants, and algae. Although the structure and components of PSI are well characterized, mechanisms that orchestrate its assembly are poorly understood. In this study, we discovered a novel nucleus-encoded protein, Photosystem I Assembly3 (PSA3), that is required for PSI accumulation. PSA3 is conserved among green photosynthetic eukaryotes but is lacking in cyanobacteria. Mutations in the psa3 gene cause the specific loss of PSI in Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). Ribosome profiling and pulse-labeling analyses showed that chloroplast- encoded PSI subunits are synthesized at normal rates in psa3 mutants, indicating that PSA3 is involved in the biogenesis of PSI at a posttranslational step. PSA3 resides on the stromal face of the thylakoid membrane, where it is found in a complex that is slightly smaller than PSI. Structural predictions suggest that PSA3 binds a basic peptide in a manner that is sensitive to the oxidation state of Cys pairs flanking the predicted peptide binding groove. PSA3 and the previously described PSI biogenesis factor PYG7 interact in yeast two-hybrid and bimolecular fluorescence complementation assays, and they are found in thylakoid membrane complexes of similar size. These and other results indicate that PSA3 cooperates with PYG7 to promote the stable assembly of PSI, and that the PsaC subunit is likely to be the primary target of their action.
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Affiliation(s)
- Jie Shen
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | | | - Alice Barkan
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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50
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van Wijk KJ, Kessler F. Plastoglobuli: Plastid Microcompartments with Integrated Functions in Metabolism, Plastid Developmental Transitions, and Environmental Adaptation. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:253-289. [PMID: 28125283 DOI: 10.1146/annurev-arplant-043015-111737] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plastoglobuli (PGs) are plastid lipoprotein particles surrounded by a membrane lipid monolayer. PGs contain small specialized proteomes and metabolomes. They are present in different plastid types (e.g., chloroplasts, chromoplasts, and elaioplasts) and are dynamic in size and shape in response to abiotic stress or developmental transitions. PGs in chromoplasts are highly enriched in carotenoid esters and enzymes involved in carotenoid metabolism. PGs in chloroplasts are associated with thylakoids and contain ∼30 core proteins (including six ABC1 kinases) as well as additional proteins recruited under specific conditions. Systems analysis has suggested that chloroplast PGs function in metabolism of prenyl lipids (e.g., tocopherols, plastoquinone, and phylloquinone); redox and photosynthetic regulation; plastid biogenesis; and senescence, including recycling of phytol, remobilization of thylakoid lipids, and metabolism of jasmonate. These functionalities contribute to chloroplast PGs' role in responses to stresses such as high light and nitrogen starvation. PGs are thus lipid microcompartments with multiple functions integrated into plastid metabolism, developmental transitions, and environmental adaptation. This review provides an in-depth overview of PG experimental observations, summarizes the present understanding of PG features and functions, and provides a conceptual framework for PG research and the realization of opportunities for crop improvement.
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Affiliation(s)
- Klaas J van Wijk
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853;
| | - Felix Kessler
- Laboratory of Plant Physiology, University of Neuchâtel, 2000 Neuchâtel, Switzerland;
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