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Srivastava R, Singh N, Kanda T, Yadav S, Yadav S, Atri N. Cyanobacterial Proteomics: Diversity and Dynamics. J Proteome Res 2024; 23:2680-2699. [PMID: 38470568 DOI: 10.1021/acs.jproteome.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Cyanobacteria (oxygenic photoautrophs) comprise a diverse group holding significance both environmentally and for biotechnological applications. The utilization of proteomic techniques has significantly influenced investigations concerning cyanobacteria. Application of proteomics allows for large-scale analysis of protein expression and function within cyanobacterial systems. The cyanobacterial proteome exhibits tremendous functional, spatial, and temporal diversity regulated by multiple factors that continuously modify protein abundance, post-translational modifications, interactions, localization, and activity to meet the dynamic needs of these tiny blue greens. Modern mass spectrometry-based proteomics techniques enable system-wide examination of proteome complexity through global identification and high-throughput quantification of proteins. These powerful approaches have revolutionized our understanding of proteome dynamics and promise to provide novel insights into integrated cellular behavior at an unprecedented scale. In this Review, we present modern methods and cutting-edge technologies employed for unraveling the spatiotemporal diversity and dynamics of cyanobacterial proteomics with a specific focus on the methods used to analyze post-translational modifications (PTMs) and examples of dynamic changes in the cyanobacterial proteome investigated by proteomic approaches.
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Affiliation(s)
| | - Nidhi Singh
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Tripti Kanda
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Sadhana Yadav
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
| | - Shivam Yadav
- Department of Botany, University of Allahabad, Allahabad 211002, India
| | - Neelam Atri
- Department of Botany, M.M.V., Banaras Hindu University, Varanasi 221005, India
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Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
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Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
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Xu C, Wang B, Yang L, Zhongming Hu L, Yi L, Wang Y, Chen S, Emili A, Wan C. Global Landscape of Native Protein Complexes in Synechocystis sp. PCC 6803. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:715-727. [PMID: 33636367 PMCID: PMC9880817 DOI: 10.1016/j.gpb.2020.06.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 04/04/2020] [Accepted: 06/12/2020] [Indexed: 01/31/2023]
Abstract
Synechocystis sp. PCC 6803 (hereafter: Synechocystis) is a model organism for studying photosynthesis, energy metabolism, and environmental stress. Although known as the first fully sequenced phototrophic organism, Synechocystis still has almost half of its proteome without functional annotations. In this study, by using co-fractionation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS), we define 291 multi-protein complexes, encompassing 24,092 protein-protein interactions (PPIs) among 2062 distinct gene products. This information not only reveals the roles of photosynthesis in metabolism, cell motility, DNA repair, cell division, and other physiological processes, but also shows how protein functions vary from bacteria to higher plants due to changes in interaction partners. It also allows us to uncover the functions of hypothetical proteins, such as Sll0445, Sll0446, and Sll0447 involved in photosynthesis and cell motility, and Sll1334 involved in regulation of fatty acid biogenesis. Here we present the most extensive PPI data for Synechocystis so far, which provide critical insights into fundamental molecular mechanisms in cyanobacteria.
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Affiliation(s)
- Chen Xu
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Bing Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Lin Yang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Lucas Zhongming Hu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 2E8, Canada
| | - Lanxing Yi
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Yaxuan Wang
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Shenglan Chen
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 2E8, Canada,Departments of Biochemistry and Biology, Boston University, Boston, MA 02215, USA
| | - Cuihong Wan
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, China,Corresponding author.
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MacGregor-Chatwin C, Nürnberg DJ, Jackson PJ, Vasilev C, Hitchcock A, Ho MY, Shen G, Gisriel CJ, Wood WH, Mahbub M, Selinger VM, Johnson MP, Dickman MJ, Rutherford AW, Bryant DA, Hunter CN. Changes in supramolecular organization of cyanobacterial thylakoid membrane complexes in response to far-red light photoacclimation. SCIENCE ADVANCES 2022; 8:eabj4437. [PMID: 35138895 PMCID: PMC8827656 DOI: 10.1126/sciadv.abj4437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are ubiquitous in nature and have developed numerous strategies that allow them to live in a diverse range of environments. Certain cyanobacteria synthesize chlorophylls d and f to acclimate to niches enriched in far-red light (FRL) and incorporate paralogous photosynthetic proteins into their photosynthetic apparatus in a process called FRL-induced photoacclimation (FaRLiP). We characterized the macromolecular changes involved in FRL-driven photosynthesis and used atomic force microscopy to examine the supramolecular organization of photosystem I associated with FaRLiP in three cyanobacterial species. Mass spectrometry showed the changes in the proteome of Chroococcidiopsis thermalis PCC 7203 that accompany FaRLiP. Fluorescence lifetime imaging microscopy and electron microscopy reveal an altered cellular distribution of photosystem complexes and illustrate the cell-to-cell variability of the FaRLiP response.
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Affiliation(s)
| | - Dennis J. Nürnberg
- Department of Life Sciences, Imperial College London, London, UK
- Physics Department, Freie Universität Berlin, Berlin, Germany
| | - Philip J. Jackson
- School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | | | - Ming-Yang Ho
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Gaozhong Shen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Christopher J. Gisriel
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, USA
| | | | - Moontaha Mahbub
- Department of Life Sciences, Imperial College London, London, UK
| | | | | | - Mark J. Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - C. Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
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Klähn S, Mikkat S, Riediger M, Georg J, Hess WR, Hagemann M. Integrative analysis of the salt stress response in cyanobacteria. Biol Direct 2021; 16:26. [PMID: 34906211 PMCID: PMC8670252 DOI: 10.1186/s13062-021-00316-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Microorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data. A dynamic reorganization of the transcriptome occurred during the first hours after salt shock, e.g. involving the upregulation of genes to activate compatible solute biochemistry balancing osmotic pressure. The massive accumulation of glucosylglycerol then had a measurable impact on the overall carbon and nitrogen metabolism. In addition, we observed the coordinated induction of putative regulatory RNAs and of several proteins known for their involvement in other stress responses. Overall, salt-induced changes in the proteome and transcriptome showed good correlations, especially among the stably up-regulated proteins and their transcripts. We define an extended salt stimulon comprising proteins directly or indirectly related to compatible solute metabolism, ion and water movements, and a distinct set of regulatory RNAs involved in post-transcriptional regulation. Our comprehensive data set provides the basis for engineering cyanobacterial salt tolerance and to further understand its regulation.
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Affiliation(s)
- Stephan Klähn
- Department of Solar Materials, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical Center, Rostock, Germany
| | - Matthias Riediger
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Freiburg, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute of Biosciences, University of Rostock, A.-Einstein-Str. 3, 18059 Rostock, Germany
- Department Life, Light and Matter, University of Rostock, Rostock, Germany
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Wang J, Huang X, Ge H, Wang Y, Chen W, Zheng L, Huang C, Yang H, Li L, Sui N, Wang Y, Zhang Y, Lu D, Fang L, Xu W, Jiang Y, Huang F, Wang Y. The Quantitative Proteome Atlas of a Model Cyanobacterium. J Genet Genomics 2021; 49:96-108. [PMID: 34775074 DOI: 10.1016/j.jgg.2021.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are a group of oxygenic photosynthetic bacteria with great potentials in biotechnological applications and advantages as models for photosynthesis research. The subcellular locations of the majority of proteins in any cyanobacteria remain undetermined, representing a major challenge in using cyanobacteria for both basic and industrial researches. Here, using label free quantitative proteomics we mapped 2027 proteins of Synechocystis sp. PCC6803, a model cyanobacterium, to different subcellular compartments, and generated a proteome atlas with such information. The atlas leads to numerous unexpected but important findings, including the predominant localization of the histidine kinases Hik33 and Hik27 on the thylakoid but not the plasma membrane. Such information completely changes the concept regarding how the two kinases are activated. Together, the atlas provides subcellular localization information for nearly 60% proteome of a model cyanobacterium, and will serve as an important resource for the cyanobacterial research community.
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Affiliation(s)
- Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyang Chen
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haomeng Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Lingyu Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Yu Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Yuqiang Jiang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Huang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China.
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Chen W, Zheng L, Dong J, Ge H, Huang X, Wang G, Huang C, Wang Y, Lu D, Xu W, Wang Y. A Systematic Survey of the Light/Dark-dependent Protein Degradation Events in a Model Cyanobacterium. Mol Cell Proteomics 2021; 20:100162. [PMID: 34655801 PMCID: PMC8603205 DOI: 10.1016/j.mcpro.2021.100162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 11/06/2022] Open
Abstract
Light is essential for photosynthetic organisms and is involved in the regulation of protein synthesis and degradation. The significance of light-regulated protein degradation is exemplified by the well-established light-induced degradation and repair of the photosystem II reaction center D1 protein in higher plants and cyanobacteria. However, systematic studies of light-regulated protein degradation events in photosynthetic organisms are lacking. Thus, we conducted a large-scale survey of protein degradation under light or dark conditions in the model cyanobacterium Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis) using the isobaric labeling-based quantitative proteomics technique. The results revealed that 79 proteins showed light-regulated degradation, including proteins involved in photosystem II structure or function, quinone binding, and NADH dehydrogenase. Among these, 25 proteins were strongly dependent on light for degradation. Moreover, the light-dependent degradation of several proteins was sensitive to photosynthetic electron transport inhibitors (DCMU and DBMIB), suggesting that they are influenced by the redox state of the plastoquinone (PQ) pool. Together, our study comprehensively cataloged light-regulated protein degradation events, and the results serve as an important resource for future studies aimed at understanding light-regulated processes and protein quality control mechanisms in cyanobacteria. Light-/dark-regulated protein degradation events in a model Cyanobacterium were identified. Seventy-nine proteins displayed light-regulated degradation. Thirty-one proteins displayed dark-regulated degradation. Multiple light-regulated protein degradation events were regulated by the redox state of the plastoquinone pool.
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Affiliation(s)
- Weiyang Chen
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinghui Dong
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Gaojie Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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Xu W, Wang Y. Post-translational Modifications of Serine/Threonine and Histidine Kinases and Their Roles in Signal Transductions in Synechocystis Sp. PCC 6803. Appl Biochem Biotechnol 2020; 193:687-716. [PMID: 33159456 DOI: 10.1007/s12010-020-03435-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/29/2020] [Indexed: 11/25/2022]
Abstract
Cyanobacterium Synechocystis sp. PCC 6803, a popular model organism for researches in photosynthesis and biofuel production, contains plant-like photosynthetic machineries which significantly contribute to global carbon fixation. There are 12 eukaryotic-type Ser/Thr kinases (SpkA-L) and 49 His kinases (Hik1-49) of two-component systems in the genome of Synechocystis sp. PCC 6803. They are the key regulators in sensing and transmitting stimuli including light- and glucose-mediate signal transduction. Proteomic studies were able to identify all the kinases. The majority of kinases no matter whether they have a predicted transmembrane domain were identified in the membrane fractions. Six Ser/Thr kinases (SpkA-D, F and G) and ten His kinases (Hik4, 12, 14, 21, 26-27, 29, 36, 43, and 46) were identified to have one or more of the three types of post-translational modifications: phosphorylation, acetylation, and thiol oxidation. Interestingly, SpkG has the phosphorylatable threonine residue that was aligned with the phosphorylated threonine residue in the activation loop of human CDK7, demonstrating conserved phosphorylation between cyanobacterial and human kinases. Transcriptomics and proteomics revealed differential expression of the kinases in heterotrophic and photoheterotrophic compared with photoautotrophic conditions, indicating their roles in regulating the growth modes of cyanobacteria. In summary, this review focuses on the discussions on post-transcriptional modifications, transcriptomic, and proteomic studies of Ser/Thr and His kinases. This together with our published review in 2019 present a complete story of an overview of sequences, domain architectures, and biochemical and physiological functions of cyanobacterial kinases with adequate details in the context of high throughput systems. We also emphasize the importance of discovering upstream molecules and substrates to understand the exact functions of the kinases in vivo. As an attempt, a model is proposed in which Hik31, His33, Sll1334, and IcfG are hypothesized to be critical for switching between autotrophic and heterotrophic modes based on the results from the phenotypes of the gene knockout strains combined with their post-translational modifications, and gene expression profiles.
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Affiliation(s)
- Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA.
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd, Beijing, 100101, China.
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Comparative Proteomic Profiling of Marine and Freshwater Synechocystis Strains Using Liquid Chromatography-Tandem Mass Spectrometry. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8100790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Freshwater Synechocystis sp. PCC 6803 has been considered to be a platform for the production of the next generation of biofuels and is used as a model organism in various fields. Various genomics, transcriptomics, metabolomics, and proteomics studies have been performed on this strain, whereas marine Synechocystis sp. PCC 7338 has not been widely studied despite its wide distribution. This study analyzed the proteome profiles of two Synechocystis strains using a liquid chromatography–tandem mass spectrometry-based bottom-up proteomic approach. Proteomic profiling of Synechocystis sp. PCC 7338 was performed for the first time with a data-dependent acquisition method, revealing 18,779 unique peptides and 1794 protein groups. A data-independent acquisition method was carried out for the comparative quantitation of Synechocystis sp. PCC 6803 and 7338. Among 2049 quantified proteins, 185 up- and 211 down-regulated proteins were defined in Synechocystis sp. PCC 7338. Some characteristics in the proteome of Synechocystis sp. PCC 7338 were revealed, such as its adaptation to living conditions, including the down-regulation of some photosynthesis proteins, the up-regulation of kdpB, and the use of osmolyte glycine as a substrate in C1 metabolism for the regulation of carbon flow. This study will facilitate further studies on Synechocystis 7338 to define in depth the proteomic differences between it and other Synechocystis strains.
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11
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Wang J, Zhang Y, Huang X, Lu D, Wang Y. Evaluation of the Potential Risk of Advanced Peak Determination in Distorting Isobaric Labeling-Based Single-Shot Proteome Quantitation. Proteomics 2020; 20:e1900255. [PMID: 32419311 DOI: 10.1002/pmic.201900255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 05/06/2020] [Indexed: 11/09/2022]
Abstract
The recent development and implementation of the advanced peak determination (APD) algorithm with MS instrument dramatically increased the sampling of low abundance features for MS/MS fragmentation. After in-depth evaluation, it is found that with APD on, many chimeric spectra are acquired through co-fragmentation of high abundance contaminants with low abundance targets, and such co-fragmentations are largely avoided when APD is off. To evaluate whether such a co-fragmentation could significantly distort the accuracy of the isobaric-labeling based quantitation of the low abundance target, a single-shot TMT experiment is performed using a two-proteome model, whereby each TMT channel contains premixed peptides from human and a cyanobacterium with a known ratio. Unexpectedly, it is found that APD does not significantly distort TMT ratios, probably because the majority of the APD-specific chimeric spectra are not identifiable. Nevertheless, a few examples of significant distortion of TMT ratios of low abundance peptides caused by APD is found through manual inspection, and suggests that APD should be off in a single-shot TMT experiment to avoid the laborious and time-costing manual inspection.
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Affiliation(s)
- Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing, 100101, China.,University of Chinese Academy of Sciences , Beijing, 100049, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing, 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing, 100101, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement , School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing, 100101, China.,University of Chinese Academy of Sciences , Beijing, 100049, China
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12
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Lysine Propionylation is a Widespread Post-Translational Modification Involved in Regulation of Photosynthesis and Metabolism in Cyanobacteria. Int J Mol Sci 2019; 20:ijms20194792. [PMID: 31561603 PMCID: PMC6801645 DOI: 10.3390/ijms20194792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Lysine propionylation is a reversible and widely distributed post-translational modification that is known to play a regulatory role in both eukaryotes and prokaryotes. However, the extent and function of lysine propionylation in photosynthetic organisms remains unclear. Cyanobacteria are the most ancient group of Gram-negative bacteria capable of oxygenic photosynthesis, and are of great importance to global carbon and nitrogen cycles. Here, we carried out a systematic study of lysine propionylaiton in cyanobacteria where we used Synechocystis sp. PCC 6803 (Synechocystis) as a model. Combining high-affinity anti-propionyllysine pan antibodies with high-accuracy mass spectrometry (MS) analysis, we identified 111 unique lysine propionylation sites on 69 proteins in Synechocystis. Further bioinformatic analysis showed that a large fraction of the propionylated proteins were involved in photosynthesis and metabolism. The functional significance of lysine propionylation on the enzymatic activity of fructose-1,6-bisphosphatase (FbpI) was studied by site-directed mutagenesis and biochemical studies. Further functional studies revealed that the propionylation level of subunit II of photosystem I (PsaD) was obviously increased after high light (HL) treatment, suggesting that propionylation may be involved in high light adaption in Synechocystis. Thus, our findings provide novel insights into the range of functions regulated by propionylation and reveal that reversible propionylation is a functional modification with the potential to regulate photosynthesis and carbon metabolism in Synechocystis, as well as in other photosynthetic organisms.
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13
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Gordon GC, Pfleger BF. Regulatory Tools for Controlling Gene Expression in Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1080:281-315. [PMID: 30091100 PMCID: PMC6662922 DOI: 10.1007/978-981-13-0854-3_12] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are attractive hosts for converting carbon dioxide and sunlight into desirable chemical products. To engineer these organisms and manipulate their metabolic pathways, the biotechnology community has developed genetic tools to control gene expression. Many native cyanobacterial promoters and related sequence elements have been used to regulate genes of interest, and heterologous tools that use non-native small molecules to induce gene expression have been demonstrated. Overall, IPTG-based induction systems seem to be leaky and initially demonstrate small dynamic ranges in cyanobacteria. Consequently, a variety of other induction systems have been optimized to enable tighter control of gene expression. Tools require significant optimization because they function quite differently in cyanobacteria when compared to analogous use in model heterotrophs. We hypothesize that these differences are due to fundamental differences in physiology between organisms. This review is not intended to summarize all known products made in cyanobacteria nor the performance (titer, rate, yield) of individual strains, but instead will focus on the genetic tools and the inherent aspects of cellular physiology that influence gene expression in cyanobacteria.
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Affiliation(s)
- Gina C Gordon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA.
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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14
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Battchikova N, Muth-Pawlak D, Aro EM. Proteomics of cyanobacteria: current horizons. Curr Opin Biotechnol 2018; 54:65-71. [DOI: 10.1016/j.copbio.2018.02.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 12/01/2022]
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15
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Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins. Cell Rep 2018; 25:478-486.e8. [DOI: 10.1016/j.celrep.2018.09.040] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/13/2018] [Accepted: 09/11/2018] [Indexed: 11/20/2022] Open
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16
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Systematic identification of light-regulated cold-responsive proteome in a model cyanobacterium. J Proteomics 2018; 179:100-109. [DOI: 10.1016/j.jprot.2018.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 11/19/2022]
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17
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Comparative Targeted Proteomics of the Central Metabolism and Photosystems in SigE Mutant Strains of Synechocystis sp. PCC 6803. Molecules 2018; 23:molecules23051051. [PMID: 29723969 PMCID: PMC6102573 DOI: 10.3390/molecules23051051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
A targeted proteome analysis was conducted to investigate the SigE dependent-regulation of central metabolism in Synechocystis sp. PCC 6803 by directly comparing the protein abundance profiles among the wild type, a sigE deletion mutant (ΔsigE), and a sigE over-expression (sigEox) strains. Expression levels of 112 target proteins, including the central metabolism related-enzymes and the subunits of the photosystems, were determined by quantifying the tryptic peptides in the multiple reaction monitoring (MRM) mode of liquid-chromatography–triple quadrupole mass spectrometry (LC–MS/MS). Comparison with gene-expression data showed that although the abundance of Gnd protein was closely correlated with that of gnd mRNA, there were poor correlations for GdhA/gdhA and glycogen degradation-related genes such as GlgX/glgX and GlgP/glgP pairs. These results suggested that the regulation of protein translation and degradation played a role in regulating protein abundance. The protein abundance profile suggested that SigE overexpression reduced the proteins involved in photosynthesis and increased GdhA abundance, which is involved in the nitrogen assimilation pathway using NADPH. The results obtained in this study successfully demonstrated that targeted proteome analysis enables direct comparison of the abundance of central metabolism- and photosystem-related proteins.
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18
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Ge H, Fang L, Huang X, Wang J, Chen W, Liu Y, Zhang Y, Wang X, Xu W, He Q, Wang Y. Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium. Mol Cell Proteomics 2018; 16:1258-1274. [PMID: 28668777 DOI: 10.1074/mcp.m116.068080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/07/2017] [Indexed: 01/18/2023] Open
Abstract
The histidine kinase Hik33 plays important roles in mediating cyanobacterial response to divergent types of abiotic stresses including cold, salt, high light (HL), and osmotic stresses. However, how these functions are regulated by Hik33 remains to be addressed. Using a hik33-deficient strain (Δhik33) of Synechocystis sp. PCC 6803 (Synechocystis) and quantitative proteomics, we found that Hik33 depletion induces differential protein expression highly like that induced by divergent types of stresses. This typically includes downregulation of proteins in photosynthesis and carbon assimilation that are necessary for cell propagation, and upregulation of heat shock proteins, chaperons, and proteases that are important for cell survival. This observation indicates that depletion of Hik33 alone mimics divergent types of abiotic stresses, and that Hik33 could be important for preventing abnormal stress response in the normal condition. Moreover, we found most proteins of plasmid origin were significantly upregulated in Δhik33, though their biological significance remains to be addressed. Together, the systematically characterized Hik33-regulated cyanobacterial proteome, which is largely involved in stress responses, builds the molecular basis for Hik33 as a general regulator of stress responses.
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Affiliation(s)
- Haitao Ge
- From the ‡State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan 250100, China
| | - Longfa Fang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiahe Huang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Jinlong Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiyang Chen
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Liu
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanya Zhang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Xiaorong Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Xu
- ‖Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504
| | - Qingfang He
- From the ‡State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan 250100, China; .,**Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas
| | - Yingchun Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China; .,¶University of Chinese Academy of Sciences, Beijing, 100049, China
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19
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Hagemann M, Hess WR. Systems and synthetic biology for the biotechnological application of cyanobacteria. Curr Opin Biotechnol 2017; 49:94-99. [PMID: 28843192 DOI: 10.1016/j.copbio.2017.07.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Their evolutionary relation to plastids in eukaryotic phototrophs and their increasing utilization as green cell factories initiated the use of systems biology approaches early on. For select model strains, extensive 'omics' data sets have been generated, and genome-wide models have been elucidated. Moreover, the results obtained may be used for the optimization of cyanobacterial metabolism, which can direct the biotechnological production of biofuels or chemical feedstock. Synthetic biology approaches permit the rational construction of novel metabolic pathways that are based on the combination of multiple enzymatic activities of different origins. In addition, the manipulation of whole metabolic networks by CRISPR-based and sRNA-based technologies with multiple parallel targets will further stimulate the use of cyanobacteria for diverse applications in basic research and biotechnology.
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Affiliation(s)
- Martin Hagemann
- University of Rostock, Institute of Biological Sciences, Plant Physiology, A.-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany
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20
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Ma Y, Yang M, Lin X, Liu X, Huang H, Ge F. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria. J Proteome Res 2017; 16:2030-2043. [DOI: 10.1021/acs.jproteome.7b00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yanyan Ma
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingkun Yang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaohuang Lin
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Huang
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Ge
- Key
Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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21
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Fang L, Ge H, Huang X, Liu Y, Lu M, Wang J, Chen W, Xu W, Wang Y. Trophic Mode-Dependent Proteomic Analysis Reveals Functional Significance of Light-Independent Chlorophyll Synthesis in Synechocystis sp. PCC 6803. MOLECULAR PLANT 2017; 10:73-85. [PMID: 27585879 DOI: 10.1016/j.molp.2016.08.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/03/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
The photosynthetic model organism Synechocystis sp. PCC 6803 can grow in different trophic modes, depending on the availability of light and exogenous organic carbon source. However, how the protein profile changes to facilitate the cells differentially propagate in different modes has not been comprehensively investigated. Using isobaric labeling-based quantitative proteomics, we simultaneously identified and quantified 45% Synechocystis proteome across four different trophic modes, i.e., autotrophic, heterotrophic, photoheterotrophic, and mixotrophic modes. Among the 155 proteins that are differentially expressed across four trophic modes, proteins involved in nitrogen assimilation and light-independent chlorophyll synthesis are dramatically upregulated in the mixotrophic mode, concomitant with a dramatic increase of PII phosphorylation that senses carbon and nitrogen assimilation status. Moreover, functional study using a mutant defective in light-independent chlorophyll synthesis revealed that this pathway is important for chlorophyll accumulation under a cycled light/dark illumination regime, a condition mimicking day/night cycles in certain natural habitats. Collectively, these results provide the most comprehensive information on trophic mode-dependent protein expression in cyanobacterium, and reveal the functional significance of light-independent chlorophyll synthesis in trophic growth.
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Affiliation(s)
- Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Ye Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Min Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Weiyang Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Road, Beijing 100101, China.
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22
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Baumgartner D, Kopf M, Klähn S, Steglich C, Hess WR. Small proteins in cyanobacteria provide a paradigm for the functional analysis of the bacterial micro-proteome. BMC Microbiol 2016; 16:285. [PMID: 27894276 PMCID: PMC5126843 DOI: 10.1186/s12866-016-0896-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
Abstract
Background Despite their versatile functions in multimeric protein complexes, in the modification of enzymatic activities, intercellular communication or regulatory processes, proteins shorter than 80 amino acids (μ-proteins) are a systematically underestimated class of gene products in bacteria. Photosynthetic cyanobacteria provide a paradigm for small protein functions due to extensive work on the photosynthetic apparatus that led to the functional characterization of 19 small proteins of less than 50 amino acids. In analogy, previously unstudied small ORFs with similar degrees of conservation might encode small proteins of high relevance also in other functional contexts. Results Here we used comparative transcriptomic information available for two model cyanobacteria, Synechocystis sp. PCC 6803 and Synechocystis sp. PCC 6714 for the prediction of small ORFs. We found 293 transcriptional units containing candidate small ORFs ≤80 codons in Synechocystis sp. PCC 6803, also including the known mRNAs encoding small proteins of the photosynthetic apparatus. From these transcriptional units, 146 are shared between the two strains, 42 are shared with the higher plant Arabidopsis thaliana and 25 with E. coli. To verify the existence of the respective μ-proteins in vivo, we selected five genes as examples to which a FLAG tag sequence was added and re-introduced them into Synechocystis sp. PCC 6803. These were the previously annotated gene ssr1169, two newly defined genes norf1 and norf4, as well as nsiR6(nitrogen stress-induced RNA 6) and hliR1(high light-inducible RNA 1) , which originally were considered non-coding. Upon activation of expression via the Cu2+.responsive petE promoter or from the native promoters, all five proteins were detected in Western blot experiments. Conclusions The distribution and conservation of these five genes as well as their regulation of expression and the physico-chemical properties of the encoded proteins underline the likely great bandwidth of small protein functions in bacteria and makes them attractive candidates for functional studies.
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Affiliation(s)
- Desiree Baumgartner
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Matthias Kopf
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany.,Present Address: Molecular Health GmbH, Kurfürsten-Anlage 21, 69115, Heidelberg, Germany
| | - Stephan Klähn
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Claudia Steglich
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104, Freiburg, Germany.
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23
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Liberton M, Saha R, Jacobs JM, Nguyen AY, Gritsenko MA, Smith RD, Koppenaal DW, Pakrasi HB. Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium. Mol Cell Proteomics 2016; 15:2021-32. [PMID: 27056914 DOI: 10.1074/mcp.m115.057240] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 01/10/2023] Open
Abstract
Cyanobacteria are photosynthetic microbes with highly differentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems in cyanobacteria, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes, many more proteins remain to be identified, and a comprehensive catalogue of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 differentially localized proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared with the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared with a more specialized role for the thylakoid membrane in cellular energetics. Thus, our data clearly define the two membrane systems with distinct functions. Overall, the protein compositions of the Synechocystis 6803 plasma membrane and thylakoid membrane are quite similar to that of the plasma membrane of Escherichia coli and thylakoid membrane of Arabidopsis chloroplasts, respectively. Synechocystis 6803 can therefore be described as a Gram-negative bacterium with an additional internal membrane system that fulfills the energetic requirements of the cell.
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Affiliation(s)
- Michelle Liberton
- From the ‡Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Rajib Saha
- From the ‡Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Jon M Jacobs
- §Pacific Northwest National Laboratory, Richland, Washington 63130
| | - Amelia Y Nguyen
- From the ‡Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | - Richard D Smith
- §Pacific Northwest National Laboratory, Richland, Washington 63130
| | | | - Himadri B Pakrasi
- From the ‡Department of Biology, Washington University, St. Louis, Missouri 63130;
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24
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Sinetova MA, Los DA. Systemic analysis of stress transcriptomics of Synechocystis reveals common stress genes and their universal triggers. MOLECULAR BIOSYSTEMS 2016; 12:3254-3258. [DOI: 10.1039/c6mb00551a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Systemic analysis of stress transcriptomics reveals that ROS and redox changes may universally trigger stress responses in Synechocystis (cyanobacteria).
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Affiliation(s)
- M. A. Sinetova
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow
- Russia
| | - D. A. Los
- Institute of Plant Physiology
- Russian Academy of Sciences
- Moscow
- Russia
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