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Krynická V, Komenda J. The Role of FtsH Complexes in the Response to Abiotic Stress in Cyanobacteria. PLANT & CELL PHYSIOLOGY 2024; 65:1103-1114. [PMID: 38619128 PMCID: PMC11287208 DOI: 10.1093/pcp/pcae042] [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: 12/28/2023] [Revised: 03/24/2024] [Accepted: 04/12/2024] [Indexed: 04/16/2024]
Abstract
FtsH proteases (FtsHs) belong to intramembrane ATP-dependent metalloproteases which are widely distributed in eubacteria, mitochondria and chloroplasts. The best-studied roles of FtsH in Escherichia coli include quality control of membrane proteins, regulation of response to heat shock, superoxide stress and viral infection, and control of lipopolysaccharide biosynthesis. While heterotrophic bacteria mostly contain a single indispensable FtsH complex, photosynthetic cyanobacteria usually contain three FtsH complexes: two heterocomplexes and one homocomplex. The essential cytoplasmic FtsH1/3 most probably fulfills a role similar to other bacterial FtsHs, whereas the thylakoid FtsH2/3 heterocomplex and FtsH4 homocomplex appear to maintain the photosynthetic apparatus of cyanobacteria and optimize its functionality. Moreover, recent studies suggest the involvement of all FtsH proteases in a complex response to nutrient stresses. In this review, we aim to comprehensively evaluate the functions of the cyanobacterial FtsHs specifically under stress conditions with emphasis on nutrient deficiency and high irradiance. We also point to various unresolved issues concerning FtsH functions, which deserve further attention.
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Affiliation(s)
- Vendula Krynická
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický Mlýn, Novohradská 237, Třeboň 37901, The Czech Republic
| | - Josef Komenda
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Opatovický Mlýn, Novohradská 237, Třeboň 37901, The Czech Republic
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Sarasa-Buisan C, Nieves-Morión M, Arévalo S, Helm RF, Sevilla E, Luque I, Fillat MF. FurC (PerR) contributes to the regulation of peptidoglycan remodeling and intercellular molecular transfer in the cyanobacterium Anabaena sp. strain PCC 7120. mBio 2024; 15:e0323123. [PMID: 38334377 PMCID: PMC10936207 DOI: 10.1128/mbio.03231-23] [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: 12/04/2023] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
Microbial extracellular proteins and metabolites provide valuable information concerning how microbes adapt to changing environments. In cyanobacteria, dynamic acclimation strategies involve a variety of regulatory mechanisms, being ferric uptake regulator proteins as key players in this process. In the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120, FurC (PerR) is a global regulator that modulates the peroxide response and several genes involved in photosynthesis and nitrogen metabolism. To investigate the possible role of FurC in shaping the extracellular environment of Anabaena, the analysis of the extracellular metabolites and proteins of a furC-overexpressing variant was compared to that of the wild-type strain. There were 96 differentially abundant proteins, 78 of which were found for the first time in the extracellular fraction of Anabaena. While these proteins belong to different functional categories, most of them are predicted to be secreted or have a peripheral location. Several stress-related proteins, including PrxA, flavodoxin, and the Dps homolog All1173, accumulated in the exoproteome of furC-overexpressing cells, while decreased levels of FurA and a subset of membrane proteins, including several export proteins and amiC gene products, responsible for nanopore formation, were detected. Direct repression by FurC of some of those genes, including amiC1 and amiC2, could account for odd septal nanopore formation and impaired intercellular molecular transfer observed in the furC-overexpressing variant. Assessment of the exometabolome from both strains revealed the release of two peptidoglycan fragments in furC-overexpressing cells, namely 1,6-anhydro-N-acetyl-β-D-muramic acid (anhydroMurNAc) and its associated disaccharide (β-D-GlcNAc-(1-4)-anhydroMurNAc), suggesting alterations in peptidoglycan breakdown and recycling.IMPORTANCECyanobacteria are ubiquitous photosynthetic prokaryotes that can adapt to environmental stresses by modulating their extracellular contents. Measurements of the organization and composition of the extracellular milieu provide useful information about cyanobacterial adaptive processes, which can potentially lead to biomimetic approaches to stabilizing biological systems to adverse conditions. Anabaena sp. strain PCC 7120 is a multicellular, nitrogen-fixing cyanobacterium whose intercellular molecular exchange is mediated by septal junctions that traverse the septal peptidoglycan through nanopores. FurC (PerR) is an essential transcriptional regulator in Anabaena, which modulates the response to several stresses. Here, we show that furC-overexpressing cells result in a modified exoproteome and the release of peptidoglycan fragments. Phenotypically, important alterations in nanopore formation and cell-to-cell communication were observed. Our results expand the roles of FurC to the modulation of cell-wall biogenesis and recycling, as well as in intercellular molecular transfer.
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Affiliation(s)
- Cristina Sarasa-Buisan
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Mercedes Nieves-Morión
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Sergio Arévalo
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - Richard F. Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA
| | - Emma Sevilla
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Sevilla, Spain
| | - María F. Fillat
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias e Instituto de Biocomputación y Física de Sistemas Complejos. Universidad de Zaragoza, Zaragoza, Spain
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Koník P, Skotnicová P, Gupta S, Tichý M, Sharma S, Komenda J, Sobotka R, Krynická V. The cyanobacterial FtsH4 protease controls accumulation of protein factors involved in the biogenesis of photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149017. [PMID: 37827327 DOI: 10.1016/j.bbabio.2023.149017] [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: 05/30/2023] [Revised: 09/18/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Membrane-bound FtsH proteases are universally present in prokaryotes and in mitochondria and chloroplasts of eukaryotic cells. These metalloproteases are often critical for viability and play both protease and chaperone roles to maintain cellular homeostasis. In contrast to most bacteria bearing a single ftsH gene, cyanobacteria typically possess four FtsH proteases (FtsH1-4) forming heteromeric (FtsH1/3 and FtsH2/3) and homomeric (FtsH4) complexes. The functions and substrate repertoire of each complex are however poorly understood. To identify substrates of the FtsH4 protease complex we established a trapping assay in the cyanobacterium Synechocystis PCC 6803 utilizing a proteolytically inactivated trapFtsH4-His. Around 40 proteins were specifically enriched in trapFtsH4 pulldown when compared with the active FtsH4. As the list of putative FtsH4 substrates contained Ycf4 and Ycf37 assembly factors of Photosystem I (PSI), its core PsaB subunit and the IsiA chlorophyll-binding protein that associates with PSI during iron stress, we focused on these PSI-related proteins. Therefore, we analysed their degradation by FtsH4 in vivo in Synechocystis mutants and in vitro using purified substrates. The data confirmed that FtsH4 degrades Ycf4, Ycf37, IsiA, and also the individual PsaA and PsaB subunits in the unassembled state but not when assembled within the PSI complexes. A possible role of FtsH4 in the PSI life-cycle is discussed.
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Affiliation(s)
- Peter Koník
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Petra Skotnicová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic
| | - Sadanand Gupta
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Martin Tichý
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic
| | - Surbhi Sharma
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Josef Komenda
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Vendula Krynická
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Třeboň 379 01, Czech Republic.
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Masuda T, Bečková M, Turóczy Z, Pilný J, Sobotka R, Trinugroho JP, Nixon PJ, Prášil O, Komenda J. Accumulation of Cyanobacterial Photosystem II Containing the 'Rogue' D1 Subunit Is Controlled by FtsH Protease and Synthesis of the Standard D1 Protein. PLANT & CELL PHYSIOLOGY 2023; 64:660-673. [PMID: 36976618 DOI: 10.1093/pcp/pcad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/16/2023]
Abstract
Unicellular diazotrophic cyanobacteria contribute significantly to the photosynthetic productivity of the ocean and the fixation of molecular nitrogen, with photosynthesis occurring during the day and nitrogen fixation during the night. In species like Crocosphaera watsonii WH8501, the decline in photosynthetic activity in the night is accompanied by the disassembly of oxygen-evolving photosystem II (PSII) complexes. Moreover, in the second half of the night phase, a small amount of rogue D1 (rD1), which is related to the standard form of the D1 subunit found in oxygen-evolving PSII, but of unknown function, accumulates but is quickly degraded at the start of the light phase. We show here that the removal of rD1 is independent of the rD1 transcript level, thylakoid redox state and trans-thylakoid pH but requires light and active protein synthesis. We also found that the maximal level of rD1 positively correlates with the maximal level of chlorophyll (Chl) biosynthesis precursors and enzymes, which suggests a possible role for rogue PSII (rPSII) in the activation of Chl biosynthesis just before or upon the onset of light, when new photosystems are synthesized. By studying strains of Synechocystis PCC 6803 expressing Crocosphaera rD1, we found that the accumulation of rD1 is controlled by the light-dependent synthesis of the standard D1 protein, which triggers the fast FtsH2-dependent degradation of rD1. Affinity purification of FLAG-tagged rD1 unequivocally demonstrated the incorporation of rD1 into a non-oxygen-evolving PSII complex, which we term rPSII. The complex lacks the extrinsic proteins stabilizing the oxygen-evolving Mn4CaO5 cluster but contains the Psb27 and Psb28-1 assembly factors.
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Affiliation(s)
- Takako Masuda
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Martina Bečková
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Zoltán Turóczy
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Jan Pilný
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice 370 05, Czech Republic
| | - Joko P Trinugroho
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Peter J Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Ondřej Prášil
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
| | - Josef Komenda
- Institute of Microbiology, The Czech Academy of Sciences, Centre Algatech, Opatovický mlýn, Třeboň 37901, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice 370 05, Czech Republic
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Wang Y, Ge H, Xiao Z, Huang C, Wang G, Duan X, Zheng L, Dong J, Huang X, Zhang Y, An H, Xu W, Wang Y. Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses. J Proteome Res 2023; 22:1255-1269. [PMID: 36930737 DOI: 10.1021/acs.jproteome.2c00759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Spatial proteome reorganization in response to a changing environment represents a different layer of adaptation mechanism in addition to differential expression of a subset of stress responsive genes in photosynthetic organisms. Profiling such reorganization events is critically important to extend our understanding how photosynthetic organisms adapt to adverse environments. Thus, we treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis), with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble fractions using a quantitative proteomics approach. A number of proteins showing such a redistribution in response to a single or multiple types of abiotic stresses were identified. These include 12 ribosomal proteins displaying unanimous cold-induced redistribution to the membrane and the protein FurA, a master regulator of iron acquisition, displaying iron deficiency- and nitrogen starvation-induced redistribution to the membrane. Such findings shed light on a novel regulatory mechanism underlying the corresponding stress responses, and establish the results in the present study as an important resource for future studies intended to understand how photosynthetic organisms cope with adverse environments.
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Affiliation(s)
- 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, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, 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, No.1 West Beichen Road, Beijing 100101, China
| | - Zhen Xiao
- 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 Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, 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, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, 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, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Xiaoxiao Duan
- 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 Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, 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, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, 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, No.1 West Beichen Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, 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 Road, Beijing 100101, 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 Road, Beijing 100101, China
| | - Hongyu An
- 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 Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, United States
| | - 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 Road, Beijing 100101, China.,University of Chinese Academy of Sciences, Huairou District, Beijing 101408, China
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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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Krynická V, Skotnicová P, Jackson PJ, Barnett S, Yu J, Wysocka A, Kaňa R, Dickman MJ, Nixon PJ, Hunter CN, Komenda J. FtsH4 protease controls biogenesis of the PSII complex by dual regulation of high light-inducible proteins. PLANT COMMUNICATIONS 2023; 4:100502. [PMID: 36463410 PMCID: PMC9860182 DOI: 10.1016/j.xplc.2022.100502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
FtsH proteases are membrane-embedded proteolytic complexes important for protein quality control and regulation of various physiological processes in bacteria, mitochondria, and chloroplasts. Like most cyanobacteria, the model species Synechocystis sp. PCC 6803 contains four FtsH homologs, FtsH1-FtsH4. FtsH1-FtsH3 form two hetero-oligomeric complexes, FtsH1/3 and FtsH2/3, which play a pivotal role in acclimation to nutrient deficiency and photosystem II quality control, respectively. FtsH4 differs from the other three homologs by the formation of a homo-oligomeric complex, and together with Arabidopsis thaliana AtFtsH7/9 orthologs, it has been assigned to another phylogenetic group of unknown function. Our results exclude the possibility that Synechocystis FtsH4 structurally or functionally substitutes for the missing or non-functional FtsH2 subunit in the FtsH2/3 complex. Instead, we demonstrate that FtsH4 is involved in the biogenesis of photosystem II by dual regulation of high light-inducible proteins (Hlips). FtsH4 positively regulates expression of Hlips shortly after high light exposure but is also responsible for Hlip removal under conditions when their elevated levels are no longer needed. We provide experimental support for Hlips as proteolytic substrates of FtsH4. Fluorescent labeling of FtsH4 enabled us to assess its localization using advanced microscopic techniques. Results show that FtsH4 complexes are concentrated in well-defined membrane regions at the inner and outer periphery of the thylakoid system. Based on the identification of proteins that co-purified with the tagged FtsH4, we speculate that FtsH4 concentrates in special compartments in which the biogenesis of photosynthetic complexes takes place.
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Affiliation(s)
- Vendula Krynická
- The Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, Novohradská 237, 379 01 Třeboň, Czech Republic.
| | - Petra Skotnicová
- The Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, Novohradská 237, 379 01 Třeboň, Czech Republic
| | - 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
| | - Samuel Barnett
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Jianfeng Yu
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Anna Wysocka
- The Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, Novohradská 237, 379 01 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Radek Kaňa
- The Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, Novohradská 237, 379 01 Třeboň, Czech Republic
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Peter J Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Josef Komenda
- The Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, Novohradská 237, 379 01 Třeboň, Czech Republic
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Yi L, Liu B, Nixon PJ, Yu J, Chen F. Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases. FRONTIERS IN PLANT SCIENCE 2022; 13:837528. [PMID: 35463435 PMCID: PMC9020784 DOI: 10.3389/fpls.2022.837528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/24/2022] [Indexed: 05/18/2023]
Abstract
The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.
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Affiliation(s)
- Lanbo Yi
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Bin Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Peter J. Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Peter J. Nixon, ; orcid.org/0000-0003-1952-6937
| | - Jianfeng Yu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, London, United Kingdom
- Jianfeng Yu, ; orcid.org/0000-0001-7174-3803
| | - Feng Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
- Feng Chen, ; orcid.org/0000-0002-9054-943X
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Jia A, Zheng Y, Chen H, Wang Q. Regulation and Functional Complexity of the Chlorophyll-Binding Protein IsiA. Front Microbiol 2021; 12:774107. [PMID: 34867913 PMCID: PMC8635728 DOI: 10.3389/fmicb.2021.774107] [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: 09/11/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
As the oldest known lineage of oxygen-releasing photosynthetic organisms, cyanobacteria play the key roles in helping shaping the ecology of Earth. Iron is an ideal transition metal for redox reactions in biological systems. Cyanobacteria frequently encounter iron deficiency due to the environmental oxidation of ferrous ions to ferric ions, which are highly insoluble at physiological pH. A series of responses, including architectural changes to the photosynthetic membranes, allow cyanobacteria to withstand this condition and maintain photosynthesis. Iron-stress-induced protein A (IsiA) is homologous to the cyanobacterial chlorophyll (Chl)-binding protein, photosystem II core antenna protein CP43. IsiA is the major Chl-containing protein in iron-starved cyanobacteria, binding up to 50% of the Chl in these cells, and this Chl can be released from IsiA for the reconstruction of photosystems during the recovery from iron limitation. The pigment–protein complex (CPVI-4) encoded by isiA was identified and found to be expressed under iron-deficient conditions nearly 30years ago. However, its precise function is unknown, partially due to its complex regulation; isiA expression is induced by various types of stresses and abnormal physiological states besides iron deficiency. Furthermore, IsiA forms a range of complexes that perform different functions. In this article, we describe progress in understanding the regulation and functions of IsiA based on laboratory research using model cyanobacteria.
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Affiliation(s)
- Anqi Jia
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yanli Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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10
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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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11
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Riediger M, Hernández-Prieto MA, Song K, Hess WR, Futschik ME. Genome-wide identification and characterization of Fur-binding sites in the cyanobacteria Synechocystis sp. PCC 6803 and PCC 6714. DNA Res 2021; 28:6407143. [PMID: 34672328 PMCID: PMC8634477 DOI: 10.1093/dnares/dsab023] [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: 06/21/2021] [Accepted: 10/16/2021] [Indexed: 11/16/2022] Open
Abstract
The Ferric uptake regulator (Fur) is crucial to both pathogenic and non-pathogenic bacteria for the maintenance of iron homeostasis as well as the defence against reactive oxygen species. Based on datasets from the genome-wide mapping of transcriptional start sites and transcriptome data, we identified a high confidence regulon controlled by Fur for the model cyanobacterium Synechocystis sp. PCC 6803 and its close relative, strain 6714, based on the conserved strong iron starvation response and Fur-binding site occurrence. This regulon comprises 33 protein-coding genes and the sRNA IsaR1 that are under the control of 16 or 14 individual promoters in strains 6803 and 6714, respectively. The associated gene functions are mostly restricted to transporters and enzymes involved in the uptake and storage of iron ions, with few exceptions or unknown functional relevance. Within the isiABC operon, we identified a previously neglected gene encoding a small cysteine-rich protein, which we suggest calling, IsiE. The regulation of iron uptake, storage, and utilization ultimately results from the interplay between the Fur regulon, several other transcription factors, the FtsH3 protease, and the sRNA IsaR1.
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Affiliation(s)
- Matthias Riediger
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Miguel A Hernández-Prieto
- ARC Centre of Excellence for Translational Photosynthesis & School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kuo Song
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Wolfgang R Hess
- Institute of Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Matthias E Futschik
- SysBioLab, Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.,MRC London Institute of Medical Sciences (LMS), Faculty of Medicine, Imperial College London, London W12 0NN, UK
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12
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New insights into the function of the proteins IsiC and IsiD from Synechocystis sp. PCC 6803 under iron limitation. Appl Microbiol Biotechnol 2021; 105:4693-4707. [PMID: 34019114 DOI: 10.1007/s00253-021-11347-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 10/25/2022]
Abstract
Iron is a common cofactor in biological processes such as respiration, photosynthesis, and nitrogen fixation. The genes isiC and isiD encode unknown proteins, and the growth of ΔisiC and ΔisiD mutants is inhibited under iron-deficient conditions. To study the regulatory mechanisms of IsiC and IsiD during iron starvation, we carried out transcriptome and metabolome sequencing. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the photosynthesis, nitrogen metabolism, and ABC transporter pathways play a vital role in regulating iron deficiency. Upon iron repletion, IsiC and IsiD also have a regulatory effect on these pathways. Additionally, KEGG analysis of the differential metabolites of wild type (WT) and mutants showed that they were all enriched in starch and sucrose metabolism after iron limitation. Weighted gene co-expression network analysis (WGCNA) constructed a co-expression network of differentially expressed genes with phenotypes and metabolites, and finally identified five modules. The turquoise module was positively correlated with iron deficiency. In contrast, the WT and blue module exhibited a negative correlation, and the mutants ΔisiC and ΔisiD were positively correlated with the gray and brown modules, respectively. WGCNA also analyzed the relationship between metabolites and phenotypes, and the green module was related to iron starvation. The co-expression network determined the hub genes and metabolites of each module. This study lays a foundation for a better understanding of cyanobacteria in response to iron deficiency. KEY POINTS: • Nitrogen metabolism and ABC transporters are involved in iron regulation. • Starch and sucrose metabolism is related to the regulation of iron deficiency. • WGCNA analyzes the correlation between genes and metabolites.
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13
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Lambrecht SJ, Steglich C, Hess WR. A minimum set of regulators to thrive in the ocean. FEMS Microbiol Rev 2020; 44:232-252. [DOI: 10.1093/femsre/fuaa005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.
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Affiliation(s)
- S Joke Lambrecht
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
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14
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Muro-Pastor AM, Hess WR. Regulatory RNA at the crossroads of carbon and nitrogen metabolism in photosynthetic cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194477. [PMID: 31884117 DOI: 10.1016/j.bbagrm.2019.194477] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are photosynthetic bacteria that populate widely different habitats. Accordingly, cyanobacteria exhibit a wide spectrum of lifestyles, physiologies, and morphologies and possess genome sizes and gene numbers which may vary by up to a factor of ten within the phylum. Consequently, large differences exist between individual species in the size and complexity of their regulatory networks. Several non-coding RNAs have been identified that play crucial roles in the acclimation responses of cyanobacteria to changes in the environment. Some of these regulatory RNAs are conserved throughout the cyanobacterial phylum, while others exist only in a few taxa. Here we give an overview on characterized regulatory RNAs in cyanobacteria, with a focus on regulators of photosynthesis, carbon and nitrogen metabolism. However, chances are high that these regulators represent just the tip of the iceberg.
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Affiliation(s)
- Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, E-41092 Sevilla, Spain
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
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15
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Gale GAR, Schiavon Osorio AA, Mills LA, Wang B, Lea-Smith DJ, McCormick AJ. Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology. Microorganisms 2019; 7:E409. [PMID: 31569579 PMCID: PMC6843473 DOI: 10.3390/microorganisms7100409] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 09/22/2019] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Recent advances in synthetic biology and an emerging algal biotechnology market have spurred a prolific increase in the availability of molecular tools for cyanobacterial research. Nevertheless, work to date has focused primarily on only a small subset of model species, which arguably limits fundamental discovery and applied research towards wider commercialisation. Here, we review the requirements for uptake of new strains, including several recently characterised fast-growing species and promising non-model species. Furthermore, we discuss the potential applications of new techniques available for transformation, genetic engineering and regulation, including an up-to-date appraisal of current Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein (CRISPR/Cas) and CRISPR interference (CRISPRi) research in cyanobacteria. We also provide an overview of several exciting molecular tools that could be ported to cyanobacteria for more advanced metabolic engineering approaches (e.g., genetic circuit design). Lastly, we introduce a forthcoming mutant library for the model species Synechocystis sp. PCC 6803 that promises to provide a further powerful resource for the cyanobacterial research community.
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Affiliation(s)
- Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - Alejandra A Schiavon Osorio
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK.
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, UK.
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16
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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: 12] [Impact Index Per Article: 2.4] [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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Kamal SM, Rybtke ML, Nimtz M, Sperlein S, Giske C, Trček J, Deschamps J, Briandet R, Dini L, Jänsch L, Tolker-Nielsen T, Lee C, Römling U. Two FtsH Proteases Contribute to Fitness and Adaptation of Pseudomonas aeruginosa Clone C Strains. Front Microbiol 2019; 10:1372. [PMID: 31338071 PMCID: PMC6629908 DOI: 10.3389/fmicb.2019.01372] [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] [Received: 04/19/2019] [Accepted: 05/31/2019] [Indexed: 12/30/2022] Open
Abstract
Pseudomonas aeruginosa is an environmental bacterium and a nosocomial pathogen with clone C one of the most prevalent clonal groups. The P. aeruginosa clone C specific genomic island PACGI-1 harbors a xenolog of ftsH encoding a functionally diverse membrane-spanning ATP-dependent metalloprotease on the core genome. In the aquatic isolate P. aeruginosa SG17M, the core genome copy ftsH1 significantly affects growth and dominantly mediates a broad range of phenotypes, such as secretion of secondary metabolites, swimming and twitching motility and resistance to aminoglycosides, while the PACGI-1 xenolog ftsH2 backs up the phenotypes in the ftsH1 mutant background. The two proteins, with conserved motifs for disaggregase and protease activity present in FtsH1 and FtsH2, have the ability to form homo- and hetero-oligomers with ftsH2 distinctively expressed in the late stationary phase of growth. However, mainly FtsH1 degrades a major substrate, the heat shock transcription factor RpoH. Pull-down experiments with substrate trap-variants inactive in proteolytic activity indicate both FtsH1 and FtsH2 to interact with the inhibitory protein HflC, while the phenazine biosynthesis protein PhzC was identified as a substrate of FtsH1. In summary, as an exception in P. aeruginosa, clone C harbors two copies of the ftsH metallo-protease, which cumulatively are required for the expression of a diversity of phenotypes.
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Affiliation(s)
- Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, New Cairo, Egypt
| | - Morten Levin Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manfred Nimtz
- Department of Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefanie Sperlein
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christian Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | - Julien Deschamps
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Luciana Dini
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Lothar Jänsch
- Department of Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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18
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Riediger M, Kadowaki T, Nagayama R, Georg J, Hihara Y, Hess WR. Biocomputational Analyses and Experimental Validation Identify the Regulon Controlled by the Redox-Responsive Transcription Factor RpaB. iScience 2019; 15:316-331. [PMID: 31103851 PMCID: PMC6525291 DOI: 10.1016/j.isci.2019.04.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/05/2019] [Accepted: 04/24/2019] [Indexed: 11/24/2022] Open
Abstract
Oxygenic photosynthesis requires the coordination of environmental stimuli with the regulation of transcription. The transcription factor RpaB is conserved from the simplest unicellular cyanobacteria to complex eukaryotic algae, representing more than 1 billion years of evolution. To predict the RpaB-controlled regulon in the cyanobacterium Synechocystis, we analyzed the positional distribution of binding sites together with high-resolution mapping data of transcriptional start sites (TSSs). We describe more than 150 target promoters whose activity responds to fluctuating light conditions. Binding sites close to the TSS mediate repression, whereas sites centered ∼50 nt upstream mediate activation. Using complementary experimental approaches, we found that RpaB controls genes involved in photoprotection, cyclic electron flow and state transitions, photorespiration, and nirA and isiA for which we suggest cross-regulation with the transcription factors NtcA or FurA. The deep integration of RpaB with diverse photosynthetic gene functions makes it one of the most important and versatile transcriptional regulators. RpaB controls a complex regulon, widely beyond the photosynthetic machinery The expression of the RNA regulators IsrR, PsrR1, and others depends on RpaB RpaB exhibits cross-regulations with other transcription factors, NtcA and Fur RpaB is a crucial transcriptional regulator in a photosynthetic microorganism
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Affiliation(s)
- Matthias Riediger
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Ryuta Nagayama
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Jens Georg
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan.
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany; Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany.
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19
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Bonisteel EM, Turner BE, Murphy CD, Melanson JR, Duff NM, Beardsall BD, Xu K, Campbell DA, Cockshutt AM. Strain specific differences in rates of Photosystem II repair in picocyanobacteria correlate to differences in FtsH protein levels and isoform expression patterns. PLoS One 2018; 13:e0209115. [PMID: 30566504 PMCID: PMC6300248 DOI: 10.1371/journal.pone.0209115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/29/2018] [Indexed: 12/23/2022] Open
Abstract
Picocyanobacteria are the numerically dominant photoautotrophs of the oligotrophic regions of Earth’s oceans. These organisms are characterized by their small size and highly reduced genomes. Strains partition to different light intensity and nutrient level niches, with differing photosynthetic apparatus stoichiometry, light harvesting machinery and susceptibility to photoinactivation. In this study, we grew three strains of picocyanobacteria: the low light, high nutrient strain Prochlorococcus marinus MIT 9313; the high light, low nutrient Prochlorococcus marinus MED 4; and the high light, high nutrient marine Synechococcus strain WH 8102; under low and high growth light levels. We then performed matched photophysiology, protein and transcript analyses. The strains differ significantly in their rates of Photosystem II repair under high light and in their capacity to remove the PsbA protein as the first step in the Photosystem II repair process. Notably, all strains remove the PsbD subunit at the same rate that they remove PsbA. When grown under low light, MIT 9313 loses active Photosystem II quickly when shifted to high light, but has no measurable capacity to remove PsbA. MED 4 and WH 8102 show less rapid loss of Photosystem II and considerable capacity to remove PsbA. MIT 9313 has less of the FtsH protease thought to be responsible for the removal of PsbA in other cyanobacteria. Furthermore, by transcript analysis the predominant FtsH isoform expressed in MIT 9313 is homologous to the FtsH 4 isoform characterized in the model strain Synechocystis PCC 6803, rather than the FtsH 2 and 3 isoforms thought to be responsible for PsbA degradation. MED 4 on the other hand shows high light inducible expression of the isoforms homologous to FtsH 2 and 3, consistent with its faster rate of PsbA removal. MIT 9313 has adapted to its low light environment by diverting resources away from Photosystem II content and repair.
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Affiliation(s)
- Erin M. Bonisteel
- Department of Chemistry & Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
| | - Brooke E. Turner
- Department of Chemistry & Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
| | - Cole D. Murphy
- Department of Chemistry & Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
| | - Jenna-Rose Melanson
- Department of Chemistry & Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
| | - Nicole M. Duff
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Brian D. Beardsall
- Department of Chemistry & Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
| | - Kui Xu
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Douglas A. Campbell
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Amanda M. Cockshutt
- Department of Chemistry & Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
- * E-mail:
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20
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Skotnicová P, Sobotka R, Shepherd M, Hájek J, Hrouzek P, Tichý M. The cyanobacterial protoporphyrinogen oxidase HemJ is a new b-type heme protein functionally coupled with coproporphyrinogen III oxidase. J Biol Chem 2018; 293:12394-12404. [PMID: 29925590 DOI: 10.1074/jbc.ra118.003441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/14/2018] [Indexed: 12/27/2022] Open
Abstract
Protoporphyrinogen IX oxidase (PPO), the last enzyme that is common to both chlorophyll and heme biosynthesis pathways, catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX. PPO has several isoforms, including the oxygen-dependent HemY and an oxygen-independent enzyme, HemG. However, most cyanobacteria encode HemJ, the least characterized PPO form. We have characterized HemJ from the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) as a bona fide PPO; HemJ down-regulation resulted in accumulation of tetrapyrrole precursors and in the depletion of chlorophyll precursors. The expression of FLAG-tagged Synechocystis 6803 HemJ protein (HemJ.f) and affinity isolation of HemJ.f under native conditions revealed that it binds heme b The most stable HemJ.f form was a dimer, and higher oligomeric forms were also observed. Using both oxygen and artificial electron acceptors, we detected no enzymatic activity with the purified HemJ.f, consistent with the hypothesis that the enzymatic mechanism for HemJ is distinct from those of other PPO isoforms. The heme absorption spectra and distant HemJ homology to several membrane oxidases indicated that the heme in HemJ is redox-active and involved in electron transfer. HemJ was conditionally complemented by another PPO, HemG from Escherichia coli. If grown photoautotrophically, the complemented strain accumulated tripropionic tetrapyrrole harderoporphyrin, suggesting a defect in enzymatic conversion of coproporphyrinogen III to protoporphyrinogen IX, catalyzed by coproporphyrinogen III oxidase (CPO). This observation supports the hypothesis that HemJ is functionally coupled with CPO and that this coupling is disrupted after replacement of HemJ by HemG.
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Affiliation(s)
- Petra Skotnicová
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Roman Sobotka
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Mark Shepherd
- the School of Biosciences, RAPID Group, University of Kent, Canterbury CT2 7NZ,United Kingdom
| | - Jan Hájek
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Pavel Hrouzek
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic.,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
| | - Martin Tichý
- From the Czech Academy of Sciences, Institute of Microbiology, Centre Algatech, 379 81 Třeboň, Czech Republic, .,the Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic, and
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21
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Bec Ková M, Yu J, Krynická V, Kozlo A, Shao S, Koník P, Komenda J, Murray JW, Nixon PJ. Structure of Psb29/Thf1 and its association with the FtsH protease complex involved in photosystem II repair in cyanobacteria. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0394. [PMID: 28808107 PMCID: PMC5566888 DOI: 10.1098/rstb.2016.0394] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2017] [Indexed: 12/15/2022] Open
Abstract
One strategy for enhancing photosynthesis in crop plants is to improve their ability to repair photosystem II (PSII) in response to irreversible damage by light. Despite the pivotal role of thylakoid-embedded FtsH protease complexes in the selective degradation of PSII subunits during repair, little is known about the factors involved in regulating FtsH expression. Here we show using the cyanobacterium Synechocystis sp. PCC 6803 that the Psb29 subunit, originally identified as a minor component of His-tagged PSII preparations, physically interacts with FtsH complexes in vivo and is required for normal accumulation of the FtsH2/FtsH3 hetero-oligomeric complex involved in PSII repair. We show using X-ray crystallography that Psb29 from Thermosynechococcus elongatus has a unique fold consisting of a helical bundle and an extended C-terminal helix and contains a highly conserved region that might be involved in binding to FtsH. A similar interaction is likely to occur in Arabidopsis chloroplasts between the Psb29 homologue, termed THF1, and the FTSH2/FTSH5 complex. The direct involvement of Psb29/THF1 in FtsH accumulation helps explain why THF1 is a target during the hypersensitive response in plants induced by pathogen infection. Downregulating FtsH function and the PSII repair cycle via THF1 would contribute to the production of reactive oxygen species, the loss of chloroplast function and cell death. This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
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Affiliation(s)
- Martina Bec Ková
- Institute of Microbiology, Center Algatech, Opatovický mlýn, 37981 Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Jianfeng Yu
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Vendula Krynická
- Institute of Microbiology, Center Algatech, Opatovický mlýn, 37981 Třeboň, Czech Republic
| | - Amanda Kozlo
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Shengxi Shao
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Peter Koník
- Institute of Microbiology, Center Algatech, Opatovický mlýn, 37981 Třeboň, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Josef Komenda
- Institute of Microbiology, Center Algatech, Opatovický mlýn, 37981 Třeboň, Czech Republic .,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - James W Murray
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Peter J Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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22
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Zhan J, Wang Q. Photoresponse Mechanism in Cyanobacteria: Key Factor in Photoautotrophic Chassis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:75-96. [PMID: 30091092 DOI: 10.1007/978-981-13-0854-3_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
As the oldest oxygenic photoautotrophic prokaryotes, cyanobacteria have outstanding advantages as the chassis cell in the research field of synthetic biology. Cognition of photosynthetic mechanism, including the photoresponse mechanism under high-light (HL) conditions, is important for optimization of the cyanobacteria photoautotrophic chassis for synthesizing biomaterials as "microbial cell factories." Cyanobacteria are well-established model organisms for the study of oxygenic photosynthesis and have evolved various acclimatory responses to HL conditions to protect the photosynthetic apparatus from photodamage. Here, we reviewed the latest progress in the mechanism of HL acclimation in cyanobacteria. The subsequent acclimatory responses and the corresponding molecular mechanisms are included: (1) acclimatory responses of PSII and PSI; (2) the degradation of phycobilisome; (3) induction of the photoprotective mechanisms such as state transitions, OCP-dependent non-photochemical quenching, and the induction of HLIP family; and (4) the regulation mechanisms of the gene expression under HL.
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Affiliation(s)
- Jiao Zhan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, Hubei, China.
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23
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Zer H, Margulis K, Georg J, Shotland Y, Kostova G, Sultan LD, Hess WR, Keren N. Resequencing of a mutant bearing an iron starvation recovery phenotype defines Slr1658 as a new player in the regulatory network of a model cyanobacterium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:235-245. [PMID: 29161470 DOI: 10.1111/tpj.13770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria. We set out to study the role of bacterioferritin co-migratory proteins during transitions in iron bioavailability in the cyanobacterium Synechocystis sp. PCC 6803 using knockout strains coupled with physiological and biochemical measurements. One of the mutants displayed slow recovery from iron limitation. However, we discovered that the cause of the phenotype was not the intended knockout but rather the serendipitous selection of a mutation in an unrelated locus, slr1658. Bioinformatics analysis suggested similarities to two-component systems and a possible regulatory role. Transcriptomic analysis of the recovery from iron limitation showed that the slr1658 mutation had an extensive effect on the expression of genes encoding regulatory proteins, proteins involved in the remodeling and degradation of the photosynthetic apparatus and proteins modulating electron transport. Most significantly, expression of the cyanobacterial homologue of the cyclic electron transport protein PGR5 was upregulated 1000-fold in slr1658 disruption mutants. pgr5 transcripts in the Δslr1658 mutant retained these high levels under a range of stress and recovery conditions. The results suggest that slr1658 is part of a regulatory operon that, among other aspects, affects the regulation of alternative electron flow. Disruption of its function has deleterious results under oxidative stress promoting conditions.
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Affiliation(s)
- Hagit Zer
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Ketty Margulis
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Jens Georg
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Yoram Shotland
- Department of Chemical Engineering, Shamoon College of Engineering, Beer Sheva, 84100, Israel
| | - Gergana Kostova
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Laure D Sultan
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Wolfgang R Hess
- Faculty of Biology, Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, D-79104, Freiburg, Germany
| | - Nir Keren
- Department of Plant and Environmental Sciences, Edmond J. Safra Campus, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
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24
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Georg J, Kostova G, Vuorijoki L, Schön V, Kadowaki T, Huokko T, Baumgartner D, Müller M, Klähn S, Allahverdiyeva Y, Hihara Y, Futschik ME, Aro EM, Hess WR. Acclimation of Oxygenic Photosynthesis to Iron Starvation Is Controlled by the sRNA IsaR1. Curr Biol 2017; 27:1425-1436.e7. [PMID: 28479323 DOI: 10.1016/j.cub.2017.04.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 01/01/2023]
Abstract
Oxygenic photosynthesis crucially depends on proteins that possess Fe2+ or Fe/S complexes as co-factors or prosthetic groups. Here, we show that the small regulatory RNA (sRNA) IsaR1 (Iron-Stress-Activated RNA 1) plays a pivotal role in acclimation to low-iron conditions. The IsaR1 regulon consists of more than 15 direct targets, including Fe2+-containing proteins involved in photosynthetic electron transfer, detoxification of anion radicals, citrate cycle, and tetrapyrrole biogenesis. IsaR1 is essential for maintaining physiological levels of Fe/S cluster biogenesis proteins during iron deprivation. Consequently, IsaR1 affects the acclimation of the photosynthetic apparatus to iron starvation at three levels: (1) directly, via posttranscriptional repression of gene expression; (2) indirectly, via suppression of pigment; and (3) Fe/S cluster biosynthesis. Homologs of IsaR1 are widely conserved throughout the cyanobacterial phylum. We conclude that IsaR1 is a critically important riboregulator. These findings provide a new perspective for understanding the regulation of iron homeostasis in photosynthetic organisms.
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Affiliation(s)
- Jens Georg
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Gergana Kostova
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Linda Vuorijoki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Verena Schön
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Taro Kadowaki
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Tuomas Huokko
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Desirée Baumgartner
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Maximilian Müller
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Stephan Klähn
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Yagut Allahverdiyeva
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Yukako Hihara
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Matthias E Futschik
- CCMAR - Center of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, Devon PL4 8AA, UK
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Biochemistry, University of Turku, 20014 Turku, Finland
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany.
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25
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Bao H, Burnap RL. Photoactivation: The Light-Driven Assembly of the Water Oxidation Complex of Photosystem II. FRONTIERS IN PLANT SCIENCE 2016; 7:578. [PMID: 27200051 PMCID: PMC4853684 DOI: 10.3389/fpls.2016.00578] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/14/2016] [Indexed: 05/10/2023]
Abstract
Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II. The assembly of the Mn4O5Ca requires light and involves a sequential process called photoactivation. This process harnesses the charge-separation of the photochemical reaction center and the coordination environment provided by the amino acid side chains of the protein to oxidize and organize the incoming manganese ions to form the oxo-bridged metal cluster capable of H2O-oxidation. Although most aspects of this assembly process remain poorly understood, recent advances in the elucidation of the crystal structure of the fully assembled cyanobacterial PSII complex help in the interpretation of the rich history of experiments designed to understand this process. Moreover, recent insights on the structure and stability of the constituent ions of the Mn4CaO5 cluster may guide future experiments. Here we consider the literature and suggest possible models of assembly including one involving single Mn(2+) oxidation site for all Mn but requiring ion relocation.
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Affiliation(s)
| | - Robert L. Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State UniversityStillwater, OK, USA
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26
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Komenda J, Sobotka R. Cyanobacterial high-light-inducible proteins — Protectors of chlorophyll–protein synthesis and assembly. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:288-95. [DOI: 10.1016/j.bbabio.2015.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/28/2015] [Accepted: 08/30/2015] [Indexed: 12/24/2022]
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27
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Hernández-Prieto MA, Semeniuk TA, Giner-Lamia J, Futschik ME. The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803. Sci Rep 2016; 6:22168. [PMID: 26923200 PMCID: PMC4770689 DOI: 10.1038/srep22168] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/09/2016] [Indexed: 01/03/2023] Open
Abstract
Cyanobacteria exhibit a great capacity to adapt to different environmental conditions through changes in gene expression. Although this plasticity has been extensively studied in the model cyanobacterium Synechocystis sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditions is lacking. Here, we report a meta-analysis of 756 individual microarray measurements conducted in 37 independent studies-the most comprehensive study of the Synechocystis transcriptome to date. Using stringent statistical evaluation, we characterized the coordinated adaptation of Synechocystis' gene expression on systems level. Evaluation of the data revealed that the photosynthetic apparatus is subjected to greater changes in expression than other cellular components. Nevertheless, network analyses indicated a significant degree of transcriptional coordination of photosynthesis and various metabolic processes, and revealed the tight co-regulation of components of photosystems I, II and phycobilisomes. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Intriguingly, global clustering analyses suggested contrasting transcriptional response of metabolic and regulatory genes stress to conditions. The integrated Synechocystis transcriptome can be accessed and interactively analyzed via the CyanoEXpress website (http://cyanoexpress.sysbiolab.eu).
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Affiliation(s)
- Miguel A. Hernández-Prieto
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Trudi Ann Semeniuk
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
| | - Matthias E. Futschik
- Systems Biology and Bioinformatics Laboratory, Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal
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28
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Steinbach G, Schubert F, Kaňa R. Cryo-imaging of photosystems and phycobilisomes in Anabaena sp. PCC 7120 cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:395-9. [DOI: 10.1016/j.jphotobiol.2015.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 01/03/2023]
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29
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Kaushik MS, Singh P, Tiwari B, Mishra AK. Ferric Uptake Regulator (FUR) protein: properties and implications in cyanobacteria. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1134-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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30
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Sacharz J, Bryan SJ, Yu J, Burroughs NJ, Spence EM, Nixon PJ, Mullineaux CW. Sub-cellular location of FtsH proteases in the cyanobacterium Synechocystis sp. PCC 6803 suggests localised PSII repair zones in the thylakoid membranes. Mol Microbiol 2015; 96:448-62. [PMID: 25601560 PMCID: PMC4949578 DOI: 10.1111/mmi.12940] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2015] [Indexed: 12/21/2022]
Abstract
In cyanobacteria and chloroplasts, exposure to HL damages the photosynthetic apparatus, especially the D1 subunit of Photosystem II. To avoid chronic photoinhibition, a PSII repair cycle operates to replace damaged PSII subunits with newly synthesised versions. To determine the sub-cellular location of this process, we examined the localisation of FtsH metalloproteases, some of which are directly involved in degrading damaged D1. We generated transformants of the cyanobacterium Synechocystis sp. PCC6803 expressing GFP-tagged versions of its four FtsH proteases. The ftsH2-gfp strain was functional for PSII repair under our conditions. Confocal microscopy shows that FtsH1 is mainly in the cytoplasmic membrane, while the remaining FtsH proteins are in patches either in the thylakoid or at the interface between the thylakoid and cytoplasmic membranes. HL exposure which increases the activity of the Photosystem II repair cycle led to no detectable changes in FtsH distribution, with the FtsH2 protease involved in D1 degradation retaining its patchy distribution in the thylakoid membrane. We discuss the possibility that the FtsH2-GFP patches represent Photosystem II 'repair zones' within the thylakoid membranes, and the possible advantages of such functionally specialised membrane zones. Anti-GFP affinity pull-downs provide the first indication of the composition of the putative repair zones.
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Affiliation(s)
- Joanna Sacharz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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31
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Busch AW, Montgomery BL. Interdependence of tetrapyrrole metabolism, the generation of oxidative stress and the mitigative oxidative stress response. Redox Biol 2015; 4:260-71. [PMID: 25618582 PMCID: PMC4315935 DOI: 10.1016/j.redox.2015.01.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/12/2015] [Accepted: 01/14/2015] [Indexed: 01/01/2023] Open
Abstract
Tetrapyrroles are involved in light harvesting and light perception, electron-transfer reactions, and as co-factors for key enzymes and sensory proteins. Under conditions in which cells exhibit stress-induced imbalances of photosynthetic reactions, or light absorption exceeds the ability of the cell to use photoexcitation energy in synthesis reactions, redox imbalance can occur in photosynthetic cells. Such conditions can lead to the generation of reactive oxygen species (ROS) associated with alterations in tetrapyrrole homeostasis. ROS accumulation can result in cellular damage and detrimental effects on organismal fitness, or ROS molecules can serve as signals to induce a protective or damage-mitigating oxidative stress signaling response in cells. Induced oxidative stress responses include tetrapyrrole-dependent and -independent mechanisms for mitigating ROS generation and/or accumulation. Thus, tetrapyrroles can be contributors to oxidative stress, but are also essential in the oxidative stress response to protect cells by contributing to detoxification of ROS. In this review, we highlight the interconnection and interdependence of tetrapyrrole metabolism with the occurrence of oxidative stress and protective oxidative stress signaling responses in photosynthetic organisms. Tetrapyrroles are involved in light sensing and oxidative stress mitigation. Reactive oxygen species (ROS) can form upon light exposure of free tetrapyrroles. Tetrapyrrole homeostasis must be tightly regulated to avoid oxidative stress. ROS can result in cellular damage or oxidative stress signaling in cells.
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32
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Responses to oxidative and heavy metal stresses in cyanobacteria: recent advances. Int J Mol Sci 2014; 16:871-86. [PMID: 25561236 PMCID: PMC4307280 DOI: 10.3390/ijms16010871] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/24/2014] [Indexed: 12/24/2022] Open
Abstract
Cyanobacteria, the only known prokaryotes that perform oxygen-evolving photosynthesis, are receiving strong attention in basic and applied research. In using solar energy, water, CO2 and mineral salts to produce a large amount of biomass for the food chain, cyanobacteria constitute the first biological barrier against the entry of toxics into the food chain. In addition, cyanobacteria have the potential for the solar-driven carbon-neutral production of biofuels. However, cyanobacteria are often challenged by toxic reactive oxygen species generated under intense illumination, i.e., when their production of photosynthetic electrons exceeds what they need for the assimilation of inorganic nutrients. Furthermore, in requiring high amounts of various metals for growth, cyanobacteria are also frequently affected by drastic changes in metal availabilities. They are often challenged by heavy metals, which are increasingly spread out in the environment through human activities, and constitute persistent pollutants because they cannot be degraded. Consequently, it is important to analyze the protection against oxidative and metal stresses in cyanobacteria because these ancient organisms have developed most of these processes, a large number of which have been conserved during evolution. This review summarizes what is known regarding these mechanisms, emphasizing on their crosstalk.
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