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Shahbazi M, Tohidfar M, Azimzadeh Irani M, Moheb Seraj RG. Functional annotation and evaluation of hypothetical proteins in cyanobacterium Synechocystis sp. PCC 6803. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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2
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Rachedi R, Foglino M, Latifi A. Stress Signaling in Cyanobacteria: A Mechanistic Overview. Life (Basel) 2020; 10:life10120312. [PMID: 33256109 PMCID: PMC7760821 DOI: 10.3390/life10120312] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Cyanobacteria are highly diverse, widely distributed photosynthetic bacteria inhabiting various environments ranging from deserts to the cryosphere. Throughout this range of niches, they have to cope with various stresses and kinds of deprivation which threaten their growth and viability. In order to adapt to these stresses and survive, they have developed several global adaptive responses which modulate the patterns of gene expression and the cellular functions at work. Sigma factors, two-component systems, transcriptional regulators and small regulatory RNAs acting either separately or collectively, for example, induce appropriate cyanobacterial stress responses. The aim of this review is to summarize our current knowledge about the diversity of the sensors and regulators involved in the perception and transduction of light, oxidative and thermal stresses, and nutrient starvation responses. The studies discussed here point to the fact that various stresses affecting the photosynthetic capacity are transduced by common mechanisms.
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Hasegawa H, Tsurumaki T, Kobayashi I, Imamura S, Tanaka K. Identification and analysis of a principal sigma factor interacting protein SinA, essential for growth at high temperatures in a cyanobacterium Synechococcus elongatus PCC 7942. J GEN APPL MICROBIOL 2020; 66:66-72. [DOI: 10.2323/jgam.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Hazuki Hasegawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Tatsuhiro Tsurumaki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Ikki Kobayashi
- Department of Applied Chemistry and Biotechnology, Chiba University
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology
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Transcription in cyanobacteria: a distinctive machinery and putative mechanisms. Biochem Soc Trans 2019; 47:679-689. [DOI: 10.1042/bst20180508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 02/03/2023]
Abstract
Abstract
Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. The vast majority of bacterial species encode at least one of these highly conserved factors and so their absence in cyanobacteria is intriguing. Additionally, the largest subunit of bacterial RNAP has undergone a split in cyanobacteria to form two subunits and the SI3 insertion within the integral trigger loop element is roughly 3.5 times larger than in Escherichia coli. The Rho termination factor also appears to be absent, leaving cyanobacteria to rely solely on an intrinsic termination mechanism. Furthermore, cyanobacteria must be able to respond to environment signals such as light intensity and tightly synchronise gene expression and other cell activities to a circadian rhythm.
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Sawa N, Tatsuke T, Ogawa A, Hirokawa Y, Osanai T, Hanai T. Modification of carbon metabolism in Synechococcus elongatus PCC 7942 by cyanophage-derived sigma factors for bioproduction improvement. J Biosci Bioeng 2019; 127:256-264. [DOI: 10.1016/j.jbiosc.2018.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022]
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6
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Sun D, Liu C, Zhu J, Liu W. Connecting Metabolic Pathways: Sigma Factors in Streptomyces spp. Front Microbiol 2017; 8:2546. [PMID: 29312231 PMCID: PMC5742136 DOI: 10.3389/fmicb.2017.02546] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/07/2017] [Indexed: 11/13/2022] Open
Abstract
The gram-positive filamentous bacterium Streptomyces is one of the largest resources for bioactive metabolites, particularly antibiotics. Antibiotic production and other metabolic processes are tightly regulated at the transcriptional level. Sigma (σ) factors are components of bacterial RNA polymerases that determine promoter specificity. In Streptomyces, σ factors also play essential roles in signal transduction and in regulatory networks, thereby assisting in their survival in complex environments. However, our current understanding of σ factors in Streptomyces is still limited. In this mini-review, we demonstrate the roles of Streptomyces σ factors, illustrating that these serve as linkers of different metabolic pathways. Further investigations on σ factors may improve our knowledge of Streptomyces physiology and benefit exploitation of Streptomyces resources.
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Affiliation(s)
- Di Sun
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Cong Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingrong Zhu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Weijie Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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7
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6S RNA plays a role in recovery from nitrogen depletion in Synechocystis sp. PCC 6803. BMC Microbiol 2017; 17:229. [PMID: 29216826 PMCID: PMC5721685 DOI: 10.1186/s12866-017-1137-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
Background The 6S RNA is a global transcriptional riboregulator, which is exceptionally widespread among most bacterial phyla. While its role is well-characterized in some heterotrophic bacteria, we subjected a cyanobacterial homolog to functional analysis, thereby extending the scope of 6S RNA action to the special challenges of photoautotrophic lifestyles. Results Physiological characterization of a 6S RNA deletion strain (ΔssaA) demonstrates a delay in the recovery from nitrogen starvation. Significantly decelerated phycobilisome reassembly and glycogen degradation are accompanied with reduced photosynthetic activity compared to the wild type. Transcriptome profiling further revealed that predominantly genes encoding photosystem components, ATP synthase, phycobilisomes and ribosomal proteins were negatively affected in ΔssaA. In vivo pull-down studies of the RNA polymerase complex indicated that the presence of 6S RNA promotes the recruitment of the cyanobacterial housekeeping σ factor SigA, concurrently supporting dissociation of group 2 σ factors during recovery from nitrogen starvation. Conclusions The combination of genetic, physiological and biochemical studies reveals the homologue of 6S RNA as an integral part of the cellular response of Synechocystis sp. PCC 6803 to changing nitrogen availability. According to these results, 6S RNA supports a rapid acclimation to changing nitrogen supply by accelerating the switch from group 2 σ factors SigB, SigC and SigE to SigA-dependent transcription. We therefore introduce the cyanobacterial 6S RNA as a novel candidate regulator of RNA polymerase sigma factor recruitment in Synechocystis sp. PCC 6803. Further studies on mechanistic features of the postulated interaction should shed additional light on the complexity of transcriptional regulation in cyanobacteria. Electronic supplementary material The online version of this article (10.1186/s12866-017-1137-9) contains supplementary material, which is available to authorized users.
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Kobayashi I, Watanabe S, Kanesaki Y, Shimada T, Yoshikawa H, Tanaka K. Conserved two-component Hik34-Rre1 module directly activates heat-stress inducible transcription of major chaperone and other genes in Synechococcus elongatus PCC 7942. Mol Microbiol 2017; 104:260-277. [PMID: 28106321 DOI: 10.1111/mmi.13624] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2017] [Indexed: 11/28/2022]
Abstract
Bacteria and other organisms, including cyanobacteria, employ two-component signal transducing modules comprising histidine kinases and response regulators to acclimate to changing environments. While the number and composition of these modules differ among cyanobacteria, two response regulators that contain DNA binding domains, RpaB and Rre1, are conserved in all sequenced cyanobacterial genomes and are essential for viability. Although RpaB negatively or positively regulates high light and other stress-responsive gene expression, little is known about the function of Rre1. Here, they investigated the direct regulatory targets of Rre1 in the cyanobacterium Synechococcus elongatus PCC 7942. Chromatin immunoprecipitation and high-density tiling array analysis were used to map Rre1 binding sites. The sites included promoter regions for chaperone genes such as dnaK2, groESL-1, groEL-2, hspA and htpG, as well as the group 2 sigma factor gene rpoD2. In vivo and in vitro analyses revealed that Rre1 phosphorylation level, DNA binding activity and adjacent gene transcription increased in response to heat stress. These responses were much diminished in a knock-out mutant of Hik34, a previously identified heat shock regulator. Based on our results, we propose Hik34-Rre1 is the heat shock-responsive signaling module that positively regulates major chaperone and other genes in cyanobacteria.
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Affiliation(s)
- Ikki Kobayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Graduate School of Interdisciplinary Science, Tokyo Institute of Technology, Nagatsuta 4259-R1-29, Midori-ku, Yokohama, 226-8503, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Tomohiro Shimada
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, 4259-R1-29 Nagatsuta, Midori-ku, Yokohama, 226-8503, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
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Sinetova MA, Los DA. New insights in cyanobacterial cold stress responses: Genes, sensors, and molecular triggers. Biochim Biophys Acta Gen Subj 2016; 1860:2391-2403. [PMID: 27422804 DOI: 10.1016/j.bbagen.2016.07.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/16/2016] [Accepted: 07/09/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Cold stress strongly induces the expression of ~100 genes in cyanobacteria. Some of these genes are necessary to protect cellular functions by adjustment of membranes, as well as transcriptional and translational machineries. About a half of cold-induced genes are not functionally characterized. A part of cold-induced genes is under control of a two-component regulatory system, consisting of histidine kinase Hik33 and response regulator Rre26. The mechanism(s) that control another part of cold-inducible genes are still unknown. SCOPE OF REVIEW The aim of this review is to summarise the latest findings in cyanobacterial cold-stress responses including transcriptomics, cold sensing, and molecular triggers. MAJOR CONCLUSIONS A feedback loop between the membrane fluidity and transcription of genes for fatty acid desaturases operates via the transmembrane red-light-activated cold sensor Hik33, which perceives cold-induced membrane rigidification as a change in its thickness. The cold-induced kinase activity of Hik33 is facilitated by interaction with a small protein, Ssl3451 - the third contributor to a canonical two-component regulatory system, which may explain the ability of some cyanobacterial histidine kinases to interact with different response regulators under different stress conditions. Other regulatory systems that control cold-stress responses operate via Ser/Thr protein kinase, SpkE, and via temperature-dependent changes in DNA supercoiling. Transcriptomic analysis shows that universal triggers of stress responses are reactive oxygen species and changes in redox status of plastoquinone pool. GENERAL SIGNIFICANCE Deeper understanding of molecular mechanisms of temperature sensing and regulation of cold-stress responses in photosynthetic cells provide a background for generation of cold-resistant crops.
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Affiliation(s)
- Maria A Sinetova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russian Federation
| | - Dmitry A Los
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russian Federation.
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10
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Antal T, Kurkela J, Parikainen M, Kårlund A, Hakkila K, Tyystjärvi E, Tyystjärvi T. Roles of Group 2 Sigma Factors in Acclimation of the Cyanobacterium Synechocystis sp. PCC 6803 to Nitrogen Deficiency. PLANT & CELL PHYSIOLOGY 2016; 57:1309-1318. [PMID: 27095737 DOI: 10.1093/pcp/pcw079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/10/2016] [Indexed: 06/05/2023]
Abstract
Acclimation of cyanobacteria to environmental conditions is mainly controlled at the transcriptional level, and σ factors of the RNA polymerase have a central role in this process. The model cyanobacterium Synechocystis sp. PCC 6803 has four non-essential group 2 σ factors (SigB, SigC, SigD and SigE) that regulate global metabolic responses to various adverse environmental conditions. Here we show that although none of the group 2 σ factors is essential for the major metabolic realignments induced by a short period of nitrogen starvation, the quadruple mutant without any group 2 σ factors and triple mutants missing both SigB and SigD grow slowly in BG-11 medium containing only 5% of the nitrate present in standard BG-11. These ΔsigBCDE, ΔsigBCD and ΔsigBDE strains lost PSII activity rapidly in low nitrogen and accumulated less glycogen than the control strain. An abnormally high glycogen content was detected in ΔsigBCE (SigD is active), while the carotenoid content became high in ΔsigCDE (SigB is active), indicating that SigB and SigD regulate the partitioning of carbon skeletons in low nitrogen. Long-term survival and recovery of the cells after nitrogen deficiency was strongly dependent on group 2 σ factors. The quadruple mutant and the ΔsigBDE strain (only SigC is active) recovered more slowly from nitrogen deficiency than the control strain, and ΔsigBCDE in particular lost viability during nitrogen starvation. Nitrogen deficiency-induced changes in the pigment content of the control strain recovered essentially in 1 d in nitrogen-replete medium, but little recovery occurred in ΔsigBCDE and ΔsigBDE.
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Affiliation(s)
- Taras Antal
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland Biological Faculty, Moscow State University, Vorobyevi Gory 119992, Moscow, Russia
| | - Juha Kurkela
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | | | - Anna Kårlund
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Kaisa Hakkila
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Esa Tyystjärvi
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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11
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Mueller TJ, Welsh EA, Pakrasi HB, Maranas CD. Identifying Regulatory Changes to Facilitate Nitrogen Fixation in the Nondiazotroph Synechocystis sp. PCC 6803. ACS Synth Biol 2016; 5:250-8. [PMID: 26692191 DOI: 10.1021/acssynbio.5b00202] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The incorporation of biological nitrogen fixation into a nondiazotrophic photosynthetic organism provides a promising solution to the increasing fixed nitrogen demand, but is accompanied by a number of challenges for accommodating two incompatible processes within the same organism. Here we present regulatory influence networks for two cyanobacteria, Synechocystis PCC 6803 and Cyanothece ATCC 51142, and evaluate them to co-opt native transcription factors that may be used to control the nif gene cluster once it is transferred to Synechocystis. These networks were further examined to identify candidate transcription factors for other metabolic processes necessary for temporal separation of photosynthesis and nitrogen fixation, glycogen catabolism and cyanophycin synthesis. Two transcription factors native to Synechocystis, LexA and Rcp1, were identified as promising candidates for the control of the nif gene cluster and other pertinent metabolic processes, respectively. Lessons learned in the incorporation of nitrogen fixation into a nondiazotrophic prokaryote may be leveraged to further progress the incorporation of nitrogen fixation in plants.
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Affiliation(s)
- Thomas J. Mueller
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16801, United States
| | - Eric A. Welsh
- Cancer
Informatics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Himadri B. Pakrasi
- Department
of Energy, Environmental, and Chemical Engineering, Washington University, St. Louis, Missouri 63130, United States
- Department
of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Costas D. Maranas
- Department
of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16801, United States
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Kuwahara A, Arisaka S, Takeya M, Iijima H, Hirai MY, Osanai T. Modification of photosynthetic electron transport and amino acid levels by overexpression of a circadian-related histidine kinase hik8 in Synechocystis sp. PCC 6803. Front Microbiol 2015; 6:1150. [PMID: 26539179 PMCID: PMC4611142 DOI: 10.3389/fmicb.2015.01150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/05/2015] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria perform oxygenic photosynthesis, and the maintenance of photosynthetic electron transport chains is indispensable to their survival in various environmental conditions. Photosynthetic electron transport in cyanobacteria can be studied through genetic analysis because of the natural competence of cyanobacteria. We here show that a strain overexpressing hik8, a histidine kinase gene related to the circadian clock, exhibits an altered photosynthetic electron transport chain in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Respiratory activity was down-regulated under nitrogen-replete conditions. Photosynthetic activity was slightly lower in the hik8-overexpressing strain than in the wild-type after nitrogen depletion, and the values of photosynthetic parameters were altered by hik8 overexpression under nitrogen-replete and nitrogen-depleted conditions. Transcripts of genes encoding Photosystem I and II were increased by hik8 overexpression under nitrogen-replete conditions. Nitrogen starvation triggers increase in amino acids but the magnitude of the increase in several amino acids was diminished by hik8 overexpression. These genetic data indicate that Hik8 regulates the photosynthetic electron transport, which in turn alters primary metabolism during nitrogen starvation in this cyanobacterium.
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Affiliation(s)
- Ayuko Kuwahara
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Satomi Arisaka
- Department of Agricultural Chemistry, School of Agriculture, Meiji UniversityKawasaki, Japan
| | - Masahiro Takeya
- Department of Agricultural Chemistry, School of Agriculture, Meiji UniversityKawasaki, Japan
| | - Hiroko Iijima
- Department of Agricultural Chemistry, School of Agriculture, Meiji UniversityKawasaki, Japan
| | | | - Takashi Osanai
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Department of Agricultural Chemistry, School of Agriculture, Meiji UniversityKawasaki, Japan
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Koskinen S, Hakkila K, Gunnelius L, Kurkela J, Wada H, Tyystjärvi T. In vivorecruitment analysis and a mutant strain without any group 2 σ factor reveal roles of different σ factors in cyanobacteria. Mol Microbiol 2015; 99:43-54. [DOI: 10.1111/mmi.13214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Satu Koskinen
- Department of Biochemistry; University of Turku; FIN-20014 Turku Finland
| | - Kaisa Hakkila
- Department of Biochemistry; University of Turku; FIN-20014 Turku Finland
| | - Liisa Gunnelius
- Department of Biochemistry; University of Turku; FIN-20014 Turku Finland
| | - Juha Kurkela
- Department of Biochemistry; University of Turku; FIN-20014 Turku Finland
| | - Hajime Wada
- Department of Life Sciences; University of Tokyo; Komaba 3-8-1, Meguro-ku Tokyo 153-8902 Japan
| | - Taina Tyystjärvi
- Department of Biochemistry; University of Turku; FIN-20014 Turku Finland
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Paget MS. Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution. Biomolecules 2015; 5:1245-65. [PMID: 26131973 PMCID: PMC4598750 DOI: 10.3390/biom5031245] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/20/2015] [Accepted: 06/01/2015] [Indexed: 12/18/2022] Open
Abstract
Sigma factors are multi-domain subunits of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. This review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (Group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (Groups 2-4) that control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. Sigma factors are then released through a wide variety of mechanisms, often involving branched signal transduction pathways that allow the integration of distinct signals. Three major strategies for sigma release are discussed: regulated proteolysis, partner-switching, and direct sensing by the anti-sigma factor.
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Affiliation(s)
- Mark S Paget
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
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15
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Overexpression of sigma factor SigB improves temperature and butanol tolerance of Synechocystis sp. PCC6803. J Biotechnol 2014; 182-183:54-60. [DOI: 10.1016/j.jbiotec.2014.04.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/17/2014] [Accepted: 04/25/2014] [Indexed: 11/21/2022]
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16
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Nagarajan S, Srivastava S, Sherman LA. Essential role of the plasmid hik31 operon in regulating central metabolism in the dark in Synechocystis sp. PCC 6803. Mol Microbiol 2013; 91:79-97. [PMID: 24237382 DOI: 10.1111/mmi.12442] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2013] [Indexed: 12/13/2022]
Abstract
The plasmid hik31 operon (P3, slr6039-slr6041) is located on the pSYSX plasmid in Synechocystis sp. PCC 6803. A P3 mutant (ΔP3) had a growth defect in the dark and a pigment defect that was worsened by the addition of glucose. The glucose defect was from incomplete metabolism of the substrate, was pH dependent, and completely overcome by the addition of bicarbonate. Addition of organic carbon and nitrogen sources partly alleviated the defects of the mutant in the dark. Electron micrographs of the mutant revealed larger cells with division defects, glycogen limitation, lack of carboxysomes, deteriorated thylakoids and accumulation of polyhydroxybutyrate and cyanophycin. A microarray experiment over two days of growth in light-dark plus glucose revealed downregulation of several photosynthesis, amino acid biosynthesis, energy metabolism genes; and an upregulation of cell envelope and transport and binding genes in the mutant. ΔP3 had an imbalance in carbon and nitrogen levels and many sugar catabolic and cell division genes were negatively affected after the first dark period. The mutant suffered from oxidative and osmotic stress, macronutrient limitation, and an energy deficit. Therefore, the P3 operon is an important regulator of central metabolism and cell division in the dark.
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Affiliation(s)
- Sowmya Nagarajan
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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Osanai T, Kuwahara A, Iijima H, Toyooka K, Sato M, Tanaka K, Ikeuchi M, Saito K, Hirai MY. Pleiotropic effect of sigE over-expression on cell morphology, photosynthesis and hydrogen production in Synechocystis sp. PCC 6803. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:456-65. [PMID: 23941239 DOI: 10.1111/tpj.12310] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 08/07/2013] [Accepted: 08/09/2013] [Indexed: 05/04/2023]
Abstract
Over-expression of sigE, a gene encoding an RNA polymerase sigma factor in the unicellular cyanobacterium Synechocystis sp. PCC 6803, is known to activate sugar catabolism and bioplastic production. In this study, we investigated the effects of sigE over-expression on cell morphology, photosynthesis and hydrogen production in this cyanobacterium. Transmission electron and scanning probe microscopic analyses revealed that sigE over-expression increased the cell size, possibly as a result of aberrant cell division. Over-expression of sigE reduced respiration and photosynthesis activities via changes in gene expression and chlorophyll fluorescence. Hydrogen production under micro-oxic conditions is enhanced in sigE over-expressing cells. Despite these pleiotropic phenotypes, the sigE over-expressing strain showed normal cell viability under both nitrogen-replete and nitrogen-depleted conditions. These results provide insights into the inter-relationship among metabolism, cell morphology, photosynthesis and hydrogen production in this unicellular cyanobacterium.
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Affiliation(s)
- Takashi Osanai
- RIKEN Plant Science Center, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan
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18
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Hakkila K, Antal T, Gunnelius L, Kurkela J, Matthijs HCP, Tyystjärvi E, Tyystjärvi T. Group 2 sigma factor mutant ΔsigCDE of the cyanobacterium Synechocystis sp. PCC 6803 reveals functionality of both carotenoids and flavodiiron proteins in photoprotection of photosystem II. PLANT & CELL PHYSIOLOGY 2013; 54:1780-1790. [PMID: 24009334 DOI: 10.1093/pcp/pct123] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Adjustment of gene expression during acclimation to stress conditions, such as bright light, in the cyanobacterium Synechocystis sp. PCC 6803 depends on four group 2 σ factors (SigB, SigC, SigD, SigE). A ΔsigCDE strain containing the stress-responsive SigB as the only functional group 2 σ factor appears twice as resistant to photoinhibition of photosystem II (PSII) as the control strain. Microarray analyses of the ΔsigCDE strain indicated that 77 genes in standard conditions and 79 genes in high light were differently expressed compared with the control strain. Analysis of possible photoprotective mechanisms revealed that high carotenoid content and up-regulation of the photoprotective flavodiiron operon flv4-sll0218-flv2 protected PSII in ΔsigCDE, while up-regulation of pgr5-like, hlipB or isiA genes in the mutant strain did not offer particular protection against photoinhibition. Photoinhibition resistance was lost if ΔsigCDE was grown in high CO2, where carotenoid and Flv4, Sll0218, and Flv2 contents were low. Additionally, photoinhibition resistance of the ΔrpoZ strain (lacking the omega subunit of RNA polymerase), with high carotenoid but low Flv4-Sll0218-Flv2 content, supported the importance of carotenoids in PSII protection. Carotenoids likely protect mainly by quenching of singlet oxygen, but efficient nonphotochemical quenching in ΔsigCDE might offer some additional protection. Comparison of photoinhibition kinetics in control, ΔsigCDE, and ΔrpoZ strains showed that protection by the flavodiiron operon was most efficient during the first minutes of high-light illumination.
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Affiliation(s)
- Kaisa Hakkila
- Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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Muramatsu M, Hihara Y. Acclimation to high-light conditions in cyanobacteria: from gene expression to physiological responses. JOURNAL OF PLANT RESEARCH 2012; 125:11-39. [PMID: 22006212 DOI: 10.1007/s10265-011-0454-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Accepted: 08/23/2011] [Indexed: 05/04/2023]
Abstract
Photosynthetic organisms have evolved various acclimatory responses to high-light (HL) conditions to maintain a balance between energy supply (light harvesting and electron transport) and consumption (cellular metabolism) and to protect the photosynthetic apparatus from photodamage. The molecular mechanism of HL acclimation has been extensively studied in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Whole genome DNA microarray analyses have revealed that the change in gene expression profile under HL is closely correlated with subsequent acclimatory responses such as (1) acceleration in the rate of photosystem II turnover, (2) downregulation of light harvesting capacity, (3) development of a protection mechanism for the photosystems against excess light energy, (4) upregulation of general protection mechanism components, and (5) regulation of carbon and nitrogen assimilation. In this review article, we survey recent progress in the understanding of the molecular mechanisms of these acclimatory responses in Synechocystis sp. PCC 6803. We also briefly describe attempts to understand HL acclimation in various cyanobacterial species in their natural environments.
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Affiliation(s)
- Masayuki Muramatsu
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Ibaraki, 305-8602, Japan
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Nikkinen HL, Hakkila K, Gunnelius L, Huokko T, Pollari M, Tyystjärvi T. The SigB σ factor regulates multiple salt acclimation responses of the cyanobacterium Synechocystis sp. PCC 6803. PLANT PHYSIOLOGY 2012; 158:514-23. [PMID: 22095043 PMCID: PMC3252095 DOI: 10.1104/pp.111.190058] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Changing of principal σ factor in RNA polymerase holoenzyme to a group 2 σ factor redirects transcription when cyanobacteria acclimate to suboptimal environmental conditions. The group 2 sigma factor SigB was found to be important for the growth of the cyanobacterium Synechocystis sp. PCC 6803 in high-salt (0.7 m NaCl) stress but not in mild heat stress at 43°C although the expression of the sigB gene was similarly highly, but only transiently up-regulated at both conditions. The SigB factor was found to regulate many salt acclimation processes. The amount of glucosylglycerol-phosphate synthase, a key enzyme in the production of the compatible solute glucosylglycerol, was lower in the inactivation strain ΔsigB than in the control strain. Addition of the compatible solute trehalose almost completely restored the growth of the ΔsigB strain at 0.7 m NaCl. High-salt conditions lowered the chlorophyll and phycobilin contents of the cells while protective carotenoid pigments, especially zeaxanthin and myxoxanthophyll, were up-regulated in the control strain. These carotenoids were up-regulated in the ΔsigCDE strain (SigB is the only functional group 2 σ factor) and down-regulated in the ΔsigB strain under standard conditions. In addition, the HspA heat shock protein was less abundant and more abundant in the ΔsigB and ΔsigCDE strains, respectively, than in the control strain in high-salt conditions. Some cellular responses are common to heat and salt stresses, but pretreatment with mild heat did not protect cells against salt shock although protection against heat shock was evident.
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Osanai T, Oikawa A, Azuma M, Tanaka K, Saito K, Hirai MY, Ikeuchi M. Genetic engineering of group 2 sigma factor SigE widely activates expressions of sugar catabolic genes in Synechocystis species PCC 6803. J Biol Chem 2011; 286:30962-30971. [PMID: 21757761 PMCID: PMC3162455 DOI: 10.1074/jbc.m111.231183] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/25/2011] [Indexed: 11/06/2022] Open
Abstract
Metabolic engineering of photosynthetic organisms is required for utilization of light energy and for reducing carbon emissions.Control of transcriptional regulators is a powerful approach for changing cellular dynamics, because a set of genes is concomitantly regulated. Here, we show that overexpression of a group 2 σ factor, SigE, enhances the expressions of sugar catabolic genes in the unicellular cyanobacterium, Synechocystis sp. PCC 6803. Transcriptome analysis revealed that genes for the oxidative pentose phosphate pathway and glycogen catabolism are induced by overproduction of SigE. Immunoblotting showed that protein levels of sugar catabolic enzymes, such as glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, glycogen phosphorylase, and isoamylase, are increased. Glycogen levels are reduced in the SigE-overexpressing strain grown under light. Metabolome analysis revealed that metabolite levels of the TCA cycle and acetyl-CoA are significantly altered by SigE overexpression. The SigE-overexpressing strain also exhibited defective growth under mixotrophic or dark conditions. Thus, SigE overexpression changes sugar catabolism at the transcript to phenotype levels, suggesting a σ factor-based engineering method for modifying carbon metabolism in photosynthetic bacteria.
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Affiliation(s)
- Takashi Osanai
- Department of Life Sciences (Biology), University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902; RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012.
| | - Akira Oikawa
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045
| | - Miyuki Azuma
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032
| | - Kan Tanaka
- Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032; Graduate School of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510
| | - Kazuki Saito
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045; Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Masami Yokota Hirai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
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Mella-Herrera RA, Neunuebel MR, Kumar K, Saha SK, Golden JW. The sigE gene is required for normal expression of heterocyst-specific genes in Anabaena sp. strain PCC 7120. J Bacteriol 2011; 193:1823-32. [PMID: 21317330 PMCID: PMC3133031 DOI: 10.1128/jb.01472-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 01/31/2011] [Indexed: 11/20/2022] Open
Abstract
The filamentous cyanobacterium Anabaena (Nostoc) sp. strain PCC 7120 produces specialized cells for nitrogen fixation called heterocysts. Previous work showed that the group 2 sigma factor sigE (alr4249; previously called sigF) is upregulated in differentiating heterocysts 16 h after nitrogen step-down. We now show that the sigE gene is required for normal heterocyst development and normal expression levels of several heterocyst-specific genes. Mobility shift assays showed that the transcription factor NtcA binds to sites in the upstream region of sigE and that this binding is enhanced by 2-oxoglutarate (2-OG). Deletions of the region containing the NtcA binding sites in P(sigE)-gfp reporter plasmids showed that the sites contribute to normal developmental regulation but are not essential for upregulation in heterocysts. Northern RNA blot analysis of nifH mRNA revealed delayed and reduced transcript levels during heterocyst differentiation in a sigE mutant background. Quantitative reverse transcription-PCR (qRT-PCR) analyses of the sigE mutant showed lower levels of transcripts for nifH, fdxH, and hglE2 but normal levels for hupL. We developed a P(nifHD)-gfp reporter construct that showed strong heterocyst-specific expression. Time-lapse microscopy of the P(nifHD)-gfp reporter in a sigE mutant background showed delayed development and undetectable green fluorescent protein (GFP) fluorescence. Overexpression of sigE caused accelerated heterocyst development, an increased heterocyst frequency, and premature expression of GFP fluorescence from the P(nifHD)-gfp reporter.
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Affiliation(s)
- Rodrigo A. Mella-Herrera
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
- Division of Biological Sciences, University of California—San Diego, La Jolla, California 92093-0116
| | - M. Ramona Neunuebel
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Krithika Kumar
- Department of Biology, Texas A&M University, College Station, Texas 77843-3258
| | - Sushanta K. Saha
- Division of Biological Sciences, University of California—San Diego, La Jolla, California 92093-0116
| | - James W. Golden
- Division of Biological Sciences, University of California—San Diego, La Jolla, California 92093-0116
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Azuma M, Osanai T, Hirai MY, Tanaka K. A Response Regulator Rre37 and an RNA Polymerase Sigma Factor SigE Represent Two Parallel Pathways to Activate Sugar Catabolism in a Cyanobacterium Synechocystis sp. PCC 6803. ACTA ACUST UNITED AC 2011; 52:404-12. [DOI: 10.1093/pcp/pcq204] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Effects of deficiency and overdose of group 2 sigma factors in triple inactivation strains of Synechocystis sp. strain PCC 6803. J Bacteriol 2010; 193:265-73. [PMID: 20971916 DOI: 10.1128/jb.01045-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acclimation of cyanobacteria to environmental changes includes major changes in the gene expression patterns partly orchestrated by the replacement of a particular σ subunit with another in the RNA polymerase holoenzyme. The cyanobacterium Synechocystis sp. strain PCC 6803 encodes nine σ factors, all belonging to the σ(70) family. Cyanobacteria typically encode many group 2 σ factors that closely resemble the principal σ factor. We inactivated three out of the four group 2 σ factors of Synechocystis simultaneously in all possible combinations and found that all triple inactivation strains grow well under standard conditions. Unlike the other strains, the ΔsigBCD strain, which contains SigE as the only functional group 2 σ factor, did not grow faster under mixotrophic than under autotrophic conditions. The SigB and SigD factors were important in low-temperature acclimation, especially under diurnal light rhythm. The ΔsigBCD, ΔsigBCE, and ΔsigBDE strains were sensitive to high-light-induced photoinhibition, indicating a central role of the SigB factor in high-light tolerance. Furthermore, the ΔsigBCE strain (SigD is the only functional group 2 σ factor) appeared to be locked in the high-fluorescence state (state 1) and grew slowly in blue but not in orange or white light. Our results suggest that features of the triple inactivation strains can be categorized as (i) direct consequences of the inactivation of a particular σ factor(s) and (ii) effects resulting from the higher probability that the remaining group 2 σ factors associate with the RNA polymerase core.
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Kolowrat C, Partensky F, Mella-Flores D, Le Corguillé G, Boutte C, Blot N, Ratin M, Ferréol M, Lecomte X, Gourvil P, Lennon JF, Kehoe DM, Garczarek L. Ultraviolet stress delays chromosome replication in light/dark synchronized cells of the marine cyanobacterium Prochlorococcus marinus PCC9511. BMC Microbiol 2010; 10:204. [PMID: 20670397 PMCID: PMC2921402 DOI: 10.1186/1471-2180-10-204] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2010] [Accepted: 07/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The marine cyanobacterium Prochlorococcus is very abundant in warm, nutrient-poor oceanic areas. The upper mixed layer of oceans is populated by high light-adapted Prochlorococcus ecotypes, which despite their tiny genome (approximately 1.7 Mb) seem to have developed efficient strategies to cope with stressful levels of photosynthetically active and ultraviolet (UV) radiation. At a molecular level, little is known yet about how such minimalist microorganisms manage to sustain high growth rates and avoid potentially detrimental, UV-induced mutations to their DNA. To address this question, we studied the cell cycle dynamics of P. marinus PCC9511 cells grown under high fluxes of visible light in the presence or absence of UV radiation. Near natural light-dark cycles of both light sources were obtained using a custom-designed illumination system (cyclostat). Expression patterns of key DNA synthesis and repair, cell division, and clock genes were analyzed in order to decipher molecular mechanisms of adaptation to UV radiation. RESULTS The cell cycle of P. marinus PCC9511 was strongly synchronized by the day-night cycle. The most conspicuous response of cells to UV radiation was a delay in chromosome replication, with a peak of DNA synthesis shifted about 2 h into the dark period. This delay was seemingly linked to a strong downregulation of genes governing DNA replication (dnaA) and cell division (ftsZ, sepF), whereas most genes involved in DNA repair (such as recA, phrA, uvrA, ruvC, umuC) were already activated under high visible light and their expression levels were only slightly affected by additional UV exposure. CONCLUSIONS Prochlorococcus cells modified the timing of the S phase in response to UV exposure, therefore reducing the risk that mutations would occur during this particularly sensitive stage of the cell cycle. We identified several possible explanations for the observed timeshift. Among these, the sharp decrease in transcript levels of the dnaA gene, encoding the DNA replication initiator protein, is sufficient by itself to explain this response, since DNA synthesis starts only when the cellular concentration of DnaA reaches a critical threshold. However, the observed response likely results from a more complex combination of UV-altered biological processes.
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Affiliation(s)
- Christian Kolowrat
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
| | - Frédéric Partensky
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
| | - Daniella Mella-Flores
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
| | - Gildas Le Corguillé
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, FR 2424, Service Informatique et Génomique, 29680 Roscoff, France
| | - Christophe Boutte
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
| | - Nicolas Blot
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
- Clermont Université, Université Blaise Pascal, UMR CNRS 6023, Laboratoire Microorganismes: Génome et Environnement, BP 10448, 63000 Clermont-Ferrand, France
| | - Morgane Ratin
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
| | - Martial Ferréol
- CEMAGREF, UR Biologie des Ecosystèmes Aquatiques, Laboratoire d'Hydroécologie Quantitative, 3 bis quai Chauveau, CP 220, 69336 Lyon Cedex 09, France
| | - Xavier Lecomte
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
| | - Priscillia Gourvil
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
| | - Jean-François Lennon
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
| | - David M Kehoe
- Department of Biology, 1001 East Third Street, Indiana University, Bloomington, IN 47405, USA
| | - Laurence Garczarek
- UPMC-Université Paris 06, Station Biologique, Place Georges Teissier, 29680 Roscoff, France
- CNRS, UMR 7144, Groupe Plancton Océanique, 29680 Roscoff, France
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Fujisawa T, Narikawa R, Okamoto S, Ehira S, Yoshimura H, Suzuki I, Masuda T, Mochimaru M, Takaichi S, Awai K, Sekine M, Horikawa H, Yashiro I, Omata S, Takarada H, Katano Y, Kosugi H, Tanikawa S, Ohmori K, Sato N, Ikeuchi M, Fujita N, Ohmori M. Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39. DNA Res 2010; 17:85-103. [PMID: 20203057 PMCID: PMC2853384 DOI: 10.1093/dnares/dsq004] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A filamentous non-N2-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an important organism for industrial applications and as a food supply. Almost the complete genome of A. platensis NIES-39 was determined in this study. The genome structure of A. platensis is estimated to be a single, circular chromosome of 6.8 Mb, based on optical mapping. Annotation of this 6.7 Mb sequence yielded 6630 protein-coding genes as well as two sets of rRNA genes and 40 tRNA genes. Of the protein-coding genes, 78% are similar to those of other organisms; the remaining 22% are currently unknown. A total 612 kb of the genome comprise group II introns, insertion sequences and some repetitive elements. Group I introns are located in a protein-coding region. Abundant restriction-modification systems were determined. Unique features in the gene composition were noted, particularly in a large number of genes for adenylate cyclase and haemolysin-like Ca2+-binding proteins and in chemotaxis proteins. Filament-specific genes were highlighted by comparative genomic analysis.
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Affiliation(s)
- Takatomo Fujisawa
- Bioresource Information Center, Department of Biotechnology, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan
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Cervený J, Nedbal L. Metabolic rhythms of the cyanobacterium Cyanothece sp. ATCC 51142 correlate with modeled dynamics of circadian clock. J Biol Rhythms 2009; 24:295-303. [PMID: 19625731 DOI: 10.1177/0748730409338367] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
These experiments aim to reveal the dynamic features that occur during the metabolism of the unicellular, nitrogen fixing cyanobacterium Cyanothece sp. when exposed to diverse circadian forcing patterns (LD 16:8, LD 12:12, LD 8:16, LD 6:6). The chlorophyll concentration grew rapidly from subjective morning when first illuminated to around noon, then remained stable from later in the afternoon and throughout the night. The optical density measured at 735 nm was stable during the morning chlorophyll accumulation, then increased in the early afternoon toward a peak, followed at dusk by a rapid decline toward the late night steady state. The authors propose that these dynamics largely reflect accumulation and subsequent consumption of glycogen granules. This hypothesis is consistent with the sharp peak of respiration that coincides with the putative hydrocarbon catabolism. In the long-day regimen (LD 16:8), these events may mark the transition from the aerobic photosynthetic metabolism to microaerobic nitrogen metabolism that occurs at dusk, and thus cannot be triggered by the darkness that comes later. Rather, control is likely to originate in the circadian clock signaling an approaching night. To explore the dynamics of the link between respiration and circadian oscillations, the authors extrapolated an earlier model of the KaiABC oscillator from Synechococcus elongatus to Cyanothece sp. The measured peak of respiratory activity at dusk correlated strongly in its timing and time width with the modeled peak in accumulation of the KaiB(4) complex, which marks the late afternoon phase of the circadian clock. The authors propose a hypothesis that high levels of KaiB(4) (or of its Cyanothece sp. analog) trigger the glycogen catabolism that is reflected in the experiments in the respiratory peak. The degree of the correlation between the modeled KaiB(4) dynamics and the dynamics of experimentally measured peaks of respiratory activity was further tested during the half-circadian regimen (LD 6:6). The model predicted an irregular pattern of the KaiABC oscillator, quite unlike mechanical or electrical clock pacemakers that are strongly damped when driven at double their endogenous frequency. This highly unusual dynamic pattern was confirmed experimentally, supporting strongly the validity of the circadian model and of the proposed direct link to respiration.
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Affiliation(s)
- Jan Cervený
- Institute of Systems Biology and Ecology, Academy of Sciences CR, Nové Hrady, Czech Republic
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Cyanobacterial daily life with Kai-based circadian and diurnal genome-wide transcriptional control in Synechococcus elongatus. Proc Natl Acad Sci U S A 2009; 106:14168-73. [PMID: 19666549 DOI: 10.1073/pnas.0902587106] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the unicellular cyanobacterium Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock under continuous light (LL) conditions. Here, we used high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild-type, kaiABC-null, and kaiC-overexpressor strains under LL and continuous dark (DD) conditions. In the wild-type strains, >30% of transcripts oscillated significantly in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was severely attenuated in kaiABC-null strains. Although it has been proposed that KaiC globally represses gene expression, our analysis revealed that dawn-expressed genes were up-regulated by kaiC-overexpression so that the clock was arrested at subjective dawn. Transfer of cells to DD conditions from LL immediately suppressed expression of most of the genes, while the clock kept even time in the absence of transcriptional feedback. Thus, the Synechococcus genome seems to be primarily regulated by light/dark cycles and is dramatically modified by the protein-based circadian oscillator.
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Imamura S, Asayama M. Sigma factors for cyanobacterial transcription. GENE REGULATION AND SYSTEMS BIOLOGY 2009; 3:65-87. [PMID: 19838335 PMCID: PMC2758279 DOI: 10.4137/grsb.s2090] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cyanobacteria are photosynthesizing microorganisms that can be used as a model for analyzing gene expression. The expression of genes involves transcription and translation. Transcription is performed by the RNA polymerase (RNAP) holoenzyme, comprising a core enzyme and a sigma (sigma) factor which confers promoter selectivity. The unique structure, expression, and function of cyanobacterial sigma factors (and RNAP core subunits) are summarized here based on studies, reported previously. The types of promoter recognized by the sigma factors are also discussed with regard to transcriptional regulation.
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Affiliation(s)
- Sousuke Imamura
- Laboratory of Molecular Genetics, School of Agriculture, Ibaraki University, 3-21-1 Ami, Inashiki, Ibaraki 300-0393, Japan
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Simultaneous inactivation of sigma factors B and D interferes with light acclimation of the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 2009; 191:3992-4001. [PMID: 19363110 DOI: 10.1128/jb.00132-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In cyanobacteria, gene expression is regulated mainly at the level of transcription initiation, which is mediated by the RNA polymerase holoenzyme. The RNA polymerase core is catalytically active, while the sigma factor recognizes promoter sequences. Group 2 sigma factors are similar to the principal sigma factor but are nonessential. Group 2 sigma factors SigB and SigD are structurally the most similar sigma factors in Synechocystis sp. strain PCC 6803. Under standard growth conditions, simultaneous inactivation of sigB and sigD genes did not affect the growth, but the photosynthesis and growth of the DeltasigBD strain were slower than in the control strain at double light intensity. Light-saturated electron transfer rates and the fluorescence and thermoluminescence measurements showed that photosynthetic light reactions are fully functional in the DeltasigBD strain, but absorption and 77 K emission spectra measurements suggest that the light-harvesting system of the DeltasigBD strain does not acclimate normally to higher light intensity. Furthermore, the DeltasigBD strain is more sensitive to photoinhibition under bright light because impaired upregulation of psbA genes leads to insufficient PSII repair.
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