1
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Collart L, Jiang D, Halsey KH. The volatilome reveals microcystin concentration, microbial composition, and oxidative stress in a critical Oregon freshwater lake. mSystems 2023; 8:e0037923. [PMID: 37589463 PMCID: PMC10654074 DOI: 10.1128/msystems.00379-23] [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: 04/20/2023] [Accepted: 07/03/2023] [Indexed: 08/18/2023] Open
Abstract
IMPORTANCE Harmful algal blooms are among the most significant threats to drinking water safety. Blooms dominated by cyanobacteria can produce potentially harmful toxins and, despite intensive research, toxin production remains unpredictable. We measured gaseous molecules in Upper Klamath Lake, Oregon, over 2 years and used them to predict the presence and concentration of the cyanotoxin, microcystin, and microbial community composition. Subsets of gaseous compounds were identified that are associated with microcystin production during oxidative stress, pointing to ecosystem-level interactions leading to microcystin contamination. Our approach shows potential for gaseous molecules to be harnessed in monitoring critical waterways.
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Affiliation(s)
- Lindsay Collart
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, USA
| | - Kimberly H. Halsey
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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2
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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: 0] [Impact Index Per Article: 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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3
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Ostermeier M, Heinz S, Hamm J, Zabret J, Rast A, Klingl A, Nowaczyk MM, Nickelsen J. Thylakoid attachment to the plasma membrane in Synechocystis sp. PCC 6803 requires the AncM protein. THE PLANT CELL 2022; 34:655-678. [PMID: 34665262 PMCID: PMC8846179 DOI: 10.1093/plcell/koab253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Thylakoids are the highly specialized internal membrane systems that harbor the photosynthetic electron transport machinery in cyanobacteria and in chloroplasts. In Synechocystis sp. PCC 6803, thylakoid membranes (TMs) are arranged in peripheral sheets that occasionally converge on the plasma membrane (PM) to form thylakoid convergence membranes (TCMs). TCMs connect several thylakoid sheets and form local contact sites called thylapses between the two membrane systems, at which the early steps of photosystem II (PSII) assembly occur. The protein CurT is one of the main drivers of TCM formation known so far. Here, we identify, by whole-genome sequencing of a curT- suppressor strain, the protein anchor of convergence membranes (AncM) as a factor required for the attachment of thylakoids to the PM at thylapses. An ancM- mutant is shown to have a photosynthetic phenotype characterized by reductions in oxygen-evolution rate, PSII accumulation, and PS assembly. Moreover, the ancM- strain exhibits an altered thylakoid ultrastructure with additional sheets and TCMs detached from the PM. By combining biochemical studies with fluorescence and correlative light-electron microscopy-based approaches, we show that AncM is an integral membrane protein located in biogenic TCMs that form thylapses. These data suggest an antagonistic function of AncM and CurT in shaping TM ultrastructure.
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Affiliation(s)
- Matthias Ostermeier
- Department of Molecular Plant Science, LMU Munich, Planegg-Martinsried, 82152, Germany
| | - Steffen Heinz
- Department of Molecular Plant Science, LMU Munich, Planegg-Martinsried, 82152, Germany
| | - Julia Hamm
- Department of Molecular Plant Science, LMU Munich, Planegg-Martinsried, 82152, Germany
| | - Jure Zabret
- Department of Plant Biochemistry, Ruhr-University Bochum, Bochum 44801, Germany
| | - Anna Rast
- Department of Molecular Plant Science, LMU Munich, Planegg-Martinsried, 82152, Germany
| | - Andreas Klingl
- Department of Plant Development, LMU Munich, Planegg-Martinsried, 82152, Germany
| | - Marc M Nowaczyk
- Department of Plant Biochemistry, Ruhr-University Bochum, Bochum 44801, Germany
| | - Jörg Nickelsen
- Department of Molecular Plant Science, LMU Munich, Planegg-Martinsried, 82152, Germany
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4
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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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5
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Different Regulatory Modes of Synechocystis sp. PCC 6803 in Response to Photosynthesis Inhibitory Conditions. mSystems 2021; 6:e0094321. [PMID: 34874777 PMCID: PMC8651088 DOI: 10.1128/msystems.00943-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Cyanobacteria are promising industrial platforms owing to their ability to produce diverse natural secondary metabolites and nonnative value-added biochemicals from CO2 and light. To fully utilize their industrial potency, it is critical to understand their photosynthetic efficiency under various environmental conditions. In this study, we elucidated the inhibitory mechanisms of photosynthesis under high-light and low-temperature stress conditions in the model cyanobacterium Synechocystis sp. PCC 6803. Under each stress condition, the transcript abundance and translation efficiency were measured using transcriptome sequencing (RNA-seq) and ribosome profiling, and the genome-wide transcription unit architecture was constructed by data integration of transcription start sites and transcript 3′-end positions obtained from differential RNA-seq and sequencing of 3′-ends (Term-seq), respectively. Our results suggested that the mode of photosynthesis inhibition differed between the two stress conditions; high light stress induced photodamage responses, while low temperature stress impaired the translation efficiency of photosynthesis-associated genes. In particular, poor translation of photosystem I resulted from ribosome stalling at the untranslated regions, affecting the overall photosynthetic yield under low temperature stress. Our comprehensive multiomics analysis with transcription unit architecture provides foundational information on photosynthesis for future industrial strain development. IMPORTANCE Cyanobacteria are a compelling biochemical production platform for their ability to propagate using light and atmospheric CO2 via photosynthesis. However, the engineering of strains is hampered by limited understanding of photosynthesis under diverse environmental conditions such as high-light and low-temperature stresses. Herein, we decipher the transcriptomic and translatomic responses of the photosynthetic efficiency to stress conditions using the integrative analysis of multiomic data generated by RNA-seq and ribosome profiling, respectively. Through the generated massive data, along with the guide of the genome-wide transcription unit architecture constructed by transcription start sites and transcript 3′-end positions, we identified the factors affecting photosynthesis at transcription, posttranscription, and translation levels. Importantly, the high-light stress induces photodamage responses, and the low-temperature stress cripples the translation efficiency of photosynthesis-associated genes. The resulting insights provide pivotal information for future cyanobacterial cell factories powered by the engineering toward robust photosynthesis ability.
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6
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Cardoso D, Lima S, Matinha-Cardoso J, Tamagnini P, Oliveira P. The Role of Outer Membrane Protein(s) Harboring SLH/OprB-Domains in Extracellular Vesicles’ Production in Synechocystis sp. PCC 6803. PLANTS 2021; 10:plants10122757. [PMID: 34961227 PMCID: PMC8707739 DOI: 10.3390/plants10122757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023]
Abstract
Cyanobacteria are a group of photosynthetic prokaryotes that contribute to primary production on a global scale. These microorganisms release vesicles to the extracellular environment, spherical nanosized structures, derived essentially from the outer membrane. Even though earlier works in model Gram-negative bacteria have hypothesized that outer membrane stability is crucial in vesicle formation, the mechanisms determining vesicle biogenesis in cyanobacteria remain unknown. Here, we report on the identification of six candidate genes encoding outer membrane proteins harboring SLH/OprB-domains in the genome of the model cyanobacterium Synechocystis sp. PCC 6803. Using a genetics-based approach, one gene was found to encode an essential protein (Slr1841), while the remaining five are not essential for growth under standard conditions. Vesicle production was monitored, and it was found that a mutant in the gene encoding the second most abundant SLH/OprB protein in Synechocystis sp. PCC 6803 outer membrane (Slr1908) produces more vesicles than any of the other tested strains. Moreover, the Slr1908-protein was also found to be important for iron uptake. Altogether, our results suggest that proteins containing the SLH/OprB-domains may have dual biological role, related to micronutrient uptake and to outer membrane stability, which, together or alone, seem to be involved in cyanobacterial vesicle biogenesis.
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Affiliation(s)
- Delfim Cardoso
- MABBS—Mestrado em Aplicações em Biotecnologia e Biologia Sintética, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007 Porto, Portugal;
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (S.L.); (J.M.-C.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Steeve Lima
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (S.L.); (J.M.-C.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal
- MCbiology Doctoral Program, ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, R. Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Jorge Matinha-Cardoso
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (S.L.); (J.M.-C.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Paula Tamagnini
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (S.L.); (J.M.-C.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Paulo Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal; (S.L.); (J.M.-C.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre s/n, 4169-007 Porto, Portugal
- Correspondence: ; Tel.: +351-22-607-4900
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7
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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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8
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Shabestary K, Hernández HP, Miao R, Ljungqvist E, Hallman O, Sporre E, Branco Dos Santos F, Hudson EP. Cycling between growth and production phases increases cyanobacteria bioproduction of lactate. Metab Eng 2021; 68:131-141. [PMID: 34601120 DOI: 10.1016/j.ymben.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/03/2021] [Accepted: 09/25/2021] [Indexed: 01/23/2023]
Abstract
Decoupling growth from product synthesis is a promising strategy to increase carbon partitioning and maximize productivity in cell factories. However, reduction in both substrate uptake rate and metabolic activity in the production phase are an underlying problem for upscaling. Here, we used CRISPR interference to repress growth in lactate-producing Synechocystis sp. PCC 6803. Carbon partitioning to lactate in the production phase exceeded 90%, but CO2 uptake was severely reduced compared to uptake during the growth phase. We characterized strains during the onset of growth arrest using transcriptomics and proteomics. Multiple genes involved in ATP homeostasis were regulated once growth was inhibited, which suggests an alteration of energy charge that may lead to reduced substrate uptake. In order to overcome the reduced metabolic activity and take advantage of increased carbon partitioning, we tested a novel production strategy that involved alternating growth arrest and recovery by periodic addition of an inducer molecule to activate CRISPRi. Using this strategy, we maintained lactate biosynthesis in Synechocystis for 30 days in a constant light turbidostat cultivation. Cumulative lactate titers were also increased by 100% compared to a constant growth-arrest regime, and reached 1 g/L. Further, the cultivation produced lactate for 30 days, compared to 20 days for the non-growth arrest cultivation. Periodic growth arrest could be applicable for other products, and in cyanobacteria, could be linked to internal circadian rhythms that persist in constant light.
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Affiliation(s)
- Kiyan Shabestary
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Hugo Pineda Hernández
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Rui Miao
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emil Ljungqvist
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Olivia Hallman
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emil Sporre
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, the Netherlands
| | - Elton P Hudson
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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9
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Oeser S, Wallner T, Schuergers N, Bučinská L, Sivabalasarma S, Bähre H, Albers SV, Wilde A. Minor pilins are involved in motility and natural competence in the cyanobacterium Synechocystis sp. PCC 6803. Mol Microbiol 2021; 116:743-765. [PMID: 34115422 DOI: 10.1111/mmi.14768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria synthesize type IV pili, which are known to be essential for motility, adhesion and natural competence. They consist of long flexible fibers that are primarily composed of the major pilin PilA1 in Synechocystis sp. PCC 6803. In addition, Synechocystis encodes less abundant pilin-like proteins, which are known as minor pilins. In this study, we show that the minor pilin PilA5 is essential for natural transformation but is dispensable for motility and flocculation. In contrast, a set of minor pilins encoded by the pilA9-slr2019 transcriptional unit are necessary for motility but are dispensable for natural transformation. Neither pilA5-pilA6 nor pilA9-slr2019 are essential for pilus assembly as mutant strains showed type IV pili on the cell surface. Three further gene products with similarity to PilX-like minor pilins have a function in flocculation of Synechocystis. The results of our study indicate that different minor pilins facilitate distinct pilus functions. Further, our microarray analysis demonstrated that the transcription levels of the minor pilin genes change in response to surface contact. A total of 122 genes were determined to have altered transcription between planktonic and surface growth, including several plasmid genes which are involved exopolysaccharide synthesis and the formation of bloom-like aggregates.
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Affiliation(s)
- Sabrina Oeser
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Thomas Wallner
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Nils Schuergers
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Lenka Bučinská
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Trebon, Czech Republic
| | - Shamphavi Sivabalasarma
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Medical School Hannover, Hannover, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
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10
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Jeong Y, Hong SJ, Cho SH, Yoon S, Lee H, Choi HK, Kim DM, Lee CG, Cho S, Cho BK. Multi-Omic Analyses Reveal Habitat Adaptation of Marine Cyanobacterium Synechocystis sp. PCC 7338. Front Microbiol 2021; 12:667450. [PMID: 34054774 PMCID: PMC8155712 DOI: 10.3389/fmicb.2021.667450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are considered as promising microbial cell factories producing a wide array of bio-products. Among them, Synechocystis sp. PCC 7338 has the advantage of growing in seawater, rather than requiring arable land or freshwater. Nonetheless, how this marine cyanobacterium grows under the high salt stress condition remains unknown. Here, we determined its complete genome sequence with the embedded regulatory elements and analyzed the transcriptional changes in response to a high-salt environment. Complete genome sequencing revealed a 3.70 mega base pair genome and three plasmids with a total of 3,589 genes annotated. Differential RNA-seq and Term-seq data aligned to the complete genome provided genome-wide information on genetic regulatory elements, including promoters, ribosome-binding sites, 5'- and 3'-untranslated regions, and terminators. Comparison with freshwater Synechocystis species revealed Synechocystis sp. PCC 7338 genome encodes additional genes, whose functions are related to ion channels to facilitate the adaptation to high salt and high osmotic pressure. Furthermore, a ferric uptake regulator binding motif was found in regulatory regions of various genes including SigF and the genes involved in energy metabolism, suggesting the iron-regulatory network is connected to not only the iron acquisition, but also response to high salt stress and photosynthesis. In addition, the transcriptomics analysis demonstrated a cyclic electron transport through photosystem I was actively used by the strain to satisfy the demand for ATP under high-salt environment. Our comprehensive analyses provide pivotal information to elucidate the genomic functions and regulations in Synechocystis sp. PCC 7338.
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Affiliation(s)
- Yujin Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seong-Joo Hong
- Department of Biological Engineering, Inha University, Incheon, South Korea.,Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Sang-Hyeok Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Seonghoon Yoon
- Department of Biological Engineering, Inha University, Incheon, South Korea.,Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Hookeun Lee
- Institute of Pharmaceutical Research, College of Pharmacy, Gachon University, Incheon, South Korea
| | | | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
| | - Choul-Gyun Lee
- Department of Biological Engineering, Inha University, Incheon, South Korea.,Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Innovative Biomaterials Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Innovative Biomaterials Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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11
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Jaiswal KK, Kumar V, Verma R, Verma M, Kumar A, Vlaskin MS, Nanda M, Kim H. Graphitic bio-char and bio-oil synthesis via hydrothermal carbonization-co-liquefaction of microalgae biomass (oiled/de-oiled) and multiple heavy metals remediations. JOURNAL OF HAZARDOUS MATERIALS 2021; 409:124987. [PMID: 33450509 DOI: 10.1016/j.jhazmat.2020.124987] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/14/2020] [Accepted: 12/26/2020] [Indexed: 05/27/2023]
Abstract
Thermochemical transformation of microalgae biomass into graphitic bio-chars entices as proficient bio-adsorbents for heavy metal contaminants. This study explores the synergistic impact of Chlorella sorokiniana on biomass generation and wastewater remediation in high rate algae pond (HRAP). Biomass produced was applied for hydrothermal carbonization-co-liquefaction (HTCL). The structural and morphological characteristics of HTCL products (i.e. bio-chars and bio-oils) have been systematically studied by XRD, Raman, FTIR, elemental analyzer, SEM, BET, and 1H NMR spectroscopy. The crystallite size of the graphite 2H indexing planes was to be 4.65 nm and 14.07 nm in the bio-chars of oiled biomass (MB-OB) and de-oiled biomass (MB-DOB), respectively. The increase in the ID/IG ratio of MB-DOB indicated the highly disordered graphitic structure due to the appearance of carbonyl, hydroxyl, and epoxy functionalities in the line of high C/N and low C/H ratio. Also, the multiple heavy metals remediation of MB-DOB revealed better efficiency as ~100% in 720 min. The kinetics analysis shows the correlation coefficient of pseudo-second-order is well fitted compared to the pseudo-first-order. The Langmuir adsorption model signifies the adsorption of heavy metal ions in a monolayer adsorption manner. The study proposes the microalgae bio-char potential for multiple heavy metals remediation alongside bio-oils.
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Affiliation(s)
- Krishna Kumar Jaiswal
- Algae Research & Bio-Energy Laboratory, Department of Chemistry, Uttaranchal University, Dehradun, Uttarakhand 248007, India
| | - Vinod Kumar
- Algae Research & Bio-Energy Laboratory, Department of Chemistry, Uttaranchal University, Dehradun, Uttarakhand 248007, India.
| | - Ravikant Verma
- Department of Ecology and Environmental Sciences, Pondicherry University, Puducherry 605014, India
| | - Monu Verma
- Department of Environmental Engineering, University of Seoul, Seoul 130743, South Korea
| | - Arvind Kumar
- Department of Ecology and Environmental Sciences, Pondicherry University, Puducherry 605014, India
| | - Mikhail S Vlaskin
- Joint Institute for High Temperatures of the Russian Academy of Sciences, 13/2 Izhorskaya St, Moscow 125412, Russia.
| | - Manisha Nanda
- Department of Biotechnology, Dolphin (P.G.) Institute of Biomedical and Natural Sciences, Dehradun 248001, India
| | - Hyunook Kim
- Department of Environmental Engineering, University of Seoul, Seoul 130743, South Korea
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12
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Xie Y, Chen L, Sun T, Zhang W. Deciphering and engineering high-light tolerant cyanobacteria for efficient photosynthetic cell factories. Chin J Chem Eng 2021. [DOI: 10.1016/j.cjche.2020.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Qiao Y, Wang W, Lu X. High Light Induced Alka(e)ne Biodegradation for Lipid and Redox Homeostasis in Cyanobacteria. Front Microbiol 2020; 11:1659. [PMID: 32765469 PMCID: PMC7379126 DOI: 10.3389/fmicb.2020.01659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/25/2020] [Indexed: 01/09/2023] Open
Abstract
Cyanobacteria are the oldest photosynthetic microorganisms with good environmental adaptability. They are ubiquitous in light-exposed habitats on Earth. In recent years, cyanobacteria have become an ideal platform for producing biofuels and biochemicals from solar energy and carbon dioxide. Alka(e)nes are the main constituents of gasoline, diesel, and jet fuels. Alka(e)ne biosynthesis pathways are present in all sequenced cyanobacteria. Most cyanobacteria biosynthesize long chain alka(e)nes via acyl-acyl-carrier proteins reductase (AAR) and aldehyde-deformylating oxygenase (ADO). Alka(e)nes can be biodegraded by a variety of cyanobacteria, which lack a β-oxidation pathway. However, the mechanisms of alka(e)ne biodegradation in cyanobacteria remain elusive. In this study, a cyanobacterial alka(e)ne biodegradation pathway was uncovered by in vitro enzyme assays. Under high light, alka(e)nes in the membrane can be converted into alcohols and aldehydes by ADO, and aldehyde dehydrogenase (ALDH) can then convert the aldehydes into fatty acids to maintain lipid homeostasis in cyanobacteria. As highly reduced molecules, alka(e)nes could serve as electron donors to further reduce partially reduced reactive oxygen species (ROS) in cyanobacteria under high light. Alka(e)ne biodegradation may serve as an emergency mechanism for responding to the oxidative stress generated by excess light exposure. This study will shed new light on the roles of alka(e)ne metabolism in cyanobacteria. It is important to reduce the content of ROS by optimization of cultivation and genetic engineering for efficient alka(e)ne biosynthesis in cyanobacteria.
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Affiliation(s)
- Yue Qiao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Weihua Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,Dalian National Laboratory for Clean Energy, Dalian, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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14
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Prathiviraj R, Chellapandi P. Modeling a global regulatory network of Methanothermobacter thermautotrophicus strain ∆H. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s13721-020-0223-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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15
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Jin H, Lindblad P, Bhaya D. Building an Inducible T7 RNA Polymerase/T7 Promoter Circuit in Synechocystis sp. PCC6803. ACS Synth Biol 2019; 8:655-660. [PMID: 30935196 DOI: 10.1021/acssynbio.8b00515] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To develop tightly regulated orthogonal gene expression circuits in the photoautotrophic cyanobacterium Synechocystis sp. PCC6803 (Syn6803), we designed a circuit in which a native inducible promoter drives the expression of phage T7 RNA polymerase (T7RNAP). T7RNAP, in turn, specifically recognizes the T7 promoter that is designed to drive GFP expression. In Syn6803, this T7RNAP/T7promoter-GFP circuit produces high GFP fluorescence, which was further enhanced by using mutant T7 promoters. We also tested two orthogonal inducible promoters, Trc1O and L03, but these promoters drive T7RNAP to levels that are toxic in E. coli. Introduction of a protein degradation tag alleviated this problem. However, in Syn6803, these circuits did not function successfully. This highlights the underappreciated fact that similar circuits work with varying efficiencies in different chassis organisms. This lays the groundwork for developing new orthogonally controlled phage RNA polymerase-dependent expression systems in Syn6803.
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Affiliation(s)
- Haojie Jin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, United States
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE 75120, Uppsala, Sweden
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, United States
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16
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Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, Burton RL, Saechao C, Sloan NB, Cheng X, Chan LJG, Petzold CJ, Fuentes-Cabrera M, Ralston CY, Kerfeld CA. Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells. PLANT PHYSIOLOGY 2019; 179:156-167. [PMID: 30389783 PMCID: PMC6324227 DOI: 10.1104/pp.18.01190] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/26/2018] [Indexed: 05/10/2023]
Abstract
Bacterial microcompartments (BMCs) encapsulate enzymes within a selectively permeable, proteinaceous shell. Carboxysomes are BMCs containing ribulose-1,5-bisphosphate carboxylase oxygenase and carbonic anhydrase that enhance carbon dioxide fixation. The carboxysome shell consists of three structurally characterized protein types, each named after the oligomer they form: BMC-H (hexamer), BMC-P (pentamer), and BMC-T (trimer). These three protein types form cyclic homooligomers with pores at the center of symmetry that enable metabolite transport across the shell. Carboxysome shells contain multiple BMC-H paralogs, each with distinctly conserved residues surrounding the pore, which are assumed to be associated with specific metabolites. We studied the regulation of β-carboxysome shell composition by investigating the BMC-H genes ccmK3 and ccmK4 situated in a locus remote from other carboxysome genes. We made single and double deletion mutants of ccmK3 and ccmK4 in Synechococcus elongatus PCC7942 and show that, unlike CcmK3, CcmK4 is necessary for optimal growth. In contrast to other CcmK proteins, CcmK3 does not form homohexamers; instead CcmK3 forms heterohexamers with CcmK4 with a 1:2 stoichiometry. The CcmK3-CcmK4 heterohexamers form stacked dodecamers in a pH-dependent manner. Our results indicate that CcmK3-CcmK4 heterohexamers potentially expand the range of permeability properties of metabolite channels in carboxysome shells. Moreover, the observed facultative formation of dodecamers in solution suggests that carboxysome shell permeability may be dynamically attenuated by "capping" facet-embedded hexamers with a second hexamer. Because β-carboxysomes are obligately expressed, heterohexamer formation and capping could provide a rapid and reversible means to alter metabolite flux across the shell in response to environmental/growth conditions.
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Affiliation(s)
- Manuel Sommer
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Markus Sutter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Sayan Gupta
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Henning Kirst
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Aiko Turmo
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Sigal Lechno-Yossef
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rodney L Burton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Christine Saechao
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Nancy B Sloan
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy and Biophysics Graduate Program, Ohio State University, Columbus, Ohio 43210
| | - Leanne-Jade G Chan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Miguel Fuentes-Cabrera
- Center for Nanophase Materials Sciences and Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennesse 37831
| | - Corie Y Ralston
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Michigan State University-U.S. Department of Energy Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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17
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Alcamán-Arias ME, Pedrós-Alió C, Tamames J, Fernández C, Pérez-Pantoja D, Vásquez M, Díez B. Diurnal Changes in Active Carbon and Nitrogen Pathways Along the Temperature Gradient in Porcelana Hot Spring Microbial Mat. Front Microbiol 2018; 9:2353. [PMID: 30333812 PMCID: PMC6176055 DOI: 10.3389/fmicb.2018.02353] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 09/13/2018] [Indexed: 01/14/2023] Open
Abstract
Composition, carbon and nitrogen uptake, and gene transcription of microbial mat communities in Porcelana neutral hot spring (Northern Chilean Patagonia) were analyzed using metagenomics, metatranscriptomics and isotopically labeled carbon (H13CO3) and nitrogen (15NH4Cl and K15NO3) assimilation rates. The microbial mat community included 31 phyla, of which only Cyanobacteria and Chloroflexi were dominant. At 58°C both phyla co-occurred, with similar contributions in relative abundances in metagenomes and total transcriptional activity. At 66°C, filamentous anoxygenic phototrophic Chloroflexi were >90% responsible for the total transcriptional activity recovered, while Cyanobacteria contributed most metagenomics and metatranscriptomics reads at 48°C. According to such reads, phototrophy was carried out both through oxygenic photosynthesis by Cyanobacteria (mostly Mastigocladus) and anoxygenic phototrophy due mainly to Chloroflexi. Inorganic carbon assimilation through the Calvin-Benson cycle was almost exclusively due to Mastigocladus, which was the main primary producer at lower temperatures. Two other CO2 fixation pathways were active at certain times and temperatures as indicated by transcripts: 3-hydroxypropionate (3-HP) bi-cycle due to Chloroflexi and 3-hydroxypropionate-4-hydroxybutyrate (HH) cycle carried out by Thaumarchaeota. The active transcription of the genes involved in these C-fixation pathways correlated with high in situ determined carbon fixation rates. In situ measurements of ammonia assimilation and nitrogen fixation (exclusively attributed to Cyanobacteria and mostly to Mastigocladus sp.) showed these were the most important nitrogen acquisition pathways at 58 and 48°C. At 66°C ammonia oxidation genes were actively transcribed (mostly due to Thaumarchaeota). Reads indicated that denitrification was present as a nitrogen sink at all temperatures and that dissimilatory nitrate reduction to ammonia (DNRA) contributed very little. The combination of metagenomic and metatranscriptomic analysis with in situ assimilation rates, allowed the reconstruction of day and night carbon and nitrogen assimilation pathways together with the contribution of keystone microorganisms in this natural hot spring microbial mat.
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Affiliation(s)
- María E. Alcamán-Arias
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research, Universidad de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Programa de Biología de Sistemas, Centro Nacional de Biotecnología – Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Javier Tamames
- Programa de Biología de Sistemas, Centro Nacional de Biotecnología – Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Camila Fernández
- Department of Oceanography, Universidad de Concepción, Concepción, Chile
- Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre-et-Marie-Curie, Centre National de la Recherche Scientifique, Banyuls-sur-Mer, France
- Fondap IDEAL, Universidad Austral de Chile, Valdivia, Chile
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Mónica Vásquez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for Climate and Resilience Research, Universidad de Chile, Santiago, Chile
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18
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Synthetic Gene Regulation in Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:317-355. [DOI: 10.1007/978-981-13-0854-3_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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19
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Cordara A, Re A, Pagliano C, Van Alphen P, Pirone R, Saracco G, Branco Dos Santos F, Hellingwerf K, Vasile N. Analysis of the light intensity dependence of the growth of Synechocystis and of the light distribution in a photobioreactor energized by 635 nm light. PeerJ 2018; 6:e5256. [PMID: 30065870 PMCID: PMC6065478 DOI: 10.7717/peerj.5256] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/26/2018] [Indexed: 12/05/2022] Open
Abstract
Synechocystis gathered momentum in modelling studies and biotechnological applications owing to multiple factors like fast growth, ability to fix carbon dioxide into valuable products, and the relative ease of genetic manipulation. Synechocystis physiology and metabolism, and consequently, the productivity of Synechocystis-based photobioreactors (PBRs), are heavily light modulated. Here, we set up a turbidostat-controlled lab-scale cultivation system in order to study the influence of varying orange–red light intensities on Synechocystis growth characteristics and photosynthetic activity. Synechocystis growth and photosynthetic activity were found to raise as supplied light intensity increased up to 500 μmol photons m−2 s−1 and to enter the photoinhibition state only at 800 μmol photons m−2 s−1. Interestingly, reverting the light to a non-photo-inhibiting intensity unveiled Synechocystis to be able to promptly recover. Furthermore, our characterization displayed a clear correlation between variations in growth rate and cell size, extending a phenomenon previously observed in other cyanobacteria. Further, we applied a modelling approach to simulate the effects produced by varying the incident light intensity on its local distribution within the PBR vessel. Our model simulations suggested that the photosynthetic activity of Synechocystis could be enhanced by finely regulating the intensity of the light incident on the PBR in order to prevent cells from experiencing light-induced stress and induce their exploitation of areas of different local light intensity formed in the vessel. In the latter case, the heterogeneous distribution of the local light intensity would allow Synechocystis for an optimized usage of light.
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Affiliation(s)
- Alessandro Cordara
- Applied Science and Technology Department-Biosolar Lab, Politecnico di Torino, Turin, Italy.,Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Turin, Italy
| | - Angela Re
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Turin, Italy
| | - Cristina Pagliano
- Applied Science and Technology Department-Biosolar Lab, Politecnico di Torino, Turin, Italy
| | - Pascal Van Alphen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Raffaele Pirone
- Applied Science and Technology Department, Politecnico di Torino, Turin, Italy
| | - Guido Saracco
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Turin, Italy
| | | | - Klaas Hellingwerf
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Nicolò Vasile
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Turin, Italy
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20
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Ge H, Fang L, Huang X, Wang J, Chen W, Liu Y, Zhang Y, Wang X, Xu W, He Q, Wang Y. Translating Divergent Environmental Stresses into a Common Proteome Response through the Histidine Kinase 33 (Hik33) in a Model Cyanobacterium. Mol Cell Proteomics 2018; 16:1258-1274. [PMID: 28668777 DOI: 10.1074/mcp.m116.068080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/07/2017] [Indexed: 01/18/2023] Open
Abstract
The histidine kinase Hik33 plays important roles in mediating cyanobacterial response to divergent types of abiotic stresses including cold, salt, high light (HL), and osmotic stresses. However, how these functions are regulated by Hik33 remains to be addressed. Using a hik33-deficient strain (Δhik33) of Synechocystis sp. PCC 6803 (Synechocystis) and quantitative proteomics, we found that Hik33 depletion induces differential protein expression highly like that induced by divergent types of stresses. This typically includes downregulation of proteins in photosynthesis and carbon assimilation that are necessary for cell propagation, and upregulation of heat shock proteins, chaperons, and proteases that are important for cell survival. This observation indicates that depletion of Hik33 alone mimics divergent types of abiotic stresses, and that Hik33 could be important for preventing abnormal stress response in the normal condition. Moreover, we found most proteins of plasmid origin were significantly upregulated in Δhik33, though their biological significance remains to be addressed. Together, the systematically characterized Hik33-regulated cyanobacterial proteome, which is largely involved in stress responses, builds the molecular basis for Hik33 as a general regulator of stress responses.
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Affiliation(s)
- Haitao Ge
- From the ‡State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan 250100, China
| | - Longfa Fang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiahe Huang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Jinlong Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiyang Chen
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Liu
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanya Zhang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China
| | - Xiaorong Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China.,¶University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wu Xu
- ‖Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana 70504
| | - Qingfang He
- From the ‡State Key Laboratory of Microbial Technology, College of Life Science, Shandong University, Jinan 250100, China; .,**Department of Applied Science, University of Arkansas at Little Rock, Little Rock, Arkansas
| | - Yingchun Wang
- §State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No.1 West Beichen Rd., Beijing 100101, China; .,¶University of Chinese Academy of Sciences, Beijing, 100049, China
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21
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Giner-Lamia J, Robles-Rengel R, Hernández-Prieto MA, Muro-Pastor MI, Florencio FJ, Futschik ME. Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803. Nucleic Acids Res 2017; 45:11800-11820. [PMID: 29036481 PMCID: PMC5714215 DOI: 10.1093/nar/gkx860] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022] Open
Abstract
In cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.
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Affiliation(s)
- Joaquín Giner-Lamia
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Laboratory of Intracellular Bacterial Pathogens, Department of Microbial Biotechnology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain
| | - Rocío Robles-Rengel
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Miguel A Hernández-Prieto
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - M Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis. Universidad de Sevilla-CSIC, Av. Américo Vespucio 49, E-41092 Seville, Spain
| | - Matthias E Futschik
- Systems Biology and Bioinformatics Laboratory, CBMR, University of Algarve, 8005-139 Faro, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal.,School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, Plymouth PL6 8BU, UK
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Hernández-Prieto MA, Li Y, Postier BL, Blankenship RE, Chen M. Far-red light promotes biofilm formation in the cyanobacteriumAcaryochloris marina. Environ Microbiol 2017; 20:535-545. [DOI: 10.1111/1462-2920.13961] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/11/2017] [Accepted: 10/13/2017] [Indexed: 01/07/2023]
Affiliation(s)
- Miguel A. Hernández-Prieto
- ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences; University of Sydney; NSW 2006 Australia
| | - Yaqiong Li
- ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences; University of Sydney; NSW 2006 Australia
| | - Bradley L. Postier
- Departments of Biology and Chemistry; Washington University in St. Louis; St. Louis MO 63130 USA
| | - Robert E. Blankenship
- Departments of Biology and Chemistry; Washington University in St. Louis; St. Louis MO 63130 USA
| | - Min Chen
- ARC Centre of Excellence for Translational Photosynthesis and School of Life and Environmental Sciences; University of Sydney; NSW 2006 Australia
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Hagemann M, Hess WR. Systems and synthetic biology for the biotechnological application of cyanobacteria. Curr Opin Biotechnol 2017; 49:94-99. [PMID: 28843192 DOI: 10.1016/j.copbio.2017.07.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis. Their evolutionary relation to plastids in eukaryotic phototrophs and their increasing utilization as green cell factories initiated the use of systems biology approaches early on. For select model strains, extensive 'omics' data sets have been generated, and genome-wide models have been elucidated. Moreover, the results obtained may be used for the optimization of cyanobacterial metabolism, which can direct the biotechnological production of biofuels or chemical feedstock. Synthetic biology approaches permit the rational construction of novel metabolic pathways that are based on the combination of multiple enzymatic activities of different origins. In addition, the manipulation of whole metabolic networks by CRISPR-based and sRNA-based technologies with multiple parallel targets will further stimulate the use of cyanobacteria for diverse applications in basic research and biotechnology.
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Affiliation(s)
- Martin Hagemann
- University of Rostock, Institute of Biological Sciences, Plant Physiology, A.-Einstein-Str. 3, D-18059 Rostock, Germany.
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany
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24
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The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels. G3-GENES GENOMES GENETICS 2017; 7:517-532. [PMID: 27974439 PMCID: PMC5295598 DOI: 10.1534/g3.116.036855] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels.
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Bečková M, Gardian Z, Yu J, Konik P, Nixon PJ, Komenda J. Association of Psb28 and Psb27 Proteins with PSII-PSI Supercomplexes upon Exposure of Synechocystis sp. PCC 6803 to High Light. MOLECULAR PLANT 2017; 10:62-72. [PMID: 27530366 DOI: 10.1016/j.molp.2016.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 06/29/2016] [Accepted: 08/04/2016] [Indexed: 05/23/2023]
Abstract
Formation of the multi-subunit oxygen-evolving photosystem II (PSII) complex involves a number of auxiliary protein factors. In this study we compared the localization and possible function of two homologous PSII assembly factors, Psb28-1 and Psb28-2, from the cyanobacterium Synechocystis sp. PCC 6803. We demonstrate that FLAG-tagged Psb28-2 is present in both the monomeric PSII core complex and a PSII core complex lacking the inner antenna CP43 (RC47), whereas Psb28-1 preferentially binds to RC47. When cells are exposed to increased irradiance, both tagged Psb28 proteins additionally associate with oligomeric forms of PSII and with PSII-PSI supercomplexes composed of trimeric photosystem I (PSI) and two PSII monomers as deduced from electron microscopy. The presence of the Psb27 accessory protein in these complexes suggests the involvement of PSI in PSII biogenesis, possibly by photoprotecting PSII through energy spillover. Under standard culture conditions, the distribution of PSII complexes is similar in the wild type and in each of the single psb28 null mutants except for loss of RC47 in the absence of Psb28-1. In comparison with the wild type, growth of mutants lacking Psb28-1 and Psb27, but not Psb28-2, was retarded under high-light conditions and, especially, intermittent high-light/dark conditions, emphasizing the physiological importance of PSII assembly factors for light acclimation.
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Affiliation(s)
- Martina Bečková
- Institute of Microbiology, Center Algatech, Opatovický mlýn, 37981 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Zdenko Gardian
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic; Institute of Plant Molecular Biology, Biology Centre Academy of Sciences, Branišovská 31, 37005 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
| | - Peter Konik
- Institute of Microbiology, Center Algatech, Opatovický mlýn, 37981 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Peter J Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Josef Komenda
- Institute of Microbiology, Center Algatech, Opatovický mlýn, 37981 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic.
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26
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Fujisawa T, Narikawa R, Maeda SI, Watanabe S, Kanesaki Y, Kobayashi K, Nomata J, Hanaoka M, Watanabe M, Ehira S, Suzuki E, Awai K, Nakamura Y. CyanoBase: a large-scale update on its 20th anniversary. Nucleic Acids Res 2016; 45:D551-D554. [PMID: 27899668 PMCID: PMC5210588 DOI: 10.1093/nar/gkw1131] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/26/2016] [Accepted: 11/11/2016] [Indexed: 01/18/2023] Open
Abstract
The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface for large genomic data to include the use of semantic web technologies and JBrowse and have extended community-based reannotation resources through the re-annotation of Synechocystis sp. PCC 6803 by the cyanobacterial research community. These updates have markedly improved CyanoBase, providing cyanobacterial genome annotations as references for cyanobacterial research.
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Affiliation(s)
- Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
| | - Shin-Ichi Maeda
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601 Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Koichi Kobayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Jiro Nomata
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Nagatsuta 4259, Midori-ku, Yokohama 226-8503, Japan
| | - Mitsumasa Hanaoka
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510 Japan
| | - Mai Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeki Ehira
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami Osawa, Hachioji, Tokyo 192-0397, Japan
| | - Eiji Suzuki
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan
| | - Koichiro Awai
- Department of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan
| | - Yasukazu Nakamura
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan
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Cassier-Chauvat C, Veaudor T, Chauvat F. Comparative Genomics of DNA Recombination and Repair in Cyanobacteria: Biotechnological Implications. Front Microbiol 2016; 7:1809. [PMID: 27881980 PMCID: PMC5101192 DOI: 10.3389/fmicb.2016.01809] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/27/2016] [Indexed: 12/16/2022] Open
Abstract
Cyanobacteria are fascinating photosynthetic prokaryotes that are regarded as the ancestors of the plant chloroplast; the purveyors of oxygen and biomass for the food chain; and promising cell factories for an environmentally friendly production of chemicals. In colonizing most waters and soils of our planet, cyanobacteria are inevitably challenged by environmental stresses that generate DNA damages. Furthermore, many strains engineered for biotechnological purposes can use DNA recombination to stop synthesizing the biotechnological product. Hence, it is important to study DNA recombination and repair in cyanobacteria for both basic and applied research. This review reports what is known in a few widely studied model cyanobacteria and what can be inferred by mining the sequenced genomes of morphologically and physiologically diverse strains. We show that cyanobacteria possess many E. coli-like DNA recombination and repair genes, and possibly other genes not yet identified. E. coli-homolog genes are unevenly distributed in cyanobacteria, in agreement with their wide genome diversity. Many genes are extremely well conserved in cyanobacteria (mutMS, radA, recA, recFO, recG, recN, ruvABC, ssb, and uvrABCD), even in small genomes, suggesting that they encode the core DNA repair process. In addition to these core genes, the marine Prochlorococcus and Synechococcus strains harbor recBCD (DNA recombination), umuCD (mutational DNA replication), as well as the key SOS genes lexA (regulation of the SOS system) and sulA (postponing of cell division until completion of DNA reparation). Hence, these strains could possess an E. coli-type SOS system. In contrast, several cyanobacteria endowed with larger genomes lack typical SOS genes. For examples, the two studied Gloeobacter strains lack alkB, lexA, and sulA; and Synechococcus PCC7942 has neither lexA nor recCD. Furthermore, the Synechocystis PCC6803 lexA product does not regulate DNA repair genes. Collectively, these findings indicate that not all cyanobacteria have an E. coli-type SOS system. Also interestingly, several cyanobacteria possess multiple copies of E. coli-like DNA repair genes, such as Acaryochloris marina MBIC11017 (2 alkB, 3 ogt, 7 recA, 3 recD, 2 ssb, 3 umuC, 4 umuD, and 8 xerC), Cyanothece ATCC51142 (2 lexA and 4 ruvC), and Nostoc PCC7120 (2 ssb and 3 xerC).
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Affiliation(s)
- Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell, CEA, Centre Nationnal de la Recherche Scientifique (CNRS), Universite Paris-Sud, Université Paris-Saclay Gif-sur-Yvette Cedex, France
| | - Théo Veaudor
- Institute for Integrative Biology of the Cell, CEA, Centre Nationnal de la Recherche Scientifique (CNRS), Universite Paris-Sud, Université Paris-Saclay Gif-sur-Yvette Cedex, France
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell, CEA, Centre Nationnal de la Recherche Scientifique (CNRS), Universite Paris-Sud, Université Paris-Saclay Gif-sur-Yvette Cedex, France
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28
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Heinz S, Rast A, Shao L, Gutu A, Gügel IL, Heyno E, Labs M, Rengstl B, Viola S, Nowaczyk MM, Leister D, Nickelsen J. Thylakoid Membrane Architecture in Synechocystis Depends on CurT, a Homolog of the Granal CURVATURE THYLAKOID1 Proteins. THE PLANT CELL 2016; 28:2238-2260. [PMID: 27543090 PMCID: PMC5059811 DOI: 10.1105/tpc.16.00491] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 08/05/2016] [Accepted: 08/17/2016] [Indexed: 05/21/2023]
Abstract
Photosynthesis occurs in thylakoids, a highly specialized membrane system. In the cyanobacterium Synechocystis sp PCC 6803 (hereafter Synechocystis 6803), the thylakoids are arranged parallel to the plasma membrane and occasionally converge toward it to form biogenesis centers. The initial steps in PSII assembly are thought to take place in these regions, which contain a membrane subcompartment harboring the early assembly factor PratA and are referred to as PratA-defined membranes (PDMs). Loss of CurT, the Synechocystis 6803 homolog of Arabidopsis thaliana grana-shaping proteins of the CURVATURE THYLAKOID1 family, results in disrupted thylakoid organization and the absence of biogenesis centers. As a consequence, PSII is less efficiently assembled and accumulates to only 50% of wild-type levels. CurT induces membrane curvature in vitro and is distributed all over the thylakoids, with local concentrations at biogenesis centers. There it forms a sophisticated tubular network at the cell periphery, as revealed by live-cell imaging. CurT is part of several high molecular mass complexes, and Blue Native/SDS-PAGE and isoelectric focusing demonstrated that different isoforms associate with PDMs and thylakoids. Moreover, CurT deficiency enhances sensitivity to osmotic stress, adding a level of complexity to CurT function. We propose that CurT is crucial for the differentiation of membrane architecture, including the formation of PSII-related biogenesis centers, in Synechocystis 6803.
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Affiliation(s)
- Steffen Heinz
- Molekulare Pflanzenwissenschaften, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
| | - Anna Rast
- Molekulare Pflanzenwissenschaften, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
| | - Lin Shao
- Molekulare Pflanzenwissenschaften, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
| | - Andrian Gutu
- Department of Molecular and Cellular Biology, FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Irene L Gügel
- Biochemie und Physiologie der Pflanzen, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
- Munich Centre for Integrated Protein Science CiPSM, Ludwig-Maximilians-Universität München, Department of Chemistry and Biochemistry, 81377 Munich, Germany
| | - Eiri Heyno
- Biochemie der Pflanzen, Ruhr-Universität Bochum, 44801 Bochum, Germany
- Max-Planck-Institut für Chemische Energiekonversion, 45470 Mülheim an der Ruhr, Germany
| | - Mathias Labs
- Molekularbiologie der Pflanzen, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
| | - Birgit Rengstl
- Molekulare Pflanzenwissenschaften, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
| | - Stefania Viola
- Molekularbiologie der Pflanzen, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
| | - Marc M Nowaczyk
- Biochemie der Pflanzen, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Dario Leister
- Molekularbiologie der Pflanzen, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
| | - Jörg Nickelsen
- Molekulare Pflanzenwissenschaften, Ludwig-Maximilians-Universität München, Biozentrum, 82152 Planegg-Martinsried, Germany
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29
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Galmozzi CV, Florencio FJ, Muro-Pastor MI. The Cyanobacterial Ribosomal-Associated Protein LrtA Is Involved in Post-Stress Survival in Synechocystis sp. PCC 6803. PLoS One 2016; 11:e0159346. [PMID: 27442126 PMCID: PMC4956104 DOI: 10.1371/journal.pone.0159346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/30/2016] [Indexed: 02/06/2023] Open
Abstract
A light-repressed transcript encodes the LrtA protein in cyanobacteria. We show that half-life of lrtA transcript from Synechocystis sp. PCC 6803 is higher in dark-treated cells as compared to light-grown cells, suggesting post-transcriptional control of lrtA expression. The lrtA 5´ untranslated leader region is involved in that darkness-dependent regulation. We also found that Synechocystis sp. PCC 6803 LrtA is a ribosome-associated protein present in both 30S and 70S ribosomal particles. In order to investigate the function of this protein we have constructed a deletion mutant of the lrtA gene. Cells lacking LrtA (∆lrtA) had significantly lower amount of 70S particles and a greater amount of 30S and 50S particles, suggesting a role of LrtA in stabilizing 70S particles. Synechocystis strains with different amounts of LrtA protein: wild-type, ∆lrtA, and LrtAS (overexpressing lrtA) showed no differences in their growth rate under standard laboratory conditions. However, a clear LrtA dose-dependent effect was observed in the presence of the antibiotic tylosin, being the LrtAS strains the most sensitive. Similar results were obtained under hyperosmotic stress caused by sorbitol. Conversely, after prolonged periods of starvation, ∆lrtA strains were delayed in their growth with respect to the wild-type and the LrtAS strains. A positive role of LrtA protein in post-stress survival is proposed.
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Affiliation(s)
- Carla V. Galmozzi
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Francisco J. Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
| | - M. Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, Sevilla, Spain
- * E-mail:
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