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Srivastava A, Kumar A, Biswas S, Kumar R, Srivastava V, Rajaram H, Mishra Y. Gamma (γ)-radiation stress response of the cyanobacterium Anabaena sp. PCC7120: Regulatory role of LexA and photophysiological changes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111529. [PMID: 36332765 DOI: 10.1016/j.plantsci.2022.111529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
High radioresistance of the cyanobacterium, Anabaena sp. PCC7120 has been attributed to efficient DNA repair, protein recycling, and oxidative stress management. However, the regulatory network involved in these batteries of responses remains unexplored. In the present study, the role of a global regulator, LexA in modulating gamma (γ)-radiation stress response of Anabaena was investigated. Comparison of the cytosolic proteome profiles upon γ-radiation in recombinant Anabaena strains, AnpAM (vector-control) and AnlexA+ (LexA-overexpressing), revealed 41 differentially accumulated proteins, corresponding to 29 distinct proteins. LexA was found to be involved in the regulation of 27 of the corresponding genes based on the presence of AnLexA-Box, EMSA, and/or qRT-PCR studies. The majority of the regulated genes were found to be involved in C-assimilation either through photosynthesis or C-catabolism and oxidative stress alleviation. Photosynthesis, measured in terms of PSII photophysiological parameters and thylakoid membrane proteome was found to be affected by γ-radiation in both AnpAM and AnlexA+ cells, with LexA affecting them even under control growth conditions. Thus, LexA functioned as one of the transcriptional regulators involved in modulating γ-radiation stress response in Anabaena. This study could pave the way for a deeper understanding of the regulation of γ-radiation-responsive genes in cyanobacteria at large.
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Affiliation(s)
- Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arvind Kumar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Subhankar Biswas
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Kumar A, Kirti A, Rajaram H. Regulation of multiple abiotic stress tolerance by LexA in the cyanobacterium Anabaena sp. strain PCC7120. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30185-8. [PMID: 30055321 DOI: 10.1016/j.bbagrm.2018.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 11/28/2022]
Abstract
The paradigm of involvement of LexA in regulation of only SOS-response in bacteria through the down-regulation of DNA repair genes was challenged in the unicellular cyanobacterium, Synechocystis PCC6803, wherein it was originally shown not to be associated with DNA repair and later also involved in management of carbon-starvation through up-regulation of C-metabolism genes. In the filamentous cyanobacterium, Anabaena sp. strain PCC7120, global stress management role for LexA and a consensus LexA-binding box (AnLexA-box) has been established using a LexA-overexpressing recombinant strain, AnlexA+. High levels of LexA rendered Anabaena cells sensitive to different DNA damage and oxidative stress-inducing agents, through the transcriptional down-regulation of the genes involved in DNA repair and alleviation of oxidative stress. LexA overexpression enhanced the ability of Anabaena to tolerate C-depletion, induced by inhibiting photosynthesis, by up-regulating genes involved in C-fixation and down-regulating those involved in C-breakdown, while maintaining the overall photosynthetic efficiency. A consensus LexA-binding box, AnLexA-box [AGT-N4-11-ACT] was identified upstream of both up- and down-regulated genes using a subset of Anabaena genes identified on the basis of proteomic analysis of AnlexA+ strain along with a few DNA repair genes. A short genome search revealed the presence of AnLexA box in at least 40 more genes, with functional roles in fatty acid biosynthesis, toxin-antitoxin systems in addition to DNA repair, oxidative stress, metal tolerance and C-metabolism. Thus, Anabaena LexA modulates the tolerance to multitude of stresses through transcriptional up/down-regulation of their functional genes directly by binding to the AnLexA Box present in their promoter region.
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Affiliation(s)
- Arvind Kumar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Trombay, Mumbai 400094, India
| | - Anurag Kirti
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Trombay, Mumbai 400094, India.
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Kizawa A, Kawahara A, Takimura Y, Nishiyama Y, Hihara Y. RNA-seq Profiling Reveals Novel Target Genes of LexA in the Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2016; 7:193. [PMID: 26925056 PMCID: PMC4759255 DOI: 10.3389/fmicb.2016.00193] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/04/2016] [Indexed: 11/13/2022] Open
Abstract
LexA is a well-established transcriptional repressor of SOS genes induced by DNA damage in Escherichia coli and other bacterial species. However, LexA in the cyanobacterium Synechocystis sp. PCC 6803 has been suggested not to be involved in SOS response. In this study, we performed RNA-seq analysis of the wild-type strain and the lexA-disrupted mutant to obtain the comprehensive view of LexA-regulated genes in Synechocystis. Disruption of lexA positively or negatively affected expression of genes related to various cellular functions such as phototactic motility, accumulation of the major compatible solute glucosylglycerol and subunits of bidirectional hydrogenase, photosystem I, and phycobilisome complexes. We also observed increase in the expression level of genes related to iron and manganese uptake in the mutant at the later stage of cultivation. However, none of the genes related to DNA metabolism were affected by disruption of lexA. DNA gel mobility shift assay using the recombinant LexA protein suggested that LexA binds to the upstream region of pilA7, pilA9, ggpS, and slr1670 to directly regulate their expression, but changes in the expression level of photosystem I genes by disruption of lexA is likely a secondary effect.
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Affiliation(s)
- Ayumi Kizawa
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Saitama, Japan
| | - Akihito Kawahara
- Biological Science Laboratories, KAO Corporation Wakayama, Japan
| | - Yasushi Takimura
- Biological Science Laboratories, KAO Corporation Wakayama, Japan
| | - Yoshitaka Nishiyama
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University Saitama, Japan
| | - Yukako Hihara
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama UniversitySaitama, Japan; Core Research of Evolutional Science and Technology, Japan Science and Technology AgencySaitama, Japan
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Oliveira P, Pinto F, Pacheco CC, Mota R, Tamagnini P. HesF
, an exoprotein required for filament adhesion and aggregation in
A
nabaena
sp.
PCC
7120. Environ Microbiol 2014; 17:1631-48. [DOI: 10.1111/1462-2920.12600] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 08/14/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Paulo Oliveira
- IBMC – Institute for Molecular and Cell Biology University of Porto R. do Campo Alegre, 823 4150‐180 Porto Portugal
| | - Filipe Pinto
- IBMC – Institute for Molecular and Cell Biology University of Porto R. do Campo Alegre, 823 4150‐180 Porto Portugal
| | - Catarina C. Pacheco
- IBMC – Institute for Molecular and Cell Biology University of Porto R. do Campo Alegre, 823 4150‐180 Porto Portugal
| | - Rita Mota
- IBMC – Institute for Molecular and Cell Biology University of Porto R. do Campo Alegre, 823 4150‐180 Porto Portugal
- Department of Biology Faculty of Sciences University of Porto Porto Portugal
| | - Paula Tamagnini
- IBMC – Institute for Molecular and Cell Biology University of Porto R. do Campo Alegre, 823 4150‐180 Porto Portugal
- Department of Biology Faculty of Sciences University of Porto Porto Portugal
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Schwarz C, Poss Z, Hoffmann D, Appel J. Hydrogenases and Hydrogen Metabolism in Photosynthetic Prokaryotes. RECENT ADVANCES IN PHOTOTROPHIC PROKARYOTES 2010; 675:305-48. [DOI: 10.1007/978-1-4419-1528-3_18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Oliveira P, Lindblad P. Transcriptional regulation of the cyanobacterial bidirectional Hox-hydrogenase. Dalton Trans 2009:9990-6. [PMID: 19904424 DOI: 10.1039/b908593a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The overall processes of transcription and its regulation have advanced significantly in the last years, making our understanding of prokaryotic biology more complex and detailed. In fact, a systematic study of different aspects of transcriptional regulation opens up outstanding opportunities to improve and develop the perception of complex reaction mechanisms, genetic processes and cell functions. In close connection to the cyanobacterial bidirectional hydrogenase, the main hydrogen-evolving enzyme in non-nitrogen fixing strains, two novel transcription factors have received increasing attention over the past five years: a LexA-related protein and the AbrB-like family members. Recent work on these regulators has produced new insights and advances towards the understanding (and possible interconnection) of several regulatory networks in cyanobacteria, namely nitrogen metabolism, redox response, toxin production, CO2 concentrating mechanisms and hydrogen metabolism. The fact that a LexA-related protein and AbrB-like family members have been co-purified in independent laboratories studying different sets of cyanobacterial genes suggests a possible common and/or complementary function of these regulators. In this review, we summarize the knowledge gained thus far regarding the transcriptional regulation of the cyanobacterial bidirectional hydrogenase, with special focus on the above mentioned transcription factors. Moreover, we discuss several additional points that warrants further investigation to increase our knowledge in this fast evolving research field.
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Affiliation(s)
- Paulo Oliveira
- Department of Photochemistry and Molecular Science, Angström Laboratories, Uppsala University, P. O. Box 523, SE-751 20, Uppsala, Sweden
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Ferreira D, Stal LJ, Moradas-Ferreira P, Mendes MV, Tamagnini P. THE RELATION BETWEEN N2 FIXATION AND H2 METABOLISM IN THE MARINE FILAMENTOUS NONHETEROCYSTOUS CYANOBACTERIUM LYNGBYA AESTUARII CCY 9616(1). JOURNAL OF PHYCOLOGY 2009; 45:898-905. [PMID: 27034220 DOI: 10.1111/j.1529-8817.2009.00714.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The marine filamentous nonheterocystous nitrogen-fixing cyanobacterium Lyngbya aestuarii (F. K. Mert.) Liebman ex Gomont CCY 9616 was grown under diazotrophic and nondiazotrophic conditions and under an alternating 16:8 light:dark (L:D) regime. Nitrogenase activity appeared just before the onset of the dark period, reaching its maximum 1-2 h in the dark, subsequently decreasing to zero at the beginning of the following light period. Nitrogenase activity was only detected at low levels of O2 (5%) and when the culture was grown in the absence of combined nitrogen. Quantitative reverse transcriptase-PCR (RT-PCR) analysis of one of the structural genes encoding nitrogenase, nifK, showed that the highest levels of transcription preceded the maximum activity of nitrogenase by 2-4 h. nifK transcription was not completely abolished during the remaining time of the 24 h cycle. Even in the presence of nitrate, when nitrogenase activity was undetectable, nifK was still transcribed. The H2 -uptake activity seemed to follow the nitrogenase, but the transcription of hupL (gene encoding the large subunit of uptake hydrogenase) preceded the nifK transcription. However, H2 -uptake and hupL transcription occurred throughout the 24 h cycle as well as under nondiazotrophic conditions, albeit at much lower levels. The hoxH transcript levels (a structural gene coding for the bidirectional hydrogenase) were similar under diazotrophic or nondiazotrophic conditions but slightly higher during the dark period. All three enzymes investigated are involved in H2 metabolism. It is concluded that the uptake hydrogenase is mainly responsible for H2 uptake. Nevertheless, uptake hydrogenase and nitrogenase do not seem to be coregulated.
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Affiliation(s)
- Daniela Ferreira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, PortugalDepartment of Marine Microbiology, NIOO-KNAW, PO Box 140, 4400 AC Yerseke, the NetherlandsIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Largo Abel Salazar 2, 4099-003 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, Portugal
| | - Lucas J Stal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, PortugalDepartment of Marine Microbiology, NIOO-KNAW, PO Box 140, 4400 AC Yerseke, the NetherlandsIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Largo Abel Salazar 2, 4099-003 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, Portugal
| | - Pedro Moradas-Ferreira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, PortugalDepartment of Marine Microbiology, NIOO-KNAW, PO Box 140, 4400 AC Yerseke, the NetherlandsIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Largo Abel Salazar 2, 4099-003 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, Portugal
| | - Marta V Mendes
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, PortugalDepartment of Marine Microbiology, NIOO-KNAW, PO Box 140, 4400 AC Yerseke, the NetherlandsIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Largo Abel Salazar 2, 4099-003 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, Portugal
| | - Paula Tamagnini
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, PortugalDepartment of Marine Microbiology, NIOO-KNAW, PO Box 140, 4400 AC Yerseke, the NetherlandsIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Largo Abel Salazar 2, 4099-003 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, PortugalIBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/nº 4169-007 Porto, Portugal
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Ferreira D, Pinto F, Moradas-Ferreira P, Mendes MV, Tamagnini P. Transcription profiles of hydrogenases related genes in the cyanobacterium Lyngbya majuscula CCAP 1446/4. BMC Microbiol 2009; 9:67. [PMID: 19351394 PMCID: PMC2674450 DOI: 10.1186/1471-2180-9-67] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 04/07/2009] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Lyngbya majuscula CCAP 1446/4 is a N2-fixing filamentous nonheterocystous strain that contains two NiFe-hydrogenases: an uptake (encoded by hupSL) and a bidirectional enzyme (encoded by hoxEFUYH). The biosynthesis/maturation of NiFe-hydrogenases is a complex process requiring several accessory proteins for e.g. for the incorporation of metals and ligands in the active center (large subunit), and the insertion of the FeS clusters (small subunit). The last step in the maturation of the large subunit is the cleavage of a C-terminal peptide from its precursor by a specific endopeptidase. Subsequently, the mature large and small subunits can assemble forming a functional enzyme. RESULTS In this work we demonstrated that, in L. majuscula, the structural genes encoding the bidirectional hydrogenase are cotranscribed, and that hoxW (the gene encoding its putative specific endopeptidase) is in the same chromosomal region but transcribed from a different promoter. The gene encoding the putative specific uptake hydrogenase endopeptidase, hupW, can be cotranscribed with the structural genes but it has its own promoter. hoxH, hupL, hoxW and hupW transcription was followed in L. majuscula cells grown under N2-fixing and non-N2-fixing conditions over a 12 h light/12 h dark cycle. The transcription of hoxH, hoxW and hupW did not vary remarkably in the conditions tested, while the hupL transcript levels are significantly higher under N2-fixing conditions with a peak occurring in the transition between the light and the dark phase. Furthermore, the putative endopeptidases transcript levels, in particular hoxW, are lower than those of the respective hydrogenase structural genes. CONCLUSION The data presented here indicate that in L. majuscula the genes encoding the putative hydrogenases specific endopeptidases, hoxW and hupW, are transcribed from their own promoters. Their transcript levels do not vary notably in the conditions tested, suggesting that HoxW and HupW are probably constantly present and available in the cells. These results, together with the fact that the putative endopeptidases transcript levels, in particular for hoxW, are lower than those of the structural genes, imply that the activity of the hydrogenases is mainly correlated to the transcription levels of the structural genes. The analysis of the promoter regions indicates that hupL and hupW might be under the control of different transcription factor(s), while both hoxH and xisH (hoxW) promoters could be under the control of LexA.
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Affiliation(s)
- Daniela Ferreira
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
| | - Filipe Pinto
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
| | - Pedro Moradas-Ferreira
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Largo Abel Salazar 2, 4099-003 Porto, Portugal
| | - Marta V Mendes
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Paula Tamagnini
- IBMC – Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
- Faculdade de Ciências, Universidade do Porto, Departamento de Botânica, Edifício FC4, Rua do Campo Alegre, s/n°, 4169-007 Porto, Portugal
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Devine E, Holmqvist M, Stensjö K, Lindblad P. Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120. BMC Microbiol 2009; 9:53. [PMID: 19284580 PMCID: PMC2670836 DOI: 10.1186/1471-2180-9-53] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 03/11/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The last step in the maturation process of the large subunit of [NiFe]-hydrogenases is a proteolytic cleavage of the C-terminal by a hydrogenase specific protease. Contrary to other accessory proteins these hydrogenase proteases are believed to be specific whereby one type of hydrogenases specific protease only cleaves one type of hydrogenase. In cyanobacteria this is achieved by the gene product of either hupW or hoxW, specific for the uptake or the bidirectional hydrogenase respectively. The filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Nostoc sp strain PCC 7120 may contain a single uptake hydrogenase or both an uptake and a bidirectional hydrogenase respectively. RESULTS In order to examine these proteases in cyanobacteria, transcriptional analyses were performed of hupW in Nostoc punctiforme ATCC 29133 and hupW and hoxW in Nostoc sp. strain PCC 7120. These studies revealed numerous transcriptional start points together with putative binding sites for NtcA (hupW) and LexA (hoxW). In order to investigate the diversity and specificity among hydrogeanse specific proteases we constructed a phylogenetic tree which revealed several subgroups that showed a striking resemblance to the subgroups previously described for [NiFe]-hydrogenases. Additionally the proteases specificity was also addressed by amino acid sequence analysis and protein-protein docking experiments with 3D-models derived from bioinformatic studies. These studies revealed a so called "HOXBOX"; an amino acid sequence specific for protease of Hox-type which might be involved in docking with the large subunit of the hydrogenase. CONCLUSION Our findings suggest that the hydrogenase specific proteases are under similar regulatory control as the hydrogenases they cleave. The result from the phylogenetic study also indicates that the hydrogenase and the protease have co-evolved since ancient time and suggests that at least one major horizontal gene transfer has occurred. This co-evolution could be the result of a close interaction between the protease and the large subunit of the [NiFe]-hydrogenases, a theory supported by protein-protein docking experiments performed with 3D-models. Finally we present data that may explain the specificity seen among hydrogenase specific proteases, the so called "HOXBOX"; an amino acid sequence specific for proteases of Hox-type. This opens the door for more detailed studies of the specificity found among hydrogenase specific proteases and the structural properties behind it.
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Affiliation(s)
- Ellenor Devine
- Department of Photochemistry and Molecular Science, The Angström Laboratories, Uppsala University, Uppsala, Sweden.
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Patterson-Fortin LM, Owttrim GW. A Synechocystis LexA-orthologue binds direct repeats in target genes. FEBS Lett 2008; 582:2424-30. [PMID: 18555801 DOI: 10.1016/j.febslet.2008.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 06/03/2008] [Accepted: 06/04/2008] [Indexed: 10/21/2022]
Abstract
Although evidence for LexA-orthologues, which do not regulate DNA damage repair, is accumulating, identification of binding sites and regulon members remains poorly characterized. In the cyanobacterium, Synechocystis sp. strain PCC 6803, we have recently identified a LexA-related protein that regulates expression of the crhR RNA helicase gene. Here we show that the Synechocystis LexA-orthologue binds as a dimer to 12 bp direct repeats containing a CTA-N9-CTA sequence conserved in two target genes, lexA and crhR. Characterization of this site provides the basis for identification of additional LexA targets and further evidence for LexA's divergence during evolution.
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11
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Agervald Å, Stensjö K, Holmqvist M, Lindblad P. Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120. BMC Microbiol 2008; 8:69. [PMID: 18442387 PMCID: PMC2408588 DOI: 10.1186/1471-2180-8-69] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 04/28/2008] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120. RESULTS RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome. CONCLUSION This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme.
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Affiliation(s)
- Åsa Agervald
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Karin Stensjö
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Marie Holmqvist
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Peter Lindblad
- Department of Photochemistry and Molecular Science, The Ångström Laboratories, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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Oliveira P, Lindblad P. An AbrB-Like protein regulates the expression of the bidirectional hydrogenase in Synechocystis sp. strain PCC 6803. J Bacteriol 2008; 190:1011-9. [PMID: 18039761 PMCID: PMC2223582 DOI: 10.1128/jb.01605-07] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 11/05/2007] [Indexed: 11/20/2022] Open
Abstract
In the unicellular cyanobacterium Synechocystis sp. strain PCC 6803, the pentameric bidirectional Ni-Fe hydrogenase (HoxEFUYH) is the sole enzyme involved in hydrogen metabolism. Recent investigations implicated the transcription factor LexA in the regulation of the hox genes in this cyanobacterium, suggesting the factor to work as an activator. In this work, we show evidence that LexA cannot account exclusively for the regulation of the hox genes in this cyanobacterium. Therefore, we investigated which additional transcription factors interact in and may regulate the expression of the hox genes in Synechocystis sp. strain PCC 6803. By using DNA affinity assays, a transcription factor with similarity to the transition state regulator AbrB from Bacillus subtilis was isolated. Electrophoretic mobility shift assays showed that the AbrB-like protein specifically interacts with the promoter region of the hox genes as well as with its own promoter region. In addition, results obtained with two genetically modified strains of Synechocystis sp. strain PCC 6803, one with a not fully segregated inactivation mutation of the abrB-like gene and the other overexpressing the same abrB-like gene, suggest that this transcription factor functions as a regulator of hox gene expression.
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Affiliation(s)
- Paulo Oliveira
- Department of Photochemistry and Molecular Science, Angström Laboratories, Uppsala University, P.O. Box 523, SE-751 20 Uppsala, Sweden
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Tamagnini P, Leitão E, Oliveira P, Ferreira D, Pinto F, Harris DJ, Heidorn T, Lindblad P. Cyanobacterial hydrogenases: diversity, regulation and applications. FEMS Microbiol Rev 2007; 31:692-720. [PMID: 17903205 DOI: 10.1111/j.1574-6976.2007.00085.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Cyanobacteria may possess two distinct nickel-iron (NiFe)-hydrogenases: an uptake enzyme found in N(2)-fixing strains, and a bidirectional one present in both non-N(2)-fixing and N(2)-fixing strains. The uptake hydrogenase (encoded by hupSL) catalyzes the consumption of the H(2) produced during N(2) fixation, while the bidirectional enzyme (hoxEFUYH) probably plays a role in fermentation and/or acts as an electron valve during photosynthesis. hupSL constitute a transcriptional unit, and are essentially transcribed under N(2)-fixing conditions. The bidirectional hydrogenase consists of a hydrogenase and a diaphorase part, and the corresponding five hox genes are not always clustered or cotranscribed. The biosynthesis/maturation of NiFe-hydrogenases is highly complex, requiring several core proteins. In cyanobacteria, the genes that are thought to affect hydrogenases pleiotropically (hyp), as well as the genes presumably encoding the hydrogenase-specific endopeptidases (hupW and hoxW) have been identified and characterized. Furthermore, NtcA and LexA have been implicated in the transcriptional regulation of the uptake and the bidirectional enzyme respectively. Recently, the phylogenetic origin of cyanobacterial and algal hydrogenases was analyzed, and it was proposed that the current distribution in cyanobacteria reflects a differential loss of genes according to their ecological needs or constraints. In addition, the possibilities and challenges of cyanobacterial-based H(2) production are addressed.
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Affiliation(s)
- Paula Tamagnini
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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