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Curren E, Leong SCY. Global phylogeography of toxic cyanobacteria Moorea producens reveals distinct genetic partitioning influenced by Proterozoic glacial cycles. HARMFUL ALGAE 2019; 86:10-19. [PMID: 31358269 DOI: 10.1016/j.hal.2019.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 06/10/2023]
Abstract
Lyngbya majuscula is a marine filamentous cyanobacteria belonging to the family Oscillatoriaceae. Recent phylogenetic analyses of L. majuscula have reclassified a subset of this species into various genera such as Moorea, Okeania and Dapis. From the genus Moorea, Moorea producens is a toxic invasive cyanobacterium that produces bioactive secondary metabolites that can cause severe inflammation and blistering. Despite the global distribution of M. producens, little information is available on their origin, patterns of dispersal and population structure. In this study, the spatial population structure of M. producens was investigated using near-complete 16S rRNA sequences. Analysis of the global population of M. producens by Isolation by Distance and STRUCTURE revealed two significantly distinct cosmopolitan populations that were separated by a genetic break. Lineage-specific divergence estimates of 147 cyanobacterial taxa, based on a relaxed molecular clock indicated the first global emergence of M. producens during the Mesoarchean and a subsequent global recolonization during the Mesoproterozoic period. We conclude that the genetic discontinuity between both cosmopolitan populations is attributed to refugia associated with Proterozoic glacial cycles.
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Affiliation(s)
- Emily Curren
- Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, 117555, Singapore; St. John's Island National Marine Laboratory (SJINML), Tropical Marine Science Institute (TMSI), National University of Singapore, 18 Kent Ridge Road, 119227, Singapore.
| | - Sandric Chee Yew Leong
- St. John's Island National Marine Laboratory (SJINML), Tropical Marine Science Institute (TMSI), National University of Singapore, 18 Kent Ridge Road, 119227, Singapore
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Pinto F, Pacheco CC, Oliveira P, Montagud A, Landels A, Couto N, Wright PC, Urchueguía JF, Tamagnini P. Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites. DNA Res 2015; 22:425-37. [PMID: 26490728 PMCID: PMC4675711 DOI: 10.1093/dnares/dsv024] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/15/2015] [Indexed: 01/04/2023] Open
Abstract
The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms.
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Affiliation(s)
- Filipe Pinto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto 4150-171, Portugal
| | - Catarina C Pacheco
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal
| | - Paulo Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal
| | - Arnau Montagud
- Instituto Universitario de Matemática Pura y Aplicada, Universitat Politècnica de València, Valencia 46022, Spain
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S10 2TN, UK
| | - Narciso Couto
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S10 2TN, UK
| | - Phillip C Wright
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S10 2TN, UK
| | - Javier F Urchueguía
- Instituto Universitario de Matemática Pura y Aplicada, Universitat Politècnica de València, Valencia 46022, Spain
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto 4150-171, Portugal
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Pereira SB, Ow SY, Barrios-Llerena ME, Wright PC, Moradas-Ferreira P, Tamagnini P. iTRAQ-based quantitative proteomic analysis of Gloeothece sp. PCC 6909: Comparison with its sheathless mutant and adaptations to nitrate deficiency and sulfur limitation. J Proteomics 2011; 75:270-83. [DOI: 10.1016/j.jprot.2011.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 07/25/2011] [Accepted: 09/09/2011] [Indexed: 11/25/2022]
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Pinto F, van Elburg KA, Pacheco CC, Lopo M, Noirel J, Montagud A, Urchueguía JF, Wright PC, Tamagnini P. Construction of a chassis for hydrogen production: physiological and molecular characterization of a Synechocystis sp. PCC 6803 mutant lacking a functional bidirectional hydrogenase. MICROBIOLOGY-SGM 2011; 158:448-464. [PMID: 22096147 DOI: 10.1099/mic.0.052282-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cyanobacteria are photosynthetic prokaryotes that are promising 'low-cost' microbial cell factories due to their simple nutritional requirements and metabolic plasticity, and the availability of tools for their genetic manipulation. The unicellular non-nitrogen-fixing Synechocystis sp. PCC 6803 is the best studied cyanobacterial strain and its genome was the first to be sequenced. The vast amount of physiological and molecular data available, together with a relatively small genome, makes Synechocystis suitable for computational metabolic modelling and to be used as a photoautotrophic chassis in synthetic biology applications. To prepare it for the introduction of a synthetic hydrogen producing device, a Synechocystis sp. PCC 6803 deletion mutant lacking an active bidirectional hydrogenase (ΔhoxYH) was produced and characterized at different levels: physiological, proteomic and transcriptional. The results showed that, under conditions favouring hydrogenase activity, 17 of the 210 identified proteins had significant differential fold changes in comparisons of the mutant with the wild-type. Most of these proteins are related to the redox and energy state of the cell. Transcriptional studies revealed that only six genes encoding those proteins exhibited significant differences in transcript levels. Moreover, the mutant exhibits similar growth behaviour compared with the wild-type, reflecting Synechocystis plasticity and metabolic adaptability. Overall, this study reveals that the Synechocystis ΔhoxYH mutant is robust and can be used as a photoautotrophic chassis for the integration of synthetic constructs, i.e. molecular constructs assembled from well characterized biological and/or synthetic parts (e.g. promoters, regulators, coding regions, terminators) designed for a specific purpose.
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Affiliation(s)
- Filipe Pinto
- Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Karin A van Elburg
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mapping Street, Sheffield S1 3JD, UK
| | - Catarina C Pacheco
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Miguel Lopo
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Josselin Noirel
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mapping Street, Sheffield S1 3JD, UK
| | - Arnau Montagud
- Instituto Universitario de Matemática Pura y Aplicada, Universidad Politécnica de Valencia, Camí de Vera, E-46071 Valencia, Spain
| | - Javier F Urchueguía
- Instituto Universitario de Matemática Pura y Aplicada, Universidad Politécnica de Valencia, Camí de Vera, E-46071 Valencia, Spain
| | - Phillip C Wright
- Biological and Environmental Systems Group, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mapping Street, Sheffield S1 3JD, UK
| | - Paula Tamagnini
- Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
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Bothe H, Schmitz O, Yates MG, Newton WE. Nitrogen fixation and hydrogen metabolism in cyanobacteria. Microbiol Mol Biol Rev 2010; 74:529-51. [PMID: 21119016 PMCID: PMC3008169 DOI: 10.1128/mmbr.00033-10] [Citation(s) in RCA: 181] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N(2) fixation and/or H(2) formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H(2) as a source of combustible energy. To enhance the rates of H(2) production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H(2) formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.
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Affiliation(s)
- Hermann Bothe
- Botanical Institute, The University of Cologne, Zülpicher Str. 47b, D-50923 Cologne, Germany.
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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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