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Ohdate K, Sakata M, Maeda K, Sakamaki Y, Nimura-Matsune K, Ohbayashi R, Hess WR, Watanabe S. Discovery of novel replication proteins for large plasmids in cyanobacteria and their potential applications in genetic engineering. Front Microbiol 2024; 15:1311290. [PMID: 38419637 PMCID: PMC10899382 DOI: 10.3389/fmicb.2024.1311290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Numerous cyanobacteria capable of oxygenic photosynthesis possess multiple large plasmids exceeding 100 kbp in size. These plasmids are believed to have distinct replication and distribution mechanisms, as they coexist within cells without causing incompatibilities between plasmids. However, information on plasmid replication proteins (Rep) in cyanobacteria is limited. Synechocystis sp. PCC 6803 hosts four large plasmids, pSYSM, pSYSX, pSYSA, and pSYSG, but Rep proteins for these plasmids, except for CyRepA1 on pSYSA, are unknown. Using Autonomous Replication sequencing (AR-seq), we identified two potential Rep genes in Synechocystis 6803, slr6031 and slr6090, both located on pSYSX. The corresponding Rep candidates, Slr6031 and Slr6090, share structural similarities with Rep-associated proteins of other bacteria and homologs were also identified in various cyanobacteria. We observed autonomous replication activity for Slr6031 and Slr6090 in Synechococcus elongatus PCC 7942 by fusing their genes with a construct expressing GFP and introducing them via transformation. The slr6031/slr6090-containing plasmids exhibited lower copy numbers and instability in Synechococcus 7942 cells compared to the expression vector pYS. While recombination occurred in the case of slr6090, the engineered plasmid with slr6031 coexisted with plasmids encoding CyRepA1 or Slr6090 in Synechococcus 7942 cells, indicating the compatibility of Slr6031 and Slr6090 with CyRepA1. Based on these results, we designated Slr6031 and Slr6090 as CyRepX1 (Cyanobacterial Rep-related protein encoded on pSYSX) and CyRepX2, respectively, demonstrating that pSYSX is a plasmid with "two Reps in one plasmid." Furthermore, we determined the copy number and stability of plasmids with cyanobacterial Reps in Synechococcus 7942 and Synechocystis 6803 to elucidate their potential applications. The novel properties of CyRepX1 and 2, as revealed by this study, hold promise for the development of innovative genetic engineering tools in cyanobacteria.
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Affiliation(s)
- Kazuma Ohdate
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Minori Sakata
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Kaisei Maeda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yutaka Sakamaki
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Kaori Nimura-Matsune
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryudo Ohbayashi
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics Group, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Satoru Watanabe
- Department of Bioscience, Faculty of Life Science, Tokyo University of Agriculture, Tokyo, Japan
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Jin H, Zhang J, Wang Y, Ge W, Jing Y, Cao X, Huo Y, Fu Y. A codon-based live-cell biomonitoring system for assessing intracellular phenylalanine bioavailability in cyanobacteria. Biosens Bioelectron 2024; 244:115792. [PMID: 37922807 DOI: 10.1016/j.bios.2023.115792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Phenylalanine, as an essential aromatic amino acid, is not only needed for protein and vital molecules such as neurotransmitter and hormone synthesis but also a substrate for the biosynthesis of phenylpropanoids and various bioactive compounds. The metabolism of phenylalanine is dynamic and transitory, which would otherwise inhibit cell growth. Therefore, it is challenging and imperative to monitor intracellular phenylalanine bioavailability in real time, which has great significance for evaluating the effectiveness of introducing pathway-specific genetic modifications to enhance phenylalanine generation. In this study, we proposed a live-cell biomonitoring system to assess phenylalanine bioavailability in real time in cyanobacteria based on codon degeneracy and species-specific usage bias. The biomonitoring system was generated through genetic modification of phenylalanine codons in the chloramphenicol antibiotic resistance gene to wholly preferred and rare codons, in combination with an orthogonal constitutive promoter Trc to express these genes. Cyanobacterial cells equipped with a preferred codon-based gene showed a significant growth advantage over those with rare codons under antibiotic pressure, while the delayed growth caused by rare codon-based genes could be rescued by supplementing phenylalanine in the cultivation medium. Increasing intracellular phenylalanine bioavailability could promote rare codon-based gene containing cell growth to a similar level as wild-type strains harboring preferred codon-based gene, providing a live-cell visualized screening method to relatively define phenylalanine content from either random mutation libraries or pathway-specific engineering cyanobacterial chassis before conducting labor-intensive quantitative measurements.
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Affiliation(s)
- Haojie Jin
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, PR China; Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, PR China
| | - Jiaqi Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, PR China
| | - Yan Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, 100191, PR China
| | - Wanzhao Ge
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, PR China
| | - Yike Jing
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, PR China
| | - Xiaoyu Cao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, PR China
| | - Yixin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Yujie Fu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, 100083, PR China; Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, 518000, PR China.
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3
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Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:656-668. [PMID: 37794696 PMCID: PMC10667661 DOI: 10.1111/1758-2229.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid-encoded genes is similar to that of chromosome-encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.
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Affiliation(s)
- Fabian Nies
- Institute of General MicrobiologyKiel UniversityKielGermany
| | - Tanita Wein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | | | - Benjamin L. Springstein
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences FacultyPontifical Catholic University of ChileSantiagoChile
| | - Claudia Taubenheim
- Institute of General MicrobiologyKiel UniversityKielGermany
- Present address:
Department of Internal Medicine IIUniversity Medical Center Schleswig‐HolsteinKielGermany
| | - Tal Dagan
- Institute of General MicrobiologyKiel UniversityKielGermany
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Opel F, Siebert NA, Klatt S, Tüllinghoff A, Hantke JG, Toepel J, Bühler B, Nürnberg DJ, Klähn S. Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria. ACS Synth Biol 2022; 11:1758-1771. [PMID: 35405070 DOI: 10.1021/acssynbio.1c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria have raised great interest in biotechnology due to their potential for a sustainable, photosynthesis-driven production of fuels and value-added chemicals. This has led to a concomitant development of molecular tools to engineer the metabolism of those organisms. In this regard, however, even cyanobacterial model strains lag behind compared to their heterotrophic counterparts. For instance, replicative shuttle vectors that allow gene transfer independent of recombination into host DNA are still scarce. Here, we introduce the pSOMA shuttle vector series comprising 10 synthetic plasmids for comprehensive genetic engineering of Synechocystis sp. PCC 6803. The series is based on the small endogenous plasmids pCA2.4 and pCB2.4, each combined with a replicon from Escherichia coli, different selection markers as well as features facilitating molecular cloning and the insulated introduction of gene expression cassettes. We made use of genes encoding green fluorescent protein (GFP) and a Baeyer-Villiger monooxygenase (BVMO) to demonstrate functional gene expression from the pSOMA plasmids in vivo. Moreover, we demonstrate the expression of distinct heterologous genes from individual plasmids maintained in the same strain and thereby confirmed compatibility between the two pSOMA subseries as well as with derivatives of the broad-host-range plasmid RSF1010. We also show that gene transfer into the filamentous model strain Anabaena sp. PCC 7120 is generally possible, which is encouraging to further explore the range of cyanobacterial host species that could be engineered via pSOMA plasmids. Altogether, the pSOMA shuttle vector series displays an attractive alternative to existing plasmid series and thus meets the current demand for the introduction of complex genetic setups and to perform extensive metabolic engineering of cyanobacteria.
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Affiliation(s)
- Franz Opel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Nina A. Siebert
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Sabine Klatt
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Adrian Tüllinghoff
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Janis G. Hantke
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Toepel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stephan Klähn
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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Nagy C, Thiel K, Mulaku E, Mustila H, Tamagnini P, Aro EM, Pacheco CC, Kallio P. Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number. Microb Cell Fact 2021; 20:130. [PMID: 34246263 PMCID: PMC8272380 DOI: 10.1186/s12934-021-01622-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Synechocystis sp. PCC 6803 provides a well-established reference point to cyanobacterial metabolic engineering as part of basic photosynthesis research, as well as in the development of next-generation biotechnological production systems. This study focused on expanding the current knowledge on genomic integration of expression constructs in Synechocystis, targeting a range of novel sites in the chromosome and in the native plasmids, together with established loci used in literature. The key objective was to obtain quantitative information on site-specific expression in reference to replicon copy numbers, which has been speculated but never compared side by side in this host. Results An optimized sYFP2 expression cassette was successfully integrated in two novel sites in Synechocystis chromosome (slr0944; sll0058) and in all four endogenous megaplasmids (pSYSM/slr5037-slr5038; pSYSX/slr6037; pSYSA/slr7023; pSYSG/slr8030) that have not been previously evaluated for the purpose. Fluorescent analysis of the segregated strains revealed that the expression levels between the megaplasmids and chromosomal constructs were very similar, and reinforced the view that highest expression in Synechocystis can be obtained using RSF1010-derived replicative vectors or the native small plasmid pCA2.4 evaluated in comparison. Parallel replicon copy number analysis by RT-qPCR showed that the expression from the alternative loci is largely determined by the gene dosage in Synechocystis, thereby confirming the dependence formerly proposed based on literature. Conclusions This study brings together nine different integrative loci in the genome of Synechocystis to demonstrate quantitative differences between target sites in the chromosome, the native plasmids, and a RSF1010-based replicative expression vector. To date, this is the most comprehensive comparison of alternative integrative sites in Synechocystis, and provides the first direct reference between expression efficiency and replicon gene dosage in the context. In the light of existing literature, the findings support the view that the small native plasmids can be notably more difficult to target than the chromosome or the megaplasmids, and that the RSF1010-derived vectors may be surprisingly well maintained under non-selective culture conditions in this cyanobacterial host. Altogether, the work broadens our views on genomic integration and the rational use of different integrative loci versus replicative plasmids, when aiming at expressing heterologous genes in Synechocystis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01622-2.
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Affiliation(s)
- Csaba Nagy
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Kati Thiel
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Edita Mulaku
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Henna Mustila
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007, Porto, Portugal
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Catarina C Pacheco
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland.
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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Madsen MA, Hamilton G, Herzyk P, Amtmann A. Environmental Regulation of PndbA600, an Auto-Inducible Promoter for Two-Stage Industrial Biotechnology in Cyanobacteria. Front Bioeng Biotechnol 2021; 8:619055. [PMID: 33542914 PMCID: PMC7853294 DOI: 10.3389/fbioe.2020.619055] [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: 10/19/2020] [Accepted: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are photosynthetic prokaryotes being developed as sustainable platforms that use renewable resources (light, water, and air) for diverse applications in energy, food, environment, and medicine. Despite the attractive promise that cyanobacteria offer to industrial biotechnology, slow growth rates pose a major challenge in processes which typically require large amounts of biomass and are often toxic to the cells. Two-stage cultivation strategies are an attractive solution to prevent any undesired growth inhibition by de-coupling biomass accumulation (stage I) and the industrial process (stage II). In cyanobacteria, two-stage strategies involve costly transfer methods between stages I and II, and little work has been focussed on using the distinct growth and stationary phases of batch cultures to autoregulate stage transition. In the present study, we identified and characterised a growth phase-specific promoter, which can serve as an auto-inducible switch to regulate two-stage bioprocesses in cyanobacteria. First, growth phase-specific genes were identified from a new RNAseq dataset comparing two growth phases and six nutrient conditions in Synechocystis sp. PCC 6803, including two new transcriptomes for low Mg and low K. A type II NADH dehydrogenase (ndbA) showed robust induction when the cultures transitioned from exponential to stationary phase growth. Behaviour of a 600-bp promoter sequence (PndbA600) was then characterised in detail following the expression of PndbA600:GFP in Synechococcus sp. PCC 7002. Culture density and growth media analyses showed that PndbA600 activation was not dependent on increases in culture density per se but on N availability and on another activating factor present in the spent media of stationary phase cultures (Factor X). PndbA600 deactivation was dependent on the changes in culture density and in either N availability or Factor X. Electron transport inhibition studies revealed a photosynthesis-specific enhancement of active PndbA600 levels. Our findings are summarised in a model describing the environmental regulation of PndbA600, which can now inform the rational design of two-stage industrial processes in cyanobacteria.
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Affiliation(s)
- Mary Ann Madsen
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Graham Hamilton
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Pawel Herzyk
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom.,Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Anna Amtmann
- College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
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8
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Ganesan V, Raja R, Hemaiswarya S, Carvalho IS, Anand N. Isolation and characterization of two novel plasmids pCYM01 and pCYM02 of Cylindrospermum stagnale. Saudi J Biol Sci 2020; 27:535-542. [PMID: 31889879 PMCID: PMC6933252 DOI: 10.1016/j.sjbs.2019.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/02/2019] [Accepted: 11/17/2019] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria play a vital role in supplying nitrogen into the soil and aquatic ecosystem. It has an extra chromosomal DNA, whose role is not yet defined well. Isolation and characterization of extra chromosomal DNA in cyanobacteria might help to understand its survival mechanism. Cylindrospermum stagnale isolated (and deposited in NRMCF 3001) from soil showed presence of four plasmids namely pCYLM01, pCYLM02, pCYLM03, and pCYLM04. The following plasmids pCYLM01 and pCYLM02 were subjected to restriction digestion using HindIII restriction enzyme and cloned into pBlueScriptSK(-) vector. The sequence of pCYLM01 contained 4 potential open reading frames (ORFs) that have amino acids in the range of 59–299. Among them, ORF1 shows high sequence homology to the bacterial replication initiator family protein as evident from BLASTP analysis. The analysis of 4359 bp plasmid pCYLM02 sequence revealed 7 ORFs which are longer than 50 amino acids in length. The ORF2 of pCYLM02 has 243 amino acids and is represented in the plasmid sequence from 3045 to 3776 bp. The ORF3 of pCYLM02 corresponds to the plasmid sequence from 2323 to 2976 and codes for a putative protein of 217 amino acids long. A number of small ORFs below 50 bp were also found in the sequence analysis.
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Affiliation(s)
- Venkatesan Ganesan
- Acme ProGen Biotech (India) Private Limited, Balaji Nagar, Salem 636 004, India.,Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Rathinam Raja
- Food Science Laboratory, Center for Mediterranean Bioresources and Food, FCT, University of Algarve, Gambelas, Faro 8005 139, Portugal
| | | | - Isabel S Carvalho
- Food Science Laboratory, Center for Mediterranean Bioresources and Food, FCT, University of Algarve, Gambelas, Faro 8005 139, Portugal
| | - Narayanaswamy Anand
- Centre for Advanced Studies in Botany, University of Madras, Guindy Campus, Chennai 600 025, India
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9
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Wang M, Luan G, Lu X. Systematic identification of a neutral site on chromosome of Synechococcus sp. PCC7002, a promising photosynthetic chassis strain. J Biotechnol 2019; 295:37-40. [PMID: 30853638 DOI: 10.1016/j.jbiotec.2019.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/01/2019] [Accepted: 02/08/2019] [Indexed: 12/01/2022]
Abstract
Cyanobacteria based photosynthetic biomanufacturing is supposed to be one of the alternative routes for sustainable production of biofuels and biochemicals. Synechococcus sp. PCC 7002 is a promising cyanobacterial chassis strain possessing desired properties for scaled cultivation in future. Development of cyanobacterial cell factories requires modifications of PCC7002 chromosome to expand the photosynthesis-based metabolism networks. Therefore, mining genomic neutral sites for stable integration of heterologous genes and pathways would be of great significance for expanding the toolbox for PCC7002 genome engineering. Here we demonstrate a paradigm for identification of potential neutral sites from chromosome of PCC7002 based on genomic and transcriptomics data. By refining the massive omics information from database, 51 putative sites with no significant physiological or metabolism effects were extracted as candidates. Combining genomic context analysis, a locus termed as NS0027 between two neighboring putative neutral genes was selected and evaluated as a neutral site for genetic integration. In addition, an ethanol synthesis pathway was introduced into the NS0027 site to assess the functionality of this site. The sites we identified and the strategy we adopted in this work would benefit the development of effective genetic toolbox and efficient photosynthetic cell factories based on PCC7002.
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Affiliation(s)
- Min Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China
| | - Guodong Luan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China.
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, 266101, 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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10
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Jin H, Wang Y, Idoine A, Bhaya D. Construction of a Shuttle Vector Using an Endogenous Plasmid From the Cyanobacterium Synechocystis sp. PCC6803. Front Microbiol 2018; 9:1662. [PMID: 30087668 PMCID: PMC6066503 DOI: 10.3389/fmicb.2018.01662] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 07/04/2018] [Indexed: 12/21/2022] Open
Abstract
To advance synthetic biology in the photosynthetic cyanobacterium Synechocystis sp. PCC6803 (Syn6803), we constructed a shuttle vector with some versatile features. This shuttle vector, pSCB-YFP, consists of a putative replicon identified on the plasmid pCC5.2, the origin of replication of pMB1 from E. coli, as well as the YFP reporter gene and a spectinomycin/streptomycin resistance cassette. pSCB-YFP is stably maintained in Syn6803M (a motile strain that lacks the endogenous pCC5.2) and expresses YFP. In addition, we engineered a fragment into pSCB-YFP that has multiple cloning sites and other features such that this plasmid can also be used as an expression vector (pSCBe). The shuttle vector pSCB-YFP can be stably maintained for at least 50 generations without antibiotic selection. It is a high copy number plasmid and can stably co-exist with the RSF1010-based pPMQAK1-GFP.
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Affiliation(s)
- Haojie Jin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Yan Wang
- Department of Neurosurgery and Stanford Stroke Center, Stanford University, Stanford, CA, United States
| | - Adam Idoine
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
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Xiao Y, Wang S, Rommelfanger S, Balassy A, Barba-Ostria C, Gu P, Galazka JM, Zhang F. Developing a Cas9-based tool to engineer native plasmids in Synechocystis sp. PCC 6803. Biotechnol Bioeng 2018; 115:2305-2314. [PMID: 29896914 DOI: 10.1002/bit.26747] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/06/2018] [Accepted: 06/05/2018] [Indexed: 01/05/2023]
Abstract
The oxygenic photosynthetic bacterium Synechocystis sp. PCC 6803 (S6803) is a model cyanobacterium widely used for fundamental research and biotechnology applications. Due to its polyploidy, existing methods for genome engineering of S6803 require multiple rounds of selection to modify all genome copies, which is time-consuming and inefficient. In this study, we engineered the Cas9 tool for one-step, segregation-free genome engineering. We further used our Cas9 tool to delete three of seven S6803 native plasmids. Our results show that all three small-size native plasmids, but not the large-size native plasmids, can be deleted with this tool. To further facilitate heterologous gene expression in S6803, a shuttle vector based on the native plasmid pCC5.2 was created. The shuttle vector can be introduced into Cas9-containing S6803 in one step without requiring segregation and can be stably maintained without antibiotic pressure for at least 30 days. Moreover, genes encoded on the shuttle vector remain functional after 30 days of continuous cultivation without selective pressure. Thus, this study provides a set of new tools for rapid modification of the S6803 genome and for stable expression of heterologous genes, potentially facilitating both fundamental research and biotechnology applications using S6803.
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Affiliation(s)
- Yi Xiao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Present address: State Key Laboratory for Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaojie Wang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Sarah Rommelfanger
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missori
| | - Andrea Balassy
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Carlos Barba-Ostria
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Present address: Department of Health Sciences, Ambato Technical University, Ambato, Ecuador
| | - Pengfei Gu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Jonathan M Galazka
- Space Biosciences Division, Ames Research Center, National Aeronautics and Space Administration, Mountain View, California
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missori
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Misssori
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12
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Liu D, Pakrasi HB. Exploring native genetic elements as plug-in tools for synthetic biology in the cyanobacterium Synechocystis sp. PCC 6803. Microb Cell Fact 2018; 17:48. [PMID: 29580240 PMCID: PMC5868059 DOI: 10.1186/s12934-018-0897-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/21/2018] [Indexed: 11/24/2022] Open
Abstract
Background The unicellular cyanobacterium Synechocystis sp. PCC 6803 has been widely used as a photoautotrophic host for synthetic biology studies. However, as a green chassis to capture CO2 for biotechnological applications, the genetic toolbox for Synechocystis 6803 is still a limited factor. Results We systematically characterized endogenous genetic elements of Synechocystis 6803, including promoters, ribosome binding sites, transcription terminators, and plasmids. Expression from twelve native promoters was compared by measuring fluorescence from the reporter protein EYFP in an identical setup, exhibiting an 8000-fold range of promoter activities. Moreover, we measured the strength of twenty native ribosome binding sites and eight native terminators, indicating their influence on the expression of the reporter genes. In addition, two shuttle vectors, pCA-UC118 and pCB-SC101, capable of replication in both Synechocystis 6803 and E. coli were constructed. Expression of reporter proteins were significantly enhanced in cells containing these new plasmids, thus providing superior gene expression platforms in this cyanobacterium. Conclusions The results of this study provide useful and well characterized native tools for bioengineering work in the model cyanobacterium Synechocystis 6803. Electronic supplementary material The online version of this article (10.1186/s12934-018-0897-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deng Liu
- Department of Biology, Washington University, Campus Box 1137, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, Campus Box 1137, One Brookings Drive, St. Louis, MO, 63130, USA.
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13
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Du W, Burbano PC, Hellingwerf KJ, Branco Dos Santos F. Challenges in the Application of Synthetic Biology Toward Synthesis of Commodity Products by Cyanobacteria via "Direct Conversion". ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:3-26. [PMID: 30091089 DOI: 10.1007/978-981-13-0854-3_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyanobacterial direct conversion of CO2 to several commodity chemicals has been recognized as a potential contributor to support the much-needed sustainable development of human societies. However, the feasibility of this "green conversion" hinders on our ability to overcome the hurdles presented by the natural evolvability of microbes. The latter may result in the genetic instability of engineered cyanobacterial strains leading to impaired productivity. This challenge is general to any "cell factory" approach in which the cells grow for multiple generations, and based on several studies carried out in different microbial hosts, we could identify that three distinct strategies have been proposed to tackle it. These are (1) to reduce microbial evolvability by decreasing the native mutation rate, (2) to align product formation with cell growth/fitness, and, paradoxically, (3) to efficiently reallocate cellular resources to product formation by uncoupling it from growth. The implementation of either of these strategies requires an advanced synthetic biology toolkit. Here, we review the existing methods available for cyanobacteria and identify areas of focus in which specific developments are still needed. Furthermore, we discuss how potentially stabilizing strategies may be used in combination leading to further increases of productivity while ensuring the stability of the cyanobacterial-based direct conversion process.
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Affiliation(s)
- Wei Du
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Patricia Caicedo Burbano
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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14
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Metabolic engineering of the pentose phosphate pathway for enhanced limonene production in the cyanobacterium Synechocysti s sp. PCC 6803. Sci Rep 2017; 7:17503. [PMID: 29235513 PMCID: PMC5727528 DOI: 10.1038/s41598-017-17831-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 11/30/2017] [Indexed: 11/08/2022] Open
Abstract
Isoprenoids are diverse natural compounds, which have various applications as pharmaceuticals, fragrances, and solvents. The low yield of isoprenoids in plants makes them difficult for cost-effective production, and chemical synthesis of complex isoprenoids is impractical. Microbial production of isoprenoids has been considered as a promising approach to increase the yield. In this study, we engineered the model cyanobacterium Synechocystis sp. PCC 6803 for sustainable production of a commercially valuable isoprenoid, limonene. Limonene synthases from the plants Mentha spicata and Citrus limon were expressed in cyanobacteria for limonene production. Production of limonene was two-fold higher with limonene synthase from M. spicata than that from C. limon. To enhance isoprenoid production, computational strain design was conducted by applying the OptForce strain design algorithm on Synechocystis 6803. Based on the metabolic interventions suggested by this algorithm, genes (ribose 5-phosphate isomerase and ribulose 5-phosphate 3-epimerase) in the pentose phosphate pathway were overexpressed, and a geranyl diphosphate synthase from the plant Abies grandis was expressed to optimize the limonene biosynthetic pathway. The optimized strain produced 6.7 mg/L of limonene, a 2.3-fold improvement in productivity. Thus, this study presents a feasible strategy to engineer cyanobacteria for photosynthetic production of isoprenoids.
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15
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Esteves-Ferreira AA, Inaba M, Obata T, Fort A, Fleming GTA, Araújo WL, Fernie AR, Sulpice R. A Novel Mechanism, Linked to Cell Density, Largely Controls Cell Division in Synechocystis. PLANT PHYSIOLOGY 2017; 174:2166-2182. [PMID: 28646084 PMCID: PMC5543973 DOI: 10.1104/pp.17.00729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/20/2017] [Indexed: 05/28/2023]
Abstract
Many studies have investigated the various genetic and environmental factors regulating cyanobacterial growth. Here, we investigated the growth and metabolism of Synechocystis sp. PCC 6803 under different nitrogen sources, light intensities, and CO2 concentrations. Cells grown on urea showed the highest growth rates. However, for all conditions tested, the daily growth rates in batch cultures decreased steadily over time, and stationary phase was obtained with similar cell densities. Unexpectedly, metabolic and physiological analyses showed that growth rates during log phase were not controlled primarily by the availability of photoassimilates. Further physiological investigations indicated that nutrient limitation, quorum sensing, light quality, and light intensity (self-shading) were not the main factors responsible for the decrease in the growth rate and the onset of the stationary phase. Moreover, cell division rates in fed-batch cultures were positively correlated with the dilution rates. Hence, not only light, CO2, and nutrients can affect growth but also a cell-cell interaction. Accordingly, we propose that cell-cell interaction may be a factor responsible for the gradual decrease of growth rates in batch cultures during log phase, culminating with the onset of stationary phase.
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Affiliation(s)
- Alberto A Esteves-Ferreira
- National University of Ireland-Galway, Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
- CAPES Foundation, Ministry of Education of Brazil, Brasilia DF 70040 020, Brazil
| | - Masami Inaba
- National University of Ireland-Galway, Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
| | - Toshihiro Obata
- Central Metabolism Laboratory, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, 14476 Potsdam-Golm, Germany
| | - Antoine Fort
- National University of Ireland-Galway, Genetics and Biotechnology Research Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
| | - Gerard T A Fleming
- National University of Ireland-Galway, Microbiology, School of Natural Sciences, Galway, Ireland
| | - Wagner L Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Vicosa, Minas Gerais, Brazil
| | - Alisdair R Fernie
- Central Metabolism Laboratory, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, 14476 Potsdam-Golm, Germany
| | - Ronan Sulpice
- National University of Ireland-Galway, Plant Systems Biology Laboratory, Plant and AgriBiosciences Research Centre, School of Natural Sciences, Galway, Ireland
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16
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Chen Y, Taton A, Go M, London RE, Pieper LM, Golden SS, Golden JW. Self-replicating shuttle vectors based on pANS, a small endogenous plasmid of the unicellular cyanobacterium Synechococcus elongatus PCC 7942. Microbiology (Reading) 2016; 162:2029-2041. [DOI: 10.1099/mic.0.000377] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- You Chen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Arnaud Taton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Michaela Go
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ross E. London
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Lindsey M. Pieper
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Susan S. Golden
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - James W. Golden
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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17
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Armshaw P, Carey D, Sheahan C, Pembroke JT. Utilising the native plasmid, pCA2.4, from the cyanobacterium Synechocystis sp. strain PCC6803 as a cloning site for enhanced product production. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:201. [PMID: 26628915 PMCID: PMC4665902 DOI: 10.1186/s13068-015-0385-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/16/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND The use of photosynthetic autotrophs and in particular the model organism Synechocystis PCC6803 is receiving much attention for the production of sustainable biofuels and other economically useful products through metabolic engineering. Optimisation of metabolic-engineered organisms for high-level sustained production of product is a key element in the manipulation of this organism. A limitation to the utilisation of metabolically-engineered Synechocystis PCC6803 is the availability of strong controllable promoters and stable gene dosage methods for maximising gene expression and subsequent product formation following genetic manipulation. RESULTS A native Synechocystis PCC6803 small plasmid, pCA2.4, is consistently maintained at a copy level of up to 7 times that of the polyploid chromosome. As this plasmid is stable during cell division, it is potentially an ideal candidate for maximising gene dosage levels within the organism. Here, we describe the construction of a novel expression vector generated from the native plasmid, pCA2.4. To investigate the feasibility of this new expression system, a yellow fluorescent protein (YFP) encoding gene was cloned downstream of the strong Ptrc promoter and integrated into a predicted neutral site within the pCA2.4 plasmid. The stability of the integrated construct was monitored over time compared to a control strain containing an identical YFP-expressing construct integrated at a known neutral site in a chromosomal location. CONCLUSIONS A significantly higher fluorescence level of the yellow fluorescent protein was observed when its encoded gene was integrated into the pCA2.4 native plasmid when compared to the isogenic chromosomally integrated control strain. On average, a minimum of 20-fold higher fluorescence level could be achieved from integration into the native plasmid. Fluorescence was also monitored as a function of culture time and demonstrated to be stable over multiple sub-cultures even after the removal of selective pressure. Therefore, the native small plasmid, pCA2.4 may be utilised to stably increase gene expression levels in Synechocystis PCC6803. With the complementary utilisation of an inducible promoter system, rapid generation of commodity-producing Synechocystis PCC6803 strains having high level, controlled expression may be more achievable.
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Affiliation(s)
- Patricia Armshaw
- />Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences; Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Dawn Carey
- />Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences; Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Con Sheahan
- />Department of Manufacturing and Operations Engineering, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland
| | - J. Tony Pembroke
- />Molecular and Structural Biochemistry Laboratory, Department of Chemical and Environmental Sciences; Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
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18
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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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Immethun CM, Ng KM, DeLorenzo DM, Waldron-Feinstein B, Lee YC, Moon TS. Oxygen-responsive genetic circuits constructed in Synechocystis sp. PCC 6803. Biotechnol Bioeng 2015; 113:433-42. [PMID: 26264210 DOI: 10.1002/bit.25722] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/18/2015] [Accepted: 08/04/2015] [Indexed: 02/03/2023]
Abstract
As photoautotrophic prokaryotes, cyanobacteria are promising platforms for producing value-added bioproducts. However, few regulatory genetic parts and devices (e.g., inducible promoters and regulatory circuits) have been developed for these potential hosts. Furthermore, the devices that have been created respond only to a single input. To address these issues, we developed an inducible genetic circuit that generates heterologous proteins in response to oxygen, an environmental signal. To test its performance and utility in Synechocystis sp. PCC 6803, a model cyanobacterial strain, we connected this circuit to either heterologous nifHDK genes, which encode oxygen-sensitive nitrogenase's structural proteins, or a fluorescent protein gene. The circuit was transcriptionally activated to generate nifHDK transcripts or fluorescent output only in low oxygen conditions. We expanded the oxygen-responsive circuit into a more complex circuit by building a two-input AND gate, which allows Synechocystis to specifically control expression of the fluorescent reporter in response to two signals, low oxygen and high anhydrotetracycline. To our knowledge, the AND gate is the first complex logic circuit built in a cyanobacterial strain. This work expands the synthetic biology tools available for complex gene expression in cyanobacteria, increasing their potential as biotechnology platforms.
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Affiliation(s)
- Cheryl M Immethun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Kenneth M Ng
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Drew M DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Ben Waldron-Feinstein
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Ying-Chiang Lee
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri.
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Watanabe S, Ohbayashi R, Kanesaki Y, Saito N, Chibazakura T, Soga T, Yoshikawa H. Intensive DNA Replication and Metabolism during the Lag Phase in Cyanobacteria. PLoS One 2015; 10:e0136800. [PMID: 26331851 PMCID: PMC4558043 DOI: 10.1371/journal.pone.0136800] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/07/2015] [Indexed: 12/20/2022] Open
Abstract
Unlike bacteria such as Escherichia coli and Bacillus subtilis, several species of freshwater cyanobacteria are known to contain multiple chromosomal copies per cell, at all stages of their cell cycle. We have characterized the replication of multi-copy chromosomes in the cyanobacterium Synechococcus elongatus PCC 7942 (hereafter Synechococcus 7942). In Synechococcus 7942, the replication of multi-copy chromosome is asynchronous, not only among cells but also among multi-copy chromosomes. This suggests that DNA replication is not tightly coupled to cell division in Synechococcus 7942. To address this hypothesis, we analysed the relationship between DNA replication and cell doubling at various growth phases of Synechococcus 7942 cell culture. Three distinct growth phases were characterised in Synechococcus 7942 batch culture: lag phase, exponential phase, and arithmetic (linear) phase. The chromosomal copy number was significantly higher during the lag phase than during the exponential and linear phases. Likewise, DNA replication activity was higher in the lag phase cells than in the exponential and linear phase cells, and the lag phase cells were more sensitive to nalidixic acid, a DNA gyrase inhibitor, than cells in other growth phases. To elucidate physiological differences in Synechococcus 7942 during the lag phase, we analysed the metabolome at each growth phase. In addition, we assessed the accumulation of central carbon metabolites, amino acids, and DNA precursors at each phase. The results of these analyses suggest that Synechococcus 7942 cells prepare for cell division during the lag phase by initiating intensive chromosomal DNA replication and accumulating metabolites necessary for the subsequent cell division and elongation steps that occur during the exponential growth and linear phases.
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Affiliation(s)
- Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryudo Ohbayashi
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Yu Kanesaki
- Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Natsumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Taku Chibazakura
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
- * E-mail:
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21
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Fine-Tuning of Photoautotrophic Protein Production by Combining Promoters and Neutral Sites in the Cyanobacterium Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 2015. [PMID: 26209663 DOI: 10.1128/aem.01349-15] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cyanobacteria are photosynthetic cell factories that use solar energy to convert CO2 into useful products. Despite this attractive feature, the development of tools for engineering cyanobacterial chassis has lagged behind that for heterotrophs such as Escherichia coli or Saccharomyces cerevisiae. Heterologous genes in cyanobacteria are often integrated at presumptively "neutral" chromosomal sites, with unknown effects. We used transcriptome sequencing (RNA-seq) data for the model cyanobacterium Synechocystis sp. strain PCC 6803 to identify neutral sites from which no transcripts are expressed. We characterized the two largest such sites on the chromosome, a site on an endogenous plasmid, and a shuttle vector by integrating an enhanced yellow fluorescent protein (EYFP) expression cassette expressed from either the Pcpc560 or the Ptrc1O promoter into each locus. Expression from the endogenous plasmid was as much as 14-fold higher than that from the chromosome, with intermediate expression from the shuttle vector. The expression characteristics of each locus correlated predictably with the promoters used. These findings provide novel, characterized tools for synthetic biology and metabolic engineering in cyanobacteria.
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22
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Angermayr SA, Gorchs Rovira A, Hellingwerf KJ. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends Biotechnol 2015; 33:352-61. [DOI: 10.1016/j.tibtech.2015.03.009] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 11/24/2022]
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Berla BM, Saha R, Immethun CM, Maranas CD, Moon TS, Pakrasi HB. Synthetic biology of cyanobacteria: unique challenges and opportunities. Front Microbiol 2013; 4:246. [PMID: 24009604 PMCID: PMC3755261 DOI: 10.3389/fmicb.2013.00246] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/05/2013] [Indexed: 12/31/2022] Open
Abstract
Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria's potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as “chassis” strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a “green E. coli.” In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.
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Affiliation(s)
- Bertram M Berla
- Department of Energy, Environmental, and Chemical Engineering, Washington University St. Louis, MO, USA
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