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Nguyen TT, Kim YK, Ko D, Kim J, Yi H, Bang YJ. Development of the First Shuttle Vector System and Optimization of Transformation in Selenomonas sputigena. J Microbiol Biotechnol 2025; 35:e2501011. [PMID: 40295217 PMCID: PMC12089946 DOI: 10.4014/jmb.2501.01011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/03/2025] [Accepted: 03/05/2025] [Indexed: 04/30/2025]
Abstract
Selenomonas sputigena, an anaerobic bacterium found in the human respiratory tract, has recently gained significant attention due to its dual role in human health - as both a periodontal pathogen and a protective agent against severe asthma. However, the absence of genetic tools for this organism has severely limited our understanding of its molecular mechanisms and therapeutic potential. Here, we report the first successful development of a genetic modification system for S. sputigena ATCC 35185. We constructed a shuttle vector carrying the Rep191 replication protein from Selenomonas ruminantium and systematically optimized transformation conditions. Through careful optimization of key parameters including DNA quantity, bacterial growth phase, membrane permeabilization, and post-pulse recovery time, we achieved a 22.5-fold improvement in transformation efficiency (from ~2,000 to ~45,000 CFU/μg DNA). The broad applicability of our system was demonstrated through successful transformation of multiple Selenomonas species, establishing the first standardized genetic modification system for this genus. We further validated the system's functionality by achieving stable GFP expression in S. sputigena, representing the first demonstration of ectopic protein expression in this organism. This work provides essential tools for investigating the molecular basis of S. sputigena's therapeutic effects and pathogenic capabilities, potentially accelerating the development of novel microbiome-based treatments for both respiratory and oral diseases.
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Affiliation(s)
- Trinh Thi Nguyen
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Yu-Kyung Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Duhyun Ko
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Jeeyou Kim
- Integrated Biomedical and Life Science, Graduate School, Korea University, Seoul 02841, Republic of Korea
| | - Hana Yi
- Integrated Biomedical and Life Science, Graduate School, Korea University, Seoul 02841, Republic of Korea
- School of Biosystems and Biomedical Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ye-Ji Bang
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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Groom J, Chung D, Olson DG, Lynd LR, Guss AM, Westpheling J. Promiscuous plasmid replication in thermophiles: Use of a novel hyperthermophilic replicon for genetic manipulation of Clostridium thermocellum at its optimum growth temperature. Metab Eng Commun 2016; 3:30-38. [PMID: 29468112 PMCID: PMC5779722 DOI: 10.1016/j.meteno.2016.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/15/2016] [Accepted: 01/28/2016] [Indexed: 12/22/2022] Open
Abstract
Clostridium thermocellum is a leading candidate for the consolidated bioprocessing of lignocellulosic biomass for the production of fuels and chemicals. A limitation to the engineering of this strain is the availability of stable replicating plasmid vectors for homologous and heterologous expression of genes that provide improved and/or novel pathways for fuel production. Current vectors relay on replicons from mesophilic bacteria and are not stable at the optimum growth temperature of C. thermocellum. To develop more thermostable genetic tools for C. thermocellum, we constructed vectors based on the hyperthermophilic Caldicellulosiruptor bescii replicon pBAS2. Autonomously replicating shuttle vectors based on pBAS2 reproducibly transformed C. thermocellum at 60 °C and were maintained in multiple copy. Promoters, selectable markers and plasmid replication proteins from C. bescii were functional in C. thermocellum. Phylogenetic analyses of the proteins contained on pBAS2 revealed that the replication initiation protein RepL is unique among thermophiles. These results suggest that pBAS2 may be a broadly useful replicon for other thermophilic Firmicutes.
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Affiliation(s)
- Joseph Groom
- Department of Genetics, University of Georgia, Athens, GA, USA
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daehwan Chung
- Department of Genetics, University of Georgia, Athens, GA, USA
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA
| | - Daniel G. Olson
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Thayer School of Engineering at Dartmouth College, Hanover, NH, USA
| | - Lee R. Lynd
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Thayer School of Engineering at Dartmouth College, Hanover, NH, USA
| | - Adam M. Guss
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, GA, USA
- The BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Barbosa TM, Phelan RW, Leong D, Morrissey JP, Adams C, Dobson ADW, O’Gara F. A novel erythromycin resistance plasmid from Bacillus sp. strain HS24, isolated from the marine sponge Haliclona simulans. PLoS One 2014; 9:e115583. [PMID: 25548909 PMCID: PMC4280177 DOI: 10.1371/journal.pone.0115583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/01/2014] [Indexed: 11/19/2022] Open
Abstract
A better understanding of the origin and natural reservoirs of resistance determinants is fundamental to efficiently tackle antibiotic resistance. This paper reports the identification of a novel 5.8 kb erythromycin resistance plasmid, from Bacillus sp. HS24 isolated from the marine sponge Haliclona simulans. pBHS24B has a mosaic structure and carries the erythromycin resistance gene erm(T). This is the first report of an erythromycin resistance plasmid from a sponge associated bacteria and of the Erm(T) determinant in the genus Bacillus.
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Affiliation(s)
| | - Robert W. Phelan
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
| | - Dara Leong
- Department of Microbiology, University College Cork, Cork, Ireland
| | - John P. Morrissey
- Department of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Claire Adams
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
| | - Alan D. W. Dobson
- Department of Microbiology, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
| | - Fergal O’Gara
- Department of Microbiology, University College Cork, Cork, Ireland
- Biomerit Research Centre, University College Cork, Cork, Ireland
- Marine Biotechnology Centre, Environmental Research Institute, University College Cork, Cork, Ireland
- Curtin University, School of Biomedical Sciences, Perth WA 6845, Australia
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Fecskeová L, Ivan J, Javorský P, Pristaš P. Variability of putative repgene cassettes in Selenomonas ruminantiumplasmids. FEMS Microbiol Lett 2012; 336:98-103. [DOI: 10.1111/j.1574-6968.2012.02659.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 08/09/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Lívia Fecskeová
- Institute of Animal Physiology; Slovak Academy of Sciences; Košice; Slovakia
| | - Jozef Ivan
- Institute of Animal Physiology; Slovak Academy of Sciences; Košice; Slovakia
| | - Peter Javorský
- Institute of Animal Physiology; Slovak Academy of Sciences; Košice; Slovakia
| | - Peter Pristaš
- Institute of Animal Physiology; Slovak Academy of Sciences; Košice; Slovakia
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Pristas P, Ivan J, Javorsky P. Structural instability of small rolling circle replication plasmids from Selenomonas ruminantium. Plasmid 2010; 64:74-8. [DOI: 10.1016/j.plasmid.2010.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 04/26/2010] [Accepted: 04/29/2010] [Indexed: 10/19/2022]
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Nakayama S, Irie R, Kosaka T, Matsuura K, Yoshino S, Furukawa K. New host-vector system in solvent-producing Clostridium saccharoperbutylacetonicum strain N1-4. J GEN APPL MICROBIOL 2007; 53:53-6. [PMID: 17429161 DOI: 10.2323/jgam.53.53] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Shunichi Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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Ivan J, Sprincová A, Javorský P, Pristas P. Spreading and mutability of Selenomonas ruminantium plasmids. Folia Microbiol (Praha) 2006; 51:283-5. [PMID: 17007426 DOI: 10.1007/bf02931814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Two small plasmids from Selenomonas ruminantium strain 19D were cloned in Escherichia coli and completely characterized. Sequence comparison indicated that the plasmids are similar to those reported in genetically vaguely related S. ruminantium strain S20. Small 1.4-kb plasmids pSRD191 and pONE430 are only distantly related (approximately 30 % for deduced Rep protein amino acid sequence) but possess a short highly conserved region outside rep gene. Larger plasmids pSRD192 and pONE429 possess large identical DNA regions in an otherwise dissimilar background. Recombination is proposed as an important mechanism of evolution and spreading of S. ruminantium plasmids.
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Affiliation(s)
- J Ivan
- Institute of Animal Physiology, Slovak Academy of Sciences, Kosice, Slovakia
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