1
|
Lossouarn J, Nesbø CL, Bienvenu N, Geslin C. Plasmid pMO1 from Marinitoga okinawensis, first non-cryptic plasmid reported within Thermotogota. Res Microbiol 2023; 174:104044. [PMID: 36805054 DOI: 10.1016/j.resmic.2023.104044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
Mobile genetic elements (MGEs), such as viruses and plasmids, drive the evolution and adaptation of their cellular hosts from all three domains of life. This includes microorganisms thriving in the most extreme environments, like deep-sea hydrothermal vents. However, our knowledge about MGEs still remains relatively sparse in these abyssal ecosystems. Here we report the isolation, sequencing, assembly, and functional annotation of pMO1, a 28.2 kbp plasmid associated with the reference strain Marinitoga okinawensis. Carrying restriction/modification and chemotaxis protein-encoding genes, pMO1 likely affects its host's phenotype and represents the first non-cryptic plasmid described among the phylum Thermotogota.
Collapse
Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Biozone, Department of Chemical Engineering and Applied Chemistry and BioZone, University of Toronto, 200 College Street, Toronto, Ontario, Canada, M5S 3E5.
| | - Nadège Bienvenu
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France.
| | - Claire Geslin
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France. mailto:
| |
Collapse
|
2
|
Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea. World J Microbiol Biotechnol 2022; 38:135. [PMID: 35695998 DOI: 10.1007/s11274-022-03327-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.
Collapse
|
3
|
Guler HI, Ceylan E, Canakci S, Belduz AO. A novel cryptic and theta type plasmid (pHIG22) from Thermus scodotuctus sp. K6. Gene 2018; 679:282-290. [PMID: 30092344 DOI: 10.1016/j.gene.2018.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/04/2018] [Indexed: 11/29/2022]
Abstract
A cryptic plasmid pHIG22 from Thermus scotoductus sp. K6, an isolate from the Alangullu Hot Spring (Aydin, Turkey), was sequenced and characterized. The pHIG22 plasmid is a multicopy, double stranded and 2222 bp circular molecule with 62.78% GC content, which shows a characteristical nucleotide sequence without any homology to other known plasmids. Five open reading frames were predicted based on the nucleotide sequence analysis. The deduced amino acid sequence of all predicted ORFs didn't show any similarity with any known proteins. Three palindroms were detected and two promoter sequences were predicted in both strands. With electron microscopy (TEM) analysis, the replication intermediates were seen as typical Q-shaped molecules that committing pHIG22 replicates via the Theta replication mechanism. A 2012 bp region among 387 and 614 bp of pHIG22 was determined as minimal replicon which carries the elements necessary for plasmid replication and ori region. Furthermore, quantitative real-time PCR showed that the relative copy number of pHIG22 was estimated to be 148.2 ± 4.7 copies per chromosome equivalent. The new Theta type plasmid would be useful and beneficial to build vectors for cloning of thermophilic genes and in vivo protein engineering.
Collapse
Affiliation(s)
- Halil Ibrahim Guler
- Karadeniz Technical University, Faculty of Science, Department of Molecular Biology and Genetics, 61080 Trabzon, Turkey
| | - Esma Ceylan
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Sabriye Canakci
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Ali Osman Belduz
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey.
| |
Collapse
|
4
|
Xu Z, Puranik R, Hu J, Xu H, Han D. Complete genome sequence of Thermotoga sp. strain RQ7. Stand Genomic Sci 2017; 12:62. [PMID: 29046741 PMCID: PMC5637354 DOI: 10.1186/s40793-017-0271-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 09/21/2017] [Indexed: 12/26/2022] Open
Abstract
Thermotoga sp. strain RQ7 is a member of the family Thermotogaceae in the order Thermotogales. It is a Gram negative, hyperthermophilic, and strictly anaerobic bacterium. It grows on diverse simple and complex carbohydrates and can use protons as the final electron acceptor. Its complete genome is composed of a chromosome of 1,851,618 bp and a plasmid of 846 bp. The chromosome contains 1906 putative genes, including 1853 protein coding genes and 53 RNA genes. The genetic features pertaining to various lateral gene transfer mechanisms are analyzed. The genome carries a complete set of putative competence genes, 8 loci of CRISPRs, and a deletion of a well-conserved Type II R-M system.
Collapse
Affiliation(s)
- Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Rutika Puranik
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Junxi Hu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
- School of Life Sciences, Minnan Normal University, 36 Xianqianzhi Street, Zhangzhou, Fujian 363000 China
| | - Hui Xu
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
| | - Dongmei Han
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403 USA
| |
Collapse
|
5
|
Loder AJ, Zeldes BM, Conway JM, Counts JA, Straub CT, Khatibi PA, Lee LL, Vitko NP, Keller MW, Rhaesa AM, Rubinstein GM, Scott IM, Lipscomb GL, Adams MW, Kelly RM. Extreme Thermophiles as Metabolic Engineering Platforms: Strategies and Current Perspective. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Andrew J. Loder
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Benjamin M. Zeldes
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Jonathan M. Conway
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - James A. Counts
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Christopher T. Straub
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Piyum A. Khatibi
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Laura L. Lee
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Nicholas P. Vitko
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| | - Matthew W. Keller
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Amanda M. Rhaesa
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gabe M. Rubinstein
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Israel M. Scott
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Gina L. Lipscomb
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Michael W.W. Adams
- University of Georgia; Department of Biochemistry and Molecular Biology; Life Sciences Bldg., University of Georgia, Athens GA 30602-7229, USA
| | - Robert M. Kelly
- North Carolina State University; Department of Chemical and Biomolecular Engineering; EB-1, 911 Partners Way Raleigh NC 27695-7905 USA
| |
Collapse
|
6
|
Lossouarn J, Dupont S, Gorlas A, Mercier C, Bienvenu N, Marguet E, Forterre P, Geslin C. An abyssal mobilome: viruses, plasmids and vesicles from deep-sea hydrothermal vents. Res Microbiol 2015; 166:742-52. [DOI: 10.1016/j.resmic.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/11/2023]
|
7
|
Expression of Heterologous Cellulases in Thermotoga sp. Strain RQ2. BIOMED RESEARCH INTERNATIONAL 2015; 2015:304523. [PMID: 26273605 PMCID: PMC4529897 DOI: 10.1155/2015/304523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 01/21/2015] [Accepted: 02/06/2015] [Indexed: 11/18/2022]
Abstract
The ability of Thermotoga spp. to degrade cellulose is limited due to a lack of exoglucanases. To address this deficiency, cellulase genes Csac_1076 (celA) and Csac_1078 (celB) from Caldicellulosiruptor saccharolyticus were cloned into T. sp. strain RQ2 for heterologous overexpression. Coding regions of Csac_1076 and Csac_1078 were fused to the signal peptide of TM1840 (amyA) and TM0070 (xynB), resulting in three chimeric enzymes, namely, TM1840-Csac_1078, TM0070-Csac_1078, and TM0070-Csac_1076, which were carried by Thermotoga-E. coli shuttle vectors pHX02, pHX04, and pHX07, respectively. All three recombinant enzymes were successfully expressed in E. coli DH5α and T. sp. strain RQ2, rendering the hosts with increased endo- and/or exoglucanase activities. In E. coli, the recombinant enzymes were mainly bound to the bacterial cells, whereas in T. sp. strain RQ2, about half of the enzyme activities were observed in the culture supernatants. However, the cellulase activities were lost in T. sp. strain RQ2 after three consecutive transfers. Nevertheless, this is the first time heterologous genes bigger than 1 kb (up to 5.3 kb in this study) have ever been expressed in Thermotoga, demonstrating the feasibility of using engineered Thermotoga spp. for efficient cellulose utilization.
Collapse
|
8
|
Lossouarn J, Nesbø CL, Mercier C, Zhaxybayeva O, Johnson MS, Charchuck R, Farasin J, Bienvenu N, Baudoux AC, Michoud G, Jebbar M, Geslin C. ‘Ménage à trois’: a selfish genetic element uses a virus to propagate withinThermotogales. Environ Microbiol 2015; 17:3278-88. [DOI: 10.1111/1462-2920.12783] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Julien Lossouarn
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Camilla L. Nesbø
- CEES; Department of Biology; University of Oslo; Oslo 0316 Norway
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G2R3 Canada
| | - Coraline Mercier
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Olga Zhaxybayeva
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | - Milo S. Johnson
- Department of Biological Sciences; Dartmouth College; Hanover NH 03755 USA
| | | | - Julien Farasin
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Nadège Bienvenu
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Anne-Claire Baudoux
- Sorbonne Universités; UPMC Univ Paris 06; Paris 75005 France
- UMR 7144; Equipe DIPO; Station Biologique de Roscoff; Roscoff 29680 France
- CNRS; UMR 7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Roscoff 29680 France
| | - Grégoire Michoud
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Mohamed Jebbar
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| | - Claire Geslin
- Université de Bretagne Occidentale (UBO, UEB); Institut Universitaire Européen de la Mer (IUEM) - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- CNRS; IUEM - UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer; UMR 6197; Laboratoire de Microbiologie des Environnements Extrêmes (LMEE); Technopôle Pointe du diablea; F-29280 Plouzané France
| |
Collapse
|
9
|
Han D, Xu H, Puranik R, Xu Z. Natural transformation of Thermotoga sp. strain RQ7. BMC Biotechnol 2014; 14:39. [PMID: 24884561 PMCID: PMC4029938 DOI: 10.1186/1472-6750-14-39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 05/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Thermotoga species are organisms of enormous interest from a biotechnological as well as evolutionary point of view. Genetic modifications of Thermotoga spp. are often desired in order to fully release their multifarious potentials. Effective transformation of recombinant DNA into these bacteria constitutes a critical step of such efforts. This study aims to establish natural competency in Thermotoga spp. and to provide a convenient method to transform these organisms. RESULTS Foreign DNA was found to be relatively stable in the supernatant of a Thermotoga culture for up to 6 hours. Adding donor DNA to T. sp. strain RQ7 at its early exponential growth phase (OD600 0.18 ~ 0.20) resulted in direct acquisition of the DNA by the cells. Both T. neapolitana chromosomal DNA and Thermotoga-E. coli shuttle vectors effectively transformed T. sp. strain RQ7, rendering the cells resistance to kanamycin. The kan gene carried by the shuttle vector pDH10 was detected by PCR from the plasmid extract of the transformants, and the amplicons were verified by restriction digestions. A procedure for natural transformation of Thermotoga spp. was established and optimized. With the optimized method, T. sp. strain RQ7 sustained a transformation frequency in the order of 10⁻⁷ with both genomic and plasmid DNA. CONCLUSIONS T. sp. strain RQ7 cells are naturally transformable during their early exponential phase. They acquire DNA from both closely and distantly related species. Both chromosomal DNA and plasmid DNA serve as suitable substrates for transformation. Our findings lend a convenient technical tool for the genetic engineering of Thermotoga spp.
Collapse
Affiliation(s)
| | | | | | - Zhaohui Xu
- Department of Biological Sciences, Bowling Green State University, 43403 Bowling Green, OH, USA.
| |
Collapse
|
10
|
Abstract
Small DNA circles can occur in Nature, for example as protein-constrained loops, and can be synthesized by a number of methods. Such small circles provide tractable systems for the study of the structure, thermodynamics and molecular dynamics of closed-circular DNA. In the present article, we review the occurrence and synthesis of small DNA circles, and examine their utility in studying the properties of DNA and DNA–protein interactions. In particular, we highlight the analysis of small circles using atomistic simulations.
Collapse
|
11
|
Zhaxybayeva O, Swithers KS, Foght J, Green AG, Bruce D, Detter C, Han S, Teshima H, Han J, Woyke T, Pitluck S, Nolan M, Ivanova N, Pati A, Land ML, Dlutek M, Doolittle WF, Noll KM, Nesbø CL. Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date. Genome Biol Evol 2012; 4:700-8. [PMID: 22798451 PMCID: PMC3516359 DOI: 10.1093/gbe/evs059] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Here we describe the genome of Mesotoga prima MesG1.Ag4.2, the first genome of a mesophilic Thermotogales bacterium. Mesotoga prima was isolated from a polychlorinated biphenyl (PCB)-dechlorinating enrichment culture from Baltimore Harbor sediments. Its 2.97 Mb genome is considerably larger than any previously sequenced Thermotogales genomes, which range between 1.86 and 2.30 Mb. This larger size is due to both higher numbers of protein-coding genes and larger intergenic regions. In particular, the M. prima genome contains more genes for proteins involved in regulatory functions, for instance those involved in regulation of transcription. Together with its closest relative, Kosmotoga olearia, it also encodes different types of proteins involved in environmental and cell-cell interactions as compared with other Thermotogales bacteria. Amino acid composition analysis of M. prima proteins implies that this lineage has inhabited low-temperature environments for a long time. A large fraction of the M. prima genome has been acquired by lateral gene transfer (LGT): a DarkHorse analysis suggests that 766 (32%) of predicted protein-coding genes have been involved in LGT after Mesotoga diverged from the other Thermotogales lineages. A notable example of a lineage-specific LGT event is a reductive dehalogenase gene-a key enzyme in dehalorespiration, indicating M. prima may have a more active role in PCB dechlorination than was previously assumed.
Collapse
Affiliation(s)
- Olga Zhaxybayeva
- Department of Biology, West Virginia University
- Department of Biological Sciences, Dartmouth College
| | | | - Julia Foght
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Anna G. Green
- Department of Molecular and Cell Biology, University of Connecticut
| | - David Bruce
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Chris Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Shunsheng Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - James Han
- DOE Joint Genome Institute, Walnut Creek, California
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California
| | | | - Marlena Dlutek
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - W. Ford Doolittle
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Kenneth M. Noll
- Department of Molecular and Cell Biology, University of Connecticut
| | - Camilla L. Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
- *Corresponding author: E-mail:
| |
Collapse
|
12
|
Han D, Norris SM, Xu Z. Construction and transformation of a Thermotoga-E. coli shuttle vector. BMC Biotechnol 2012; 12:2. [PMID: 22225774 PMCID: PMC3398313 DOI: 10.1186/1472-6750-12-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 01/06/2012] [Indexed: 11/29/2022] Open
Abstract
Background Thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. They may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. A lack of genetic tools has hampered the investigation and application of these organisms. This study aims to develop a genetic transfer system for Thermotoga spp. Results Methods for preparing and handling Thermotoga solid cultures under aerobic conditions were optimized. A plating efficiency of ~50% was achieved when the bacterial cells were embedded in 0.3% Gelrite. A Thermotoga-E. coli shuttle vector pDH10 was constructed using pRQ7, a cryptic mini-plasmid found in T. sp. RQ7. Plasmid pDH10 was introduced to T. maritima and T. sp. RQ7 by electroporation and liposome-mediated transformation. Transformants were isolated, and the transformed kanamycin resistance gene (kan) was detected from the plasmid DNA extracts of the recombinant strains by PCR and was confirmed by restriction digestions. The transformed DNA was stably maintained in both Thermotoga and E. coli even without the selective pressure. Conclusions Thermotoga are transformable by multiple means. Recombinant Thermotoga strains have been isolated for the first time. A heterologous kan gene is functionally expressed and stably maintained in Thermotoga.
Collapse
Affiliation(s)
- Dongmei Han
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | | | | |
Collapse
|
13
|
Soler N, Marguet E, Cortez D, Desnoues N, Keller J, van Tilbeurgh H, Sezonov G, Forterre P. Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. Nucleic Acids Res 2010; 38:5088-104. [PMID: 20403814 PMCID: PMC2926602 DOI: 10.1093/nar/gkq236] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (∼12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication.
Collapse
Affiliation(s)
- Nicolas Soler
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
- *To whom correspondence should be addressed. Tel: +33 1 40 51 65 76; Fax: +0033 140516570;
| | - Evelyne Marguet
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Diego Cortez
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Nicole Desnoues
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Jenny Keller
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Herman van Tilbeurgh
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Guennadi Sezonov
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, Univ Paris-Sud, 91405 Orsay Cedex, CNRS UMR 8621, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Université Paris-Sud, IFR115, UMR8619-CNRS, 91405 Orsay and Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France
- *To whom correspondence should be addressed. Tel: +33 1 40 51 65 76; Fax: +0033 140516570;
| |
Collapse
|
14
|
Conners SB, Mongodin EF, Johnson MR, Montero CI, Nelson KE, Kelly RM. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species. FEMS Microbiol Rev 2006; 30:872-905. [PMID: 17064285 DOI: 10.1111/j.1574-6976.2006.00039.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
High-throughput sequencing of microbial genomes has allowed the application of functional genomics methods to species lacking well-developed genetic systems. For the model hyperthermophile Thermotoga maritima, microarrays have been used in comparative genomic hybridization studies to investigate diversity among Thermotoga species. Transcriptional data have assisted in prediction of pathways for carbohydrate utilization, iron-sulfur cluster synthesis and repair, expolysaccharide formation, and quorum sensing. Structural genomics efforts aimed at the T. maritima proteome have yielded hundreds of high-resolution datasets and predicted functions for uncharacterized proteins. The information gained from genomics studies will be particularly useful for developing new biotechnology applications for T. maritima enzymes.
Collapse
Affiliation(s)
- Shannon B Conners
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
| | | | | | | | | | | |
Collapse
|
15
|
Chu SF, Shu HY, Lin LC, Chen MY, Tsay SS, Lin GH. Characterization of a rolling-circle replication plasmid from Thermus aquaticus NTU103. Plasmid 2006; 56:46-52. [PMID: 16675012 DOI: 10.1016/j.plasmid.2006.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Revised: 01/25/2006] [Accepted: 01/31/2006] [Indexed: 10/24/2022]
Abstract
The thermophilic bacterium Thermus aquaticus NTU103 harbors a 1,965-bp plasmid, pTA103. Sequencing analysis revealed that pTA103 contains two open reading frames. One of the open reading frames (orf2) shares no significant homology with protein in the data bank. The other one has 50% similarity and 34% identity with RepA-like protein of pRm1132f, which is a rolling-circle replication (RCR) plasmid isolated from Sinorhizobium meliloti. S1 nuclease analysis demonstrated that pTA103 contains a single-stranded intermediate, confirming that pTA103 replicates via RCR mechanism. Sequence data also revealed putative double-stranded origin and single-stranded origin sites, indicating the importance of these cis elements in pTA103 replication.
Collapse
Affiliation(s)
- Sheng-Fen Chu
- Microbial Genetics Laboratory, Institute of Microbiology, Immunology and Molecular Medicine, Tzu-Chi University, Hualien 970, Taiwan
| | | | | | | | | | | |
Collapse
|
16
|
DeBoy RT, Mongodin EF, Emerson JB, Nelson KE. Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J Bacteriol 2006; 188:2364-74. [PMID: 16547022 PMCID: PMC1428405 DOI: 10.1128/jb.188.7.2364-2374.2006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 01/16/2006] [Indexed: 11/20/2022] Open
Abstract
In the present study, the chromosomes of two members of the Thermotogales were compared. A whole-genome alignment of Thermotoga maritima MSB8 and Thermotoga neapolitana NS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same replichore, i.e., the same replicating half of the chromosome (delimited by the replication origin and terminus). Based on cumulative GC skew analysis, both the T. maritima and T. neapolitana lineages contain one or two major inverted DNA segments. Also, based on PCR amplification and sequence analysis of the DNA joints that are associated with the major rearrangements, the overall chromosome architecture was found to be conserved at most DNA joints for other strains of T. neapolitana. Taken together, the results from this analysis suggest that the observed chromosomal rearrangements in the Thermotogales likely occurred by successive inversions after their divergence from a common ancestor and before strain diversification. Finally, sequence analysis shows that size polymorphisms in the DNA joints associated with CRISPRs can be explained by expansion and possibly contraction of the DNA repeat and spacer unit, providing a tool for discerning the relatedness of strains from different geographic locations.
Collapse
Affiliation(s)
- Robert T DeBoy
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
| | | | | | | |
Collapse
|
17
|
Nesbø CL, Dlutek M, Doolittle WF. Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 2005; 172:759-69. [PMID: 16322518 PMCID: PMC1456242 DOI: 10.1534/genetics.105.049312] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we characterize regions of the genomes of eight members of the hyperthermophilic genus Thermotoga. These bacteria differ from each other physiologically and by 3-20% in gene content and occupy physically distinct environments in widely disparate regions of the globe. Among the four different lineages (represented by nine different strains) that we compare, no two are closer than 96% in the average sequences of their genes. By most accepted recent definitions these are different "ecotypes" and different "species." And yet we find compelling evidence for recombination between them. We suggest that no single prokaryotic species concept can accommodate such uncoupling of ecotypic and genetic aspects of cohesion and diversity, and that without a single concept, the question of whether or not prokaryotic species might in general be cosmopolitan cannot be sensibly addressed. We can, however, recast biogeographical questions in terms of the distribution of genes and their alleles.
Collapse
Affiliation(s)
- Camilla L Nesbø
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada.
| | | | | |
Collapse
|
18
|
Zhou M, Xiang H, Sun C, Li Y, Liu J, Tan H. Complete sequence and molecular characterization of pNB101, a rolling-circle replicating plasmid from the haloalkaliphilic archaeon Natronobacterium sp. strain AS7091. Extremophiles 2003; 8:91-8. [PMID: 15064975 DOI: 10.1007/s00792-003-0366-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2003] [Accepted: 10/20/2003] [Indexed: 11/29/2022]
Abstract
A new plasmid was isolated from the haloalkaliphilic archaeon, Natronobacterium sp. strain AS7091 and named pNB101. Sequence analysis revealed that pNB101 consists of 2,538 bp, in which three major open reading frames (ORF1, ORF2, and ORF3) were identified in the same strand. The ORF1 encodes a putative replication (Rep) protein with three typical motifs (I, II, and III) found in rolling-circle (RC) replicating plasmids. The putative double-stranded origin (DSO) and single-stranded origin (SSO) were detected within ORF3 and downstream of ORF1, respectively. S1 nuclease digestion and Southern blot analysis demonstrated the existence of the single-stranded DNA (ssDNA) intermediate from pNB101, which corresponds to the leading strand in RC replication and was further confirmed by strand-specific RNA probes. A single transcript for ORF1 ( rep) was detected by Northern blotting, and the 5' end of this transcript was determined by primer extension. Both results indicate that the three motifs (I-III) are located at the very end of the N-terminal of this Rep protein. Northern blot analysis also revealed that the ORF3 was transcribed at a very high level, which may play an important role in plasmid replication because the putative DSO is located in this gene. Together, our results indicate that pNB101, the first plasmid isolated from haloalkaliphilic Archaea, represents a novel RC-replicating plasmid.
Collapse
Affiliation(s)
- Meixian Zhou
- State Key Laboratory of Microbial Resources and Center for Molecular Microbiology, Institute of Microbiology, Chinese Academy of Sciences, 100080, Beijing, People's Republic of China
| | | | | | | | | | | |
Collapse
|
19
|
Ward DE, Revet IM, Nandakumar R, Tuttle JH, de Vos WM, van der Oost J, DiRuggiero J. Characterization of plasmid pRT1 from Pyrococcus sp. strain JT1. J Bacteriol 2002; 184:2561-6. [PMID: 11948174 PMCID: PMC134983 DOI: 10.1128/jb.184.9.2561-2566.2002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We discovered a 3,373-bp plasmid (pRT1) in the hyperthermophilic archaeon Pyrococcus sp. strain JT1. Two major open reading frames were identified, and analysis of the sequence revealed some resemblance to motifs typically found in plasmids that replicate via a rolling-circle mechanism. The presence of single-stranded DNA replication intermediates of pRT1 was detected, confirming this mode of replication.
Collapse
Affiliation(s)
- Donald E Ward
- Laboratory for Microbiology, Wageningen University, 6703CT Wageningen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
20
|
Akimkina T, Ivanov P, Kostrov S, Sokolova T, Bonch-Osmolovskaya E, Firman K, Dutta CF, McClellan JA. A highly conserved plasmid from the extreme thermophile Thermotoga maritima MC24 is a member of a family of plasmids distributed worldwide. Plasmid 1999; 42:236-40. [PMID: 10545265 DOI: 10.1006/plas.1999.1429] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have screened Thermotoga strains, isolated from hydrothermal vents near the Kuril Islands, for the presence of plasmid DNA. The miniplasmid pMC24 was isolated from the extreme thermophilic eubacteria Thermotoga maritima and sequenced, showing it to be a plasmid of 846 bp. It was found, from a search of the databases, to be closely related to the previously described Thermotoga miniplasmid pRQ7, isolated from a strain found on the Azore Islands, and was distinguished by only two point mutations. These changes resulted in two consecutive frameshifts altering a region encoding 9 amino acids in the Rep-coding region. We have also shown that pMC24, as with pRQ7, is negatively supercoiled. It seems that negatively supercoiled miniplasmids related to pRQ7 are spread worldwide and strongly maintained among Thermotoga strains.
Collapse
Affiliation(s)
- T Akimkina
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square 46, Moscow, Russia
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Yu JS, Noll KM. Plasmid pRQ7 from the hyperthermophilic bacterium Thermotoga species strain RQ7 replicates by the rolling-circle mechanism. J Bacteriol 1997; 179:7161-4. [PMID: 9371465 PMCID: PMC179659 DOI: 10.1128/jb.179.22.7161-7164.1997] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The hyperthermophilic bacterium Thermotoga species strain RQ7 harbors an 846-bp plasmid, pRQ7, with a single open reading frame. Previously published analyses of the DNA sequence of pRQ7 suggested that it may replicate by a rolling-circle (RC) replication mechanism, and this report provides experimental evidence supporting this hypothesis. Single-stranded pRQ7 DNA accumulates in strain RQ7, as evidenced by the facts that this DNA bound to nitrocellulose membranes under nondenaturing conditions, was sensitive to S1 nuclease digestion, and hybridized to only one of two homologous DNA probes specific for each strand of the plasmid. The DNA encoding the open reading frame was cloned and expressed in Escherichia coli and gave a protein with a molecular mass of 26 kDa, similar to that deduced by sequence analysis. This protein bound to a fragment of pRQ7 that contains a putative double-stranded replication region in a magnesium-dependent reaction and made this fragment sensitive to S1 nuclease activity. It did not cause this same S1 nuclease sensitivity in the remainder of pRQ7. This activity on pRQ7 DNA suggests that this protein plays a role in plasmid replication.
Collapse
Affiliation(s)
- J S Yu
- Department of Molecular and Cell Biology, The University of Connecticut, Storrs 06269-3125, USA
| | | |
Collapse
|
22
|
Guipaud O, Marguet E, Noll KM, de la Tour CB, Forterre P. Both DNA gyrase and reverse gyrase are present in the hyperthermophilic bacterium Thermotoga maritima. Proc Natl Acad Sci U S A 1997; 94:10606-11. [PMID: 9380682 PMCID: PMC23419 DOI: 10.1073/pnas.94.20.10606] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Like all hyperthermophiles yet tested, the bacterium Thermotoga maritima contains a reverse gyrase. Here we show that it contains also a DNA gyrase. The genes top2A and top2B encoding the two subunits of a DNA gyrase-like enzyme have been cloned and sequenced. The Top2A (type II DNA topoisomerase A protein) is more similar to GyrA (DNA gyrase A protein) than to ParC [topoisomerase IV (Topo IV) C protein]. The difference is especially striking at the C-terminal domain, which differentiates DNA gyrases from Topo IV. DNA gyrase activity was detected in T. maritima and purified to homogeneity using a novobiocin-Sepharose column. This hyperhermophilic DNA gyrase has an optimal activity around 82-86 degrees C. In contrast to plasmids from hyperthermophilic archaea, which are from relaxed to positively supercoiled, we found that the plasmid pRQ7 from Thermotoga sp. RQ7 is negatively supercoiled. pRQ7 became positively supercoiled after addition of novobiocin to cell cultures, indicating that its negative supercoiling is due to the DNA gyrase of the host strain. The findings concerning DNA gyrase and negative supercoiling in Thermotogales put into question the role of reverse gyrase in hyperthermophiles.
Collapse
Affiliation(s)
- O Guipaud
- Laboratoire de Biologie Moléculaire du Gène chez les Extrémophiles, Institut de Génétique et Microbiologie, Université Paris-Sud, 91405 Orsay Cedex, France.
| | | | | | | | | |
Collapse
|
23
|
Erauso G, Marsin S, Benbouzid-Rollet N, Baucher MF, Barbeyron T, Zivanovic Y, Prieur D, Forterre P. Sequence of plasmid pGT5 from the archaeon Pyrococcus abyssi: evidence for rolling-circle replication in a hyperthermophile. J Bacteriol 1996; 178:3232-7. [PMID: 8655503 PMCID: PMC178075 DOI: 10.1128/jb.178.11.3232-3237.1996] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The plasmid pGT5 (3,444 bp) from the hyperthermophilic archaeon Pyrococcus abyssi GE5 has been completely sequenced. Two major open reading frames with a good coding probability are located on the same strand and cover 85% of the total sequence. The larger open reading frame encodes a putative polypeptide which exhibits sequence similarity with Rep proteins of plasmids using the rolling-circle mechanism for replication. Upstream of this open reading frame, we have detected an 11-bp motif identical to the double-stranded origin of several bacterial plasmids that replicate via the rolling-circle mechanism. A putative single-stranded origin exhibits similarities both to bacterial primosome-dependent single-stranded initiation sites and to bacterial primase (dnaG) start sites. A single-stranded form of pGT5 corresponding to the plus strand was detected in cells of P. abyssi. These data indicate that pGT5 replicates via the rolling-circle mechanism and suggest that members of the domain Archaea contain homologs of several bacterial proteins involved in chromosomal DNA replication. Phylogenetic analysis of Rep proteins from rolling-circle replicons suggest that diverse families diverged before the separation of the domains Archaea, Bacteria, and Eucarya.
Collapse
Affiliation(s)
- G Erauso
- Station Biologique de Roscoff, UPR 9042 Centre National de la Recherche Scientifique, Université Paris-Sud, France
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Bacillus stearothermophilus plasmid pSTK1 replicon is functional in Escherichia coli. Biotechnol Lett 1995. [DOI: 10.1007/bf00132013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|