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Krupovic M, Makarova KS, Wolf YI, Medvedeva S, Prangishvili D, Forterre P, Koonin EV. Integrated mobile genetic elements in Thaumarchaeota. Environ Microbiol 2019; 21:2056-2078. [PMID: 30773816 PMCID: PMC6563490 DOI: 10.1111/1462-2920.14564] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/10/2019] [Accepted: 02/13/2019] [Indexed: 12/20/2022]
Abstract
To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence-like transposons, (iv) integrative-conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly-roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I-B CRISPR-Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Sofia Medvedeva
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sorbonne Université, Collège doctoral, 75005, Paris, France
| | - David Prangishvili
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France
| | - Patrick Forterre
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, 75015, Paris, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris- Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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Das S, Mitra S, Sahoo S, Chakrabarti J. Viral/plasmid captures in Crenarchaea. J Biomol Struct Dyn 2013; 32:546-54. [DOI: 10.1080/07391102.2013.782826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Michael GB, Kadlec K, Sweeney MT, Brzuszkiewicz E, Liesegang H, Daniel R, Murray RW, Watts JL, Schwarz S. ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer. J Antimicrob Chemother 2011; 67:91-100. [DOI: 10.1093/jac/dkr411] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fouts DE. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res 2006; 34:5839-51. [PMID: 17062630 PMCID: PMC1635311 DOI: 10.1093/nar/gkl732] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phage_Finder, a heuristic computer program, was created to identify prophage regions in completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose prophages have been manually identified, Phage_Finder found 91% of the regions, resulting in 7% false positive and 9% false negative prophages. A search of 302 complete bacterial genomes predicted 403 putative prophage regions, accounting for 2.7% of the total bacterial DNA. Analysis of the 285 putative attachment sites revealed tRNAs are targets for integration slightly more frequently (33%) than intergenic (31%) or intragenic (28%) regions, while tmRNAs were targeted in 8% of the regions. The most popular tRNA targets were Arg, Leu, Ser and Thr. Mapping of the insertion point on a consensus tRNA molecule revealed novel insertion points on the 5′ side of the D loop, the 3′ side of the anticodon loop and the anticodon. A novel method of constructing phylogenetic trees of phages and prophages was developed based on the mean of the BLAST score ratio (BSR) of the phage/prophage proteomes. This method verified many known bacteriophage groups, making this a useful tool for predicting the relationships of prophages from bacterial genomes.
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Affiliation(s)
- Derrick E Fouts
- The Institute for Genomic research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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McGrath BM, Pembroke J. Detailed analysis of the insertion site of the mobile elements R997, pMERPH, R392, R705 and R391 inE. coliK12. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09673.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Mantri Y, Williams KP. Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. Nucleic Acids Res 2004; 32:D55-8. [PMID: 14681358 PMCID: PMC308793 DOI: 10.1093/nar/gkh059] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic chromosomes often contain islands, such as temperate phages or pathogenicity islands, delivered by site-specific integrases. Integration usually occurs within a tRNA or tmRNA gene, splitting the gene, yet sequences within the island restore the disrupted gene. The regenerated RNA gene and the displaced fragment of that gene thus mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm generates a list of tRNA and tmRNA genes, uses each as the query for a BLAST search of the starting DNA and removes unlikely hits through a series of filters. A search for islands in 106 whole bacterial genomes produced 143 candidates, with the search itself providing an estimate of three false candidates among these. Preliminary phylogenetic analysis of the associated integrases reduced this set to 89 cases of independently evolved site specificity, which showed strong bias for the tmRNA gene. The website Islander (http://www.indiana.edu/ approximately islander) presents the candidate islands in GenBank-style files and correlates integrase phylogeny with site specificity.
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Affiliation(s)
- Yogita Mantri
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA
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Böltner D, MacMahon C, Pembroke JT, Strike P, Osborn AM. R391: a conjugative integrating mosaic comprised of phage, plasmid, and transposon elements. J Bacteriol 2002; 184:5158-69. [PMID: 12193633 PMCID: PMC135318 DOI: 10.1128/jb.184.18.5158-5169.2002] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The conjugative, chromosomally integrating element R391 is the archetype of the IncJ class of mobile genetic elements. Originally found in a South African Providencia rettgeri strain, R391 carries antibiotic and mercury resistance traits, as well as genes involved in mutagenic DNA repair. While initially described as a plasmid, R391 has subsequently been shown to be integrated into the bacterial chromosome, employing a phage-like integration mechanism closely related to that of the SXT element from Vibrio cholerae O139. Analysis of the complete 89-kb nucleotide sequence of R391 has revealed a mosaic structure consisting of elements originating in bacteriophages and plasmids and of transposable elements. A total of 96 open reading frames were identified; of these, 30 could not be assigned a function. Sequence similarity suggests a relationship of large sections of R391 to sequences from Salmonella, in particular those corresponding to the putative conjugative transfer proteins, which are related to the IncHI1 plasmid R27. A composite transposon carrying the kanamycin resistance gene and a novel insertion element were identified. Challenging the previous assumption that IncJ elements are plasmids, no plasmid replicon was identified on R391, suggesting that they cannot replicate autonomously.
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Affiliation(s)
- Dietmar Böltner
- Department of Biological Sciences, University of Essex, Colchester, United Kingdom
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Williams KP. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies. Nucleic Acids Res 2002; 30:866-75. [PMID: 11842097 PMCID: PMC100330 DOI: 10.1093/nar/30.4.866] [Citation(s) in RCA: 231] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most classical integrases of prokaryotic genetic elements specify integration into tRNA or tmRNA genes. Sequences shared between element and host integration sites suggest that crossover can occur at any of three sublocations within a tRNA gene, two with flanking symmetry (anticodon-loop and T-loop tDNA) and the third at the asymmetric 3' end of the gene. Integrase phylogeny matches this classification: integrase subfamilies use exclusively either the symmetric sublocations or the asymmetric sublocation, although tRNA genes of several different aminoacylation identities may be used within any subfamily. These two familial sublocation preferences imply two modes by which new integration site usage evolves. The tmRNA gene has been adopted as an integration site in both modes, and its distinctive structure imposes some constraints on proposed evolutionary mechanisms.
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Affiliation(s)
- Kelly P Williams
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA.
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