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Eppinger M, Radnedge L, Andersen G, Vietri N, Severson G, Mou S, Ravel J, Worsham PL. Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance. PLoS One 2012; 7:e32911. [PMID: 22479347 PMCID: PMC3316555 DOI: 10.1371/journal.pone.0032911] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 02/06/2012] [Indexed: 12/21/2022] Open
Abstract
Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.
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Affiliation(s)
- Mark Eppinger
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Lyndsay Radnedge
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Gary Andersen
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Nicholas Vietri
- United States Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, Maryland, United States of America
| | - Grant Severson
- United States Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, Maryland, United States of America
| | - Sherry Mou
- United States Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland, School of Medicine, Baltimore, Maryland, United States of America
| | - Patricia L. Worsham
- United States Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, Maryland, United States of America
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Kholodii GY, Yurieva OV, Gorlenko ZM, Mindlin SZ, Bass IA, Lomovskay OL, Kopteva AV, Nikiforov VG. Tn5041: a chimeric mercury resistance transposon closely related to the toluene degradative transposon Tn4651. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 8):2549-2556. [PMID: 9274008 DOI: 10.1099/00221287-143-8-2549] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This paper reports the discovery and characterization of Tn5041, a novel-type transposon vehicle for dissemination of mercury resistance in natural bacterial populations. Tn5041 (14876 bp), identified in a Pseudomonas strain from a mercury mine, is a Tn3 family mercury resistance transposon far outside the Tn21 subgroup. As in other Tn3 family transposons, Tn5041 duplicates 5 bp of the target sequence following insertion. Tn5041 apparently acquired its mer operon as a single-ended relic of a transposon belonging to the classical mercury resistance transposons of the Tn21 subgroup. The putative transposase and the 47 bp terminal inverted repeats of Tn5041 are closely related to those of the toluene degradative transposon Tn4651 and fall into a distinct subgroup on the fringe of the Tn3 family. The amino acid sequence of the putative resolvase of Tn5041 resembles site-specific recombinases of the integrase family. Besides the mer operon and putative transposition genes, Tn5041 contains a 4 kb region that accommodates a number of apparently defective genes and mobile elements.
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Affiliation(s)
- G Ya Kholodii
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - O V Yurieva
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Zh M Gorlenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - S Z Mindlin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - I A Bass
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - O L Lomovskay
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - A V Kopteva
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - V G Nikiforov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
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Fan WH, Woelfle MA, Mosig G. Two copies of a DNA element, 'Wendy', in the chloroplast chromosome of Chlamydomonas reinhardtii between rearranged gene clusters. PLANT MOLECULAR BIOLOGY 1995; 29:63-80. [PMID: 7579168 DOI: 10.1007/bf00019119] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We have characterized two copies of a 2.4 kb DNA element that we call 'Wendy', in the chloroplast chromosome of Chlamydomonas reinhardtii. The two copies of Wendy reside in different single-copy regions at opposite positions in the chloroplast genome. Like many mobile DNA elements, both copies of Wendy are bordered by inverted repeats and contain several additional degenerate copies of these repeat sequences in direct or inverted orientation. In addition, four basepairs are repeated in direct orientation. Two major open reading frames (ORFs) are predicted from the DNA sequence of Wendy I. These ORFs are co-transcribed from a promoter inside the element. The deduced amino acid sequence of the larger of these ORFs shares some weak similarities with sequence motifs of transposases and integrases of other mobile elements. Wendy II appears to be altered relative to Wendy I by point mutations and small deletions and insertions which destroy the ORFs. The leader sequence of the Wendy transcript is nearly identical with the leader sequence of the rbcL transcript of C. reinhardtii, but not of C. moewusii (where the complete Wendy was also undetectable). Furthermore, both copies of Wendy are bracketed by gene clusters that are separated in C. reinhardtii but are contiguous in C. moewusii where they exist in an inverted orientation compared with C. reinhardtii. Wendy was not found in any of the completely sequenced chloroplast genomes of rice, tobacco, pine, Euglena or Marchantia, nor in any other GenBank entry. Our results suggest that Wendy has invaded C. reinhardtii after divergence from other species. Subsequent Wendy-dependent illegitimate homologous or site-specific recombination events or both may have contributed to scrambling of the C. reinhardtii chloroplast genome relative to genomes of other species.
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Affiliation(s)
- W H Fan
- Department of Molecular Biology, Vanderbilt University, Nashville, TN 37235, USA
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Rinkel M, Hubert JC, Roux B, Lett MC. Transposon Tn5403, a mobilization-helper element: Complete nucleotide sequence and distribution in aquatic strains. FEMS Microbiol Ecol 1994. [DOI: 10.1111/j.1574-6941.1994.tb00233.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Chiou CS, Jones AL. Nucleotide sequence analysis of a transposon (Tn5393) carrying streptomycin resistance genes in Erwinia amylovora and other gram-negative bacteria. J Bacteriol 1993; 175:732-40. [PMID: 8380801 PMCID: PMC196212 DOI: 10.1128/jb.175.3.732-740.1993] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A class II Tn3-type transposable element, designated Tn5393 and located on plasmid pEa34 from streptomycin-resistant strain CA11 of Erwinia amylovora, was identified by its ability to move from pEa34 to different sites in plasmids pGEM3Zf(+) and pUCD800. Nucleotide sequence analysis reveals that Tn5393 consists of 6,705 bp with 81-bp terminal inverted repeats and generates 5-bp duplications of the target DNA following insertion. Tn5393 contains open reading frames that encode a putative transposase (tnpA) and resolvase (tnpR) of 961 and 181 amino acids, respectively. The two open reading frames are separated by a putative recombination site (res) consisting of 194 bp. Two streptomycin resistance genes, strA and strB, were identified on the basis of their DNA sequence homology to streptomycin resistance genes in plasmid RSF1010. StrA is separated from tnpR by a 1.2-kb insertion element designated IS1133. The tnpA-res-tnpR region of Tn5393 was detected in Pseudomonas syringae pv. papulans Psp36 and in many other gram-negative bacteria harboring strA and strB. Except for some strains of Erwinia herbicola, these other gram-negative bacteria lacked insertion sequence IS1133. The prevalence of strA and strB could be accounted for by transposition of Tn5393 to conjugative plasmids that are then disseminated widely among gram-negative bacteria.
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Affiliation(s)
- C S Chiou
- Department of Botany and Plant Pathology, Michigan State University, East Lansing 48824-1312
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Abstract
The Tn3 family of transposable elements is probably the most successful group of mobile DNA elements in bacteria: there are many different but related members and they are widely distributed in gram-negative and gram-positive bacteria. The Tn21 subgroup of the Tn3 family contains closely related elements that provide most of the currently known variation in Tn3-like elements in gram-negative bacteria and that are largely responsible for the problem of multiple resistance to antibiotics in these organisms. This paper reviews the structure, the mechanism of transposition, the mode of acquisition of accessory genes, and the evolution of these elements.
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Affiliation(s)
- J Grinsted
- Department of Microbiology, University of Bristol, Medical School, University Walk, U.K
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Abstract
The resolvase gene and the putative res site of Tn2501 are not closely related to any of the previously described resolution functions. In view of this divergence, we designed genetic experiments to confirm the localization of the res site. We analyzed the activity of the Tn2501-encoded resolvase on substrates containing either directly or invertedly repeated res sites. These experiments confirm the localization of the res site that was predicted from nucleotide sequence data and show that the Tn2501 resolvase promotes site-specific inversions in vivo.
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Affiliation(s)
- T Michiels
- Université Catholique de Louvain, Unité de Microbiologie, UCL 54-90, Brussels, Belgium
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