Genetic variation in Brachyspira: chromosomal rearrangements and sequence drift distinguish B. pilosicoli from B. hyodysenteriae

Zuerner, Richard L.; Stanton, Thad B.; Minion, F. Chris; Li, Chunhao; Charon, Nyles W.; Trott, Darren J.; Hampson, David J.

doi:10.1016/j.anaerobe.2004.05.002

Cited by 27 publications

(19 citation statements)

References 36 publications

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“…It has been suggested that VSH-1 plays a part in the genomic and population structures and the pathogenic properties of Brachyspira spp. 63,64 , and VSH-1 does transfer virulence and antibiotic resistance genes between cells [50][51][52][53] . VSH-1 is induced by treatment of Brachyspira spp.…”

Section: The D Desulfuricans Gtamentioning

confidence: 99%

Gene transfer agents: phage-like elements of genetic exchange

2012

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Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.The prevalence of horizontal gene transfer (HGT), in which DNA is exchanged between closely or distantly related lineages, has altered the way we think about evolution 1,2 , having profound effects on our views of the evolutionary relationships among living organisms. It has caused a shift from a bifurcating 'tree of life' view to a 'net of life' or 'web of life' view [3][4][5] , in which "highways of gene sharing" (REF. 6) represent major connections, with genes (or DNA segments) viewed as "public goods, available for all organisms to integrate into their genomes" (REF. 7). HGT occurs within and between all three domains of life, and it has been estimated that 0.05-80% of genes in bacterial and archaeal genomes have been affected by HGT, depending on the analytical method used and the genome analysed [8][9][10] . Although HGT is widespread, it is not random: patterns of preferential gene exchange among specific groups of organisms that share ancestry or habitat have been * Present address. aslang@mun.ca; olgazh@dartmouth.edu; j.beatty@mail.ubc.ca Competing interests statementThe authors declare no competing financial interests. 6,9,11,12 . Such patterns are probably a consequence of existing barriers to HGT, which have been reviewed in detail elsewhere 13,14 . FURTHER INFORMATIONAlthough we have known about some HGT mechanisms for decades, novel processes that expand the existing repertoire of gene exchange methods are continually being identified. Transformation was the first mechanism of gene exchange to be discovered 15 , wherein DNA is taken up directly from the environment (reviewed elsewhere 16,17 ). In transduction, DNA transfer is mediated by viral particles (BOX 1). In conjugation, which was discovered in the 1940s 18 , DNA is transferred from a donor to a recipient cell during cell-to-cell contact; conjugation is used in the transfer of plasmids, transposons, integrons, and integrative and conjugative elements (ICEs) [19][20][21] . There are other modes of gene exchange that do not fit well into any of these three canonical mechanisms, including temporary cell fusion followed by chromosomal recombination and plasmid exchange 22 , intercellular connection through nanotubes 23 , and the release of membrane vesicles containing chromosomal, plasmid and phage DNA that can then merge with nearby cells 24 . In addition, a novel mechanism of gene transfer that has feature...

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Section: The D Desulfuricans Gtamentioning

confidence: 99%

Gene transfer agents: phage-like elements of genetic exchange

2012

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“…Recent insights into Brachyspira species evolution and interactions have been obtained from investigations into gene transfer associated with a novel prophage-like agent (Stanton et al 2001;Stanton et al 2003;Matson et al 2005), analysis of the population structures and species relatedness using multilocus enzyme electrophoresis (Trott et al 1997;Trott et al 1998) and multilocus sequence typing (Råsbäck et al 2007), and investigations of genomic rearrangements between B. hyodysenteriae and B. pilosicoli by comparing limited physical genomic maps (Zuerner et al 2004). The close similarities of the 16S rRNA sequences of the various Brachyspira species indicate that Brachyspira speciation has occurred more recently than it has in many other bacterial genera (Paster and Dewhirst, 1997).…”

Section: Introductionmentioning

confidence: 99%

Intestinal Spirochaetes of the Genus Brachyspira Share a Partially Conserved 26 Kilobase Genomic Region with Enterococcus faecalis and Escherichia coli

Motro

Dunn

et al. 2008

Microbiol�Insights

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Anaerobic intestinal spirochaetes of the genus Brachyspira include both pathogenic and commensal species. The two best-studied members are the pathogenic species B. hyodysenteriae (the aetiological agent of swine dysentery) and B. pilosicoli (a cause of intestinal spirochaetosis in humans and other species). Analysis of near-complete genome sequences of these two species identifi ed a highly conserved 26 kilobase (kb) region that was shared, against a background of otherwise very little sequence conservation between the two species. PCR amplifi cation was used to identify sets of contiguous genes from this region in the related Brachyspira species B. intermedia, B. innocens, B. murdochii, B. alvinipulli, and B. aalborgi, and demonstrated the presence of at least part of this region in species from throughout the genus. Comparative genomic analysis with other sequenced bacterial species revealed that none of the completely sequenced spirochaete species from different genera contained this conserved cluster of coding sequences. In contrast, Enterococcus faecalis and Escherichia coli contained high gene cluster conservation across the 26 kb region, against an expected background of little sequence conservation between these phylogenetically distinct species. The conserved region in B. hyodysenteriae contained fi ve genes predicted to be associated with amino acid transport and metabolism, four with energy production and conversion, two with nucleotide transport and metabolism, one with ion transport and metabolism, and four with poorly characterised or uncertain function, including an ankyrin repeat unit at the 5' end. The most likely explanation for the presence of this 26 kb region in the Brachyspira species and in two unrelated enteric bacterial species is that the region has been involved in horizontal gene transfer. Abbreviation:ACT: Artemis Comparison Tool; bp: base pair; COG: clusters of orthologous groups; DNA: deoxyribonucleic acid; GC: guanine plus cytosine; GC3: guanine plus cytosine at the third base position on a codon; HGT: horizontal gene transfer; kb: kilobase; Mb: megabase; PCR: polymerase chain reaction.The GenBank accession numbers for the genome region sequences for Brachyspira hyodysenteriae WA-1 and Brachyspira pilosicoli 95/1000 are EF694538 and EF694539, respectively.

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“…Within their genome, B. hyodysenteriae cells carry a mitomycin C-inducible prophagelike element, designated VSH-1 (30,31,63). Unlike traditional prophages, VSH-1 particles contain random 7.5-kb fragments of the B. hyodysenteriae genome.…”

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Collateral Effects of Antibiotics: Carbadox and Metronidazole Induce VSH-1 and Facilitate Gene Transfer among Brachyspira hyodysenteriae Strains

Stanton

Humphrey

Sharma

et al. 2008

Appl Environ Microbiol

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Brachyspira hyodysenteriae is an anaerobic spirochete and the etiologic agent of swine dysentery. The genome of this spirochete contains a mitomycin C-inducible, prophage-like gene transfer agent designated VSH-1. VSH-1 particles package random 7.5-kb fragments of the B. hyodysenteriae genome and transfer genes between B. hyodysenteriae cells. The chemicals and conditions inducing VSH-1 production are largely unknown. Antibiotics used in swine management and stressors inducing traditional prophages might induce VSH-1 and thereby stimulate lateral gene transfer between B. hyodysenteriae cells. In these studies, VSH-1 induction was initially detected by a quantitative real-time reverse transcriptase PCR assay evaluating increased transcription of hvp38 (VSH-1 head protein gene). VSH-1 induction was confirmed by detecting VSH-1-associated 7.5-kb DNA and VSH-1 particles in B. hyodysenteriae cultures. Nine antibiotics (chlortetracycline, lincomycin, tylosin, tiamulin, virginiamycin, ampicillin, ceftriaxone, vancomycin, and florfenicol) at concentrations affecting B. hyodysenteriae growth did not induce VSH-1 production. By contrast, VSH-1 was detected in B. hyodysenteriae cultures treated with mitomycin C (10 g/ml), carbadox (0.5 g/ml), metronidazole (0.5 g/ml), and H 2 O 2 (300 M). Carbadox-and metronidazole-induced VSH-1 particles transmitted tylosin and chloramphenicol resistance determinants between B. hyodysenteriae strains. The results of these studies suggest that certain antibiotics may induce the production of prophage or prophage-like elements by intestinal bacteria and thereby impact intestinal microbial ecology.In the United States, various antimicrobials are added to feed to prevent diseases and to promote growth or to enhance the feeding efficiency of swine (14, 28). Antibiotics commonly used in feed for swine include tetracyclines, carbadox, macrolides, and lincosamides (19). At higher concentrations, carbadox, lincomycin, tylosin, and tiamulin are added to feed or drinking water for the treatment of swine intestinal diseases, notably swine dysentery (25,28). In Australia and some European countries, nitroimidazole antibiotics, such as metronidazole, ronidazole, and dimetridazole, have been used to treat swine dysentery (22,25; D. Trott, personal communication), although legislation in several countries has restricted the use of these antibiotics in food animals (2, 44).The etiologic agent of swine dysentery is the anaerobic spirochete Brachyspira hyodysenteriae. Within their genome, B. hyodysenteriae cells carry a mitomycin C-inducible prophagelike element, designated VSH-1 (30, 31, 63). Unlike traditional prophages, VSH-1 particles contain random 7.5-kb fragments of the B. hyodysenteriae genome. VSH-1 head, tail, and lysis genes total at least 16.3 kb of DNA (38). Consequently, an individual VSH-1 particle is incapable of lytic growth, and there are no bioassays (i.e., plaque formation) for measuring VSH-1 production. Although VSH-1 particles do not selfpropagate, they transfer genes between B. hyody...

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Genetic variation in Brachyspira: chromosomal rearrangements and sequence drift distinguish B. pilosicoli from B. hyodysenteriae

Cited by 27 publications

References 36 publications

Gene transfer agents: phage-like elements of genetic exchange

Gene transfer agents: phage-like elements of genetic exchange

Intestinal Spirochaetes of the Genus Brachyspira Share a Partially Conserved 26 Kilobase Genomic Region with Enterococcus faecalis and Escherichia coli

Collateral Effects of Antibiotics: Carbadox and Metronidazole Induce VSH-1 and Facilitate Gene Transfer among Brachyspira hyodysenteriae Strains

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