Genomic analysis of ICE<i>Vch</i>Ban8: An atypical genetic element in <i>Vibrio cholerae</i>

Taviani, Elisa; Spagnoletti, Matteo; Ceccarelli, Daniela; Haley, Bradd J.; Hasan, Nur A.; Chen, Arlene; Colombo, Mauro; Huq, Anwar; Colwell, Rita R.

doi:10.1016/j.febslet.2012.03.064

Cited by 21 publications

(27 citation statements)

References 31 publications

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“…Sh95 is a hybrid element that efficiently self-transfers to a new host and integrates into the chromosome, despite having a different xis/int module. The limited nucleotide identity of xis and int genes to their respective homologues found in SXT/ R391 ICEs, as well as the opposite orientation observed for xis in the ICESh95 structure, suggest that this element may have gone through a recombination event by way of its own bet/exo system, a process previously proposed for the atypical element ICEVchBan8 Taviani et al, 2012).…”

Section: Discussionmentioning

confidence: 84%

“…Once transferred, the Int SXT integrase promotes the integration through a site-specific recombination mechanism between the attP site of the ICE and the attB site of the host chromosome. Most members of the SXT/R391 family integrate specifically at the 5´end of the prfC gene (Hochhut & Waldor, 1999;Taviani et al, 2012;. Ramírez et al (2010) previously reported the presence of antimicrobial resistance genes in 10 clinical isolates of Shewanella spp.…”

Section: Introductionmentioning

confidence: 99%

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Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus

et al. 2016

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Shewanella spp. are currently considered to be emerging pathogens that can code for a bla OXA carbapenemase in their chromosome. Complete genome analysis of the clinical isolate Shewanella sp. Sh95 revealed that this strain is a novel species, which shares a lineage with marine isolates. Characterization of its resistome showed that it codes for genes drfA15, qacH and bla OXA-48. We propose that Shewanella sp. Sh95 acts as reservoir of bla . Moreover, analysis of mobilome showed that it contains a novel integrative and conjugative element (ICE), named ICESh95. Comparative analysis between the close relatives ICESpuPO1 from Shewanella sp. W3-18-1 and ICE SXT MO10 from Vibrio cholerae showed that ICESh95 encompassed two new regions, a type III restriction modification system and a multidrug resistance integron. The integron platform contained a novel arrangement formed by gene cassettes drfA15 and qacH, and a class C-attC group II intron. Furthermore, insertion of ICESh95 occurred at a unique target site, which correlated with the presence of a different xis/ int module. Mobility of ICESh95 was assessed and demonstrated its ability to self-transfer with high efficiency to different species of bacteria. Our results show that ICESh95 is a selftransmissible, mobile element, which can contribute to the dissemination of antimicrobial resistance; this is clearly a threat when natural bacteria from water ecosystems, such as Shewanella, act as vectors in its propagation.

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Section: Discussionmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus

et al. 2016

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“…This element, ICEVchBan8, carries a different integration module coding for Int Ban8 and is integrated into a tRNA Ser -coding gene, a locus usually occupied by the pathogenicity island VPI-2. Although the ability of ICEVchBan8 to transfer has not been demonstrated, it seems to be able to excise by site-specific recombination and form the circular intermediate required for transfer (49).…”

Section: Integration and Excisionmentioning

confidence: 97%

“…Interestingly, an atypical genetic element sharing most of its structural genes with SXT/R391 ICEs has been identified in a natural isolate of V. cholerae O37 (31,49). This element, ICEVchBan8, carries a different integration module coding for Int Ban8 and is integrated into a tRNA Ser -coding gene, a locus usually occupied by the pathogenicity island VPI-2.…”

Section: Integration and Excisionmentioning

confidence: 99%

Biology of Three ICE Families: SXT/R391, ICE Bs1 , and ICE St1 /ICE St3

Carraro

Burrus

2014

Microbiol Spectr

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Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.

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“…The prototypical elements of this family of ICEs i.e., SXT and R391 were derived from Vibrio cholerae O139 in India and Providencia rettgeri in South Africa, respectively (Coetzee et al, 1972; Waldor et al, 1996). All the SXT/R391 ICEs are chromosomal MGEs sharing a conserved integrase that mediates site-specific integration into the 5′ end of prfC or t-RNA-ser in the absence of a prfC site (Hochhut and Waldor, 1999; Hochhut et al, 2001; Burrus and Waldor, 2003; Burrus et al, 2006; Taviani et al, 2012; Carraro and Burrus, 2014; Luo et al, 2016). Members of this ICE family contain 52 conserved core genes, many of which are involved in integration/excision, conjugative transfer and regulation of the ICEs (Beaber et al, 2002; Burrus et al, 2006; Wozniak et al, 2009; Bi et al, 2012; Spagnoletti et al, 2014; Carraro et al, 2015; Poulin-Laprade and Burrus, 2015; Poulin-Laprade et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104

Badhai

Das

2016

Front. Microbiol.

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The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476T (ICEMfuInd1a and ICEMfuInd1b) and in Marinomonas profundimaris strain D104 (ICEMprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICEMfuInd1b and ICEMprChn1 were inserted into the genome at 5′-end of an typical host prfC gene, while ICEMfuInd1a was inserted at 5′-end of an atypical hipA-like gene. Despite their coexistence, the ICEMfuInd1a and ICEMfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the M. fungiae genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICEMfuInd1a, ICEMfuInd1b, and ICEMprChn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hotspot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICEMprChn1 from M. profundimaris. Finally, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.

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Genomic analysis of ICEVchBan8: An atypical genetic element in Vibrio cholerae

Cited by 21 publications

References 31 publications

Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus

Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus

Biology of Three ICE Families: SXT/R391, ICE Bs1 , and ICE St1 /ICE St3

Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICEMfuInd1a and ICEMfuInd1b, and ICEMprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476T and Marinomonas profundimaris Strain D104

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