Revised nomenclature for transposable genetic elements

Roberts, Adam P.; Chandler, Michaël; Courvalin, Patrice; Guédon, Gérard; Mullany, Peter; Pembroke, J. Tony; Rood, Julian I.; Smith, Jeffrey C.; Summers, Anne O.; Tsuda, Masashi; Berg, Douglas E.

doi:10.1016/j.plasmid.2008.08.001

Cited by 186 publications

(150 citation statements)

References 53 publications

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“…There are several mechanisms by which plasmids and transposons can be mobilized. Mobilizable elements typically contain an oriT and a gene (mob) that encodes a conjugative relaxase (40,46). The mob gene product nicks a site in oriT and is required for mobilization.…”

Section: Resultsmentioning

confidence: 99%

The Bacillus subtilis Conjugative Transposon ICEBs1Mobilizes Plasmids Lacking Dedicated Mobilization Functions

2012

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Integrative and conjugative elements (ICEs, also known as conjugative transposons) are mobile elements that are found integrated in a host genome and can excise and transfer to recipient cells via conjugation. ICEs and conjugative plasmids are found in many bacteria and are important agents of horizontal gene transfer and microbial evolution. Conjugative elements are capable of self-transfer and also capable of mobilizing other DNA elements that are not able to self-transfer. Plasmids that can be mobilized by conjugative elements are generally thought to contain an origin of transfer ( oriT ), from which mobilization initiates, and to encode a mobilization protein (Mob, a relaxase) that nicks a site in oriT and covalently attaches to the DNA to be transferred. Plasmids that do not have both an oriT and a cognate mob are thought to be nonmobilizable. We found that Bacillus subtilis carrying the integrative and conjugative element ICE Bs1 can transfer three different plasmids to recipient bacteria at high frequencies. Strikingly, these plasmids do not have dedicated mobilization- oriT functions. Plasmid mobilization required conjugation proteins of ICE Bs1 , including the putative coupling protein. In contrast, plasmid mobilization did not require the ICE Bs1 conjugative relaxase or cotransfer of ICE Bs1 , indicating that the putative coupling protein likely interacts with the plasmid replicative relaxase and directly targets the plasmid DNA to the ICE Bs1 conjugation apparatus. These results blur the current categorization of mobilizable and nonmobilizable plasmids and indicate that conjugative elements play a role in horizontal gene transfer even more significant than previously recognized.

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Section: Resultsmentioning

confidence: 99%

The Bacillus subtilis Conjugative Transposon ICEBs1Mobilizes Plasmids Lacking Dedicated Mobilization Functions

2012

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“…These two new elements were found to possess Ͼ95% identity to SPI-7 at the nucleotide level and yet to carry novel cargo regions. As the novel elements are less than 100% identical to SPI-7 and contain novel accessory genes, they were named ICESb1 and ICESb2, respectively, and also given systematic names (see Materials and Methods), according to transposon registry guidelines (59). Defining the core and variable portions of the novel S. bongori ICEs.…”

Section: Resultsmentioning

confidence: 99%

Structure, Diversity, and Mobility of the Salmonella Pathogenicity Island 7 Family of Integrative and Conjugative Elements within Enterobacteriaceae

et al. 2012

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Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae. Bacterial genomes are often represented as a core of conserved genes interspersed with accessory regions which are variably present throughout members of a species. The ability of an organism to sample variation through accessing a pan-genome can be strongly associated with a change in lifestyle or adaptation to a new niche (29). In some cases, acquired accessory functions become fixed and go on to define a particular lineage (30). A classical example of this is the acquisition of the Salmonella pathogenicity islands (SPIs), considered to have been fundamental to the evolution of the genus Salmonella (26). The largest of these islands identified to date is SPI-7, found within the genomes of Salmonella enterica subsp. enterica serovar Typhi (S. Typhi) (52), Salmonella enterica subsp. enterica serovar Paratyphi C (S. Paratyphi C) (43), and some strains of Salmonella enterica subsp. enterica serovar Dublin (S. Dublin) (55). SPI-7 is 120 kb in length and encodes important virulence functions, including the major virulence antigen (Vi) and type IVB pili (24, 52). Additionally, integrated within SPI-7 from strains of S. Typhi is a prophage harboring the type 3 secretion system effector protein-encoding gene sopE (47).SPI-7 possesses many similarities to integrative and conjugative elements (ICEs), a class of self-transmissible elements (7) also known as conjugativ...

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“…Open reading frames and pseudogenes were predicted using RAST 2.0 [33] combined with BLASTP/BLASTN searches [34] against the UniProtKB/Swiss-Prot database [35] and the RefSeq database [36]. Annotation of resistance genes, mobile elements, and other features was carried out using the online databases including CARD [37], ResFinder [38], BacMet [39], ISfinder [40], INTEGRALL [41], and the Tn Number Registry [42]. Multiple and pairwise sequence comparisons were performed using MUSCLE 3.8.31 [43] and BLASTN, respectively.…”

Section: Sequencing and Annotationmentioning

confidence: 99%

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

Feng¹,

Yin²,

Zhan³

et al. 2018

Oncotarget

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This study dealt with detailed genomic characterization of two multidrug resistant (MDR) plasmids p675920-1 and p675920-2 from a single clinical Klebsiella pneumoniae isolate 675920. p675920-1 was essentially a hybrid of the IncFII plasmid pHN7A8 and the IncR plasmid pKPC-LK30, and functioned as an IncFII plasmid with inactivation of the IncR replication gene. The backbone of p675920-2 was a hybrid of a novel replicon, three maintenance regions (22.0-, 2.7-, 2.6-kb in length, respectively) as found in pKPYL2, p10164-3 and pK1HV, respectively, and the entire 25.9-kb conjugal transfer region of pKPYL2. p675920-1 and p675920-2 carried a large number of resistance genes, which contributed to resistance to at least seven classes of antibiotics (β-lactams, quinolones, aminoglycosides, fosfomycins, sulphonamides, trimethoprims, and tetracyclines) and one kind of heavy mental (mercury). All of these resistance genes are associated with mobile elements such as insertion sequences, insertion sequence-based transposition units, and transposons, which constituted a total of three novel MDR regions, two in p675920-1 and another in p675920-2. Coexistence of two MDR plasmids p675920-1 and p675920-2 made K. pneumoniae 675920 tend to become extensively drug-resistant.

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Revised nomenclature for transposable genetic elements

Cited by 186 publications

References 53 publications

The Bacillus subtilis Conjugative Transposon ICEBs1Mobilizes Plasmids Lacking Dedicated Mobilization Functions

The Bacillus subtilis Conjugative Transposon ICEBs1Mobilizes Plasmids Lacking Dedicated Mobilization Functions

Structure, Diversity, and Mobility of the Salmonella Pathogenicity Island 7 Family of Integrative and Conjugative Elements within Enterobacteriaceae

WITHDRAWN: Structure genomics of two chimera plasmids p675920-1 and p675920-2 coexisting in a multi-drug resistant Klebsiella pneumoniae isolate

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