Plasmid 48 (2002) 202–212 www.academicpress.

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When phage, plasmids, and transposons collide: genomic islands, and conjugative- and mobilizable-transposons as a mosaic continuum
€ltner A. Mark Osborn* and Dietmar Bo
Department of Biological Sciences, University of Essex, Colchester, CO4 3SQ, UK Received 29 August 2002

Abstract Plasmids and bacteriophage represent the classical vectors for gene transfer within the horizontal gene pool. However, the more recent discovery of an increasing array of other mobile genetic elements (MGE) including genomic islands (GIs), conjugative transposons (CTns), and mobilizable transposons (MTns) which each integrate within the chromosome, offer an increasingly diverse assemblage contributing to bacterial adaptation and evolution. Molecular characterisation of these elements has revealed that they are comprised of functional modules derived from phage, plasmids, and transposons, and further that these modules are combined to generate a continuum of mosaic MGE. In particular, they are comprised of any one of three distinct types of recombinase, together with plasmid-derived transfer and mobilisation gene functions. This review highlights both the similarities and distinctions between these integrating transferable elements resulting from combination of the MGE toolbox. Ó 2002 Elsevier Science (USA). All rights reserved.
Keywords: Gene transfer; Genomic islands; Conjugative transposons; Conjugation; Tyrosine recombinase; Resolvase; Transposase

1. Mobile genetic elements and the horizontal gene pool The prokaryotic horizontal gene pool (HGP) represents a rich tapestry of adaptive phenotypes conveyed within and between bacterial (and archaeal) cells, by an increasingly diverse assemblage of mobile genetic elements (MGE). Fifty years on from the discovery of transduction by

Corresponding author. Fax: +44-1206-872592. E-mail address: osborn@essex.ac.uk (A. Mark Osborn).

*

Salmonella bacteriophage (Zinder and Lederberg, 1952) and the introduction of the term plasmid (Lederberg, 1952), following the earlier identification of bacterial conjugation, research has revealed numerous combinations of genetic modules derived from phage, plasmid (and transposons) to generate an array of MGE that include conjugative and mobilizable transposons, genomic islands, and integrons (Toussaint and Merlin, 2002). Whilst plasmids and bacteriophage have wellestablished genetic and phenotypic identities, the emerging families of mosaic MGE pose a considerable challenge for the systematicist as to how

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. named following the conserved aspartate and glutamate residues (Polard and Chandler. and second. 1995). (ii) serine Scocca. which from their names at least suggest vastly differing entities. 2002). whilst comparative analysis of these elements reveals fascinating evolutionary insights. the occurrence of plasmid-related transfer genes on CTns. GIs. are now recognised as important contributors to bacterial adaptation and evolution. 1997. Thus this review will focus also on the emerging groups of mobilizable transposons comprised of different combinations of recombinases and plasmid-related mobilisation functions. which are found in some bacterial strains but are absent from otherwise very closely related strains.A. Genomic islands Genomic islands. were first identified as chromosomally . and which are being discovered increasingly on GIs. the situation is complicated further by the additional inclusion on MGE of genes encoding plasmid-related mobilisation and transfer functions. and (iii) DD-E recombinases (transposases). Mark Osborn. However. 2. B€ oltner / Plasmid 48 (2002) 202–212 203 Fig. the genomic islands (GIs) and conjugative transposons (CTns). 1. Such complications arise not least from the utilisation of three distinct enzyme families catalysing the vital process of recombination between DNA molecules (Toussaint and Merlin. namely the presence of phage-related integrases belonging to the tyrosine recombinase family. 1) that are either self-transmissible or mobilizable between bacterial cells. MGE functional modules are as given in the key. Moreover. These families are named after key conserved residues in their active site: (i) tyrosine recombinases (reviewed in Esposito and €by et al. and transposons) that contribute key functional components are circled (dotted lines). Yet molecular comparison of their backbone modules identifies key similarities. phage. Nunes-Du recombinases (resolvase/invertase) (reviewed in Smith and Thorpe. Black triangles inserted within the functional modules of the Anchored Genomic Island indicate that molecular evidence exists for remnants or mutant forms of such modules (see text for further details). D. 2002). In this review we focus in particular on two groups of MGE. 1998). MGE (plasmids. it is apparent on further inspection that they represent just part of a continuum of mosaic MGE (Fig. The mosaic continuum of mobilizable and conjugative genetic elements. best to classify such elements. which vary in size between 10 and 500 kb.

the bph-sal element. 2000). 1983). the clc element encoding chlorocatechol degradation (Ravatn et al. For example the clc element (Ravatn et al. Significantly. Other integrases.and Tn916-related transfer genes. Listeria. however. Xanthomonas (No€ el et al. 2002).. a phylogeny of integrase sequences has also identified three groups that are consistent with the tRNA sub-location classification (Williams. and thus. Acquisition of such traits as functional units allows bacteria to respond rapidly to environmental challenges and explore new ecological niches. whilst a third conjugative element from Pseudomonas aeruginosa JB2 encoding degradation of hydroxy. the SRL PAI from Shigella flexneri (Turner et al. which is increasingly observed (see below). 2001). 2000) has shown this to be a mosaic containing a tyrosine recombinase related to that of the CTns Tn5276 and Tn5252.. 2000). that includes an integrase most closely related to that from Mesorhizobium loti GIs. have been demonstrated to be functional. Although mobilisation of the MMH594 PAI has been demonstrated. 1998). from non-pathogenic to pathogenic. Recent comparison of tRNA attachment sites for the broader group of elements utilising tyrosine recombinases. Phenotypes carried by genomic islands are not limited to those encoding virulence but also include antibiotic resistance e. 2002). 2000). whilst at present it is not known whether this element is capable of independent transfer. 2002).. 1998) and symbiosis (Sym islands) (Sullivan and Ronson. or near to. PAIs carry genes encoding a variety of phenotypes including adhesins. 1998) was initially identified following conjugative transfer from Pseudomonas strain B13 to P. especially if the island also carries conjugal transfer genes. In some GIs the integrase gene may be deleted or non-functional. and subsequently in the related islands from M. and Pseudomonas syringae (Jackson et al.g. As a consequence such islands have been termed ÔecologicalÕ or ÔfitnessÕ islands (Hacker and Carniel.g. Mark Osborn.. partial sequence analysis of the integrative element ICEStl (Burrus et al. given that the phenotype of bacteria receiving such islands is often altered dramatically (e. In Gram-positive bacteria an increasing number of potentially transmissible GIs are identified. 2000).. In addition to the virulence genes they typically carry an integrase gene related to that of phage lambda and belonging to the larger family of tyrosine recombinases. putida Fl. Salmonella. Helicobacter. and subsequently found to integrate using a tyrosine recombinase into either of two tRNA gene attachment sites. Conjugative transfer has also been demonstrated for the 500 kb Sym island from Mesorhizobium loti (Sullivan and Ronson. Vibrio. this phenomenon has been described as Ôevolution in quantum leapsÕ (Groisman and Ochman. Similarly. Integration of this element has been shown to be site-specific within its host. Typically PAIs are integrated into.. Whilst the presence of plasmid-related transfer genes on GIs offers conjugation as a dissemination . In addition.204 A.. 2001). In Streptococcus thermophilus. A number of the ecological islands have been demonstrated to be conjugative. and subsequently termed pathogenicity islands (PAIs) by Hacker et al.. degradation of xenobiotic compounds e. 2001). and Clostridium) (Hacker and Kaper. a 153 kb pathogenicity island has been identified in Enterococcus faecalis MMH594 PAI (Shankar et al. and also carries transfer genes related to the Enterococcus plasmids pAD1 and pAM373. differing in G + C content and codon usage from the surrounding DNA (Hacker et al. potentially capable of horizontal gene transfer. D. has revealed three sub-locations for integration within these genes. More recently PAIs have been identified in a diverse range of animal pathogens from both Gram-negative (Yersinia.. secretion systems and iron uptake systems critical to pathogenicity (reviewed in Hacker and Kaper. it is not currently known whether the element is also self-transmissible. (1990). tRNA genes and are flanked by short direct repeats resembling phage attachment sites (Hacker and Kaper. PAIs have also been identified in a number of plant pathogens including Erwinia. together with plasmid pSK41. and Neisseria) and Gram-positive genera (Staphylococcus. 1996). or from non-symbiotic to symbiotic). encoding biphenyl and salicylate metabolism functions.. 2002). B€ oltner / Plasmid 48 (2002) 202–212 located virulence genes in uropathogenic Escherichia coli.. More recently. 1998).and halo-aromatic compounds is also believed to integrate within the chromosome (Hickey et al. Other likely members of this group of Ôconjugative genomic islandsÕ include the related conjugative integrating elements R391 and SXT that carry metal and/or antibiotic resistance genes (see below). Accordingly. resulting in permanently anchored islands (see below).g. 1999). loti R7A and MAFF303099 (Sullivan et al.. from Pseudomonas putida KF715 also transfers by conjugation and is believed to integrate within a specific insertion hot-spot (Nishi et al...

However. UV-inducible excision has not been demonstrated. though now inappropriately. 2002) shows them to share conserved backbone regions. this proposed classification of R391 and SXT as conjugative transposons might at first seem appropriate. However. being variously described as a transmissible resistance factor. on the basis of sequence data and phenotypic and molecular characterisation. 1979) and pMERPH (Peters et al. B€ oltner / Plasmid 48 (2002) 202–212 205 mechanism. 2002) and SXT (Beaber et al. Mark Osborn.e. Thus these elements. In this respect.. albeit a self-transmissable one. 1999).. coli (Hochhut and Waldor. R391..A. and subsequently as a conjugative transposon (Murphy and Pembroke. 1).. with R391 and SXT only integrating into a single site on the E. the nature of R391. may in fact have been the first genomic island to be isolated. Whilst these may facilitate integration into the chromosome. these backbone regions include a phage-related integrase and associated regulatory genes. In particular. 2002) is consistent with replicon (Bo repeated failures to isolate ccc DNA and now confirms that these elements are not plasmids. coli chromosome (see Fig. classically. together with a conjugative transfer system related to that from the plasmid R27 (seen also in SGI1 from S. The absence of any identifiable plasmid €ltner et al. Following encapsulation of SaPI1 and the subsequent transfer to another cell. this island would now appear to be permanently anchored within the chromosome (Fig.. an integrating plasmid. the PAIs can be excised and circularised by certain Staphylococcal phage (80a and /13) to form circular forms of the PAIs that can then re-integrate in a site-specific manner. as indicated by both the presence of a number of ORFs related to genes from the IncHI1 plasmid R27 encoding mating pair stabilisation and pilus . isolated in India (Waldor et al. including R997 (Matthew et al. 2000) and the inability to demonstrate transfer of the multi-drug resistances (Threlfall et al. However. whilst lacking their own transfer system. The 15. 1994). in contrast to SGI1. 1995). Prior to the determination of the sequences of these elements and the earlier demonstration of the site-specific integration of SXT and R391 into the prfC gene of E. Thus. they share greater similarities with the GIs that similarly integrate into just one or two sites (typically tRNA genes) on the chromosome.. the DNA sequence of SGI1 suggests a possible previous existence as an integrative conjugative plasmid. such as Tn916. Anchored genomic islands and integrative plasmids Analysis of the 43 kb genomic island (SGI1) carrying multi-drug resistances. The recent deter€ltner mination of the DNA sequences of R391 (Bo et al. and the IncJ elements Two notable recent examples of the combination of conjugative plasmid transfer genes with phage-related integration systems are offered by two related elements. With a failure to detect excision of the SGI1 island (Boyd et al. 3. are readily transferred intact via phage transduction. However. D. and in the case of SaPI1 this is a direct consequence of SaPI1 replication interfering with that of the phage. enterica DT104—see below). with at least 95% identify to each other over 65 kb. both R391 and SXT are capable of excision and subsequent conjugative transfer to recipient cells. offering another example of the numerous mechanistic variations found in the HGP. had represented something of an enigma. GIs can also utilise other MGE and mechanisms to facilitate their dispersion... isolated 30 years ago. In retrospect. 1998) both contain a putative integrase (tyrosine recombinase) and are flanked by direct repeats. at least at the level of phenotype. 1972) and the SXT element from Vibrio cholerae. i. in a semi-parasitic manner. They form part of a larger series of elements. 1991). 1). is in the absence of random chromosomal integration (see below). R391 from a South African isolate of Providencia rettgeri (Coetzee et al.2 kb PAI SaPI1 and the related SaPI2 from Staphylococcus aureus which both carry the tst gene for toxic shock syndrome toxin-1 (Lindsay et al. Alternatively. referred to as IncJ elements (following plasmid incompatibility nomenclature). R391. suggesting an absence of an excisionase on these elements. replication of the circular form can lead to transduction of the PAIs at high frequencies.. 1996). 4. recA-independent chromosomal integration combined with conjugative transfer. 2001).. 2001) indicates a complex evolutionary history... where these elements differ from archetypal conjugative transposons. SaPI1 uses its own integrase to integrate into the recipient hostÕs chromosome (Ruzin et al. SXT. in Salmonella enterica serovar Typhimurium DT104 (Boyd et al..

3 kb plasmid pSE101 into a threonine tRNA gene in its host Saccharoployspora erythraea. it is tempting to speculate on the possibility for divergence and subsequent evolution over time of these genes to fulfil new functional roles. as evidenced by the presence of two transposon-related resolvases at either end of the PAI (Takai et al. Two such elements were originally identified: Tn916 from Enterococcus faecalis (Franke and Clewell. 1994) more akin to the relatively random integration of CTns.2 kb conjugative circular plasmid pSAM2 (Boccard et al. without requiring autolysis (Hamilton et al. though subsequent insertion mutagenesis suggests the fascinating possibility that these genes function instead as a Type IV secretion system acting as a potential DNA donation system to facilitate DNA transformation. Indeed. 1).. 2001). 2001). 1999). Whilst integration by homologous recombination enables plasmids to form stable cointegrates.. Plasmid-located genomic islands Localisation of GIs is not limited to the chromosome. the similarities between plasmid conjugative transfer systems and the type IV protein secretion systems including those carried by the cag PAI of Helicobacter pylori or. a lambda-like integrase mediates integration of the 11. sequence analysis of a 27. 1). 1980). Whereas this PAI includes an integrase gene. suggest common evolutionary origins for these systems (Christie.. We have also identified ORFs encoding potential tyrosine recombinases using the PFAM database within archaeal plasmids (Osborn and €ltner. responsible for extracellular transport of the pertussis toxin in Bordetella pertussis. Past traces of a conjugative lifestyle may also be indicated in the Neisseria gonorrhoeae Gonococcal Genetic Island (GGI) by the presence of traG and traH homologues (Dillard and Seifert. ORF439 in Bo the 41. Integration of F typically occurs by homologous recombination between IS elements (IS2 or IS3a and 3b) present on the F plasmid and chromosome. unpublished data) namely. Alternatively. In contrast. 1989) carries a tyrosine recombinase in addition to a rolling circle type replicon and conjugative transfer genes (Fig.. 6.2 kb conjugative plasmid pNOB8 from Sulfolobus sp. in particular the PAI on the Shigella flexneri virulence plasmid pWR201 (Venkatesan et al. Chromosomal integration of plasmids has long been recognised.. 2000). Similarly. 5. B€ oltner / Plasmid 48 (2002) 202–212 assembly proteins. and the related ORF457 in the pING plasmid from Sulfolobus islandicus (Stedman et al. Mark Osborn. the Streptomyces ambofaciens 11. Whilst the function of their gene products is unknown. with a number of elements found located on plasmids. 2000). which is now the accepted archetype of the CTns. which encode a DD-E type recombinase (transposase) at the flanking ends of the 44. NOB8H2 (She et al.3 kb element. introduced into Streptomyces lividans the element demonstrates integration into multiple sites (Brown et al. 1998).206 A. D. Given that the incorporation of plasmid-derived conjugative transfer genes into the chromosome is readily demonstrated. as evidenced by the presence of copies of IS1627.5 kb PAI found on the 80 kb plasmid p33071 in Rhodococcus equi again suggest involvement of transposons in PAI insertion. it is likely that its insertion into pXO1 is mediated by insertion sequences. with reversible integration of the plasmid pKLK106 into two lysine tRNA genes in Pseudomonas aeruginosa (Kiewitz et al. 1981).. 2001) but also notably in the discovery of a PAI carrying the three toxin genes on the plasmid pXO1 from Bacillus anthracis (Okinaka et al. most notably of the F plasmid in the formation of E. together with an ORF related to the replication gene (repA) from the Rhodopseudomonas plasmid pMG101. Similarly. and Tn5253 from Streptococcus pneumoniae (Shoemaker et al. an increasing number of plasmids are reported to carry a lambda-related integrase that facilitates recA-independent chromosomal integration and excision.. such similarities between DNA and protein transporters may represent divergent evolution of ancestral macromolecule secretion systems. In Gram-negative bacteria tyrosine recombinase-mediated integration of plasmids has also been reported.. coli Hfr strains. as opposed to a tyrosine recombinase (Fig. when pSE101 is. we speculate that these plasmids may represent the first examples of integrative plasmids in the archaea... 2001). 2000) These examples of PAIs that utilise transposons for insertion represent yet another intriguing illustration of the versatility of mosaic MGE. For example. Conjugative transposons Conjugative transposons were first identified as chromosomally-borne transposons that were capable of conjugative transfer. Whilst numerous CTns have .

. Tn916 does demonstrate distinct preferences for AT-rich regions with a consensus target of 50 -TT/ ATTTT(N6 )AAAAAA/TA-30 (Lu and Churchward.. albeit conjugative ones. on the basis of their preference for specific integration sites. which is involved in pilus assembly. as opposed to the more random integration exhibited by classical CTns. 1993). notwithstanding the more detailed characterisation of the Enterococcus pheromone-sensing plasmids pAD1 (Francia et al. Moreover.. 2002). A full review of the CTns is beyond the scope of this current paper. Thus. CTnscr94 from Salmonella senftenberg (Hochhut et al. 1997).. 2001). although no individual base within this generic sequence is conserved amongst the numerous integration sites identified. offer a better candidate for a conjugative transposon within the proteobacteriaceae. unpublished data) of ORF21 of Tn916 Bo shows it to be a member of the FtsK/SpoIIIE family. whilst Tn4371 carries RP4/Ti-related transfer genes.. 2000) and the increasing number of SpoIIIE homologues suggest that this may be a widespread mechanism for DNA transport. Over recent years a number of elements isolated from members of the proteobacteriaceae have been proposed as CTns. in particular tRNA genes. we again found that many of the putative ORFs described show no relationship to known transfer genes. the putative TraP protein shows homology to DNA primases. and also to a number of proteins related to the TraC protein from the F plasmid. A functional origin of transfer has been located between ORFs 20 and 21. yet many of these elements would appear to have more in common with genomic islands. 2001) and pSAM2 (Hag ege et al. the putative protein encoded by ORF1 is homologous to relaxase proteins from both conjugative plasmids and mobilizable transposons. and in particular from Bacteroides. suggesting a possible role for this ORF for DNA nicking prior to transfer. whilst the TraG protein is homologous to the BctA protein involved in conjugative transfer of the Bacteroides pBF4 plasmid (Morgan and Macrina. unpublished data) identifies (Osborn and Bo relationships to certain Vibrio phage replication proteins (Nasu et al. we refer readers to the excellent reviews by Salyers et al. 2001) and pAM373 (De Boever et al. However. SpoIIIE homologues are also responsible for conjugative transfer of the Streptomyces plasmids pIJ101 (Pettis and Cohen. However. albeit predominantly from Gram-positive bacteria. conjugative . B€ oltner / Plasmid 48 (2002) 202–212 207 subsequently been identified. This element that utilises a tyrosine recombinase demonstrates semirandom integration into a number of sites present on both the CH34 chromosome and the co-resident pMOL plasmid. Similarly the TraJ protein from CTnDOT is related to the TrwI protein from the transfer operon of R388. The CTnDOT TraA protein is related to a number of ParA proteins involved in plasmid partitioning. Of two additional ORFS upstream of the putative tra genes on the CTnDOT sequence (accession number: AF289050). and includes sequences related to both IncP and F plasmid nic sites (Jaworski and Clewell. The 55 kb catabolic biphenyl degradation transposon Tn4371 from Ralstonia eutropha CH34 does. and is thought to represent a new class of conjugal transfer system (Bonheyo et al. 2000). In contrast. Mark Osborn. CTnDOT shows greater specificity and is found to integrate into only about seven sites in the Bacteroides chromosome (Bedzyk et al. Integration of the majority of CTns utilises a tyrosine recombinase. 1992). (1995) and Scott and Churchward (1995). loti strain R7A symbiosis island (Sullivan et al. 1997). and SXT (see above). Thus it is probable that the CTnDOT transfer operon represents a distant relative of Gram-negative conjugative plasmid transfer systems.A. as is similarly the case for most GIs. For both Tn916 and CTnDOT. Less is known about the transfer system of Tn916. much of our molecular understanding of CTns stems from analyses of Tn916 and the Bacteroides element CTnDOT. including R391. 1997) and the M. however. 2000) and the rep gene from the Bacillus plasmid pGI3 (Hoflack et al... SpoIIIE genes are believed to drive DNA transport from the mother cell into the prespore during sporulation in Bacillus (Bath et al. as more plasmids are sequenced from these organisms. D. although FASTA analysis (Osborn and €ltner.. Following our own FASTA analysis. 1995). this may identify a possible closer linkage between the transfer systems of classical CTns and those from conjugative plasmids. however. FASTA analysis of ORF20 €ltner.. However.. 1995). it is possible that the difficulties in identifying relationships to well-known plasmid conjugation systems may be a consequence that these CTns have been isolated from organisms for which our knowledge of plasmid biology is relatively sparse. The transfer system of CTnDOT is unrelated to that of Tn916-like elements. Classical CTns such as Tn916 demonstrate semi-random integration in a manner more redolent of classical transposons.

Tn10. whether the element integrates into multiple sites (as is the case for Tn916). sites. Upon comparison of such classical transposons with their namesakes. consisting of a transposon that includes an oriT site. Mobilizable transposons Classical transposons utilise one of two types of recombinase. although the transfer genes have been demonstrated to be functional via mobilisation of a second transposable element Tn-bph (Merlin et al. with the Non-replicating Bacteroides Units (NBUs). Obviously. required for integration. and R391). NBU1 and NBU2. NBU1. enabling mobilisation by a co-resident conjugative plasmid. whilst others have led to highly similar MGE being classified with very different names. and additionally carry a plasmid-related mob gene (Fig.g.. such as RP4 (Crellin and Rood. they clearly share a tyrosine recombination-type integration mechanism. demonstrates semi-random integration (Shoemaker et al. Smith and Parker.. carry a putative oriT site related to that of the conjugative transposon Tn916 (Fig. or semi-randomly (Tn4555) [as is the case for Tn916. the conjugative transposons (that utilise a tyrosine recombinase). it is clear that some earlier classifications are inappropriate. a second group including Tn7. 1) to integrate into either tRNA genes (NBU1 and NBU2) (Shoemaker et al. Alternatively. this is most apparent with respect to the conjugative transposons (e. or into one. (Tribble et al. and both utilise conjugative transfer systems that are related.. Wang et al. Mobilisation of these elements utilises oriT sequences and mob genes resembling those from Gram-positive plasmids (Shoemaker et al.. We would suggest that CTn is retained for those classical CTns exhibiting random or .208 A. loti R7A symbiosis island. Conjugative transposons or conjugative genomic islands—that is the question The state of MGE nomenclature is a direct consequence of their highly mosaic composition. yet following analysis of the DNA sequence of this element. and the mobilizable transposon Tn4555 all identified as utilising a tyrosine recombinase-based integration system (Fig. conjugative MGE. B€ oltner / Plasmid 48 (2002) 202–212 transfer of the element has not been demonstrated. and the IS3 family utilise the so-called DD-E recombinase (transposase). yet an increasing number of mobilizable transposons (MTns). It does. 2000) to mediate excision and insertion. At present such systems await discovery. being mobilizable and capable of semi-random integration upon transfer to Bacillus subtilis. as is typical for the GIs. 1992). or occasionally two. Tn916 and CTn-DOT) and the increasing number of GIs that encode their own conjugation systems (e. when transferred into E. historical precedence in the naming of individual elements will lead to future researchers trying to classify newly discovered elements as part of existing groupings. Wang et al. however. 1996a. as described above for pSE 101. In contrast. On molecular comparison of these elements. 1996b). Intriguingly. The majority of these have been identified in Bacteroides isolates.. A third type of mobilizable element. coli. to those from conjugative plasmids. These transposon-encoded mob determinants permit mobilisation of Tn4551—carrying plasmids lacking their own mob system by a helper plasmid.g. It is postulated that Tn5398 utilises both resolvases and mob gene functions carried on the conjugative transposon Tn5397 which is co-resident in the same host (Farrow et al... 1). for which we propose the name Conjugative Genomic Islands. Tn5398 was found to lack both a gene encoding any recognisable recombinase. as new DNA sequences are generated and molecular mechanisms unravelled. can be delineated. 2001). as well as potential mobilisation genes. the clc element. 1997)]. have been reported. 1999). with indistinct boundaries between a number of groups of elements. perhaps combining a DD-E or serine recombinase and a complete plasmid-related conjugative transfer system. Tn5398 from C. 2000). Tn4451 and Tn4453 from Clostridium spp. it is attractive to conjecture upon the existence of truly randomly integrating. 7. Mark Osborn. represent a second type of MTn that instead utilise a serine recombinase (the TnpX resolvase) (Lyras and Rood. 1).. difficile 630 represents yet another fascinating variation on this theme. However. Perhaps on this basis alone CTns and a second group. 2000.. D. 1998. 2000). suggesting that site-specificity of tyrosine recombinase-based systems is a host-specific phenomenon.. Firstly transposons such as Tn3 and cd utilise a serine recombinase (resolvase/invertase). albeit to differing degrees. Arguably the clearest distinction between CTns and GIs is with respect to integration site preference. namely. the M. 8. Arguably.

P. M. and can be mobilised via conjugation to other cells. 2001. J. Rood. Smokvina. J. Roussel. L.. Brown. R391: a conjugative integrating mosaic comprised of phage. For MGE. E. which in many cases will be for a tRNA gene.N. R. Friedmann. 2000. 183.R.. € ltner. Boumedine.. R factors from Proteus rettgeri. 285–291. 2000. De Boever. 2002. Donadio.M. Micro. Transfer region of a Bacteroides conjugative transposon. M.. N. J. Guerineau.. 294–305.A. are termed conjugative genomic islands (a sub-family of the GIs). J.I. Shoemaker.. Science 290. 543–552... However. Microbiol. Microbiol. Coetzee..... H. as needed. K. J. Bonheyo. 1327– 1341. plasmid and transposon elements. Enterococcus faecalis conjugative plasmid pAM373: complete nucleotide sequence and genetic analyses of sex pheromone response. one approach is to accept their mosaic nature. we point towards the numerous examples of reclassification of bacterial genera and species that have resulted from ribosomal RNA-based phylogenetic studies over the last 15 years. Tn4451 from Clostridium perfringens is a mobilizable transposon that encodes the functional Mob protein.R. D.. Hedges. Gen. Peters. D. Mol.T. 1992.. J. but integration into multiple sites in other recipients.B.. K. Imberechts. A.Õ classification remains an important discipline within biology. but lack a conjugation system of their own. The integrated conjugative plasmid pSAM2 of Streptomyces ambofaciens is related to temperate bacteriophages. Errington.. Katz.J. K. 185– 193.. 8. Bo Osborn.A. G.B. and will increasingly further benefit from ongoing developments of a number of MGE-module specific websites. 66. 166–172... Wang. 5158–5169..-K. 2001. Idler. F. 2000. 4259–4269. 40. Type IV secretion: intracellular transfer of macromolecules by systems ancestrally related to conjugation machines. Role of Bacillus subtilis SpoIIIE in DNA transport across the mother cell-prespore division septum. Whilst such an approach is extremely valuable (Toussaint and Merlin.. Boccard. 2002. Bacteriol. 1972. Characterization of the genes and attachment sites for site-specific integration of plasmid pSE101 in Saccharopolyspora erythraea and Streptomyces lividans. Microbiol. M. Mulvey.S.. Y. 41–51.W. J. Partial characterization of a genomic island associated with the multidrug resistance region of Salmonella enterica Typhimurium DT104. 174. but a number of additional elements. 1749– 1753. D. Environ.K. D.M.. G... 1994. Pembroke. 2001. Backer.B... N. 973–980. D.. V. to cover MGE that integrate (irrespective of their type of recombinase) into the chromosome. Bacteriol. M. CTnDOT. Characterization of a novel integrative element.A. MacMahon. J. A. Shoemaker. B. S. L. Clewell. Appl. 28. the desire to also assign generic names to new and existing elements remains compelling. Bedzyk. Burrus. Acknowledgments The authors wish to thank Professor Julian Rood for an introduction to the serine-recombinase-based mobilizable transposons... D. Mol. As a lead. Boyd. in the lactic acid bacterium Streptococcus thermophilus.. A. B€ oltner / Plasmid 48 (2002) 202–212 209 semi-random integration. Plasmid 45.. Gen. T. even here the waters are muddied by elements such as the mobilizable transposons NBU1 and NBU2.M.. Mulvey. TnpZ. G. E.. D. As a third group we propose the adoption of the generic term mobilizable transposon. Pernodet.. 189.. References Bath. J. Mark Osborn. P. and classify all MGE on the presence of key functional modules. Salyers. 2000.K. Christie. whilst those conjugative integrating elements which have distinct sitepreference.. Complete nucleotide sequence of a 43kilobase genomic island associated with the multidrug resistance region of Salmonella enterica serovar Typhimurium DT104 and its identification in phage type DT120 and serovar Agona.C. Genet. . Beaber. N.J.... G.. Fraser. 184. A. Decaris.H.E... would clearly fall within this group. 242. Bacteriol. B. Mol.A. ICEStl.... 37. or in the case of R391 and SXT for prfC. Waldor. J. an integrating antibiotic resistance gene transfer element derived from Vibrio cholerae. Crellin. 5725–5732. Datta. J. Cloeckaert. P. 995–997. We hope that the MGE research community will face these challenges and be willing to embrace appropriate changes to nomenclature. Insertion and excision of Bacteroides conjugative chromosomal elements. Boyd. C. L. Lett. J. or the integrative plasmid pSE101 (see above) that show single-site specificity in one host. D. Genomic and functional analyses of SXT. EMBO J.P. 631–642. A. Graham. 1989. C. This term has been adopted already for a number of MGE (see above). Mol.. Microbiol.. L.. Ng. 72.A...A. Salyers. Peters. FEMS Microbiol. Whilst some may ask ÔWhat’s in a name? That which we call a rose by any other name would smell as sweet.B. 1992. Chaslus-Dancla. Gu edon. Strike.. Hochhut. Wu. Young.. 2002). 184.A. J. Bacteriol.W.L..

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