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


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: (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

0147-619X/02/$ - see front matter Ó 2002 Elsevier Science (USA). All rights reserved. PII: S 0 1 4 7 - 6 1 9 X ( 0 2 ) 0 0 1 1 7 - 8

2. 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. named following the conserved aspartate and glutamate residues (Polard and Chandler. the genomic islands (GIs) and conjugative transposons (CTns). 2002). whilst comparative analysis of these elements reveals fascinating evolutionary insights. and transposons) that contribute key functional components are circled (dotted lines). which vary in size between 10 and 500 kb. namely the presence of phage-related integrases belonging to the tyrosine recombinase family. 1995). (ii) serine Scocca.A. MGE functional modules are as given in the key. Genomic islands Genomic islands. Moreover. D. 1997. B€ oltner / Plasmid 48 (2002) 202–212 203 Fig. which are found in some bacterial strains but are absent from otherwise very closely related strains. best to classify such elements. MGE (plasmids. In this review we focus in particular on two groups of MGE. which from their names at least suggest vastly differing entities. are now recognised as important contributors to bacterial adaptation and evolution. 1998). GIs. These families are named after key conserved residues in their active site: (i) tyrosine recombinases (reviewed in Esposito and €by et al. 1. Nunes-Du recombinases (resolvase/invertase) (reviewed in Smith and Thorpe. 2002).. phage. Mark Osborn. However. Thus this review will focus also on the emerging groups of mobilizable transposons comprised of different combinations of recombinases and plasmid-related mobilisation functions. were first identified as chromosomally . and which are being discovered increasingly on GIs. and (iii) DD-E recombinases (transposases). it is apparent on further inspection that they represent just part of a continuum of mosaic MGE (Fig. Yet molecular comparison of their backbone modules identifies key similarities. The mosaic continuum of mobilizable and conjugative genetic elements. and second. the situation is complicated further by the additional inclusion on MGE of genes encoding plasmid-related mobilisation and transfer functions. the occurrence of plasmid-related transfer genes on CTns. 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). 1) that are either self-transmissible or mobilizable between bacterial cells.

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

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

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. together with an ORF related to the replication gene (repA) from the Rhodopseudomonas plasmid pMG101. when pSE101 is. 1980). In Gram-negative bacteria tyrosine recombinase-mediated integration of plasmids has also been reported. 5.. 2001).. Two such elements were originally identified: Tn916 from Enterococcus faecalis (Franke and Clewell. 2000) These examples of PAIs that utilise transposons for insertion represent yet another intriguing illustration of the versatility of mosaic MGE. 1989) carries a tyrosine recombinase in addition to a rolling circle type replicon and conjugative transfer genes (Fig. 2001). responsible for extracellular transport of the pertussis toxin in Bordetella pertussis. Chromosomal integration of plasmids has long been recognised. Whilst numerous CTns have . an increasing number of plasmids are reported to carry a lambda-related integrase that facilitates recA-independent chromosomal integration and excision. a lambda-like integrase mediates integration of the 11. in particular the PAI on the Shigella flexneri virulence plasmid pWR201 (Venkatesan et al.. 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.206 A. 2000).3 kb element. 1994) more akin to the relatively random integration of CTns. such similarities between DNA and protein transporters may represent divergent evolution of ancestral macromolecule secretion systems.. 1999). Whilst the function of their gene products is unknown. Integration of F typically occurs by homologous recombination between IS elements (IS2 or IS3a and 3b) present on the F plasmid and chromosome. 1981). In contrast. Whereas this PAI includes an integrase gene. Indeed. We have also identified ORFs encoding potential tyrosine recombinases using the PFAM database within archaeal plasmids (Osborn and €ltner. as opposed to a tyrosine recombinase (Fig. introduced into Streptomyces lividans the element demonstrates integration into multiple sites (Brown et al. most notably of the F plasmid in the formation of E. Given that the incorporation of plasmid-derived conjugative transfer genes into the chromosome is readily demonstrated.2 kb conjugative circular plasmid pSAM2 (Boccard et al. which encode a DD-E type recombinase (transposase) at the flanking ends of the 44. Similarly. with reversible integration of the plasmid pKLK106 into two lysine tRNA genes in Pseudomonas aeruginosa (Kiewitz et al. 2001). Similarly. as evidenced by the presence of two transposon-related resolvases at either end of the PAI (Takai et al. and the related ORF457 in the pING plasmid from Sulfolobus islandicus (Stedman et al. D. 1). B€ oltner / Plasmid 48 (2002) 202–212 assembly proteins. 1998). ORF439 in Bo the 41.. as evidenced by the presence of copies of IS1627. 2000).. For example..2 kb conjugative plasmid pNOB8 from Sulfolobus sp.. the Streptomyces ambofaciens 11. we speculate that these plasmids may represent the first examples of integrative plasmids in the archaea. 6. Alternatively.5 kb PAI found on the 80 kb plasmid p33071 in Rhodococcus equi again suggest involvement of transposons in PAI insertion. Whilst integration by homologous recombination enables plasmids to form stable cointegrates. sequence analysis of a 27. it is likely that its insertion into pXO1 is mediated by insertion sequences. without requiring autolysis (Hamilton et al. unpublished data) namely. Mark Osborn. Plasmid-located genomic islands Localisation of GIs is not limited to the chromosome. coli Hfr strains. NOB8H2 (She 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. 1). and Tn5253 from Streptococcus pneumoniae (Shoemaker et al. which is now the accepted archetype of the CTns.3 kb plasmid pSE101 into a threonine tRNA gene in its host Saccharoployspora erythraea.. 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.. Conjugative transposons Conjugative transposons were first identified as chromosomally-borne transposons that were capable of conjugative transfer. it is tempting to speculate on the possibility for divergence and subsequent evolution over time of these genes to fulfil new functional roles. with a number of elements found located on plasmids. suggest common evolutionary origins for these systems (Christie.

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

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

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

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