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

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

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

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

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

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

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

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

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