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

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

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

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

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

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

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

.. 2001. An.. Waldor. F.S. Microbiology 146.. J.. Deletions of chromosomal regions coding for fimbriae and hemolysins occur in vivo and in vitro in various extra-intestinal Escherichia coli isolates. M. Kiewitz. 154. W. 153–158. J. Plasmid 41..B.. 1938–1946. Ecological fitness. Franke. Microbiology 143. 4718– 4726. A Darwinian view of the evolution of microbes. E. Goebel. G. Knapp. 1952. 145. J. Klockgether.. Pembroke.. Arnold. R. J. R. Genomic analysis of the erythromycin resistance element Tn5398 from Clostridium difficile. Carniel.. Site-specific integration of the conjugal Vibrio cholerae SXT element into prfC. Hacker. J. Bacteriol. J. B. Kurepina.. Cell genetics and hereditary symbioses. Mansfield. Clewell. J. 588–601. B€ oltner / Plasmid 48 (2002) 202–212 osa strain JB2.. A.A. bctA: A novel pBF4 gene necessary for conjugal transfer in Bacteroides spp. E. Rev... A..P. K... D.. nucleotide sequencing. 177... 8. Sezonov.P. 67. J..... Bacteriol. K. CTnscr94. 1993. D. W. 1997. 1996.. Ruzin. B. Taylor. Lund. C. J.. Merlin. M. Churchward. 1999. 32. 10875–10880.. Nucleotide sequence and characterization of the cryptic Bacillus thuringiensis plasmid pG13 reveals a new type of rolling circle replicon. and RP4/Tilike transfer functions.E. 213– 225.. H. Physiol. M. A.. 657–662. Marre. Completion of the nucleotide sequence of the Enterococcus faecalis conjugative virulence plasmid pAD1 and identification of a second transfer origin. 138. Pathog. 1981. J. 134. TnpX. Rood.. Hickey. (USA) 96. Hochhut. K. 2000. Ann. G. 494–502. Insertion-duplication mutagenesis of Neisseria: use in characterization of DNA transfer genes in the Gonococcal Genetic Island. J.L. R.. Murphy. Seurinck. Microbiol. J..Y. Sabat. 179. Arment. Hacker. C.. 2000. M.J.. Ike.. B. D.. Jaworski.. E. 1999. J. J. P erez-Lesher. Dillard. L.J. J.. Ott. 791–794. 2001. Hamilton. Acad. Nucl.I. Weinel. A. J. J.S. 1995.. mobile cluster of biodegradation genes from Pseudomonas aerugin- . Ross. A. Plasmid 46.B. 54. 1997.B.. Monitoring genome evolution ex Tu vivo: reversible chromosomal integration of a 106 kb plasmid at two tRNALys gene loci in sequential Pseudomonas aeruginosa airway isolates.D.. 2000. 1999. 6644–6651. Microbiol. Weaver.W.. W. Acids Res. 1979..W. J. Micro.. A functional origin of transfer (oriT) on the conjugative transposon Tn916. J.. 183. 179. FEMS Microbiol. L. Mol.B. Pathogenicity islands: bacterial evolution in quantum leaps. A. Tn916 target DNA sequences bind the C-terminal domain of integrase protein with different affinities that correlate with transposon insertion frequency. Farrow. Lu.I.M.. 1983. Pathogenicity islands and the evolution of microbes. J. Rev. N..D. Samberger... Gilmore. R.W. Goebel. Yuroff. Hacker. Micro. Lett. A. Gerbaud... Environ.. Clewell. B. 111–127... Cloning.B. D. 175. Hedges. Lyras. Dillard... Microbiology 147. Schmid. Gibbon. Sci. D. 2155–2165. C.L. 2001. Hacker. Jahreis. Lindsay. Matthew. Seifert. Microbiol. Proc.210 A. D. 2717–2728. Pernodet. Muscholl-Silberhorn. Mahillon. W. R. The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Hoflack...L. J. Toussaint.. Microb. K. Spontaneous deletions and flanking regions of the chromosomal inherited hemolysin determinant of an Escherichia coli O6 strain. Bender. K. Bacteriol. J. 641–679.. 1995. Appl.V. D. Bacteriol. 3605–3614. Tsiamis.T. Scocca... The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. 263–277.. 2001. Types of beta-lactamase determined by plasmids in Gramnegative bacteria. 25. Microbiol. 376–381.. Murillo. Groisman. J. Lengeler. Mol...J. 32... Transfer functions of the conjugative integrating element pSAM2 from Streptomyces ambofaciens: characterization of a kil-kor system associated with transfer. 1145–1152. H. a Pseudomonas-like catabolic pathway. H. S.. and functional analysis of a novel. E. Rood.W. Bacteriol. Bacteriol. J. Transfer of the IncJ plasmid R391 to recombination deficient Escherichia coli K12: evidence that R391 behaves as a conjugal transposon.A. J. 527–543. 1995. J. EMBO Reports 2. Vivian. 4603– 4609. Lyras. Novick. a conjugative transposon found in enterobacteria.P. Tn4371: a modular structure encoding a phage-like integrase.... 99–110. 29. J. Morgan. 2001. Esposito. 38... J. Cell 87. Y. Hag ege. J. C. M. Wirth.. D. Macrina.R. Athanassopoulos. 403–430.S... J. Wingender. Mol. 5000–5008. Lederberg. Sesma. genomic islands and bacterial pathogenicity. 1990. A.. A variable genetic island specific for Neisseria gonorrhoeas is involved in providing DNA for natural transformation and is found more often in disseminated infection isolates... R. Identification of a pathogenicity island. on a large native plasmid in the bean pathogen Pseudomonas syringae pathovar phaseolicola. 2365–2373..F. Kaper. K.. Clewell.A. Smith.. J.K. A.T. 2097–2102. Bacteriol. €mmler. Springael. Jackson. J. D.. D. Transposition of Tn4451 and Tn4453 involves a circular intermediate that forms a promoter for the large resolvase.E.. G. 41. which contains genes for virulence and avirulence.. 1997. M. Larbig. Haas. Bacteriol. F.J. J. M.. 5529–5538... Bacteriol. 177. 40–54.. Gu erineau... Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of ‘‘conjugal’’ transfer in the absence of a conjugative plasmid. Francia. Mark Osborn. F. Hochhut. 1998. G. Schwartz. Natl.. Mol.. 2001. Friedmann. H. J..L. D. 1997. Ochman.

Novick..R. Okinaka. 6509–6515. 1995. and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. Shoemaker. 435–439. 26. Ricke. Gilmore...G..G. Weaver.N. K. Phan. Rowe. A.. 1995. DNA sequence and comparison of virulence plasmids from Rhodococcus equi ATCC 33701 and 103. Genet.E. Microbiol. The transfer origin for Bacteroides mobilizable transposon Tn4555 is related to a plasmid family from Gram-positive bacteria. J. Bacteriol. the large Bacillus anthracis plasmid harboring the anthrax toxin genes. L. R.. Threlfall.S. S. Elliot.. McCallum. 181..M. Ronson. Rec.. Gen.M. J. Strike.R.....R. S. G.P. Manter. H. 1995. Webby. Zillig... D.W.... Kwon. Yokoyama. 41. 1994. G. 928– 936. 1340–1348.. J... 1998. Hoffmaster. Ruzin. Toussaint. 3594– 3600. J. A. Salyers. Salyers. N. R. Wang. J. 182. Springael. 2002. Shinagawa.R. J. Mol. 13–23.. Holz. J. Stuart. 228. Smith. Sullivan..C. 59. A.. Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A.. J. a mobilizable site-specific integrated element from Bacteroides spp.J. 2001. 180. Ravatn.. integrates into the 30 end of a Leu-tRNA gene and has an integrase that is a member of the lambda integrase family... N.A...K. Mol.M. 2000.. 1999.Y. J. Ogino. She. Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Mol. 2002. Ronson.E. can integrate nonspecifically in Escherichia coli. Smith.. Shankar. Suzuki. Y.. 1996b. Martinez. Bacteriol. Prescott. Svensson. Diversity in the serine recombinases. Bacteriol. Nucl.. C. 44. Lindsay.E. Immun.B. 367–397.. 2001. Molecular genetics of SaPI1—a mobile pathogenicity island in Staphylococcus aureus. R.. (USA) 95. A.. 2000.M. F. Mobile elements as a combination of functional modules. R.. J. Cruickshank. K. Zehnder. Tribble... K. vesicatoria are encoded within the hrp pathogenicity island. M. Ward.. Acad. Hampton.. G.. A. J. D. Stevens. T. 6840– 6847. G.D.A. 184.. Chandler. A. pING family of conjugative plasmids from the extremely thermophilic archaeon Sulfolobus islandicus: insights into recombination and conjugation in Crenarchaeota.J. Sullivan. Polard. Novel mercury resistance determinants carried by IncJ plasmids pMERPH and R391. S. A. van der Meer. K. Garrett. 247–250. A. Y.. Pettis. M. Koehler. Park. W.. Parker. Nennstiel.F.. P. Shoemaker. NBU1. D.J.S. 2000. D.W. H. J. 365–377. A. 38. 577.. Nicholson... Prangishvili. 1980.. K..T.. 2002..A. Plasmid 3. Peters.. Infect. T. Shoemaker.B. Smith.. Thieme. Natl. Smith. Shoemaker. E. J. 137. Microbiol. Rossbach. P.. K. N. Q. 26– 35. No€ el. 80–87. 4360–4369.... Conjugative transposition.J.M.. 49. 417–425. Tirumalai. A.. 3086–3095. Li. Guild. Dan.. A 90kilobase conjugative chromosomal element coding for biphenyl and salicylate catabolism in Pseudomonas putida KF715. Makino.. Salyers. Tominaga.V..J. Stedman. Hill. C.C.. T.M. Trzebiatowski. A. G.M. 178... Acids Res. Honda. H...... 180.. A. C. 79.. Bacteriol. W. S. H. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements.. C.R. A. Zillig. S.B. N. A. strain B13.. 1998.. H. R. Bacteriol.. U. Gen. I. M... B€ oltner / Plasmid 48 (2002) 202–212 Nasu. L. Garrett..A. G. H. D..S.R.. Churchward. Proc. 391– 406. Modulation of virulence within a pathogenicity island in vancomycin-resistant Enterococcus faecalis.. 1996a. R. R. Cloud.. 1998.A. Cohen. J..... O.D. U.. Leeuwen. 3601–3607..A..D. F. tandem amplification. T. 182. D.. Thorpe.B. 5145–5149. R. Gouzy. 2002. Hines. J...-R. Bacteriol..A. Microbiol. Sugahara. Wang. Epidemic in cattle and humans of Salmonella typhimurium DT104 with chromosomally integrated multiple drug resistance.S. H.A.. Alperin. DNAse-resistant transfer of chromosomal cat and let insertions by filter mating in pneumococcus.. G.J. V.. N. Brown. D. Jackson. 299–307. Mol. Ritchie. Wang. Bacteriol. Studer. D. 1949–1955. 7014–7020. Two novel type III-secreted proteins of Xanthomonas campestris pv. 182. Takamatsu.. Lamke. Hobman. Osaki. Int. Bacteriol.. 2000. NBU1.A. K. S.W. 1998.. 184. K. 579–590.. Rev. J.J. J. K. N. C. 2002. 178. Mol. T. J. J. EllenNunes-Du berger. Kumano. Extremophiles 2. Iida..L. 2000. 68.. T. L. Plasmid 47.J. V.. Bonas. Stedman. S. Evolution of rhizobia by acquisition of a 500 kb symbiosis island that integrates into a phe-tRNA gene. J. Fleetwood. Baghdayan. 2156–2161. J... K. 1991.. Sekizaki.J. N.T. Singh..... P.. W. de Bruijn. Vet. Nakamura..M.. Nature 417. C. M. T. P. Phan. Takai. G. Scott.. 211 Shoemaker. Q. J. R. Merlin.. The Bacteroides mobilizable insertion element. Landy. The Bacteroides mobilizable transposon Tn4555 integrates by a site-specific recombination mechanism . S. Parker... 1997. Bacteriol. Salyers.-R. D.. Microbiol. She... Albers. Clin. N. R. B. Microbiol. D. Bacteriol.. H. M. A filamentous phage associated with recent pandemic Vibrio parahaemolyticus O3:K6 strains.S. Kakuda. Sequence and organization of pX01. Chromosomal integration. Nishi. S.A. Mark Osborn.T. Unravelling the essential role in conjugation of the Tra protein of Streptomyces lividans plasmid pIJ101 Anton. Frost. Multiple gene products and sequences required for the excision of the mobilizable integrated Bacteroides element NBU1.. Furukawa.. J. Similarities and differences among 105 members of the Int family of site-specific recombinases.B.. Ann. 1998. Keim. Microbiol. Rev. Mahillon. Yamaichi. Bacterial transposases and retroviral integrases.. €by.. J. Sci. 294–299. 15. Microbiol.S. 746–750.

J. D... Acids Res. Tschape. Blattner. S. Bacteriol. trimethoprim.P. 64. 866–875. Shoemaker.R. 2001. 2001.. Bacteriol. Adler. B€ oltner / Plasmid 48 (2002) 202–212 tance to sulfamethoxazole. Nested deletions of the SRL Pathogenicity Island of Shigella flexneri 2a. S. Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies... 1952. 5535–5543. A. H. Bacteriol.A. 679–699. Rajakumar. K... which carries a functional lincomycin resistance gene. J. G... J. 179. 4157–4165.J. 182. J. M. Characterization of a Bacteroides mobilizable transposon. M. Salyers. F. 2000.K.B. V. Sakellaris. Williams. 3271–3285. Infect. E. J. 178. Turner.. Burland...J. Genetic exchange in Salmonella. Nucl. Wang. J.. 183. Wang. NBU2. 2731–2739. Bacteriol... N.N. Mekalanos. 2002. Waldor.. K.M. J. 1996.. 3559–3571. Bacteriol.A. Mark Osborn. 30. A new type of conjugative transposon encodes resis- . Venkatesan.212 A. B. Immun. H. Lederberg. Grotbeck. J. 69. J.-R. Rose.. Luck. Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Goldberg. M.D.. N... D. Zinder. similar to that of the Gram-positive bacterial element Tn916. and streptomycin in Vibrio cholerae O139.

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