SummaryElements that excise and integrate, such as prophages, and transfer by conjugation, such as plasmids, have been found in various bacteria. These elements appear to have a diversified set of characteristics including cell-to-cell contact using pili or cell aggregation, transfer of single-stranded or double-stranded DNA, low or high specificity of integration and serine or tyrosine recombinases. This has led to a highly heterogeneous nomenclature, including conjugative transposons, integrative 'plasmids', genomic islands and numerous unclassified elements. However, all these elements excise by site-specific recombination, transfer the resulting circular form by conjugation and integrate by recombination between a specific site of this circular form and a site in the genome of their host. Whereas replication of the circular form probably occurs during conjugation, this replication is not involved in the maintenance of the element. In this review, we show that these elements share very similar characteristics and, therefore, we propose to classify them as integrative and conjugative elements (ICEs). These elements evolve by acquisition or exchanges of modules with various transferable elements including at least ICEs and plasmids. The ICEs are probably widespread among the bacteria.

Horizontal transfer of genomic islands (GEIs), that is, chromosomal regions encoding functions that can be advantageous for the host, plays a key role in bacterial evolution, but their mechanisms of transfer remained elusive for a long time. Recent data suggest that numerous GEIs belong to noncanonical classes of mobile genetic elements (MGEs) that can transfer by conjugation. Among them, the integrative and conjugative elements encode their own excision, conjugative transfer, and integration, whereas the integrative mobilizable elements are autonomous for excision and integration but require the conjugation machinery of helper elements to transfer. Others can self-transfer but require the recombination machinery of the recipient cell to integrate. All these MGEs evolve by acquisition, deletion, or exchange of modules, that is, groups of genes involved in the same function. Moreover, composite GEIs can result from the insertion of a MGE within another or from the site-specific integration of an incoming MGE into one of the recombination sites flanking a resident GEI (tandem accretion). Tandem accretion enables the cis-conjugative mobilization of highly degenerated and nonautonomous GEIs, the cis-mobilizable elements. All these mechanisms contribute to the plasticity and complex evolution of GEIs and explain the highly diverse tableau revealed by more and more genome comparisons.

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Transposable DNA elements occur naturally in the genomes of nearly all species of prokaryotes. A proposal for a uniform transposable element nomenclature was published prominently in the 1970s but is not, at present, available online even in abstract form, and many of the newly discovered elements have been named without reference to it. We propose here an updated version of the original nomenclature system for all of the various types of prokaryotic, autonomous, transposable elements excluding insertion sequences, for which a nomenclature system already exists. The use of this inclusive and sequential Tn numbering system for transposable elements described here recognizes the ease of interspecies spread of individual elements, and allows for the naming of mosaic elements containing segments from two or more previously described types of transposons or plasmids. It will guard against a future necessity to rename elements following changes in bacterial nomenclature which occurs constantly with our increased understanding of bacterial phylogenies and taxonomic groupings. It also takes into account the increasing importance of metagenomic sequencing projects and the continued identification of new mobile elements from unknown hosts.