Elsevier

Current Opinion in Microbiology

Volume 38, August 2017, Pages 106-113
Current Opinion in Microbiology

Towards a taxonomy of conjugative plasmids

https://doi.org/10.1016/j.mib.2017.05.005Get rights and content

Highlights

  • Conjugative plasmids are key mediators of Horizontal Gene Transfer in Bacteria, frequently mediating environmental adaptation.

  • In order to make sense of the increasingly amount of plasmid genomic data, there is a need of appropriate, functional ways to classify conjugative plasmids.

  • Conjugative plasmids form distinguishable clades and phylogenies, thus they are not refractory to taxonomic classification.

  • Translating criteria employed in bacterial taxonomy might be enough to provide an operational taxonomy for conjugative plasmids.

Conjugative plasmids are the keystone of horizontal gene transfer. Metagenomic research and clinical understanding of plasmid transmission beg for a taxonomical approach to conjugative plasmid classification. Up to now, a meaningful classification was difficult to achieve for lack of appropriate analytical tools. The advent of the genomic era revolutionized the landscape, offering a plethora of plasmid sequences as well as bioinformatic analytical tools. Given the need and the opportunity, in view of the available evidence, a taxonomy of conjugative plasmids is proposed in the hope that it will leverage plasmid studies.

Section snippets

Horizontal gene transfer and the origin of bacterial species

While central to evolutionary thinking, the concept of species has been problematic, especially in the prokaryotic domain [1, 2, 3]. Doolittle and Zhaxybayeva identify three main questions regarding the origin of bacterial species: whether bacterial species exist, whether a unitary definition is possible, and what are the evolutionary forces behind bacterial speciation [2]. Horizontal gene transfer (HGT) stands out because it conditions the answers to these three questions [2, 4]. If rampant,

The role of mobile genetic elements

Natural transformation, phage transduction, and bacterial conjugation are three main routes of HGT in bacteria. Phage transduction and bacterial conjugation are encoded by mobile genetic elements (MGEs) [14]. Conjugative plasmids, integrative conjugative elements (ICEs) and bacteriophages propagate both by vertical expansion (piggybacking their host reproduction), and by infectious transfer (horizontally invading new hosts). This latter ability makes MGEs essential vehicles for bacterial

Classifying plasmids

Taxonomy involves the organization of a significant classification, but not all classifications are taxonomical. Because plasmids are key in the spread of antibiotic resistances, several classification schemes have been developed for epidemiological tracking [27, 28, 29]. While both taxonomical and epidemiological classification might overlap to some extent (e.g., E. coli phylogroups [30, 31]), both endeavors have fundamentally different goals. Epidemiological classification (even when it

Defining a plasmid taxonomic hierarchy (classes, families and species)

To set up an operational taxonomy, we need to construct phylogenies using some conserved genetic marker. Bacterial taxonomy employs 16S RNA and concatenated sets of conserved proteins, but no universally conserved gene exists in plasmids. The closest to a universally conserved plasmid gene would be the replication initiation protein (RIP). However, RIP-based phylogenies are difficult to make and interpret because (i) plasmids quite often contain more than one RIP, and (ii) there are many

Operational criteria to define plasmid species

The most important clade that we should define is the functional equivalent to a bacterial species. As discussed above, a plasmid species taxonomic unit must be biologically informative and phylogenetically relevant, that is, it must fulfill three basic requirements: (i) monophyly, (ii) apomorphysm and (iii) similarity. The same requirements are the bases for the definition of species in bacteria and higher organisms [2]. Following equivalent rules, it is possible to achieve an operational

A case study: defining plasmid species in the MOBF11 family

As an example on how these general conditions apply to the particular case of conjugative plasmids, we analyzed some plasmid groups belonging to the MOBF11 family of the MOBF class. Two of them, IncW and IncP-9, were previously characterized [22, 38], while a third group (IncN3) has been recently described [55]. These three groups correspond to reciprocally monophyletic branches in the MOBF11 tree (Figure 1), thus fulfilling species condition (i). In order to test whether plasmids within these

Concluding remarks

It might seem paradoxical to propose a taxonomical classification in a time where genomics and metagenomics are increasingly blurring the boundaries of traditional bacterial species [58]. However, in doing so we are not advocating for the idea of species having an idiosyncratic and permanent quality (defined as ‘pre-Darwinian essentialism’ by Doolittle [58]), but for a practical solution to a real problem that plasmid biology is currently suffering. Rapid and cheap bacterial and metagenome

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Funding

The work performed by the FdlC group was supported by grants BFU2014-55534-C2-1-P and BFU2014-62190-EXP from the Spanish Ministry of Economy and Competitiveness and 612146/FP7-ICT-2013-10 from the European Seventh Framework Programme.

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

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