Towards a taxonomy of conjugative plasmids
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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2022, Environmental Technology and InnovationCitation Excerpt :In genetic bioaugmentation for pollutant removal a donor bacterium harboring a catabolic plasmid will transfer the plasmid to a recipient cell (transconjugant) and both donor and transconjugant can express degradation genes for removal of the contaminant. Many of these catabolic plasmids exist in the IncP incompatibility group which contains self-conjugatable plasmids that form a short, rigid pilus (Fernandez-Lopez et al., 2017). Incompatibility groups describe plasmids that are unable to coexist in a single cell due to sharing elements of the same replication system (Novick, 1987).
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2022, PlasmidCitation Excerpt :If one were to speculate perhaps presence of pRK100 plasmid helps with changed growth or metabolic capacity in urine, bacterial adhesion, or it has increased epithelial cell invasion, as it was shown for a well characterized uropathogenic strain of E. coli UTI89 carrying F-type plasmid pUTI89 (Cusumano et al., 2010). Recent efforts were made to review, to organize and to propose unifying nomenclature of the conjugative transfer or plasmid genes (Fernandez-Lopez et al., 2017; Orlek et al., 2017; Thomas et al., 2017). Several types of classification of plasmids are currently in use or proposed: (1) based on replication mechanisms and incompatibility groups (Carattoli et al., 2005); (2) Mob families for conjugative plasmids using conservation of key transfer protein – relaxase (Francia et al., 2004; Orlek et al., 2017); (3) partitioning mechanism (Bousquet et al., 2015), (4) based on ANI via a taxonomic classifier of plasmids tool (COPLA) for plasmid taxonomic units (PTUs) (Redondo-Salvo et al., 2021).
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2020, Water ResearchCitation Excerpt :Conjugative or self-transmissible plasmids contain two modules with a mobility system (relaxase and T4CP) and an MPF system (T4SS), while the mobilizable plasmids do not contain the MPF system (Smillie et al., 2010; Guglielmini et al., 2014). Compared with the control treatment, antibiotic selection pressures promoted the occurrence of these genetic elements with ARGs on plasmids and increased the number of potential mobilizable or conjugative plasmids, which could play a more critical role than non-mobilizable plasmids in increasing environmental adaptation of microbiota to antibiotics and in acquiring and horizontally transferring ARGs between the same microbial species or across species under antibiotic selection pressures (Fernandez-Lopez et al., 2017; Wang et al., 2019). The HGT of plasmid-mediated resistance to different antibiotics exacerbates antibiotic resistance challenges in clinical and natural environment.
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2020, PlasmidCitation Excerpt :The conjugal transfer/mobilization capacity of the naphthalene plasmid pNAH20 was characterized in our previous work (Heinaru et al., 2009). Later, it was classified into the same phylogenetic cluster (IncP-9δ) with the naphthalene-degrading plasmid pDTG1 from P. putida NCIB 9816–4 (Fernandez-Lopez et al., 2017). The plasmid pPHE20 carries the pheBA operon as well as the ttg operon, coding for proteins showing similarity to those of toluene efflux pumps (Fig. 1).