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Bacterial transformation: distribution, shared mechanisms and divergent control
Calum Johnston1,2, Bernard Martin1,2, Gwennaele Fichant1,2, Patrice Polard1,2 and Jean-Pierre Claverys1,2
Abstract | Natural bacterial transformation involves the internalization and chromosomal integration of DNA and has now been documented in ~80 species. Recent advances have established that phylogenetically distant species share conserved uptake and processing proteins but differ in the inducing cues and regulatory mechanisms that are involved. In this Review, we highlight divergent and common principles that govern the transformation process in different bacteria. We discuss how this cumulative knowledge enables the prediction of new transformable species and supports the idea that the main role of internalized DNA is in the generation of genetic diversity or in chromosome repair rather than in nutrition.
Natural bacterial transformation, which was first discovered in the Gram-positive bacterium Streptococcus pneumoniae (also known as pneumococcus)1, is regarded as a parasexual process that involves two partners: exogenous DNA and a recipient cell. Internalization of exogenousDNA and integration into the recipient genome by homologous recombination enables bacteria to acquire new genetic traits and to adapt to changing environmental conditions, promoting for example resistance to antibiotics and evasion of vaccines2. Unlike other mechanisms of horizontal gene transfer, such as
transduction and conjugation, transformation is entirely directed by the recipient cell and all required proteins are encoded in the core genome. Most transformable bacteria do not permanently express the proteins that are involved but instead require specific conditions to develop competence for genetic transformation. Competence is thus a transient window of opportunity for DNA internalization and thereby enables subsequent transformation.
The number of species that are known to be naturally transformable has almost doubled in 20 years3,4. A
total of 82 species have now been shown to be naturally transformable (http://www.nature.com/nrmicro/journal/v12/n3/full/nrmicro3199.html#supplementary-information
Web End =Supplementary information S1 (table)). This number could be an overestimate as, in several cases, only a single report documents transformation and molecular proof of natural transformation (such as inactivation of a key DNA-uptake or processing gene
for example, comEC or dprA; see below) is lacking. Nevertheless, an analysis of the phylogenetic distribution of 57 of these 82 species shows that transformability is spread throughout the main taxa, with Gram-positive and Gram-negative bacteria equally represented (FIG.1a).
Over the past 10 years, several...