**3. Mobile genetic elements**

Horizontal gene transfer is a significant driving force of bacterial genome evolution, including the emergence and dissemination of antibiotic resistance and virulence genes. The SOS response has been shown to play an important role in gene transfer in a number of bacterial species.

One of the first reports of the involvement of the SOS response in horizontal gene transfer was SOS induction of transfer of antibiotic resistances encoded by the *Vibrio cholerae* integrating conjugative element, SXT [13]. The SOS response has also been shown to induce lambdoid prophages due to SOS induced self cleavage of the CI phage repressor [25].

In turn, as conjugative plasmid DNA transfer and transformation, involve uptake of ssDNA, these mechanisms induce the SOS response [26, 27].

An important class of SOS controlled mobile genetic elements are the wide spread integrons. They are associated particularly with transposons and conjugative plasmids and have played an important role in the evolution of antibiotic resistance among pathogenic bacteria [28]. Integrons encode a site specific recombination system that promotes integration and expression of gene cassettes with antibiotic resistance and metabolism associated functions.

On the basis of integrase sequences, five classes of integrons are distinguished. Class 1 integrons are by far the most prevalent and clinically relevant. Recently, the class 1 integrons were found in a considerable fraction of *E. coli* isolates [29].

Integrons are composed of an *int*I gene encoding an integrase, followed by a recombination site, attI and a variable array of gene cassettes each ending in a recombination attC site [30]. Integron cassette expression is driven by the Pc promoter situated upstream of the array. Cassettes closest to the promoter are expressed at highest levels [31]. The integron integrases are frequently controlled by the LexA protein [11].

Integrons enable bacteria to evolve in response to new antibiotic challenges via rapid optimization of cassette expression. Activity of the integrase allows: (i) modulation of cassette expression, (ii) rapid gain of additional copies of selected cassettes and (iii) elimination of redundant cassettes. Integrase activity does not compromise genome integrity due to the high specificity of integrase-mediated recombination [32–34]. Thus, integrase-mediated cassette re-shuffling in stressful environments could accelerate bacterial evolution allowing bacteria to optimize cassette expression and maximize fitness. Relavant cassettes could be positioned near the Pc promoter for maximal expression, while unnecessary cassettes could be kept at the end of the array and be moved forward when required [33].

DNA acquired by HGT, including pathogenicity islands (PAIs) with virulence factor genes, must either replicate autonomously or be integrated into the bacterial chromose or plasmid. Integration is mediated by recombinases/integrases that are often encoded on PAIs and perform either integration or excision from the chromosome. It was recently shown that SOS inducing antibiotics, including clinically relevant for treatment of UTI, led to in a subpopulation, increased promoter activity as well as increased loss of PAIs [35].
