## 2 Transcriptional Regulation in Integrons
### Regulation of Integrase Transcription in MI and CI by Stress Response Mechanisms  
#### 2.5.1 The Role of SOS Response  
The SOS response is a complex regulatory network involved with DNA repair in response to damage or bypassing lesions, directly linked with adaptation and emergence of phenotypes clinically relevant [17; 18; 19; 99]. The LexA is the main transcriptional repressor that controls the SOS response, and the derepression of this system is associated with the RecA-dependent cleavage of LexA induced by the presence of abnormal rates of single-stranded DNA (ssDNA), which is a signal of genotoxic stress to the cell. The LexA binds specifically to a palindromic region of 16 bp located in the vicinity of the RNA polymerase binding site, blocking gene transcription by interfering with RNA polymerase activity [100]. Figure 7: The _blac_GS-1_/_aacA4_ fused cassette formation and their transcription dynamics. Truncation of GES-1_attC_ site involved with _blac_GS-1_/_aacA4_ fused cassette formation. Sequences of the complete and truncated GES-1_attC_ sites are shown. The _blac_GS-1 and _aacA4_ partial coding regions are underlined and in uppercase. The _attC_ sites are italicized, and their core sites (1L, 2L, 2R, 1R) are underlined and in bold. The transcription dynamics of _gcu14-blac_GS-1_/_aacA4_ gene cassette array. Transcription direction is represented by horizontal arrows. The scheme shows that all mRNA molecules originating from Pc promoter corresponded to _gcu14_ monocistronic or full-length polycistronic transcripts (curved lines), demonstrating that the fusion _blac_GS-1_/_aacA4_ is always transcribed together (bottom). Curiously, a conserved LexA-binding motif was identified overlapping the -10 hexamer of the integrase promoter region (P\({}_{\text{int}}\)) in both CIs and MIs (Figure 8) of clinical and environmental sources, and some studies experimentally determined that the LexA specifically binds to this motif in a large fraction of integrases [17; 19]. In fact, phylogenetic analysis indicated that the LexA regulation of _intl_ genes is ancient and that it is a widespread and conserved phenomenon among integrins [19]. It was demonstrated that in normal conditions, the LexA remained bound to its motif, avoiding the recruitment of RNA polymerase to P\({}_{\text{int}}\) and, therefore, repressing integrase transcription. However, upon induction of SOS response, the cleavage of LexA released the P\({}_{\text{int}}\) promoter, allowing integrase transcription. The in vitro assays revealed that this derepression by SOS induction resulted in a significant increase of excision rates by integrase (Figure 9). As aforementioned, the newly acquired cassettes in an integer are more efficiently expressed by the Pc promoter, which can become silenced by continuous integrase recombination events that move them to more distal positions in the array [2; 7]. Under steady-state conditions, SOS repression of _intl_ maintains the architecture of the existing cassette arrangement. However, the induction of SOS response by stressful conditions, such as DNA damage by the antibiotics ciprofloxacin, trimethoprim, \(\beta\)-lactams, and metronidazoleze, leads to antibiotic resistance emergence [100; 101; 102; 103; 104]. The induced SOS system upregulates the integrase expression when innovations and adaptation to novel situations are needed, ensuring cassette shuffling, which allows expression of previously silenced genes, and acquisition of new ones from the surrounding bacterial communities (Figure 9) [17]. Furthermore, the gene cassettes that have been temporarily silenced in distal positions may also contribute to bacterial evolution, since they represent a valuable source of variability, accounting for the spread of strains carrying cryptic resistance determinants [19; 104].