## 2 Transcriptional Regulation in Integrons
### Integrase Expression in Class 2 Integrons  
Although studies focusing on the transcription dynamics of integrase belonging to other integron classes are scarce, some interesting features concerning class 2 integrase regulation had been addressed. [PERSON] et al. [48] had identified that the class 2 integrase promoter sequence \(\mathrm{P_{intI2}}\) was found 40 bp upstream _intI2_ start codon. The _intI2_ transcription start site and a potential ribosomal binding site (RBS) were mapped 8 bp and 28 bp downstream this \(\mathrm{P_{intI2}}\), respectively. It was observed a potential LexA binding site overlapping \(\mathrm{P_{intI2}}\), suggesting that class 2 integrase activity could also be controlled by the SOS regulon, such as _intI1_ and _intIA_ from the class 1 integron and the _V. cholerae_ CI [17; 19]. However, [PERSON] et al. [48] experimentally demonstrated that, in spite of the presence of a LexA binding site in \(\mathrm{P_{intI2}}\), the _intI2_ expression is not regulated by the SOS response. This putative LexA box carried additional polymorphisms in its central region, which may prevent the LexA binding in this site. Moreover, as aforementioned, the functional Pc2 cassette promoters (Pc2A and Pc2B) are found embedded in _attI2_, and not within _intI2_. So, in this case, Pc2 and \(\mathrm{P_{intI2}}\) are arranged tail-to-tail, in a way that no transcriptional interference would take place. Thus, considering this regulatory scenario, neither LexA nor transcription interference would influence _intI2_ transcription, which should be constitutively expressed. [PERSON] et al. [19] correlated the lack of LexA repressor activity and the presence of inactive IntI enzymes, which probably evolved to avoid the deleterious effects of a constitutively expressed integrase. Therefore, the same correlation can be established for _intI2_, since class 2 integrons normally encode an inactive truncated gene, due to the occurrence of a premature ochre STOP codon (TAA) at position 179 [46]. Conversely, class 2 integrons coding a complete and functional integrase are rarely found, which could be related to a high fitness burden associated with the constitutive expression of _intl2_, since it is devoid of the tight regulation of the SOS system. Additionally, these rare functional class 2 integrins are associated with Pc2 cassette promoter variants (Pc2A-V2 and Pc2B-V2; see above in Section 2.1.2) less efficient in promoting gene cassette transcription. This inverse correlation is the same observed for class 1 integrins, in which weak the Pc variants determine more efficient integrases [26]. Therefore, class 2 integrins are defined by two categories. The most prevalent group carries the Pc2A and Pc2B promoters, which efficiently express a restricted subset of gene cassettes but is incapable of promoting gene cassette innovation due to an inactive integrase. On the other hand, the uncommon category codes a functional integrase that allows novel gene cassette acquisitions but transcribes gene cassettes inefficiently. Based on this evidence, it was proposed that the absence of LexA-mediated _intl2_ repression led the selection of mutations that resulted in the integrase inactivation or production of weak Pc configurations, reducing the integrin fitness burden [48].