## 2 Transcriptional Regulation in Integrons
### The Role of Pc Promoters on Gene Cassette Transcription
#### 2.1.1 Pc Promoters in Class 1 Integrons
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Pc Variant 1** & **–35** & **Spacer** & **–10** & **Transcription** & **Reference** \\  & **Sequence** & **Region (bp)** & **Sequence** & **Strength 2** & \\ \hline \multicolumn{5}{c}{Pc variants with polymorphisms inside -35 and -10 regions} \\ \hline PcS & TTGACA & 17 & TA\(\Delta\)ACT & 1240 & [2; 3; 26; 28] \\ PcH2 & TTGACA & 17 & TA\(\Delta\)GCT & 840 & [26; 27; 28] \\ PcH1 & TGGACA & 17 & TA\(\Delta\)ACT & 220 & [2; 3; 26; 28] \\ PcSS & TTGATA & 17 & TA\(\Delta\)ACT & 100 & [26; 38] \\ PcPUO & TGGACA & 17 & TA\(\Delta\)ACT & 60 & [26; 35] \\ PcW & TGGACA & 17 & TA\(\Delta\)GCT & 40 & [2; 36; 28] \\ PcH42 & TTTGCA & 17 & TA\(\Delta\)ACT & 40 & [26; 36] \\ PcLn116 & TTGACA & 17 & TGA\(\Delta\)ACT & 10 & [26; 37] \\ \hline \multicolumn{5}{c}{Pc variants with polymorphisms upstream the -10 region} \\ \hline PcSIGN-10 & TTGACA & 17 & (IGN)TAAGCT & 1160 & [26] \\ PcH2 IGN-10 & TTGACA & 17 & (IGN)TAAGCT & 860 & [26] \\ PcWIGN-10 & TGGACA & 17 & (IGN)TAAGCT & 720 & [26; 39] \\ PcH1 TIN-10 & TGGACA & 17 & (TTN)TA\(\Delta\)ACT & 375 & [26] \\ PcW\({}_{\text{TAN-10}}\) & TGGACA & 17 & (TAN)TA\(\Delta\)GCT & undetectable & [26] \\ \hline \multicolumn{5}{c}{Pc variants combined with P2} \\ \hline PcS & TTGACA & 17 & TA\(\Delta\)ACT & 1000 & [26; 28] \\ + P2 & TTGITA & 17 & TA\(\Delta\)GCT & \\ PcW\({}_{\text{TGCN-10}}\) & TGGACA & 17 & (TGNT)TAAGCT & 620 & [26] \\ + P2 & TTGITA & 17 & TA\(\Delta\)GCT & 380 & [26; 28] \\ PcW & TGGACA & 17 & TA\(\Delta\)GCT & 340 & [2; 3; 26; 28] \\ + P2 & TTGITA & 17 & TA\(\Delta\)GCT & \\ \hline \multicolumn{5}{c}{Pc variants combined with P2 variants} \\ \hline PcW\({}_{\text{TGCN-10}}\) & TGGACA & 17 & (IGN)TAAGCT & NP & [26] \\ + P2m1 & TTGITA & 17 & GACAGT & NP & [26] \\ PcH1 & TGGACA & 17 & TA\(\Delta\)ACT & NP & [26] \\ + P2m1 & TTGITA & 17 & TACACAC & NP & [26] \\ PcW & TGGACA & 17 & TA\(\Delta\)GCT & \\ + P2m3 & TTGITA & 17 & TA\(\Delta\)GCT & 720 & [29] \\ \hline \hline \end{tabular} \({}^{\dagger}\) Underlined bases represent the polymorphisms relative to \(\sigma^{70}\) consensus promoter from _Escherichia coli_ –35 TTGACA (16–18 bp) –10 TATAAT [3]. \({}^{2}\) Relative transcription strengths values were estimated by measuring the \(\beta\)-galactosidase activity of Pc-\(lacZ\) transcriptional fusions as reported in reference [26]. NP, not performed.  
\end{table} 
Table 2: Genetic and functional features of Pc and P2 variants and the different Pc + P2 combinations in class 1 integrins. Nucleotide modifications other than those found in -35 and -10 hexamers of Pc also contribute to variations in transcription efficiencies. A previous study demonstrated that the occurrence of a C/G mutation close to the -10 hexamer of PcW (2 bp upstream) was able to increase transcription of inserted gene cassettes. This mutation extended the -10 motif (TGN), which enhances transcription efficiency of _E. coli_\(\sigma^{70}\) promoters, creating a new promoter variant named PcW\({}_{\text{TGN-10}}\)[26; 39; 40]. Although rare, such TGN-10 motif has also been found in association with PcS and PcH2 [26; 34]. Two other Pc variants were raised from additional mutations upstream -10 hexamer. They were designated PcW\({}_{\text{TAN-10}}\) and PcH1\({}_{\text{TNN-10}}\), which presented the C/A and C/T mutations, respectively, 2 bp upstream -10 region, and both variants seem to be extremely rare [26; 40]. Additionally to Pc, a second promoter, named P2, is found 119 bp downstream from Pc in all integrins (Table 2), however, in most cases, this promoter is inactive due to a short spacer region (14 bp instead of 17 bp). In some integrins, insertion of three G residues increases the P2 spacer region from 14 to 17 bp, generating a functional promoter [3]. This active P2 is almost exclusively found in association with PcW (PcW + P2) and accounts for 90% of transcription when this version is present [2; 3].