For region upstream from the arp2 gene (B), horizontal lines below learn more the sequences delimitate the putative stems regions and dashed lines indicate the loop part. To determine which genes were co-transcribed, RT-PCR amplification of core region was performed by grouping ORFs two by two or three by three. For ICESt1, amplifications of orfR/arp1/orfQ and orfP/arp2, respectively, were positive while that of the orfQ/orfP junction was negative (see additional file 1: S1B). These data comfort the hypothesis of a two-operon organization for ICESt1 (see additional file 1: S1A) with a functional rho-independent transcription

terminator located between the two operons. By contrast, for ICESt3, all the RT-PCR amplifications of the regulation module were positive (see additional file 1: S1D) indicating a co-transcription of all the regulation genes (see additional file 1: S1C). The free energy of the transcriptional terminator detected between orf385B and orfQ genes in ICESt3 (Figure 1) was calculated with the mFold software [19]. It is different from the one for ICESt1 (ΔG = -4.3 kcal.mol-1 for ICESt3 and ΔG = -8.2 kcal.mol-1 for ICESt1). This difference could explain why all genes of the regulation module of ICESt3 can be co-transcribed while two independent transcriptional units were found in ICESt1. We then examined the

activity of the promoter located upstream from the orfQ gene by Rapid Amplification of cDNA ends (5′ RACE). For both elements, the start point (A nucleotide) was located seven nucleotides downstream from a -10 box separated by 17 nt PX-478 mouse from a -35 box, which overlapped the rho-independent transcription terminator (Figure 1A). This result is consistent with the S. thermophilus promoter consensus sequence (TTGACA – 17 nt – TATAAT) [20]. Therefore, both ICEs possess a functional PorfQ promoter. However, it was previously showed that ICESt3 differs from ICESt1 by a -1 frameshift in the 5′ end of its orfQ gene (orfQ1) [11]. A second RBS, that could enable the translation from an initiation codon located downstream, was identified in silico (Figure 1A). All together, buy Staurosporine these data suggest that

the orfQ2 gene of ICESt3 is truncated of 54 nucleotides at its 5′ end compared to the orfQ gene of ICESt1. All RT-PCR amplifications targeting co-transcription of the sixteen conjugation-recombination genes of ICESt1 and ICESt3 gave amplicons (see additional file 1: S1B and S1D). Therefore, these genes are transcribed as a single polycistronic mRNA of about 14.6 kb (see additional file 1: S1A and S1C). To map more precisely the 5′ end of these transcripts, other sets of primers were designed in the arp2/orfN intergenic region. For ICESt1, these results (data not shown) combined with 5′ RACE experiments confirmed the predicted conjugation-recombination promoter, Pcr, with a -10 box (TATAAT) located seven nucleotides upstream from the transcription start point (A) nucleotide (Figure 1B).