coli strains (Michel et al, 2007) Group II introns in bacteria

coli strains (Michel et al., 2007). Group II introns in bacteria are usually found only in mobile elements such as transposons (Martinez-Abarca & Toro, 2000). The sequence downstream of aidA reveals the 3′-end of another ORF. The 415-nucleotide sequence is 97% identical to the sequence of a putative large inner membrane associated with a Tn1-transposon. It is therefore highly likely that the aah-aida operon is located within a mobile genetic element. In order to map the beginning of the transcript starting upstream Apoptosis inhibitor of aah, we performed an RT-PCR

on RNA extracted from a culture of 2787 at an OD600 nm of 2.0 using forward primers hybridizing 43, 63, 194 or 247 nucleotides upstream of the aah start codon and a reverse primer hybridizing 140 nucleotides downstream of the start codon. The amplification was successful with the first two forward primers and failed with the last two (data not shown). Controls performed without reverse transcription ensured that there was no DNA contamination in our reactions. This result suggested Selleckchem Akt inhibitor that a transcription start lies between 63 and 194 nucleotides upstream of aah. We then performed 5′ RACE reactions using mRNA extracted from cultures of 2787 at an OD600 nm of 0.7 (mid-log phase) or 2.0 (early-stationary phase). Using aah-specific primers, we obtained one major fragment with both mRNA preparations.

When we performed 5′ RACE reactions with aidA-specific primers, we did not obtain any amplification fragment. ADP ribosylation factor These results suggest that the aah-aidA operon is transcribed as a bicistronic mRNA. The sequences of the fragments amplified with the aah primers were identical and revealed a transcription start 149 nucleotides upstream of the aah start codon (Fig. 1, P149). Analysis of the sequence upstream of this transcription start revealed a putative −10 sequence with the sequence ACTATATTAA, but no −35 sequence. The ACTATATTAA sequence matches the RpoS-specific −10 consensus sequence, and RpoS-controlled promoters are known to have no −35 consensus sequence (Weber et al., 2005). Our results therefore

suggest that the P149 promoter is RpoS dependent. Examination of the sequence chromatograms showed another putative, but weaker transcription start 128 nucleotides upstream of the aah start codon (Fig. 1, P128). Analysis of the sequence upstream of this transcription start revealed putative −10 and −35 sequences. These sequences weakly matched the consensus of RpoD-controlled promoters and are only 15 nucleotides apart. The promoter is therefore expected to be weak, which could explain why the transcript resulting from P128 appeared to be weaker than the one resulting from P149. A number of RpoS-controlled genes are also transcribed by RpoD through overlapping promoter sequences (Bordes et al., 2000). Our work suggests that this is also the case for the aah-aidA operon.

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