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Characterization of a Minimal Type of Promoter Containing the −10 Element and a Guanine at the −14 or −13 Position in Mycobacteria

ABSTRACT Three key promoter elements, i.e., −10, −35, and T−15G−14N, are recognized by the σ subunit of RNA polymerase. Among them, promoters with the −10 element and either −35 or T−15G−14N are known to initiate transcription efficiently, but recent systematic analyses have identified a large group of promoters in Mycobacterium tuberculosis that contain only a −10 consensus. How these promoters initiate transcription remains poorly understood. Here, we show that promoters containing the −10 element and an upstream G located at the −14 or −13 position can successfully initiate transcription in mycobacteria. Importantly, this new type of promoter is active in the absence of other promoter consensuses, suggesting that it is a minimal promoter type. Mutation of the upstream G in promoters decreased the efficiencies of their binding with RNA polymerase and their abilities to initiate transcription in both in vitro and in vivo analyses. A glutamic acid in σ region 3.0 is essential for recognizing G−14 and G−13 and is conserved in both principal and principal-like σ factors in mycobacteria, indicating that recognition of this minimal type of promoter might be a common mechanism for transcription initiation. Consistently, more than 70% of the identified promoters in M. tuberculosis contained G−14 or G−13 upstream of the conserved −10 element, and thousands of promoters in representative mycobacterial species have been predicted using the −10 consensus and G−14 or G−13. Altogether, our study presents a universal mechanism for transcription initiation from a minimal promoter in mycobacteria, which might also be applicable to other bacteria. IMPORTANCE In contrast to the detailed information for recognizing classic promoters in the model organism Escherichia coli, very little is known about how transcription is initiated in the human pathogen Mycobacterium tuberculosis. In this study, we characterized a new type of promoter in mycobacteria that requires only a −10 consensus and an upstream G−14 or G−13. Residues important for recognizing the −10 element and the upstream G are conserved in σA and σB from mycobacterial species. According to such features, thousands of promoters in mycobacteria can be predicted using the −10 consensus and G−14 or G−13, which suggests that transcription from this new type of promoter might be widespread. Our findings provide insightful information for characterizing promoters in mycobacteria.