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Background  The σ 54  factor controls unique promoters and interacts with a specialized activator (enhancer binding proteins [EBP]) for transcription initiation. Although σ 54  is present in many  Clostridiales  species that have great importance in human health and biotechnological applications, the cellular processes controlled by σ 54  remain unknown.    Results  For systematic analysis of the regulatory functions of σ 54 , we performed comparative genomic reconstruction of transcriptional regulons of σ 54  in 57 species from the  Clostridiales  order. The EBP-binding DNA motifs and regulated genes were identified for 263 EBPs that constitute 39 distinct groups. The reconstructed σ 54  regulons contain the genes involved in fermentation and amino acid catabolism. The predicted σ 54  binding sites in the genomes of  Clostridiales  spp. were verified by in vitro binding assays. To our knowledge, this is the first report about direct regulation of the Stickland reactions and butyrate and alcohols synthesis by σ 54  and the respective EBPs. Considerable variations were demonstrated in the sizes and gene contents of reconstructed σ 54  regulons between different  Clostridiales  species. It is proposed that σ 54  controls butyrate and alcohols synthesis in solvent-producing species, regulates autotrophic metabolism in acetogenic species, and affects the toxin production in pathogenic species.    Conclusions  This study reveals previously unrecognized functions of σ 54  and provides novel insights into the regulation of fermentation and amino acid metabolism in  Clostridiales  species, which could have potential applications in guiding the treatment and efficient utilization of these species.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5918-4) contains supplementary material, which is available to authorized users.

Genomic reconstruction of σ54 regulons in Clostridiales