Transcriptional landscape variability within the bacterial oppA-oppB intergenic region as revealed by computational search for the potential starts of RNA synthesis

Integral membrane proteins OppB and OppC, comprising the backbone of oligopeptide bacterial ABC-transporters, are still unexplored in terms of expressional regulation of corresponding genes. The possibility of oppB transcription from additional promoters located between oppA and oppB within the oppABCDF operon was investigated using the unified promoter-search algorithm (PlatPromU) for 13 genomes of bacteria representing different taxonomic groups. Similar patterns in the distribution of potential transcription start sites have been revealed for Enterobacteriales, while unusual intergenic region oversaturated with potential promoters (“promoter island”) was found in Bifidobacterium dentium. Phylogenetic analysis and search for nucleotide motifs homologous to this “promoter island” suggest that a part of this sequence was acquired by the regulatory region of Bifidobacterium dentium oppB laterally transferred from the coding region of the gene of evolutionary distant Geobacillus thermodenitrificans GNTG_2042. This integration can trigger the formation of an extended "promoter island", which in this case was aimed to optimize the expression of the own gene oppB of Bifidobacterium dentium, rather than to the assimilation of the novel gene.