Supervised clustering of bacterial promoter identifies two groups with different relevant positions at -10

Promoters are DNA sequences responsible for the specific recognition of the transcriptional machinery in all the biological systems. In bacteria, two main groups of promoters have been described, the σ70-like family, which includes the housekeeping σ70 and the alternative σ38, σ32, σ28, and σ24; and the σ54 family. However, promoter sequences may differ even inside the same family, and this classification may not fully capture the functional diversity of groups. In this work, we explored and classified a collection of bacterial promoters associated with six σ factor families in the bacterium Escherichia coli K-12 using a Supervised clustering workflow that uses Shapley values. From this analysis, we identified two subgroups of sequences differentiated by the conservation of the -9 to -7 positions upstream the Transcription Start Site, suggesting that this region may be employed in classification frameworks. Finally, a detailed analysis of σ70 promoter sequences identify five clusters with a conserved signal in the -10, but with different sequence composition. In summary, these signatures could provide more insights into the sigma factor-promoter interaction and the separation of the DNA double-strand.