Identification of genome-wide distribution of cyanobacterial group 2 sigma factor SigE accountable for its regulon

Abstract

Sigma factors are the subunits of bacterial RNA polymerase that govern the expression of genes by recognizing the promoter sequence. Cyanobacteria, which are oxygenic phototrophic eubacteria, have multiple alternative sigma factors that respond to various environmental stresses. The subgroup highly homologous to the primary sigma factor (SigA) is called the group 2 sigma factor. The model cyanobacterium, Synechocystis sp. PCC 6803, has four group 2 sigma factors (SigB-E) conserved within the phylum Cyanobacteria. Among the group 2 sigma factors in Synechocystis sp. PCC 6803, SigE is unique because it alters metabolism by inducing the expression of genes related to sugar catabolism and nitrogen metabolism. However, the features of promoter sequence of the SigE regulon remains elusive. Here, we identified the direct targets of SigA and SigE by chromatin immunoprecipitation sequencing (ChIP-seq). We then showed that the binding sites of SigE and SigA overlapped substantially, but SigE exclusively localized to SigE-dependent promoters. We also found consensus sequences from SigE-dependent promoters and confirmed their importance. ChIP-seq analysis showed both the redundancy and specificity of SigE compared with SigA, integrating information obtained from a previously adopted genetic approach and in vitro assays. The features of SigE elucidated in our study indicate its similarity with group 2 sigma factors of other bacteria, even though they are evolutionally irrelevant. Our approach is also applicable to other organisms and organelles, such as plant plastids, which have multiple group 2 sigma factors. ImportanceGroup 2 sigma factors are alternative sigma factors highly homologous to primary sigma factors. Cyanobacteria, which are photosynthetic eubacteria, are unique because they have multiple group 2 sigma factors. Although each sigma factor induces the expression of specific genes, the redundancy and complicated network of the primary and group 2 sigma factors hinder the identification of their regulons via a genetic approach. Here, we identified the binding sites of SigE (group 2 sigma factor) and SigA (primary sigma factor) using chromatin immunoprecipitation sequencing and identified the minimal element of SigE-dependent promoters by subsequent promoter assays. Our study provides insights into the common features of group 2 sigma factors, which, though evolutionarily irrelevant, are widespread among eubacteria and plant plastids.