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 cyanobacteriumSynechocystis sp. PCC 6803 has four group-2 sigma factors (SigB-SigE) 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 the promoter sequences of the SigE regulon remain 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 that SigE localized exclusively 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 the 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 evolutionarily irrelevant. Our approach is also applicable to other organisms and organelles, such as plant plastids, which have multiple group-2 sigma factors.