Rewiring the specificity of extracytoplasmic function sigma factors

Abstract

Bacterial genomes are being sequenced at an exponentially increasing rate, but our inability to decipher their transcriptional wiring limits our ability to derive new biology from these sequences. De novo determination of regulatory interactions requires accurate prediction of regulators’ DNA binding and precise determination of biologically significant binding sites. Here we address these challenges by solving the DNA-specificity code of extracytoplasmic function sigma factors (ECF σs), a major family of bacterial regulators, and determining their putative regulons. We generated an aligned collection of ECF σs and their promoters by leveraging the autoregulatory nature of ECF σs as a means of promoter discovery and analyzed it to identify and characterize the conserved amino acid–nucleotide interactions that determine promoter specificity. This enabled de novo prediction of ECF σ specificity, which we combined with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to predict the direct targets of ∼67% of ECF σs. This global survey indicated that some ECF σs are conserved global regulators controlling many genes throughout the genome, which are important under many conditions, while others are local regulators, controlling a few closely linked genes in response to specific stimuli in select species. This analysis reveals important organizing principles of bacterial gene regulation and presents a conceptual and computational framework for deciphering gene regulatory networks.

Multi-Omic Analyses Reveal Habitat Adaptation of Marine Cyanobacterium Synechocystis sp. PCC 7338

“…On the other hand, the region 2 sequence of HTZ78_05385 was close to an ECF sigma factor of another marine cyanobacteria, Nodularia spumigena , inferring the function of HTZ78_05385 is related to the adaptation to marine environment. Considering the promoter motifs predicted for clusters of ECF sigma factors, which had been clustered by region 2 and region 4 sequences in the previous study, we found 5′-GTC of − 10 motif and 5′-GGAAC of − 35 motif for SigG, and the extended − 10 and − 35 motifs for SigH; SigI and HTZ78_05385 were predicted to have 5′-CGTA of − 10 motif and 5′-CATCC of − 35 motif, which are distinctive from those of SigG and SigH ( Supplementary Figure 2C ) ( Todor et al, 2020 ).…”

“…The SigG and other ECF sigma factors (SigH, SigI, and HTZ78_05385) were further analyzed to investigate their functions in stress responses. The amino acid sequences of region 2 and region 4, which are the conserved domains of ECF sigma factors, were aligned with previously known bacterial ECF sigma factors ( Todor et al, 2020 ). In results, it was revealed that both region 2 and region 4 sequences of SigG, SigH, and SigI of Synechocystis sp.…”

“…PCC 6803 and Synechocystis sp. PCC 6714 ( Supplementary Figure 2B ) ( Todor et al, 2020 ). On the other hand, the region 2 sequence of HTZ78_05385 was close to an ECF sigma factor of another marine cyanobacteria, Nodularia spumigena , inferring the function of HTZ78_05385 is related to the adaptation to marine environment.…”

Extracytoplasmic Function σ Factors as Tools for Coordinating Stress Responses

“…These specific ECF-promoter interactions at the -35 and -10 boxes have been recently explored to implement a tool for promoter prediction based on the amino acid composition of key DNA contact points within the σ 2 and σ 4 domains [50]. Its application has allowed the prediction of target regulons of nearly 70% of the known ECFs and established that around 55% of them are autoregulated.…”

“…Altogether, this improvement in the classification will generally improve the ability of the scientific community to predict the function of newly annotated ECFs. Thus, it will help to: (i) define their target promoters based on over-represented motifs in those that are autoregulated, (ii) determine functionally important residues for this recognition and (iii) develop predictive tools to define target promoters, especially for those ECFs that are not autoregulated (a matter that has already started to be addressed [50]). Furthermore, a continuous update is guaranteed with the constantly increasing number of bacterial genome sequences.…”