Characterization of an ECF56-family sigma factor fromStreptomyces venezuelaereveals a highly conserved regulome

Abstract

34Bacteria often possess alternative sigma factors that initiate the transcription of 35 specific genes under environmental stresses, the largest and most diverse group being 36 the extracytoplasmic function (ECF) sigma factors. The regulation of ECF activity is 37 crucial for ensuring the distinct transcription of stress responsive genes only occurs 38 under the appropriate conditions. While most ECFs are comprised of only the core σ 2 39 and σ 4 regions, a unique form of ECF sigma factor regulation also contains a C-terminal 40 extension bearing homology to the NTF2 superfamily of protein domains. While 41 previous work has shown that this NTF2 domain can affect transcriptional activity in vivo 42 in ECF41 and ECF42, its role in the newly classified ECF56 subgroup is unknown. In 43 this work, we show that truncation of the C-terminus of the ECF56 sigma factor 44 SVEN_4562 of Streptomyces venezuelae upregulates its activity in a hybrid assay. 45 Through transcriptomics in S. venezuelae, we found that this truncated ECF56 sigma 46 factor has a highly conserved promoter sequence in vivo. Bioinformatic assays 47 ECF56 family of sigma factors is highly conserved and performs important functions yet 53 to be understood in Actinobacteria. 54 55 Importance 56 Most ECF sigma-factors rely on anti-sigma factor regulation; in contrast, the 57 unique classes of ECF sigma-factors that contain a C-terminal extension are thought to 58 respond directly to an environmental signal. Here we show that the cis-acting regulatory 59 element of the ECF56 regulon is likely highly conserved in many Actinobacteria, with 60 exact nucleotide level conservation over ~2 billion years of evolution. The high 61 conservation of this genetic architecture, as well as a conserved gene content within the 62 regulon, strongly point to a specialized and important role in Actinobacteria biology. 63 64