Overlapping SigH and SigE sigma factor regulons in Corynebacterium glutamicum

0571654 - MBÚ 2024 RIV CH eng J - Journal Article
Busche, T. - Dostálová, Hana - Rucká, Lenka - Holátko, Jiří - Barvík, I. - Štěpánek, Václav - Pátek, Miroslav - Kalinowski, J.
Overlapping SigH and SigE sigma factor regulons in Corynebacterium glutamicum.
Frontiers in Microbiology. Roč. 13, FEB 28 (2023), č. článku 1059649. ISSN 1664-302X. E-ISSN 1664-302X
R&D Projects: GA ČR(CZ) GA17-06991S
Grant - others:AV ČR(CZ) DAAD-18-11
Program: Bilaterální spolupráce
Institutional support: RVO:61388971
Keywords : Corynebacterium * sigma factor * regulon * promoter * stress * consensus sequence * transcriptional start site * RNA-seq
OECD category: Microbiology
Impact factor: 5.2, year: 2022
Method of publishing: Open access
https://www.frontiersin.org/articles/10.3389/fmicb.2022.1059649/full

The sigma H (sigma(Eta)) and sigma E (sigma(E)) subunits of Corynebacterium glutamicum RNA polymerase belong to Group 4 of sigma factors, also called extracytoplasmic function (ECF) sigma factors. Genes of the C. glutamicum sigma(Eta) regulon that are involved in heat and oxidative stress response have already been defined, whereas the genes of the sigma(E) regulon, which is involved in cell surface stress response, have not been explored until now. Using the C. glutamicum RES167 strain and its derivative C. glutamicum Delta cseE with a deletion in the anti-sigma(Epsilon) gene, differential gene expression was analyzed by RNA sequencing. We found 296 upregulated and 398 downregulated genes in C. glutamicum Delta cseE compared to C. glutamicum RES167. To confirm the functional link between sigma(Epsilon) and the corresponding promoters, we tested selected promoters using the in vivo two-plasmid system with gfpuv as a reporter gene and by in vitro transcription. Analyses with RNAP+sigma(Eta) and RNAP+sigma(Epsilon), which were previously shown to recognize similar promoters, proved that the sigma(Eta) and sigma(E) regulons significantly overlap. The sigma(E)-controlled genes were found to be involved for example in protein quality control (dnaK, dnaJ2, clpB, and clpC), the regulation of Clp proteases (clgR), and membrane integrity maintenance. The single-promoter analyses with sigma(Eta) and sigma(Epsilon) revealed that there are two groups of promoters: those which are exclusively sigma(Eta)-specific, and the other group of promoters, which are sigma(Eta)/sigma(E)-dependent. No exclusively sigma(E)-dependent promoter was detected. We defined the consensus sequences of exclusively sigma(Eta)-regulated promotors to be35 GGAAt and 10 GTT and sigma(Eta)/sigma(E)-regulated promoters to be35 GGAAC and 10 cGTT. Fifteen genes were found to belong to the sigma(Eta)/sigma(Epsilon) regulon. Homology modeling showed that there is a specific interaction between Met170 in sigma(Eta) and the nucleotides31 and 30 within the non-coding strand (AT or CT) of the sigma(Eta)-dependent promoters. In sigma(E), Arg185 was found to interact with the nucleotides GA at the same positions in the sigma(E)-dependent promoters.
Permanent Link: https://hdl.handle.net/11104/0342865