Accepted_test

Phylogenetic analysis and molecular dynamic simulations of CsqR, a transcription factor from Escherichia coli

by Rybina A. A. | Glushak R. A. | Bessonova T. A. | Dakhnovets A. I. | Rudenko A. Y. | Ozhiganov R. M. | Kaznadzey A. D. | Tutukina M. N | Gelfand M. S. | Skolkovo Institute of Science and Technology, Moscow, Russia | Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia | Institute of Cell Biophysics RAS (Federal Research Center “Pushchino Scientific Center for Biological Research RAS”), Pushchino, Russia | Skolkovo Institute of Science and Technology, Moscow, Russia | Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia | Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia | Institute for Information Transmission Problems RAS, Moscow, Russia | Skolkovo Institute of Science and Technology, Moscow, Russia | Skolkovo Institute of Science and Technology, Moscow, Russia

Abstract ID: 599

Event: BGRS-abstracts

Sections: [Sym 5] Section “Molecular phylogenetics and phylogenomics of Plants, Fungi, Protists, Prokaryotes and Viruses”

The study focuses on CsqR, a local transcription factor in Escherichia coli responsible for regulating the expression of yih genes involved in sulfoquinovose (SQ) degradation. Previous research suggested a potential regulatory role of lactose on these genes. SQ and its derivatives, sulfoquinovosyl glycerol (SQG) and sulforhamnose (SR), were identified as putative effectors of CsqR. The investigation aimed to explore CsqR evolution and its interaction patterns with SQ, SR, SQG, and lactose.

Phylogenetic analysis indicated the presence of CsqR homologs across Actinobacteria and Proteobacteria. The structure of the tree suggested a duplication event. CsqR homologs in Enterobacteriales species exhibited a conserved Met25 residue suggesting existence of CsqR as two protein variants: a full-length version (CsqR-l) and a shorter one (CsqR-s). Western blot analysis confirmed the existence of these variants, with CsqR-s being activated significantly during growth with SQ as the sole carbon source.

CsqR-s might have two potential structural arrangements, with the interdomain linker appearing either as a disordered loop or an α-helix. This helix allowed the N-terminal domain to rotate in a hinge-like motion, resulting in the transition of CsqR-s between two conformations referred to as "open" and "compact". Molecular docking suggested that CsqR-s might better discriminate between ligands and other compounds compared to CsqR-l.

The findings suggest that CsqR might exist in two protein forms, which is quite rare for transcription factors in bacteria.