Structural study to analyze the DNA-binding properties of DsrC protein from the dsr operon of sulfur-oxidizing bacterium Allochromatium vinosum.

Abstract

Our environment is densely populated with various beneficial sulfur-oxidizing prokaryotes (SOPs). These organisms are responsible for the proper maintenance of biogeochemical sulfur cycles to regulate the turnover of biological sulfur substrates in the environment. Allochromatium vinosum strain DSM 180T is a gamma-proteobacterium and is a member of SOP. The organism codes for the sulfur-oxidizing dsr operon, which is comprised of dsrABEFHCMKLJOPNRS genes. The Dsr proteins formed from dsr operon are responsible for formation of sulfur globules. However, the molecular mechanism of the regulation of the dsr operon is not yet fully established. Among the proteins encoded by dsr genes, DsrC is known to have some regulatory functions. DsrC possesses a helix-turn-helix (HTH) DNA-binding motif. Interestingly, the structural details of this interaction have not yet been fully established. Therefore, we tried to analyze the binding interactions of the DsrC protein with the promoter DNA structure of the dsr operon as well as a random DNA as the control. We also performed molecular dynamics simulations of the DsrC-DNA complexes. This structure-function relationship investigation revealed the most probable binding interactions of the DsrC protein with the promoter region present upstream of the dsrA gene in the dsr operon. As expected, the random DNA structure could not properly interact with DsrC. Our analysis will therefore help researchers to predict a plausible biochemical mechanism for the sulfur oxidation process. Graphical Abstract Interaction of Allochromatium vinosum DsrC protein with the promoter region present upstream of the dsrA gene.