Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors.

Saurabh Kumar Pandey,Rüdiger H Ettrich,Jannette Carey,David Řeha,Milan Melichercik

doi:10.3390/molecules25092247

Abstract

Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.

Highlights

Bacterial arginine repressor (ArgR) is the master regulator of the arginine regulon, sensing the intracellular concentration of L-arginine (L-arg) and exerting transcriptional control over synthesis of arginine biosynthetic and catabolic enzymes, including its own synthesis [1,2]
E. coli is the species with most available biochemical and genetic information in light of which structural data can be interpreted in terms of function, only separate N- and C-domain structures are available to date for E. coli ArgR, and a critical linker region implicated by genetic evidence is missing
The results presented here reveal that arginine repressors from E. coli and B. subtilis share a common global motion, a relative rotation of the two trimers comprising the hexamer, even though rotation is driven by different residues in distinct locations in the two proteins

Summary

Introduction

Bacterial arginine repressor (ArgR) is the master regulator of the arginine regulon, sensing the intracellular concentration of L-arginine (L-arg) and exerting transcriptional control over synthesis of arginine biosynthetic and catabolic enzymes, including its own synthesis [1,2]. E. coli is the species with most available biochemical and genetic information in light of which structural data can be interpreted in terms of function, only separate N- and C-domain structures are available to date for E. coli ArgR, and a critical linker region implicated by genetic evidence is missing. The structures and functions of all characterized ArgRs are essentially identical, their sequence identities are unexpectedly low. B. subtilis ArgR (BsArgR) can substitute for the function of E. coli ArgR (EcArgR) in vivo [6], but EcArgR and BsArgR share only ~27% sequence identity overall, with ~19% identity in the N-terminal domains, ~35% in the C-terminal domains, and distinct interdomain linker regions. Multiple alignment of EcArgR with sequences of available intact ArgR crystal structures produces results that misalign some of the secondary structures that define the highly conserved tertiary structures of the N- and C-terminal domains (Figure S1)

Methods

Results

Conclusion