Allosteric mechanism of MntR transcription factor from alkalophilic bacterium Halalkalibacterium halodurans

Abstract

Bacterium Halalkalibacterium halodurans is an industrially important alkalophilic bacteria. It is recognized as a producer of enzymes such as β-galactosidase, xylanase, amylase and protease which are able to function at higher pH values and thus can be used in textile, food, paper industry and more. This bacterium, as any other bacterium, requires a sensitive mechanism for regulation of homeostasis of manganese ions (Mn²⁺) in order to survive. The key protein regulating this mechanism in H. halodurans is MntR – a transcriptional factor that binds to DNA and regulates the transcription of genes for proteins involved in manganese homeostasis. Long range all-atom molecular dynamics (MD) simulations, from 500 ns up to 1.25 µs, were used to study different forms of H. halodurans MntR in order to investigate the differences in the protein’s structural and dynamical properties upon Mn²⁺ binding. Simulations revealed an allosteric mechanism which is activated by Mn²⁺ binding. The results of simulations show that Mn²⁺ binding alters the non-covalent interaction network of the protein structure which leads to a conformational change that primarily affects the positions of the DNA binding domains and, consequently, the DNA binding affinity of H. halodurans MntR. The key amino acid residues of the proposed mechanism were identified and their role in the proposed mechanism was computationally confirmed by MD simulations of in silico mutants.

Communicated by Ramaswamy H. Sarma

Keywords:

• Molecular dynamics
• Halalkalibacterium halodurans
• manganese homeostasis
• manganese transport regulator (MntR)
• non-covalent interaction network

Acknowledgments

This study was supported by the Croatian Science Foundation, project ‘Manganese Metallosensors’, project number IP-2020-02-3446. We thank the Zagreb University Computing Centre (SRCE) for providing computational resources available at computer cluster Isabella.

Disclosure statement

The authors declare no conflict of interest. They have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article.

Additional information

Funding

This research was funded by the Croatian Science Foundation, project “Manganese metallosensors” project number IP-2020-02-3446.