Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival

Megumi Nishinaga,Yudai Nishitani,Kouhei Tsumoto,Shigetoshi Aono,Satoru Nagatoishi,Takehiko Tosha,Seina Nagai,Hitomi Sawai,Yoshitsugu Shiro,Hiroshi Sugimoto,Norifumi Muraki

doi:10.1038/s42003-021-01987-5

Abstract

Hemes (iron-porphyrins) are critical for biological processes in all organisms. Hemolytic bacteria survive by acquiring b-type heme from hemoglobin in red blood cells from their animal hosts. These bacteria avoid the cytotoxicity of excess heme during hemolysis by expressing heme-responsive sensor proteins that act as transcriptional factors to regulate the heme efflux system in response to the cellular heme concentration. Here, the underlying regulatory mechanisms were investigated using crystallographic, spectroscopic, and biochemical studies to understand the structural basis of the heme-responsive sensor protein PefR from Streptococcus agalactiae, a causative agent of neonatal life-threatening infections. Structural comparison of heme-free PefR, its complex with a target DNA, and heme-bound PefR revealed that unique heme coordination controls a >20 Å structural rearrangement of the DNA binding domains to dissociate PefR from the target DNA. We also found heme-bound PefR stably binds exogenous ligands, including carbon monoxide, a by-product of the heme degradation reaction.

Highlights

IntroductionHemolytic bacteria survive by acquiring b-type heme from hemoglobin in red blood cells from their animal hosts
Hemes are critical for biological processes in all organisms
Fernandez et al reported that S. agalactiae PefR regulates the gene expression of two newly characterized operons, pefAB and pefRCD, which are involved in heme tolerance and homeostasis in S. agalactiae27,28. pefA and pefB were predicted to encode a drug: H+ antiporter and a functionally unknown protein, respectively, and pefC and pefD encode subunits of the ABC (ATP-binding cassette) multidrug exporter

Summary

Introduction

Hemolytic bacteria survive by acquiring b-type heme from hemoglobin in red blood cells from their animal hosts These bacteria avoid the cytotoxicity of excess heme during hemolysis by expressing heme-responsive sensor proteins that act as transcriptional factors to regulate the heme efflux system in response to the cellular heme concentration. We propose that after dissociating from the target DNA, the heme of holo-PefR can stably bind CO, which is a by-product of heme degradation by heme oxygenase These findings on a key protein required for the survival of the neonatal infection-causing hemolytic bacterium S. agalactiae might provide new leads for the development of antimicrobial agents effective against globally distributed drugresistant pathogens

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Conclusion