HrrSA orchestrates a systemic response to heme and determines prioritization of terminal cytochrome oxidase expression

Abstract

<jats:title>Abstract</jats:title> <jats:p>Heme is a multifaceted molecule. While serving as a prosthetic group for many important proteins, elevated levels are toxic to cells. The complexity of this stimulus has shaped bacterial network evolution. However, only a small number of targets controlled by heme-responsive regulators have been described to date. Here, we performed chromatin affinity purification and sequencing to provide genome-wide insights into in vivo promoter occupancy of HrrA, the response regulator of the heme-regulated two-component system HrrSA of Corynebacterium glutamicum. Time-resolved profiling revealed dynamic binding of HrrA to more than 200 different genomic targets encoding proteins associated with heme biosynthesis, the respiratory chain, oxidative stress response and cell envelope remodeling. By repression of the extracytoplasmic function sigma factor sigC, which activates the cydABCD operon, HrrA prioritizes the expression of genes encoding the cytochrome bc1-aa3 supercomplex. This is also reflected by a significantly decreased activity of the cytochrome aa3 oxidase in the ΔhrrA mutant. Furthermore, our data reveal that HrrA also integrates the response to heme-induced oxidative stress by activating katA encoding the catalase. These data provide detailed insights in the systemic strategy that bacteria have evolved to respond to the versatile signaling molecule heme.</jats:p>

A pseudokinase version of the histidine kinase ChrS promotes high heme tolerance of Corynebacterium glutamicum

“…Export of further toxic heme-related products, or even import of neutralizing compounds coping with H 2 O 2 , like e.g., described for the ribulose-5-phosphate 3-epimerase in Escherichia coli or the Mn(II) uptake system of Neisseria gonorrhoeae importing manganese ( Horsburgh et al, 2002 ; Seib et al, 2004 ; Sobota and Imlay, 2011 ), could also aid at tolerating heme. Of special interest is e.g., the operon cg2675-cg2678, which encodes an ABC-type transport system and was found also to be regulated by the heme-responsive RR HrrA ( Keppel et al, 2020 ). Future studies on these systems, are however, required to elucidate their role in heme tolerance or homeostatic processes.…”

“…After sensing heme availability via intramembrane interaction ( Ito et al, 2009 ; Keppel et al, 2018 ), the TCS ChrSA acts as an activator of the hrtBA operon encoding the heme export system ( Heyer et al, 2012 ). In contrast, the paralogous TCS HrrSA is a global regulator of heme homeostasis controlling more than 200 genomic targets including inter alia genes involved in heme biosynthesis, respiration as well as hmuO , encoding heme oxygenase ( Keppel et al, 2020 ). Strikingly, a high level of cross-phosphorylation between the systems was observed ( Keppel et al, 2019 ), while phosphatase activity of these HKs remains specific to their cognate RR ( Hentschel et al, 2014 ).…”

“…ChrSA is solely responsible for the detoxification from heme via activating the hrtBA operon and autoregulates its own expression ( Heyer et al, 2012 ). The HrrSA system was recently shown to act as regulator for heme homeostasis, controlling hmuO as well as more than 200 further genes involved in heme biosynthesis, respiratory chain, oxidative stress, or cell envelope remodeling ( Keppel et al, 2020 ). The histidine kinases ChrS as well as HrrS undergo autophosphorylation in response to heme, activating the respective response regulator ChrA and HrrA.…”

The Transcriptional Regulatory Network of Corynebacterium pseudotuberculosis

“…The hrrA gene is part of the HrrSA TCS and it was differentially expressed in both C. pseudotuberculosis T1 and CP13 under iron starvation [ 43 ]. This system both activates the expression of a heme oxygenase ( hmuO gene) and represses genes acting in heme homeostasis in C. glutamicum and Corynebacterium diphtheriae [ 91 , 92 ], and is considered the global regulator of heme in C. glutamicum [ 93 ]. In this system the HrrS is the sensor kinase and the HrrA is the response regulator.…”

FNR-Type Regulator GoxR of the Obligatorily Aerobic Acetic Acid Bacterium Gluconobacter oxydans Affects Expression of Genes Involved in Respiration and Redox Metabolism

“…Quantification of the resulting libraries was performed with the KAPA library quantification kit as described above and sequenced on a MiSeq system (Illumina) using paired-end sequencing with a read length of 2 Â 150 bases. Mapping of the sequencing data and peak detection were performed with an analysis pipeline described recently for another transcriptional regulator (71). Briefly, mapping of the reads to the G. oxydans 621H reference genome (GenBank accession numbers NC_006672.1 to NC_006677.1) was performed using Bowtie2 (72) in local alignment mode with the following parameters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50.…”