Quaternary Structure and Deoxyribonucleic Acid-Binding Properties of the Heme-Dependent, CO-Sensing Transcriptional Regulator PxRcoM
- Matthew R. Dent
- Madeleine G. Roberts
- Hannah E. BowmanHannah E. BowmanDepartment of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United StatesMore by Hannah E. Bowman
- Brian R. Weaver
- Darrell R. McCaslinDarrell R. McCaslinBiophysics Instrumentation Facility, Department of Biochemistry, University of Wisconsin−Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United StatesMore by Darrell R. McCaslin
- , and
- Judith N. Burstyn*
RcoM, a heme-containing, CO-sensing transcription factor, is one of two known bacterial regulators of CO metabolism. Unlike its analogue CooA, the structure and DNA-binding properties of RcoM remain largely uncharacterized. Using a combination of size exclusion chromatography and sedimentation equilibrium, we demonstrate that RcoM-1 from Paraburkholderia xenovorans is a dimer, wherein the heme-binding domain mediates dimerization. Using bioinformatics, we show that RcoM is found in three distinct genomic contexts, in accordance with the previous literature. We propose a refined consensus DNA-binding sequence for RcoM based on sequence alignments of coxM-associated promoters. The RcoM promoter consensus sequence bears two well-conserved direct repeats, consistent with other LytTR domain-containing transcription factors. In addition, there is a third, moderately conserved direct repeat site. Surprisingly, PxRcoM-1 requires all three repeat sites to cooperatively bind DNA with a [P]1/2 of 250 ± 10 nM and an average Hill coefficient, n, of 1.7 ± 0.1. The paralog PxRcoM-2 binds to the same triplet motif with comparable affinity and cooperativity. Considering this unusual DNA binding stoichiometry, that is, a dimeric protein with a triplet DNA repeat-binding site, we hypothesize that RcoM interacts with DNA in a manner distinct from other LytTR domain-containing transcription factors.
This article is cited by 1 publications.
- Marten H. Vos, Mayla Salman, Ursula Liebl. Early processes in heme-based CO-sensing proteins. Frontiers in Molecular Biosciences 2022, 9 https://doi.org/10.3389/fmolb.2022.1046412