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bioRxiv · 10.1101/2021.01.08.426013

Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains

Gao, Y.·Poudel, S.·Seif, Y.·Shen, Z.·Palsson, B. O.
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Abstract

CodY is a conserved broad acting transcription factor that regulates the expression of genes related to amino acid metabolism and virulence in methicillin-resistant Staphylococcus aureus (MRSA). CodY target genes have been studied by using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). Here we performed the first in vivo determination of CodY target genes using a novel CodY monoclonal antibody in established ChIP-exo protocols. Our results showed, 1) the same 135 CodY promoter binding sites regulating 165 target genes identified in two closely related virulent S. aureus USA300 TCH1516 and LAC strains; 2) The differential binding intensity for the same target genes under the same conditions was due to sequence differences in the same CodY binding site in the two strains; 3) Based on transcriptomic data, a CodY regulon comprising 72 target genes that are differentially regulated relative to a CodY deletion strain, representing genes that are mainly involved in amino acid transport and metabolism, inorganic ion transport and metabolism, transcription and translation, and virulence; and 4) CodY systematically regulated central metabolic flux to generate branched-chain amino acids (BCAAs) by mapping the CodY regulon onto a genome-scale metabolic model of S. aureus. Our study performed the first system-level analysis of CodY in two closely related USA300 TCH1516 and LAC strains giving new insights into the similarities and differences of CodY regulatory roles between the closely related strains. ImportanceWith the increasing availability of whole genome sequences for many strains within the same pathogenic species, a comparative analysis of key regulators is needed to understand how the different strains uniquely coordinate metabolism and expression of virulence. To successfully infect the human host, Staphylococcus aureus USA300 relies on the transcription factor CodY to reorganize metabolism and express virulence factors. While CodY is a known key transcription factor, its target genes are not characterized on a genome-wide basis. We performed a comparative analysis to describe the transcriptional regulation of CodY between two dominant USA300 strains. This study motivates the characterization of common pathogenic strains and an evaluation of the possibility of developing specialized treatments for major strains circulating in the population.

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Gao, Y., Poudel, S., Seif, Y., Shen, Z., Palsson, B. O.. 2021-01-09. Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains. https://doi.org/10.1101/2021.01.08.426013

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