Transcriptome profiles with and without L-cysteine supplementation

CyuR (b0447, also known as DecR or YbaO) is a recently characterized transcription regulator responsible for the generation of hydrogen sulfide (H2S) from L-cysteine (Cys), which decreases oxidative stress. Given that mitigation of oxidative stress is an important survival mechanism to achieve antibiotic resistance (AR) in many pathogenic bacteria such as Escherichia coli and Salmonella enterica, detailed studies about its effect and the regulatory network of CyuR are imperative. In this study, we investigated the roles of CyuR and its regulon genes in a Cys-dependent AR mechanism in E. coli in a microaerobic condition. We show that (1) CyuR negatively controls the expression of mdlAB encoding a transporter that may export antibiotics. (2) Cys metabolism has a significant role in AR and its effect is conserved in many E. coli strains including clinical isolates. (3) CyuR binds ‘GAAwAAATTGTxGxxATTTsyCC’ in the absence of Cys found by performing an in vitro binding assay. (4) CyuR may regulate 14 genes, in addition to previously reported 2 genes, as we suggested by in silico motif scanning and transcriptome sequencing. Collectively, our findings confirm the significant roles of CyuR and its relevance to antibiotic resistance associated with Cys. Ribosomal RNA removed RNA prepared from cell cultures of E. coli W at the exponential phase.