The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins

• Published in: Nature communications Vol. 13; no. 1; pp. 2883 - 18
• Main Authors: Chu, Liang-Cui, Arede, Pedro, Li, Wei, Urdaneta, Erika C., Ivanova, Ivayla, McKellar, Stuart W., Wills, Jimi C., Fröhlich, Theresa, von Kriegsheim, Alexander, Beckmann, Benedikt M., Granneman, Sander
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.05.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/70; 38/91; 45; 45/23; 45/88; 631/326/41; 631/326/421; 631/337/475; 631/45/500; 82/29; 82/80; 82/81; 82/83; Bacteria; Bacterial Proteins - metabolism; Binding; Deoxyribonucleic acid; DNA; DNA - metabolism; DNA-Binding Proteins - metabolism; Drug resistance; Gene expression; Gram-positive bacteria; Helix-Turn-Helix Motifs - genetics; Humanities and Social Sciences; Metabolism; Methicillin; Methicillin-Resistant Staphylococcus aureus - genetics; Methicillin-Resistant Staphylococcus aureus - metabolism; multidisciplinary; Post-transcription; Protein Binding; Proteins; Proteome - metabolism; Proteomes; Ribonucleic acid; RNA; RNA - metabolism; RNA-binding protein; Science; Science (multidisciplinary); Staphylococcus aureus; Staphylococcus infections; Transcription factors; Transcription Factors - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-30553-8

RNA-binding proteins play key roles in controlling gene expression in many organisms, but relatively few have been identified and characterised in detail in Gram-positive bacteria. Here, we globally analyse RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) using two complementary biochemical approaches. We identify hundreds of putative RNA-binding proteins, many containing unconventional RNA-binding domains such as Rossmann-fold domains. Remarkably, more than half of the proteins containing helix-turn-helix (HTH) domains, which are frequently found in prokaryotic transcription factors, bind RNA in vivo. In particular, the CcpA transcription factor, a master regulator of carbon metabolism, uses its HTH domain to bind hundreds of RNAs near intrinsic transcription terminators in vivo. We propose that CcpA, besides acting as a transcription factor, post-transcriptionally regulates the stability of many RNAs. RNA-binding proteins play key roles in controlling gene expression in many organisms. Here, Chu et al. identify hundreds of RNA-binding proteins in methicillin-resistant Staphylococcus aureus , and show that a major transcription factor uses its helix-turn-helix domain to bind RNAs near intrinsic transcription terminators.