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

Liang-Cui Chu, Pedro Arede, Wei Li, Erika C. Urdaneta, Ivayla Ivanova, Stuart W. McKellar, Jimi C. Wills, Theresa Fröhlich, Alexander Kriegsheim, Benedikt M. Beckmann and Sander Granneman ()
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Liang-Cui Chu: University of Edinburgh
Pedro Arede: University of Edinburgh
Wei Li: University of Edinburgh
Erika C. Urdaneta: Humboldt University Berlin
Ivayla Ivanova: University of Edinburgh
Stuart W. McKellar: University of Edinburgh
Jimi C. Wills: University of Edinburgh
Theresa Fröhlich: University of Edinburgh
Alexander Kriegsheim: University of Edinburgh
Benedikt M. Beckmann: Humboldt University Berlin
Sander Granneman: University of Edinburgh

Nature Communications, 2022, vol. 13, issue 1, 1-18

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-022-30553-8

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