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 Von Kriegsheim; Benedikt M. Beckmann; Sander Granneman

doi:10.1038/s41467-022-30553-8

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 Von Kriegsheim, Benedikt M. Beckmann, Sander Granneman

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	2883
Number of pages	18
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-30553-8
Publication status	Published - 24 May 2022

Keywords / Materials (for Non-textual outputs)

bacterial proteins
DNA-binding proteins
DNA
helix-loop-helix motifs
methicillin-resistant staphylococcus aureus
protein binding
proteome
RNA
transcription factors

Access to Document

10.1038/s41467-022-30553-8Licence: Creative Commons: Attribution (CC-BY)

GrannemanEtalNC2022TheRNABoundProteomeOfMRSAFinal published version, 2.92 MBLicence: Creative Commons: Attribution (CC-BY)

Unravelling post-transcriptional regulatory networks in pathogenic S. aureus
Granneman, S. (Principal Investigator)
MRC
1/01/18 → 22/08/23
Project: Research
High resolution metabolite and peptide mass spectrometry
Von Kriegsheim, A. (Principal Investigator), Christophorou, M. (Co-investigator), Finch, A. (Co-investigator), Morton, N. (Co-investigator), Ponting, C. (Co-investigator) & Walmsley, S. (Co-investigator)
UK-based charities
2/10/17 → 1/11/22
Project: Research
Wellcome Trust Four-year PhD studentship (Stuart William McKellar)
Beggs, J. (Principal Investigator)
UK-based charities
1/10/15 → 30/09/19
Project: Research

Institute for Genetics and Cancer Mass Spectrometry Facility
Von Kriegsheim, A. (Manager)
School of Genetics and Cancer
Facility/equipment: Facility

Cite this

Chu, L., Arede, P., Li, W., Urdaneta, E. C., Ivanova, I., Mckellar, S. W., Wills, J. C., Fröhlich, T., Von Kriegsheim, A., Beckmann, B. M., & Granneman, S. (2022). The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins. Nature Communications, 13(1), Article 2883. https://doi.org/10.1038/s41467-022-30553-8

@article{65cbb5adbc704360bebfbcadb5e06678,

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

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.",

keywords = "bacterial proteins, DNA-binding proteins, DNA, helix-loop-helix motifs, methicillin-resistant staphylococcus aureus, protein binding, proteome, RNA, transcription factors",

author = "Liang-cui Chu and Pedro Arede and Wei Li and Urdaneta, \{Erika C.\} and Ivayla Ivanova and Mckellar, \{Stuart W.\} and Wills, \{Jimi C.\} and Theresa Fr{\"o}hlich and \{Von Kriegsheim\}, Alexander and Beckmann, \{Benedikt M.\} and Sander Granneman",

note = "Funding Information: We are very grateful to Ross Fitzgerald, Amy Pickering (Ross Fitzgerald{\textquoteright}s group), Jai Tree, Ben Howden and Tim Stinear for providing strains, for fruitful scientific discussions and for helping us to master the genetic engineering of S. aureus. We would like to thank Juan Xie (Shiyong Liu{\textquoteright}s group) for running the RBPPred, Tomasz Turowski (David Tollervey{\textquoteright}s group) for helping with MiniSeq sequencing, Atlanta Cook for helping establish the fluorescent EMSA protocol and Hugh McCaughan for helping with the analysis of the growth curve data. We would also like to thank Emma Denham, Tatsiana Auchynnikava and the members of the Granneman lab for critically reading the manuscript. Finally, we would like to thank Iain McNae and Malcolm Walkinshaw for their support and valuable feedback. This work was supported by a Medical Research Council Non-Clinical Senior Research Fellowship (MR/R008205/1 to S.G.), a Wellcome Trust PhD scholarship (109093/Z/15/A to S.W.M.) and a Wellcome Trust Multiuser Equipment grant (208402/Z/17/Z to A.v.K.). B.M.B. is supported by the German Research Foundation (DFG; IRTG 2290) and the Plus 3 Programme of the Boehringer Ingelheim Foundation (BIS). Publisher Copyright: {\textcopyright} 2022, The Author(s).",

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doi = "10.1038/s41467-022-30553-8",

language = "English",

volume = "13",

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TY - JOUR

T1 - The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins

AU - Chu, Liang-cui

AU - Arede, Pedro

AU - Li, Wei

AU - Urdaneta, Erika C.

AU - Ivanova, Ivayla

AU - Mckellar, Stuart W.

AU - Wills, Jimi C.

AU - Fröhlich, Theresa

AU - Von Kriegsheim, Alexander

AU - Beckmann, Benedikt M.

AU - Granneman, Sander

N1 - Funding Information: We are very grateful to Ross Fitzgerald, Amy Pickering (Ross Fitzgerald’s group), Jai Tree, Ben Howden and Tim Stinear for providing strains, for fruitful scientific discussions and for helping us to master the genetic engineering of S. aureus. We would like to thank Juan Xie (Shiyong Liu’s group) for running the RBPPred, Tomasz Turowski (David Tollervey’s group) for helping with MiniSeq sequencing, Atlanta Cook for helping establish the fluorescent EMSA protocol and Hugh McCaughan for helping with the analysis of the growth curve data. We would also like to thank Emma Denham, Tatsiana Auchynnikava and the members of the Granneman lab for critically reading the manuscript. Finally, we would like to thank Iain McNae and Malcolm Walkinshaw for their support and valuable feedback. This work was supported by a Medical Research Council Non-Clinical Senior Research Fellowship (MR/R008205/1 to S.G.), a Wellcome Trust PhD scholarship (109093/Z/15/A to S.W.M.) and a Wellcome Trust Multiuser Equipment grant (208402/Z/17/Z to A.v.K.). B.M.B. is supported by the German Research Foundation (DFG; IRTG 2290) and the Plus 3 Programme of the Boehringer Ingelheim Foundation (BIS). Publisher Copyright: © 2022, The Author(s).

PY - 2022/5/24

Y1 - 2022/5/24

N2 - 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.

AB - 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.

KW - bacterial proteins

KW - DNA-binding proteins

KW - DNA

KW - helix-loop-helix motifs

KW - methicillin-resistant staphylococcus aureus

KW - protein binding

KW - proteome

KW - RNA

KW - transcription factors

U2 - 10.1038/s41467-022-30553-8

DO - 10.1038/s41467-022-30553-8

M3 - Article

C2 - 35610211

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 2883

ER -

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

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

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Projects

Unravelling post-transcriptional regulatory networks in pathogenic S. aureus

High resolution metabolite and peptide mass spectrometry

Wellcome Trust Four-year PhD studentship (Stuart William McKellar)

Equipment

Institute for Genetics and Cancer Mass Spectrometry Facility

Cite this