RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
22 06 2022
22 06 2022
Historique:
received:
06
05
2021
accepted:
03
06
2022
entrez:
22
6
2022
pubmed:
23
6
2022
medline:
25
6
2022
Statut:
epublish
Résumé
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism.
Identifiants
pubmed: 35732654
doi: 10.1038/s41467-022-31173-y
pii: 10.1038/s41467-022-31173-y
pmc: PMC9217828
doi:
Substances chimiques
RNA, Bacterial
0
RNA, Messenger
0
RNA, Small Untranslated
0
Ribonuclease III
EC 3.1.26.3
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
3560Subventions
Organisme : Medical Research Council
ID : MR/N02995X/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_UU_00007/12
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 201531/Z/16/Z
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/D/20002174
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 208402/Z/17/Z
Pays : United Kingdom
Organisme : NIAID NIH HHS
ID : R01 AI143743
Pays : United States
Organisme : Medical Research Council
ID : MR/R008205/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 109093/Z/15/A
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BBS/E/D/20002173
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 207507
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Informations de copyright
© 2022. The Author(s).
Références
Methods. 2014 Feb;65(3):263-73
pubmed: 24211736
mBio. 2019 Feb 5;10(1):
pubmed: 30723124
Cell Host Microbe. 2013 Dec 11;14(6):683-95
pubmed: 24331466
PLoS Pathog. 2011 Mar;7(3):e1002006
pubmed: 21423670
J Exp Med. 1999 Mar 15;189(6):907-18
pubmed: 10075974
PLoS Genet. 2016 Apr 01;12(4):e1005962
pubmed: 27035918
Mol Cell. 2017 Jan 5;65(1):39-51
pubmed: 28061332
EMBO Rep. 2020 May 6;21(5):e45832
pubmed: 32202364
Nucleic Acids Res. 2017 May 5;45(8):4994-5007
pubmed: 28369640
Mol Microbiol. 2000 Dec;38(5):1027-33
pubmed: 11123676
FEMS Microbiol Rev. 2014 Jul;38(4):698-719
pubmed: 24372362
J Bacteriol. 2017 May 9;199(11):
pubmed: 28289085
Nucleic Acids Res. 2021 Oct 11;49(18):10644-10656
pubmed: 34554192
Algorithms Mol Biol. 2011 Nov 24;6:26
pubmed: 22115189
Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13059-64
pubmed: 21788484
J Bacteriol. 2005 Dec;187(23):8063-80
pubmed: 16291680
Microbiol Mol Biol Rev. 2009 Jun;73(2):233-48
pubmed: 19487727
J Biol Chem. 2012 Dec 21;287(52):43454-63
pubmed: 23129767
Nat Commun. 2019 Jan 14;10(1):197
pubmed: 30643129
BMC Microbiol. 2009 May 18;9:95
pubmed: 19450265
J Bacteriol. 2004 Jul;186(13):4085-99
pubmed: 15205410
Appl Environ Microbiol. 2004 Oct;70(10):6076-85
pubmed: 15466553
Cell. 2009 Feb 20;136(4):615-28
pubmed: 19239884
Mol Cell. 2016 May 19;62(4):618-26
pubmed: 27184080
J Vis Exp. 2020 May 9;(159):
pubmed: 32449723
Nat Commun. 2022 Jun 22;13(1):3560
pubmed: 35732654
Infect Immun. 2008 May;76(5):2044-50
pubmed: 18347047
PLoS Pathog. 2014 Mar 20;10(3):e1003979
pubmed: 24651379
Infect Immun. 2002 Nov;70(11):6373-82
pubmed: 12379717
Cell. 2013 Apr 25;153(3):654-65
pubmed: 23622248
Nat Methods. 2015 Apr;12(4):323-5
pubmed: 25730492
FEMS Microbiol Rev. 2015 May;39(3):316-30
pubmed: 25934118
Genome Biol. 2014;15(12):550
pubmed: 25516281
J Bacteriol. 2018 Oct 23;200(22):
pubmed: 30150231
Nucleic Acids Res. 2009 Nov;37(21):7239-57
pubmed: 19786493
Annu Rev Microbiol. 2016 Sep 8;70:299-316
pubmed: 27482744
Cell. 2016 Sep 22;167(1):111-121.e13
pubmed: 27662085
PLoS Genet. 2012 Jun;8(6):e1002782
pubmed: 22761586
mBio. 2012 Mar 20;3(2):
pubmed: 22434850
Nucleic Acids Res. 2021 Jun 21;49(11):6399-6419
pubmed: 34096591
Proc Natl Acad Sci U S A. 1990 Jun;87(11):4179-83
pubmed: 2190215
Nucleic Acids Res. 2015 Apr 20;43(7):e47
pubmed: 25605792
Elife. 2020 May 01;9:
pubmed: 32356726
EMBO J. 1995 Sep 15;14(18):4569-77
pubmed: 7556100
Methods Mol Biol. 2014;1106:93-100
pubmed: 24222457
PLoS One. 2011;6(5):e20554
pubmed: 21655230
BMC Microbiol. 2012 Jan 24;12:17
pubmed: 22272815
Nucleic Acids Res. 2014 Apr;42(8):4892-905
pubmed: 24557948
Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):1169-74
pubmed: 15657139
RNA. 2015 May;21(5):1005-17
pubmed: 25805861
Nat Struct Mol Biol. 2011 Dec 25;19(1):105-12
pubmed: 22198463
Genes Dev. 2007 Jun 1;21(11):1353-66
pubmed: 17545468
Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):E4981-90
pubmed: 25368190
Genome Biol. 2015 Jan 13;16:1
pubmed: 25583448
Cell Rep. 2014 Apr 24;7(2):424-435
pubmed: 24703849
Mol Microbiol. 2014 May;92(4):824-39
pubmed: 24666349
J Proteome Res. 2011 Apr 1;10(4):1794-805
pubmed: 21254760
J Mol Biol. 2008 Nov 14;383(3):603-14
pubmed: 18773907
Biochim Biophys Acta. 2008 Sep;1779(9):574-82
pubmed: 18342642
Nucleic Acids Res. 2018 Nov 2;46(19):10380-10394
pubmed: 30113670
Cell Rep. 2020 Mar 24;30(12):4027-4040.e7
pubmed: 32209466
Bioinformatics. 2011 Nov 1;27(21):2957-63
pubmed: 21903629
Mol Cell. 2022 Feb 3;82(3):629-644.e4
pubmed: 35063132
Infect Immun. 2018 Jan 22;86(2):
pubmed: 29133345
Mol Microbiol. 1999 Aug;33(4):806-16
pubmed: 10447889
FEMS Microbiol Rev. 1996 Jul;18(4):301-17
pubmed: 8703508
Mol Cell. 2016 Sep 1;63(5):884-97
pubmed: 27588604
Genes (Basel). 2016 Oct 03;7(10):
pubmed: 27706107
Mol Microbiol. 2006 Aug;61(4):1038-48
pubmed: 16879652
Cell Microbiol. 2014 Apr;16(4):451-65
pubmed: 24164701
PLoS Pathog. 2019 Mar 14;15(3):e1007618
pubmed: 30870530
Nucleic Acids Res. 2017 Jun 20;45(11):6746-6760
pubmed: 28379505
Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):10010-5
pubmed: 21610164
EMBO J. 2017 Feb 1;36(3):374-387
pubmed: 27836995
Antimicrob Agents Chemother. 2013 Aug;57(8):3864-74
pubmed: 23733475
PLoS Genet. 2015 Feb 02;11(2):e1004957
pubmed: 25643072
Mol Cell. 2008 Dec 26;32(6):827-37
pubmed: 19111662
Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450
pubmed: 30395289
FEBS J. 2022 Apr;289(7):1746-1764
pubmed: 33690958
Plasmid. 2009 Mar;61(2):126-9
pubmed: 18996145
Mol Cell. 2011 Sep 16;43(6):880-91
pubmed: 21925377
Nucleic Acids Res. 2019 Jan 8;47(D1):D607-D613
pubmed: 30476243
Nat Protoc. 2016 Dec;11(12):2301-2319
pubmed: 27809316
Front Microbiol. 2018 Feb 20;9:228
pubmed: 29515534
Microbiol Spectr. 2018 Jul;6(4):
pubmed: 30003868
Cell Host Microbe. 2010 Jul 22;8(1):116-27
pubmed: 20638647
Nucleic Acids Res. 2010 Oct;38(19):6620-36
pubmed: 20511587
EMBO J. 2012 Oct 17;31(20):4005-19
pubmed: 22922465
Infect Genet Evol. 2014 Jan;21:616-26
pubmed: 24291227
Nucleic Acids Res. 2003 May 1;31(9):2381-92
pubmed: 12711683
Nat Commun. 2017 Apr 11;8(1):12
pubmed: 28400552
Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):14036-41
pubmed: 26504242
Cell Microbiol. 2013 Aug;15(8):1427-37
pubmed: 23470014
Methods Enzymol. 2008;447:309-27
pubmed: 19161850
Nucleic Acids Res. 2018 Sep 28;46(17):8803-8816
pubmed: 29986060
Genome Biol. 2014 Jan 07;15(1):R8
pubmed: 24393166
Infect Immun. 2014 Oct;82(10):4144-53
pubmed: 25047846
Nat Microbiol. 2016 Oct 10;2:16183
pubmed: 27723728
PLoS Pathog. 2010 Mar 12;6(3):e1000809
pubmed: 20300607
BMC Bioinformatics. 2006 Apr 05;7:191
pubmed: 16597342
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
EMBO J. 2015 Jun 3;34(11):1478-92
pubmed: 25630703
J Infect. 2015 Oct;71(4):447-57
pubmed: 26079275
J Biol Chem. 2004 Nov 26;279(48):49804-15
pubmed: 15383528
Nat Commun. 2022 Jun 22;13(1):3558
pubmed: 35732665
FEMS Microbiol Rev. 2010 Sep;34(5):866-82
pubmed: 20662934
Microbes Infect. 2012 Apr;14(4):380-6
pubmed: 22178792
PLoS Pathog. 2013;9(12):e1003767
pubmed: 24348246
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
EMBO J. 2019 Mar 15;38(6):
pubmed: 30760492
Appl Environ Microbiol. 2018 Aug 1;84(16):
pubmed: 29884758
PLoS Pathog. 2012;8(11):e1003016
pubmed: 23209405
RNA. 2017 Sep;23(9):1419-1431
pubmed: 28606943
Infect Immun. 2009 Oct;77(10):4256-64
pubmed: 19667045
PLoS One. 2010 May 20;5(5):e10725
pubmed: 20505759
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
FEMS Microbiol Rev. 2009 Jan;33(1):133-51
pubmed: 19076632
Front Microbiol. 2017 Jul 10;8:1276
pubmed: 28740488
Anal Chem. 2003 Feb 1;75(3):663-70
pubmed: 12585499
Nat Med. 2007 Dec;13(12):1510-4
pubmed: 17994102
EMBO J. 2005 Feb 23;24(4):824-35
pubmed: 15678100
Int J Genomics. 2015;2015:395753
pubmed: 25977913
PLoS One. 2011 Apr 15;6(4):e18617
pubmed: 21525981
Methods. 2013 Sep 15;63(2):135-43
pubmed: 23851283
Anal Biochem. 1987 Apr;162(1):156-9
pubmed: 2440339