Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae.

Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

Original Publication: London : Nature Publishing Group, copyright 2011-

DNA Restriction-Modification Enzymes/*genetics ; Gonorrhea/*genetics ; Neisseria gonorrhoeae/*genetics; Base Sequence ; DNA Methylation/genetics ; DNA Mutational Analysis ; Gene Expression Regulation, Bacterial/genetics ; Genetic Variation/genetics ; Genome, Bacterial/genetics ; Gonorrhea/microbiology ; Humans ; Neisseria gonorrhoeae/pathogenicity

Restriction-Modification systems (RMS) are one of the main mechanisms of defence against foreign DNA invasion and can have an important role in the regulation of gene expression. The obligate human pathogen Neisseria gonorrhoeae carries one of the highest loads of RMS in its genome; between 13 to 15 of the three main types. Previous work has described their organization in the reference genome FA1090 and has inferred the associated methylated motifs. Here, we studied the structure of RMS and target methylated motifs in 25 gonococcal strains sequenced with Single Molecule Real-Time (SMRT) technology, which provides data on DNA modification. The results showed a variable picture of active RMS in different strains, with phase variation switching the activity of Type III RMS, and both the activity and specificity of a Type I RMS. Interestingly, the Dam methylase was found in place of the NgoAXI endonuclease in two of the strains, despite being previously thought to be absent in the gonococcus. We also identified the real methylation target of NgoAXII as 5'-GCAGA-3', different from that previously described. Results from this work give further insights into the diversity and dynamics of RMS and methylation patterns in N. gonorrhoeae.

FEMS Microbiol Lett. 2009 Nov;300(1):25-35. (PMID: 19758331)
Mol Microbiol. 2001 Sep;41(5):1199-210. (PMID: 11555298)
Nat Rev Mol Cell Biol. 2004 Feb;5(2):148-57. (PMID: 15040447)
Nat Rev Microbiol. 2010 Mar;8(3):196-206. (PMID: 20140025)
Infect Immun. 2001 Dec;69(12):7197-204. (PMID: 11705888)
Microbiology (Reading). 2003 Nov;149(Pt 11):3311-3319. (PMID: 14600243)
Pathog Dis. 2017 Aug 31;75(6):. (PMID: 28859312)
Genome Res. 2017 May;27(5):722-736. (PMID: 28298431)
PLoS One. 2011;6(12):e27569. (PMID: 22162751)
PLoS Pathog. 2009 Apr;5(4):e1000400. (PMID: 19390608)
Sci Rep. 2016 Feb 12;6:21015. (PMID: 26867950)
Mol Biol Evol. 2000 Apr;17(4):540-52. (PMID: 10742046)
Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5. (PMID: 27095192)
Nucleic Acids Res. 2003 Jan 1;31(1):418-20. (PMID: 12520038)
Bioinformatics. 2012 Feb 15;28(4):464-9. (PMID: 22199388)
FASEB J. 2014 Dec;28(12):5197-207. (PMID: 25183669)
Microbiology (Reading). 2004 Jun;150(Pt 6):1713-1722. (PMID: 15184558)
Front Microbiol. 2015 Dec 21;6:1426. (PMID: 26733970)
Bioinformatics. 2018 Jan 15;34(2):292-293. (PMID: 29028899)
Nat Rev Microbiol. 2006 Mar;4(3):183-92. (PMID: 16489347)
Bioinformatics. 2006 Jul 1;22(13):1600-7. (PMID: 16606683)
Microbiol Mol Biol Rev. 2006 Sep;70(3):830-56. (PMID: 16959970)
BMC Biol. 2013 Jan 22;11:4. (PMID: 23339471)
Trends Genet. 2000 Jun;16(6):276-7. (PMID: 10827456)
Proc Natl Acad Sci U S A. 2016 May 17;113(20):5658-63. (PMID: 27140615)
J Antimicrob Chemother. 2016 Nov;71(11):3096-3108. (PMID: 27432602)
Nucleic Acids Res. 2002 Sep 1;30(17):3880-5. (PMID: 12202773)
Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5547-51. (PMID: 15802471)
J Bacteriol. 2010 Aug;192(15):3951-60. (PMID: 20511499)
J Mol Biol. 1989 Jan 5;205(1):115-25. (PMID: 2784505)
Nucleic Acids Res. 2010 Apr;38(7):2428-43. (PMID: 20071371)
Annu Rev Genet. 2014;48:405-31. (PMID: 25251852)
Nucleic Acids Res. 2003 Apr 1;31(7):1805-12. (PMID: 12654995)
PLoS Comput Biol. 2011 Oct;7(10):e1002195. (PMID: 22039361)
Mol Cell. 1999 Apr;3(4):435-45. (PMID: 10230396)
Nucleic Acids Res. 2001 Sep 15;29(18):3742-56. (PMID: 11557807)
Microbiol Mol Biol Rev. 2013 Mar;77(1):53-72. (PMID: 23471617)
Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85. (PMID: 26673716)
Nucleic Acids Res. 2014 Jan;42(1):20-44. (PMID: 24068554)
Methods Mol Biol. 2019;1997:37-58. (PMID: 31119616)
FEBS Lett. 2001 Apr 27;495(3):178-83. (PMID: 11334887)
Nucleic Acids Res. 2007;35(15):5242-52. (PMID: 17675301)
Nucleic Acids Res. 2013 Jan 7;41(1):405-17. (PMID: 23147004)
J Mol Biol. 1998 Jun 19;279(4):823-32. (PMID: 9642063)
FASEB J. 2011 Oct;25(10):3622-33. (PMID: 21680891)
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W5-9. (PMID: 18440982)
Front Microbiol. 2014 Dec 17;5:712. (PMID: 25566225)
Nat Commun. 2014 Nov 19;5:5471. (PMID: 25407023)
J Bacteriol. 2011 Dec;193(23):6750-9. (PMID: 21984785)
PLoS Genet. 2016 Feb 12;12(2):e1005854. (PMID: 26870957)
Syst Biol. 2010 May;59(3):307-21. (PMID: 20525638)
Nucleic Acids Res. 2015 Jan;43(Database issue):D298-9. (PMID: 25378308)
Microbiol Mol Biol Rev. 2014 Sep;78(3):544-71. (PMID: 25184565)
Mol Biol Evol. 2010 Feb;27(2):221-4. (PMID: 19854763)

United Kingdom WT_ Wellcome Trust; 098051 United Kingdom WT_ Wellcome Trust; 098051 United Kingdom WT_ Wellcome Trust

0 (DNA Restriction-Modification Enzymes)

Date Created: 20191013 Date Completed: 20201029 Latest Revision: 20210929

20250114

PMC6789123

10.1038/s41598-019-51102-2

31605008