title: CRISPR regulation of intraspecies diversification by limiting IS transposition and intercellular recombination.
abstract: Mobile genetic elements (MGEs) and genetic rearrangement are considered as major driving forces of bacterial diversification. Previous comparative genome analysis of Porphyromonas gingivalis, a pathogen related to periodontitis, implied such an important relationship. As a counterpart system to MGEs, clustered regularly interspaced short palindromic repeats (CRISPRs) in bacteria may be useful for genetic typing. We found that CRISPR typing could be a reasonable alternative to conventional methods for characterizing phylogenetic relationships among 60 highly diverse P. gingivalis isolates. Examination of genetic recombination along with multilocus sequence typing suggests the importance of such events between different isolates. MGEs appear to be strategically located at the breakpoint gaps of complicated genome rearrangements. Of these MGEs, insertion sequences (ISs) were found most frequently. CRISPR analysis identified 2,150 spacers that were clustered into 1,187 unique ones. Most of these spacers exhibited no significant nucleotide similarity to known sequences (97.6%: 1,158/1,187). Surprisingly, CRISPR spacers exhibiting high nucleotide similarity to regions of P. gingivalis genomes including ISs were predominant. The proportion of such spacers to all the unique spacers (1.6%: 19/1,187) was the highest among previous studies, suggesting novel functions for these CRISPRs. These results indicate that P. gingivalis is a bacterium with high intraspecies diversity caused by frequent insertion sequence (IS) transposition, whereas both the introduction of foreign DNA, primarily from other P. gingivalis cells, and IS transposition are limited by CRISPR interference. It is suggested that P. gingivalis CRISPRs could be an important source for understanding the role of CRISPRs in the development of bacterial diversity.
authors: Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Japan. aporceddu@uniss.it
authors: Takayasu
authors: T
authors: Watanabe
authors: Takashi
authors: T
authors: Nozawa
authors: Chihiro
authors: C
authors: Aikawa
authors: Atsuo
authors: A
authors: Amano
authors: Fumito
authors: F
authors: Maruyama
authors: Ichiro
authors: I
authors: Nakagawa
mesh_terms: D016866:Bacteroidaceae Infections / Q000382:microbiology; D001483:Base Sequence; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics*; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D016966:Porphyromonas gingivalis / Q000235:genetics*; D011995:Recombination, Genetic; D016415:Sequence Alignment
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial
keywords: Porphyromonas gingivalis; clustered regularly interspaced short palindromic repeat (CRISPR); diversification; genome rearrangement; intercellular recombination; mobile genetic element (MGE)
references: BMC Microbiol. 2007 Apr 12;7:30
references: 17430587
references: J Bacteriol. 2003 Sep;185(18):5591-601
references: 12949112
references: Bioinformatics. 2001 Dec;17(12):1230-1
references: 11751234
references: BMC Bioinformatics. 2008 Sep 16;9:376
references: 18793444
references: ISME J. 2012 May;6(5):915-26
references: 22158393
references: Mol Biol Evol. 2011 Oct;28(10):2731-9
references: 21546353
references: BMC Evol Biol. 2010 Jul 28;10:230
references: 20667132
references: PLoS One. 2012;7(5):e36995
references: 22623967
references: Microbiology (Reading). 2005 Aug;151(Pt 8):2551-2561
references: 16079334
references: J Clin Microbiol. 2006 Jan;44(1):35-41
references: 16390944
references: J Periodontol. 2003 Jan;74(1):90-6
references: 12593602
references: Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):9107-12
references: 22586109
references: Microbiology (Reading). 2006 Apr;152(Pt 4):1099-1108
references: 16549673
references: Bioinformatics. 2009 Dec 15;25(24):3317-8
references: 19846435
references: Science. 2008 May 23;320(5879):1047-50
references: 18497291
references: Mol Microbiol. 1993 Nov;10(3):465-71
references: 7968525
references: Oral Microbiol Immunol. 2009 Oct;24(5):423-6
references: 19702958
references: Genome Biol. 2004;5(2):R12
references: 14759262
references: PLoS Genet. 2008 Jul 18;4(7):e1000128
references: 18650965
references: J Bacteriol. 2008 Feb;190(4):1401-12
references: 18065539
references: J Bacteriol. 2011 Aug;193(16):4259-60
references: 21705612
references: J Bacteriol. 1999 Jun;181(11):3536-41
references: 10348867
references: J Bacteriol. 2004 Mar;186(5):1518-30
references: 14973027
references: Int J Syst Bacteriol. 1999 Apr;49 Pt 2:351-9
references: 10319455
references: Mol Biol Evol. 2006 Feb;23(2):254-67
references: 16221896
references: Science. 2008 Dec 19;322(5909):1843-5
references: 19095942
references: PLoS One. 2010 Sep 28;5(9):
references: 20927396
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7
references: 17537822
references: Microbiology (Reading). 2003 Sep;149(Pt 9):2407-2415
references: 12949166
references: Nat Rev Microbiol. 2008 Mar;6(3):181-6
references: 18157154
references: Biol Direct. 2011 Dec 21;6(1):65
references: 22188759
references: Environ Microbiol. 2012 Sep;14(9):2564-76
references: 22583485
references: Science. 2007 Mar 23;315(5819):1709-12
references: 17379808
references: J Dent Res. 1992 Feb;71(2):353-8
references: 1313462
references: Stand Genomic Sci. 2010 Nov 20;3(3):315-24
references: 21304736
references: J Clin Microbiol. 1999 May;37(5):1426-30
references: 10203499
references: Trends Microbiol. 2012 Jan;20(1):1-4
references: 22112388
references: PLoS One. 2012;7(7):e41706
references: 22860008
references: Curr Opin Microbiol. 2006 Oct;9(5):526-31
references: 16935554
references: J Bacteriol. 2011 Jul;193(14):3433-45
references: 21398535
references: ISME J. 2012 Jun;6(6):1176-85
references: 22170420
references: Genome Res. 2004 Jun;14(6):1188-90
references: 15173120
references: Microbiol Mol Biol Rev. 1998 Dec;62(4):1244-63
references: 9841671
references: Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12554-9
references: 16105942
references: Microbiology (Reading). 2011 Jul;157(Pt 7):2022-2032
references: 21527470
references: Annu Rev Genet. 2011;45:273-97
references: 22060043
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D57-61
references: 19933762
references: J Clin Microbiol. 2000 May;38(5):1909-14
references: 10790120
references: Proc Natl Acad Sci U S A. 1981 Nov;78(11):7069-72
references: 6273909
references: Genetics. 1997 Jul;146(3):745-50
references: 9215884
references: J Clin Microbiol. 2008 Jan;46(1):31-42
references: 17977992
references: DNA Res. 2008 Aug;15(4):215-25
references: 18524787
references: PLoS One. 2011 May 06;6(5):e19543
references: 21573110
references: Genetics. 2003 Aug;164(4):1279-89
references: 12930739
references: Nature. 2011 May 12;473(7346):174-80
references: 21508958
references: Genome Res. 2003 Jun;13(6A):1042-55
references: 12799345
references: Nat Commun. 2011 Jan 11;2:152
references: 21224843
references: PLoS Genet. 2008 Dec;4(12):e1000304
references: 19081788
references: Nat Rev Microbiol. 2011 Jun;9(6):467-77
references: 21552286
references: J Periodontal Res. 2004 Apr;39(2):136-42
references: 15009522
references: PLoS One. 2011;6(5):e19631
references: 21611187
references: mBio. 2012 Jan 31;3(1):
references: 22294679
references: Infect Immun. 2001 Jun;69(6):3703-12
references: 11349034
references: Trends Genet. 2010 Aug;26(8):335-40
references: 20598393
references: Nature. 2000 May 18;405(6784):299-304
references: 10830951
references: Genome Res. 2009 Oct;19(10):1809-16
references: 19564451
references: Database (Oxford). 2010 Jul 06;2010:baq013
references: 20624719
references: Clin Microbiol Rev. 2007 Oct;20(4):593-621
references: 17934076
references: FEMS Microbiol Lett. 2012 Aug;333(1):1-9
references: 22530835
references: mBio. 2012 Nov 01;3(5):
references: 23033473