Diverse CRISPRs Evolving in Human Microbiomes
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR–associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP) enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes), we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones) are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals. This work indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes.
Vyšlo v časopise:
Diverse CRISPRs Evolving in Human Microbiomes. PLoS Genet 8(6): e32767. doi:10.1371/journal.pgen.1002441
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002441
Souhrn
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR–associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human Microbiome Project (HMP) enables us to explore the distribution and diversity of known CRISPRs in human-associated microbial communities and to discover new CRISPRs. We propose a targeted assembly strategy to reconstruct CRISPR arrays, which whole-metagenome assemblies fail to identify. For each known CRISPR type (identified from reference genomes), we use its direct repeat consensus sequence to recruit reads from each HMP dataset and then assemble the recruited reads into CRISPR loci; the unique spacer sequences can then be extracted for analysis. We also identified novel CRISPRs or new CRISPR variants in contigs from whole-metagenome assemblies and used targeted assembly to more comprehensively identify these CRISPRs across samples. We observed that the distributions of CRISPRs (including 64 known and 86 novel ones) are largely body-site specific. We provide detailed analysis of several CRISPR loci, including novel CRISPRs. For example, known streptococcal CRISPRs were identified in most oral microbiomes, totaling ∼8,000 unique spacers: samples resampled from the same individual and oral site shared the most spacers; different oral sites from the same individual shared significantly fewer, while different individuals had almost no common spacers, indicating the impact of subtle niche differences on the evolution of CRISPR defenses. We further demonstrate potential applications of CRISPRs to the tracing of rare species and the virus exposure of individuals. This work indicates the importance of effective identification and characterization of CRISPR loci to the study of the dynamic ecology of microbiomes.
Zdroje
1. BarrangouRFremauxCDeveauHRichardsMBoyavalP 2007 CRISPR provides acquired resistance against viruses in prokaryotes. Science 315 1709 1712
2. HorvathPBarrangouR 2010 CRISPR/Cas, the immune system of bacteria and archaea. Science 327 167 170
3. JansenREmbdenJDGaastraWSchoulsLM 2002 Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43 1565 1575
4. SorekRKuninVHugenholtzP 2008 CRISPR–a widespread system that provides acquired resistance against phages in bacteria and archaea. Nat Rev Microbiol 6 181 186
5. van der OostJJoreMMWestraERLundgrenMBrounsSJ 2009 CRISPR-based adaptive and heritable immunity in prokaryotes. Trends Biochem Sci 34 401 407
6. GrissaIVergnaudGPourcelC 2007 The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8 172
7. KuninVSorekRHugenholtzP 2007 Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biol 8 R61
8. DeltchevaEChylinskiKSharmaCMGonzalesKChaoY 2011 CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471 602 607
9. DeveauHGarneauJEMoineauS 2010 CRISPR/Cas System and Its Role in Phage-Bacteria Interactions. Annual Review of Microbiology 64 475 493
10. DeveauHBarrangouRGarneauJELabontéJFremauxC 2008 Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilis. Journal of Bacteriology 190 1390 1400
11. ChakrabortySSnijdersAPChakravortyRAhmedMTarekAM 2010 Comparative network clustering of direct repeats (DRs) and cas genes confirms the possibility of the horizontal transfer of CRISPR locus among bacteria. Mol Phylogenet Evol 56 878 887
12. GoddeJBickertonA 2006 The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes. Journal of Molecular evolution 62 718 729
13. AnderssonAFBanfieldJF 2008 Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320 1047 1050
14. HeidelbergJFNelsonWCSchoenfeldTBhayaD 2009 Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS ONE 4 e4169 doi:10.1371/journal.pone.0004169
15. HeldNLWhitakerRJ 2009 Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ Microbiol 11 457 466
16. KuninVHeSWarneckeFPetersonSBGarcia MartinH 2008 A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research 18 293 297
17. HawleyDMAltizeSM 2011 Disease ecology meets ecological immunology: understanding the links between organismal immunity and infection dynamics in natural populations. . Functional Ecology 25 48 60
18. KeesingFHoltRDOstfeldRS 2006 Effects of species diversity on disease risk. Ecol Lett 9 485 498
19. WolinskaJSpaakP 2009 The cost of being common: evidence from natural Daphnia populations. Evolution 63 1893 1901
20. HamiltonWDAxelrodRTaneseR 1990 Sexual reproduction as an adaptation to resist parasites (a review). Proc Natl Acad Sci USA 87 3566 3573
21. AnglyFEFeltsBBreitbartMSalamonPEdwardsRA 2006 The marine viromes of four oceanic regions. PLoS Biol 4 e368 doi:10.1371/journal.pbio.0040368
22. ParadaVBaudouxACSintesEWeinbauerMGHerndlGJ 2008 Dynamics and diversity of newly produced virioplankton in the North Sea. ISME J 2 924 936
23. VenturaMSozziTTurroniFMatteuzziDvan SinderenD 2010 The impact of bacteriophages on probiotic bacteria and gut microbiota diversity. Genes Nutr
24. WoodfordNTurtonJFLivermoreDM 2011 Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiol Rev
25. GarneauJEDupuisMEVillionMRomeroDABarrangouR 2010 The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468 67 71
26. PrideDTSunCLSalzmanJRaoNLoomerP 2011 Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Genome Research 21 126 136
27. GrissaIVergnaudGPourcelC 2007 CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35 W25 57
28. BlandCRamseyTSabreeFLoweMBrownK 2007 CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8 209
29. EdgarR 2007 PILER-CR: Fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8 18
30. RousseauCGonnetMLe RomancerMNicolasJ 2009 CRISPI: a CRISPR interactive database. Bioinformatics 25 3317 3318
31. RhoMTangHYeY 2010 FragGeneScan: predicting genes in short and error-prone reads. Nucl Acids Res doi:10.1093/nar/gkq747
32. BhallyHSLemaCRomagnoliMBorekAWakefieldT 2005 Leptotrichia buccalis bacteremia in two patients with acute myelogenous leukemia. Anaerobe 11 350 353
33. HaftDHSelengutJMongodinEFNelsonKE 2005 A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol 1 e60 doi:10.1371/journal.pcbi.0010060
34. MartínREscobedoSSuárez JuanE 2010 Induction, structural characterization, and genome sequence of Lv1, a prophage from a human vaginal Lactobacillus jensenii strain. Int Microbiol 13 113 121
35. MarraffiniLASontheimerEJ 2010 CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11 181 190
36. MojicaFJMDíez-VillaseñorCsGarcía-MartínezJsSoriaE 2005 Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of Molecular evolution 60 174 182
37. MarraffiniLASontheimerEJ 2008 CRISPR interference limits horizontal gene transfer in Staphylococci by targeting DNA. Science 322 1843 1845
38. MojicaFJDiez-VillasenorCGarcia-MartinezJAlmendrosC 2008 Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155 733 740
39. LiWJaroszewskiLGodzikA 2001 Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17 282 283
40. LiRZhuHRuanJQianWFangX 2010 De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20 265 272
41. QinJLiRRaesJArumugamMBurgdorfKS 2010 A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464 59 65
42. The Human Microbiome Consortium 2012 Structure, Function and Diversity of Human Microbiome in an Adult Reference Population. Nature: doi:10.1038/nature11234
43. SmootMEOnoKRuscheinskiJWangPLIdekerT 2011 Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27 431 432
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 6
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