Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome.

Applied and Environmental Microbiology
Valery A SorokinIrena I Artamonova

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic data: in particular, the largest existing data set, generated from the Sorcerer II Global Ocean Sampling expedition. The application of three publicly available CRISPR recognition programs to the Global Ocean metagenome produced a large proportion of false-positive results. To address this problem, a filtering procedure was designed. It resulted in about 200 reliable CRISPR cassettes, which were then studied in detail. The repeat consensuses were clustered into several stable classes that differed from the existing classification. Short fragments of DNA similar to the cassette spacers were more frequently present in the same geographical location than in other locations (P, <0.0001). We developed a catalogue of elementary CRISPR-forming eve...Continue Reading

References

Jul 27, 1979·Science·W Arber
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 1, 1993·Microbiological Reviews·T A Bickle, D H Krüger
Mar 8, 2000·Microbiology and Molecular Biology Reviews : MMBR·K E Wommack, R R Colwell
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Dec 1, 2004·Annual Review of Genetics·Christian S RiesenfeldJo Handelsman
Mar 29, 2005·Journal of Molecular Evolution·Francisco J M MojicaElena Soria
Nov 9, 2006·PLoS Biology·Florent E AnglyForest Rohwer
Jan 24, 2007·BMC Bioinformatics·Robert C Edgar
Mar 24, 2007·Science·Rodolphe BarrangouPhilippe Horvath
Apr 20, 2007·Genome Biology·Victor KuninPhilip Hugenholtz
May 5, 2007·The American Naturalist·Samantha E FordeBrendan J M Bohannan
Jun 1, 2007·Nucleic Acids Research·Ibtissem GrissaChristine Pourcel
Sep 27, 2007·Environmental Microbiology·Gene W Tyson, Jillian F Banfield
Dec 11, 2007·Journal of Bacteriology·Philippe HorvathRodolphe Barrangou
Dec 11, 2007·Journal of Bacteriology·Hélène DeveauSylvain Moineau
Dec 25, 2007·Nature Reviews. Microbiology·Rotem SorekPhilip Hugenholtz
May 24, 2008·Science·Anders F Andersson, Jillian F Banfield
Aug 16, 2008·Science·Stan J J BrounsJohn van der Oost
Aug 23, 2008·The ISME Journal·Shannon J WilliamsonK Eric Wommack
Oct 31, 2008·RNA·Caryn HaleMichael P Terns
Dec 20, 2008·Science·Luciano A Marraffini, Erik J Sontheimer
Feb 7, 2009·Environmental Microbiology·Nicole L Held, Rachel J Whitaker
Feb 26, 2009·Molecular Microbiology·Reidun K LillestølRoger A Garrett
Jun 30, 2009·Environmental Microbiology·Ruth-Anne SandaaT Frede Thingstad
Oct 9, 2009·Current Opinion in Microbiology·Rebecca Vega Thurber
Nov 28, 2009·Trends in Microbiology·David M KristensenEugene V Koonin

❮ Previous
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Citations

Mar 21, 2013·Nucleic Acids Research·Connor T SkennertonGene W Tyson
Feb 28, 2013·BMC Evolutionary Biology·Anne Kupczok, Jonathan P Bollback
Dec 23, 2011·Biology Direct·Avital BrodtUri Gophna
Apr 26, 2012·PLoS Computational Biology·Ariel D WeinbergerJillian F Banfield
Mar 16, 2011·Yi chuan = Hereditas·Tie-Min Li, Bo Du
Mar 19, 2014·BMC Genomics·Anna A GoglevaIrena I Artamonova
Dec 10, 2013·Nucleic Acids Research·Quan ZhangYuzhen Ye
Mar 19, 2013·Annual Review of Biochemistry·Rotem SorekBlake Wiedenheft
Mar 31, 2012·Annual Review of Marine Science·Mya Breitbart
Nov 9, 2011·Annual Review of Genetics·Devaki BhayaRodolphe Barrangou
Jan 10, 2012·Annual Review of Food Science and Technology·Rodolphe Barrangou, Philippe Horvath
Jan 13, 2011·FEMS Microbiology Reviews·Elizabeth Skippington, Mark A Ragan
May 3, 2011·Current Opinion in Microbiology·Michael P Terns, Rebecca M Terns
Sep 3, 2016·Bioinformatics·Jikai Lei, Yanni Sun
Nov 20, 2016·Molecular Ecology·Daniel MorleyStineke van Houte
Mar 25, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Ville HoikkalaLotta-Riina Sundberg
Mar 25, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Anna LopatinaKonstantin Severinov
Mar 30, 2020·The ISME Journal·Ruonan WuJames M Tiedje

❮ Previous
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