Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

Biology Direct
Kira S MakarovaEugene V Koonin

Abstract

The CRISPR-Cas adaptive immunity systems that are present in most Archaea and many Bacteria function by incorporating fragments of alien genomes into specific genomic loci, transcribing the inserts and using the transcripts as guide RNAs to destroy the genome of the cognate virus or plasmid. This RNA interference-like immune response is mediated by numerous, diverse and rapidly evolving Cas (CRISPR-associated) proteins, several of which form the Cascade complex involved in the processing of CRISPR transcripts and cleavage of the target DNA. Comparative analysis of the Cas protein sequences and structures led to the classification of the CRISPR-Cas systems into three Types (I, II and III). A detailed comparison of the available sequences and structures of Cas proteins revealed several unnoticed homologous relationships. The Repeat-Associated Mysterious Proteins (RAMPs) containing a distinct form of the RNA Recognition Motif (RRM) domain, which are major components of the CRISPR-Cas systems, were classified into three large groups, Cas5, Cas6 and Cas7. Each of these groups includes many previously uncharacterized proteins now shown to adopt the RAMP structure. Evidence is presented that large subunits contained in most of the CRI...Continue Reading

References

Jul 6, 2012·Extremophiles : Life Under Extreme Conditions·Anita MarchfelderLennart Randau
Apr 3, 2013·Cell Research·Bin ShenXingxu Huang
Apr 16, 2013·Nature·Timothy R SampsonDavid S Weiss
Jan 31, 2013·Nature Biotechnology·Wenyan JiangLuciano A Marraffini
Dec 14, 2011·Proceedings of the National Academy of Sciences of the United States of America·Asma Hatoum-AslanLuciano A Marraffini
Apr 28, 2012·Briefings in Functional Genomics·M Senthil Kumar, Kevin C Chen
Mar 9, 2013·Nucleic Acids Research·Kira S MakarovaEugene V Koonin
Jun 30, 2012·Science·Martin JinekEmmanuelle Charpentier
Feb 26, 2013·Applied and Environmental Microbiology·Christine RomanoTimothy R McDermott
Dec 20, 2011·Journal of Bacteriology·Nobuto TakeuchiEugene V Koonin
Feb 28, 2013·BMC Evolutionary Biology·Anne Kupczok, Jonathan P Bollback
Apr 6, 2012·PloS One·Inmaculada Garcia-HerediaFrancisco Rodriguez-Valera
Jul 17, 2013·International Journal of Molecular Sciences·Hagen RichterAndré Plagens
Aug 26, 2014·PloS One·Michael DaumeLennart Randau
Oct 15, 2013·Nucleic Acids Research·Nancy F RamiaHong Li
Oct 24, 2013·Nucleic Acids Research·Ole NiewoehnerJennifer A Doudna
Aug 21, 2013·Cellular and Molecular Life Sciences : CMLS·Giedrius GasiunasVirginijus Siksnys
Jun 10, 2014·Nature Reviews. Microbiology·John van der OostBlake Wiedenheft
Feb 7, 2014·Nucleic Acids Research·André PlagensLennart Randau
Dec 10, 2013·Nucleic Acids Research·Quan ZhangYuzhen Ye
May 6, 2014·Annales d'endocrinologie·Denise R Archambeault, Martin M Matzuk
Aug 13, 2014·Extremophiles : Life Under Extreme Conditions·Kira S MakarovaEugene V Koonin
Apr 15, 2014·Nucleic Acids Research·Krzysztof ChylinskiEugene V Koonin
Jul 8, 2014·PloS One·Lauren M ChildsRachel J Whitaker

Citations

Dec 16, 1998·Trends in Biochemical Sciences·S F Altschul, Eugene V Koonin
Mar 13, 1999·Nature Structural Biology·C KleanthousA M Hemmings
Aug 16, 2000·Proceedings of the National Academy of Sciences of the United States of America·D M Lilley, M F White
Dec 19, 2000·Proteins·J Pei, Nick V Grishin
Mar 28, 2002·Nucleic Acids Research·Vivek AnantharamanL Aravind
Apr 16, 2002·Molecular Microbiology·Ruud JansenLeo M Schouls
Jul 20, 2002·Current Opinion in Structural Biology·L AravindEugene V Koonin
Apr 10, 2003·Trends in Genetics : TIG·Kira S MakarovaEugene V Koonin
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Apr 7, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Thomas A Steitz, Y Whitney Yin
Jun 25, 2004·Nucleic Acids Research·Aron Marchler-Bauer, Stephen H Bryant
Nov 9, 2004·Bioinformatics·Johannes Söding
Mar 29, 2005·Journal of Molecular Evolution·F J M MojicaElena Soria
Jul 18, 2006·Nucleic Acids Research·Johannes SödingAndrei N Lupas
Mar 24, 2007·Science·Rodolphe BarrangouPhilippe Horvath
Apr 28, 2007·Molecular Microbiology·Mitsuoki KawanoGisela Storz
May 15, 2007·Journal of Molecular Biology·Arturas JakubauskasArvydas Janulaitis
May 9, 2008·Nucleic Acids Research·Christian ColeGeoffrey J Barton
May 17, 2008·The Journal of Biological Chemistry·Natalia BeloglazovaAlexander F Yakunin
Aug 8, 2008·Biology Direct·Igor B RogozinEugene V Koonin
Aug 16, 2008·Science·Stan J J BrounsJohn van der Oost
Dec 20, 2008·Science·Luciano A Marraffini, Erik J Sontheimer
Jan 15, 2009·Genes & Development·Jason CarteMichael P Terns
Jan 24, 2009·EMBO Reports·Marcin Nowotny
Jan 29, 2009·FEBS Letters·Dong Han, Gerhard Krauss
Mar 28, 2009·PLoS Genetics·Laurence Van Melderen, Manuel Saavedra De Bast
Jun 16, 2009·Structure·Luciano A Marraffini, Erik J Sontheimer

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Zinc Fingers
Immune Response
Transverse Tubule of Muscle Cell
Polymerase
Deoxyribonuclease I
Phanaeus furiosus
Bacterial Proteins
Molecular Helix
Zinc Ion Binding
Protein Family

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