Literature DB >> 28605718

Diversity, classification and evolution of CRISPR-Cas systems.

Eugene V Koonin1, Kira S Makarova2, Feng Zhang3.   

Abstract

The bacterial and archaeal CRISPR-Cas systems of adaptive immunity show remarkable diversity of protein composition, effector complex structure, genome locus architecture and mechanisms of adaptation, pre-CRISPR (cr)RNA processing and interference. The CRISPR-Cas systems belong to two classes, with multi-subunit effector complexes in Class 1 and single-protein effector modules in Class 2. Concerted genomic and experimental efforts on comprehensive characterization of Class 2 CRISPR-Cas systems led to the identification of two new types and several subtypes. The newly characterized type VI systems are the first among the CRISPR-Cas variants to exclusively target RNA. Unexpectedly, in some of the class 2 systems, the effector protein is additionally responsible for the pre-crRNA processing. Comparative analysis of the effector complexes indicates that Class 2 systems evolved from mobile genetic elements on multiple, independent occasions. Published by Elsevier Ltd.

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Mesh：

Year:  2017        PMID： 28605718      PMCID： PMC5776717          DOI： 10.1016/j.mib.2017.05.008

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN： 1369-5274            Impact factor:   7.934


  71 in total

1.  Crystal Structure of Staphylococcus aureus Cas9.

Authors:  Hiroshi Nishimasu; Le Cong; Winston X Yan; F Ann Ran; Bernd Zetsche; Yinqing Li; Arisa Kurabayashi; Ryuichiro Ishitani; Feng Zhang; Osamu Nureki
Journal:  Cell       Date:  2015-08-27       Impact factor: 41.582

2.  CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes.

Authors:  Alexis C Komor; Ahmed H Badran; David R Liu
Journal:  Cell       Date:  2017-04-20       Impact factor: 41.582

Review 3.  Coupling immunity and programmed cell suicide in prokaryotes: Life-or-death choices.

Authors:  Eugene V Koonin; Feng Zhang
Journal:  Bioessays       Date:  2016-11-29       Impact factor: 4.345

4.  Structure and Engineering of Francisella novicida Cas9.

Authors:  Hisato Hirano; Jonathan S Gootenberg; Takuro Horii; Omar O Abudayyeh; Mika Kimura; Patrick D Hsu; Takanori Nakane; Ryuichiro Ishitani; Izuho Hatada; Feng Zhang; Hiroshi Nishimasu; Osamu Nureki
Journal:  Cell       Date:  2016-02-11       Impact factor: 41.582

5.  Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity.

Authors:  Wenyan Jiang; Poulami Samai; Luciano A Marraffini
Journal:  Cell       Date:  2016-02-04       Impact factor: 41.582

6.  Diversity and evolution of class 2 CRISPR-Cas systems.

Authors:  Sergey Shmakov; Aaron Smargon; David Scott; David Cox; Neena Pyzocha; Winston Yan; Omar O Abudayyeh; Jonathan S Gootenberg; Kira S Makarova; Yuri I Wolf; Konstantin Severinov; Feng Zhang; Eugene V Koonin
Journal:  Nat Rev Microbiol       Date:  2017-01-23       Impact factor: 60.633

7.  Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems.

Authors:  Sergey Shmakov; Omar O Abudayyeh; Kira S Makarova; Yuri I Wolf; Jonathan S Gootenberg; Ekaterina Semenova; Leonid Minakhin; Julia Joung; Silvana Konermann; Konstantin Severinov; Feng Zhang; Eugene V Koonin
Journal:  Mol Cell       Date:  2015-10-22       Impact factor: 17.970

Review 8.  An updated evolutionary classification of CRISPR-Cas systems.

Authors:  Kira S Makarova; Yuri I Wolf; Omer S Alkhnbashi; Fabrizio Costa; Shiraz A Shah; Sita J Saunders; Rodolphe Barrangou; Stan J J Brouns; Emmanuelle Charpentier; Daniel H Haft; Philippe Horvath; Sylvain Moineau; Francisco J M Mojica; Rebecca M Terns; Michael P Terns; Malcolm F White; Alexander F Yakunin; Roger A Garrett; John van der Oost; Rolf Backofen; Eugene V Koonin
Journal:  Nat Rev Microbiol       Date:  2015-09-28       Impact factor: 60.633

9.  RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus.

Authors:  Raymond H J Staals; Yifan Zhu; David W Taylor; Jack E Kornfeld; Kundan Sharma; Arjan Barendregt; Jasper J Koehorst; Marnix Vlot; Nirajan Neupane; Koen Varossieau; Keiko Sakamoto; Takehiro Suzuki; Naoshi Dohmae; Shigeyuki Yokoyama; Peter J Schaap; Henning Urlaub; Albert J R Heck; Eva Nogales; Jennifer A Doudna; Akeo Shinkai; John van der Oost
Journal:  Mol Cell       Date:  2014-11-06       Impact factor: 17.970

10.  Altered stoichiometry Escherichia coli Cascade complexes with shortened CRISPR RNA spacers are capable of interference and primed adaptation.

Authors:  Konstantin Kuznedelov; Vladimir Mekler; Sofia Lemak; Monika Tokmina-Lukaszewska; Kirill A Datsenko; Ishita Jain; Ekaterina Savitskaya; John Mallon; Sergey Shmakov; Brian Bothner; Scott Bailey; Alexander F Yakunin; Konstantin Severinov; Ekaterina Semenova
Journal:  Nucleic Acids Res       Date:  2016-10-13       Impact factor: 16.971
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  377 in total

1.  Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes.

Authors:  Beatriz A Osuna; Shweta Karambelkar; Caroline Mahendra; Kathleen A Christie; Bianca Garcia; Alan R Davidson; Benjamin P Kleinstiver; Samuel Kilcher; Joseph Bondy-Denomy
Journal:  Cell Host Microbe       Date:  2020-04-22       Impact factor: 21.023

2.  Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity.

Authors:  Ning Jia; Charlie Y Mo; Chongyuan Wang; Edward T Eng; Luciano A Marraffini; Dinshaw J Patel
Journal:  Mol Cell       Date:  2018-11-29       Impact factor: 17.970

3.  Dynamics of Cas10 Govern Discrimination between Self and Non-self in Type III CRISPR-Cas Immunity.

Authors:  Ling Wang; Charlie Y Mo; Michael R Wasserman; Jakob T Rostøl; Luciano A Marraffini; Shixin Liu
Journal:  Mol Cell       Date:  2018-11-29       Impact factor: 17.970

4.  Cas4 Nucleases Can Effect Specific Integration of CRISPR Spacers.

Authors:  Zhufeng Zhang; Saifu Pan; Tao Liu; Yingjun Li; Nan Peng
Journal:  J Bacteriol       Date:  2019-05-22       Impact factor: 3.490

5.  Francisella novicida CRISPR-Cas Systems Can Functionally Complement Each Other in DNA Defense while Providing Target Flexibility.

Authors:  Hannah K Ratner; David S Weiss
Journal:  J Bacteriol       Date:  2020-05-27       Impact factor: 3.490

Review 6.  Unveiling Human Non-Random Genome Editing Mechanisms Activated in Response to Chronic Environmental Changes: I. Where Might These Mechanisms Come from and What Might They Have Led To?

Authors:  Loris Zamai
Journal:  Cells       Date:  2020-10-27       Impact factor: 6.600

7.  PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage.

Authors:  Tautvydas Karvelis; Greta Bigelyte; Joshua K Young; Zhenglin Hou; Rimante Zedaveinyte; Karolina Budre; Sushmitha Paulraj; Vesna Djukanovic; Stephen Gasior; Arunas Silanskas; Česlovas Venclovas; Virginijus Siksnys
Journal:  Nucleic Acids Res       Date:  2020-05-21       Impact factor: 16.971

8.  Covalent Modifications of the Bacteriophage Genome Confer a Degree of Resistance to Bacterial CRISPR Systems.

Authors:  Yuepeng Liu; Li Dai; Junhua Dong; Cen Chen; Jingen Zhu; Venigalla B Rao; Pan Tao
Journal:  J Virol       Date:  2020-11-09       Impact factor: 5.103

9.  Using the Endogenous CRISPR-Cas System of Heliobacterium modesticaldum To Delete the Photochemical Reaction Center Core Subunit Gene.

Authors:  Patricia L Baker; Gregory S Orf; Kimberly Kevershan; Michael E Pyne; Taner Bicer; Kevin E Redding
Journal:  Appl Environ Microbiol       Date:  2019-11-14       Impact factor: 4.792

10.  Phosphate Lock Residues of Acidothermus cellulolyticus Cas9 Are Critical to Its Substrate Specificity.

Authors:  Travis H Hand; Anuska Das; Mitchell O Roth; Chardasia L Smith; Uriel L Jean-Baptiste; Hong Li
Journal:  ACS Synth Biol       Date:  2018-12-03       Impact factor: 5.110
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