Literature DB >> 27588603

DNA Targeting by a Minimal CRISPR RNA-Guided Cascade.

Megan L Hochstrasser1, David W Taylor2, Jack E Kornfeld3, Eva Nogales4, Jennifer A Doudna5.   

Abstract

Bacteria employ surveillance complexes guided by CRISPR (clustered, regularly interspaced, short palindromic repeats) RNAs (crRNAs) to target foreign nucleic acids for destruction. Although most type I and type III CRISPR systems require four or more distinct proteins to form multi-subunit surveillance complexes, the type I-C systems use just three proteins to achieve crRNA maturation and double-stranded DNA target recognition. We show that each protein plays multiple functional and structural roles: Cas5c cleaves pre-crRNAs and recruits Cas7 to position the RNA guide for DNA binding and unwinding by Cas8c. Cryoelectron microscopy reconstructions of free and DNA-bound forms of the Cascade/I-C surveillance complex reveal conformational changes that enable R-loop formation with distinct positioning of each DNA strand. This streamlined type I-C system explains how CRISPR pathways can evolve compact structures that retain full functionality as RNA-guided DNA capture platforms.
Copyright © 2016 Elsevier Inc. All rights reserved.

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Year:  2016        PMID: 27588603      PMCID: PMC5111854          DOI: 10.1016/j.molcel.2016.07.027

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  52 in total

1.  Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.

Authors:  Zhucheng Chen; Haijuan Yang; Nikola P Pavletich
Journal:  Nature       Date:  2008-05-22       Impact factor: 49.962

2.  Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog.

Authors:  Takuo Osawa; Hideko Inanaga; Chikara Sato; Tomoyuki Numata
Journal:  Mol Cell       Date:  2015-04-23       Impact factor: 17.970

3.  Structural Principles of CRISPR RNA Processing.

Authors:  Hong Li
Journal:  Structure       Date:  2014-11-26       Impact factor: 5.006

4.  Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system.

Authors:  Ki Hyun Nam; Charles Haitjema; Xueqi Liu; Fran Ding; Hongwei Wang; Matthew P DeLisa; Ailong Ke
Journal:  Structure       Date:  2012-07-26       Impact factor: 5.006

5.  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

6.  In vitro reconstitution of an Escherichia coli RNA-guided immune system reveals unidirectional, ATP-dependent degradation of DNA target.

Authors:  Sabin Mulepati; Scott Bailey
Journal:  J Biol Chem       Date:  2013-06-11       Impact factor: 5.157

7.  Structures of the RNA-guided surveillance complex from a bacterial immune system.

Authors:  Blake Wiedenheft; Gabriel C Lander; Kaihong Zhou; Matthijs M Jore; Stan J J Brouns; John van der Oost; Jennifer A Doudna; Eva Nogales
Journal:  Nature       Date:  2011-09-21       Impact factor: 49.962

8.  Sequence- and structure-specific RNA processing by a CRISPR endonuclease.

Authors:  Rachel E Haurwitz; Martin Jinek; Blake Wiedenheft; Kaihong Zhou; Jennifer A Doudna
Journal:  Science       Date:  2010-09-10       Impact factor: 47.728

9.  Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex.

Authors:  Timothy R Blosser; Luuk Loeff; Edze R Westra; Marnix Vlot; Tim Künne; Małgorzata Sobota; Cees Dekker; Stan J J Brouns; Chirlmin Joo
Journal:  Mol Cell       Date:  2015-03-05       Impact factor: 17.970

10.  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

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  23 in total

Review 1.  Microbiology catches the cryo-EM bug.

Authors:  Lesley A Earl; Veronica Falconieri; Sriram Subramaniam
Journal:  Curr Opin Microbiol       Date:  2018-04-12       Impact factor: 7.934

2.  Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.

Authors:  Yibei Xiao; Min Luo; Robert P Hayes; Jonathan Kim; Sherwin Ng; Fang Ding; Maofu Liao; Ailong Ke
Journal:  Cell       Date:  2017-06-29       Impact factor: 41.582

3.  Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis.

Authors:  Sergey A Shmakov; Kira S Makarova; Yuri I Wolf; Konstantin V Severinov; Eugene V Koonin
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-21       Impact factor: 11.205

4.  Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex.

Authors:  Saikat Chowdhury; Joshua Carter; MaryClare F Rollins; Sarah M Golden; Ryan N Jackson; Connor Hoffmann; Lyn'Al Nosaka; Joseph Bondy-Denomy; Karen L Maxwell; Alan R Davidson; Elizabeth R Fischer; Gabriel C Lander; Blake Wiedenheft
Journal:  Cell       Date:  2017-03-23       Impact factor: 41.582

Review 5.  Diversity, classification and evolution of CRISPR-Cas systems.

Authors:  Eugene V Koonin; Kira S Makarova; Feng Zhang
Journal:  Curr Opin Microbiol       Date:  2017-06-09       Impact factor: 7.934

6.  Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry.

Authors:  MaryClare F Rollins; Saikat Chowdhury; Joshua Carter; Sarah M Golden; Heini M Miettinen; Andrew Santiago-Frangos; Dominick Faith; C Martin Lawrence; Gabriel C Lander; Blake Wiedenheft
Journal:  Mol Cell       Date:  2019-03-11       Impact factor: 17.970

7.  Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs in the Porphyromonas gingivalis CRISPR-Cas I-C System.

Authors:  Michal Burmistrz; Jose Ignacio Rodriguez Martinez; Daniel Krochmal; Dominika Staniec; Krzysztof Pyrc
Journal:  J Bacteriol       Date:  2017-10-31       Impact factor: 3.490

8.  CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.

Authors:  Paola Soto-Perez; Jordan E Bisanz; Joel D Berry; Kathy N Lam; Joseph Bondy-Denomy; Peter J Turnbaugh
Journal:  Cell Host Microbe       Date:  2019-09-03       Impact factor: 21.023

9.  Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex.

Authors:  Tai Wei Guo; Alberto Bartesaghi; Hui Yang; Veronica Falconieri; Prashant Rao; Alan Merk; Edward T Eng; Ashleigh M Raczkowski; Tara Fox; Lesley A Earl; Dinshaw J Patel; Sriram Subramaniam
Journal:  Cell       Date:  2017-10-05       Impact factor: 41.582

10.  A compact Cascade-Cas3 system for targeted genome engineering.

Authors:  Bálint Csörgő; Lina M León; Ilea J Chau-Ly; Alejandro Vasquez-Rifo; Joel D Berry; Caroline Mahendra; Emily D Crawford; Jennifer D Lewis; Joseph Bondy-Denomy
Journal:  Nat Methods       Date:  2020-10-19       Impact factor: 28.547

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