Literature DB >> 25398355

Protein engineering of Cas9 for enhanced function.

Benjamin L Oakes1, Dana C Nadler2, David F Savage3.   

Abstract

CRISPR/Cas systems act to protect the cell from invading nucleic acids in many bacteria and archaea. The bacterial immune protein Cas9 is a component of one of these CRISPR/Cas systems and has recently been adapted as a tool for genome editing. Cas9 is easily targeted to bind and cleave a DNA sequence via a complementary RNA; this straightforward programmability has gained Cas9 rapid acceptance in the field of genetic engineering. While this technology has developed quickly, a number of challenges regarding Cas9 specificity, efficiency, fusion protein function, and spatiotemporal control within the cell remain. In this work, we develop a platform for constructing novel proteins to address these open questions. We demonstrate methods to either screen or select active Cas9 mutants and use the screening technique to isolate functional Cas9 variants with a heterologous PDZ domain inserted within the protein. As a proof of concept, these methods lay the groundwork for the future construction of diverse Cas9 proteins. Straightforward and accessible techniques for genetic editing are helping to elucidate biology in new and exciting ways; a platform to engineer new functionalities into Cas9 will help forge the next generation of genome-modifying tools.

Entities:  

Keywords:  BH; CRISPR; Cas9; DNA; EM; FACS; GFP; Gene activation/repression; Genome editing; HR; IPTG; IT dCas9; LB; NHEJ; NUC; Nuclease; PAM; PDZ; PI; Protein engineering; REC; RFP; RNA; SOB; SOC; SpCas9; Synthetic biology; WT dCas9; aTC; crRNA; dCas9; sgRNA; ssDNA; tracrRNA

Mesh:

Substances:

Year:  2014        PMID: 25398355      PMCID: PMC4641071          DOI: 10.1016/B978-0-12-801185-0.00024-6

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


  43 in total

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2.  A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

Authors:  Martin Jinek; Krzysztof Chylinski; Ines Fonfara; Michael Hauer; Jennifer A Doudna; Emmanuelle Charpentier
Journal:  Science       Date:  2012-06-28       Impact factor: 47.728

3.  Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

Authors:  Lei S Qi; Matthew H Larson; Luke A Gilbert; Jennifer A Doudna; Jonathan S Weissman; Adam P Arkin; Wendell A Lim
Journal:  Cell       Date:  2013-02-28       Impact factor: 41.582

4.  Multiplex genome engineering using CRISPR/Cas systems.

Authors:  Le Cong; F Ann Ran; David Cox; Shuailiang Lin; Robert Barretto; Naomi Habib; Patrick D Hsu; Xuebing Wu; Wenyan Jiang; Luciano A Marraffini; Feng Zhang
Journal:  Science       Date:  2013-01-03       Impact factor: 47.728

5.  RNA-guided human genome engineering via Cas9.

Authors:  Prashant Mali; Luhan Yang; Kevin M Esvelt; John Aach; Marc Guell; James E DiCarlo; Julie E Norville; George M Church
Journal:  Science       Date:  2013-01-03       Impact factor: 47.728

6.  One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering.

Authors:  Haoyi Wang; Hui Yang; Chikdu S Shivalila; Meelad M Dawlaty; Albert W Cheng; Feng Zhang; Rudolf Jaenisch
Journal:  Cell       Date:  2013-05-02       Impact factor: 41.582

7.  CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes.

Authors:  Luke A Gilbert; Matthew H Larson; Leonardo Morsut; Zairan Liu; Gloria A Brar; Sandra E Torres; Noam Stern-Ginossar; Onn Brandman; Evan H Whitehead; Jennifer A Doudna; Wendell A Lim; Jonathan S Weissman; Lei S Qi
Journal:  Cell       Date:  2013-07-11       Impact factor: 41.582

8.  CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.

Authors:  Elitza Deltcheva; Krzysztof Chylinski; Cynthia M Sharma; Karine Gonzales; Yanjie Chao; Zaid A Pirzada; Maria R Eckert; Jörg Vogel; Emmanuelle Charpentier
Journal:  Nature       Date:  2011-03-31       Impact factor: 49.962

9.  Efficient genome editing in zebrafish using a CRISPR-Cas system.

Authors:  Woong Y Hwang; Yanfang Fu; Deepak Reyon; Morgan L Maeder; Shengdar Q Tsai; Jeffry D Sander; Randall T Peterson; J-R Joanna Yeh; J Keith Joung
Journal:  Nat Biotechnol       Date:  2013-01-29       Impact factor: 54.908

10.  Linking the functions of unrelated proteins using a novel directed evolution domain insertion method.

Authors:  Wayne R Edwards; Kathy Busse; Rudolf K Allemann; D Dafydd Jones
Journal:  Nucleic Acids Res       Date:  2008-06-17       Impact factor: 16.971

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  9 in total

1.  CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification.

Authors:  Benjamin L Oakes; Christof Fellmann; Harneet Rishi; Kian L Taylor; Shawn M Ren; Dana C Nadler; Rayka Yokoo; Adam P Arkin; Jennifer A Doudna; David F Savage
Journal:  Cell       Date:  2019-01-10       Impact factor: 41.582

2.  Rapid construction of metabolite biosensors using domain-insertion profiling.

Authors:  Dana C Nadler; Stacy-Anne Morgan; Avi Flamholz; Kaitlyn E Kortright; David F Savage
Journal:  Nat Commun       Date:  2016-07-29       Impact factor: 14.919

3.  CasX enzymes comprise a distinct family of RNA-guided genome editors.

Authors:  Jun-Jie Liu; Natalia Orlova; Benjamin L Oakes; Enbo Ma; Hannah B Spinner; Katherine L M Baney; Jonathan Chuck; Dan Tan; Gavin J Knott; Lucas B Harrington; Basem Al-Shayeb; Alexander Wagner; Julian Brötzmann; Brett T Staahl; Kian L Taylor; John Desmarais; Eva Nogales; Jennifer A Doudna
Journal:  Nature       Date:  2019-02-04       Impact factor: 49.962

Review 4.  CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering.

Authors:  Maryam Saifaldeen; Dana E Al-Ansari; Dindial Ramotar; Mustapha Aouida
Journal:  Cells       Date:  2020-11-21       Impact factor: 6.600

5.  mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence.

Authors:  Gregory C Finnigan; Jeremy Thorner
Journal:  G3 (Bethesda)       Date:  2016-07-07       Impact factor: 3.154

6.  Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch.

Authors:  Benjamin L Oakes; Dana C Nadler; Avi Flamholz; Christof Fellmann; Brett T Staahl; Jennifer A Doudna; David F Savage
Journal:  Nat Biotechnol       Date:  2016-05-02       Impact factor: 54.908

7.  RNA-guided retargeting of Sleeping Beauty transposition in human cells.

Authors:  Adrian Kovač; Csaba Miskey; Michael Menzel; Esther Grueso; Andreas Gogol-Döring; Zoltán Ivics
Journal:  Elife       Date:  2020-03-06       Impact factor: 8.140

8.  Engineering of the genome editing protein Cas9 to slide along DNA.

Authors:  Trishit Banerjee; Hiroto Takahashi; Dwiky Rendra Graha Subekti; Kiyoto Kamagata
Journal:  Sci Rep       Date:  2021-07-08       Impact factor: 4.379

9.  Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules.

Authors:  Arik Shams; Sean A Higgins; Christof Fellmann; Thomas G Laughlin; Benjamin L Oakes; Rachel Lew; Shin Kim; Maria Lukarska; Madeline Arnold; Brett T Staahl; Jennifer A Doudna; David F Savage
Journal:  Nat Commun       Date:  2021-09-27       Impact factor: 14.919

  9 in total

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