Literature DB >> 33483498

CRISPR technologies and the search for the PAM-free nuclease.

Daphne Collias1, Chase L Beisel2,3,4.   

Abstract

The ever-expanding set of CRISPR technologies and their programmable RNA-guided nucleases exhibit remarkable flexibility in DNA targeting. However, this flexibility comes with an ever-present constraint: the requirement for a protospacer adjacent motif (PAM) flanking each target. While PAMs play an essential role in self/nonself discrimination by CRISPR-Cas immune systems, this constraint has launched a far-reaching expedition for nucleases with relaxed PAM requirements. Here, we review ongoing efforts toward realizing PAM-free nucleases through natural ortholog mining and protein engineering. We also address potential consequences of fully eliminating PAM recognition and instead propose an alternative nuclease repertoire covering all possible PAM sequences.

Entities:  

Year:  2021        PMID: 33483498      PMCID: PMC7822910          DOI: 10.1038/s41467-020-20633-y

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  112 in total

1.  Protein building blocks preserved by recombination.

Authors:  Christopher A Voigt; Carlos Martinez; Zhen-Gang Wang; Stephen L Mayo; Frances H Arnold
Journal:  Nat Struct Biol       Date:  2002-07

2.  Applications of CRISPR technologies in research and beyond.

Authors:  Rodolphe Barrangou; Jennifer A Doudna
Journal:  Nat Biotechnol       Date:  2016-09-08       Impact factor: 54.908

3.  High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli.

Authors:  Suhyung Cho; Donghui Choe; Eunju Lee; Sun Chang Kim; Bernhard Palsson; Byung-Kwan Cho
Journal:  ACS Synth Biol       Date:  2018-03-21       Impact factor: 5.110

4.  Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems.

Authors:  Ryan T Leenay; Kenneth R Maksimchuk; Rebecca A Slotkowski; Roma N Agrawal; Ahmed A Gomaa; Alexandra E Briner; Rodolphe Barrangou; Chase L Beisel
Journal:  Mol Cell       Date:  2016-03-31       Impact factor: 17.970

Review 5.  Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.

Authors:  Kira S Makarova; Yuri I Wolf; Jaime Iranzo; Sergey A Shmakov; Omer S Alkhnbashi; Stan J J Brouns; Emmanuelle Charpentier; David Cheng; Daniel H Haft; Philippe Horvath; Sylvain Moineau; Francisco J M Mojica; David Scott; Shiraz A Shah; Virginijus Siksnys; Michael P Terns; Česlovas Venclovas; Malcolm F White; Alexander F Yakunin; Winston Yan; Feng Zhang; Roger A Garrett; Rolf Backofen; John van der Oost; Rodolphe Barrangou; Eugene V Koonin
Journal:  Nat Rev Microbiol       Date:  2019-12-19       Impact factor: 60.633

6.  A system for the continuous directed evolution of biomolecules.

Authors:  Kevin M Esvelt; Jacob C Carlson; David R Liu
Journal:  Nature       Date:  2011-04-10       Impact factor: 49.962

7.  Engineered Cpf1 variants with altered PAM specificities.

Authors:  Linyi Gao; David B T Cox; Winston X Yan; John C Manteiga; Martin W Schneider; Takashi Yamano; Hiroshi Nishimasu; Osamu Nureki; Nicola Crosetto; Feng Zhang
Journal:  Nat Biotechnol       Date:  2017-06-05       Impact factor: 54.908

8.  Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9.

Authors:  Seiichi Hirano; Omar O Abudayyeh; Jonathan S Gootenberg; Takuro Horii; Ryuichiro Ishitani; Izuho Hatada; Feng Zhang; Hiroshi Nishimasu; Osamu Nureki
Journal:  Nat Commun       Date:  2019-04-29       Impact factor: 14.919

9.  Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes.

Authors:  Shayesteh R Ferdosi; Radwa Ewaisha; Farzaneh Moghadam; Sri Krishna; Jin G Park; Mo R Ebrahimkhani; Samira Kiani; Karen S Anderson
Journal:  Nat Commun       Date:  2019-04-23       Impact factor: 14.919

10.  Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs.

Authors:  Thomas Jacobsen; Fani Ttofali; Chunyu Liao; Srinivas Manchalu; Benjamin N Gray; Chase L Beisel
Journal:  Nucleic Acids Res       Date:  2020-06-04       Impact factor: 16.971

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  25 in total

1.  A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes.

Authors:  Franziska Wimmer; Frank Englert; Chase L Beisel
Journal:  Methods Mol Biol       Date:  2022

Review 2.  Fine-tuning gene expression for improved biosynthesis of natural products: From transcriptional to post-translational regulation.

Authors:  Chenyi Li; Tian Jiang; Michelle Li; Yusong Zou; Yajun Yan
Journal:  Biotechnol Adv       Date:  2021-10-09       Impact factor: 14.227

3.  Precise DNA cleavage using CRISPR-SpRYgests.

Authors:  Kathleen A Christie; Jimmy A Guo; Rachel A Silverstein; Roman M Doll; Megumu Mabuchi; Hannah E Stutzman; Jiecong Lin; Linyuan Ma; Russell T Walton; Luca Pinello; G Brett Robb; Benjamin P Kleinstiver
Journal:  Nat Biotechnol       Date:  2022-10-06       Impact factor: 68.164

Review 4.  Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses.

Authors:  Md Mamunul Islam; Dipak Koirala
Journal:  Anal Chim Acta       Date:  2021-12-01       Impact factor: 6.911

5.  Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons.

Authors:  Sanne E Klompe; Nora Jaber; Leslie Y Beh; Jason T Mohabir; Aude Bernheim; Samuel H Sternberg
Journal:  Mol Cell       Date:  2022-01-19       Impact factor: 19.328

Review 6.  CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security.

Authors:  Susheel Kumar Sharma; Om Prakash Gupta; Neeta Pathaw; Devender Sharma; Albert Maibam; Parul Sharma; Jyotsana Sanasam; Suhas Gorakh Karkute; Sandeep Kumar; Bijoya Bhattacharjee
Journal:  Front Nutr       Date:  2021-12-16

Review 7.  Genome Editing for Improving Crop Nutrition.

Authors:  Ai Nagamine; Hiroshi Ezura
Journal:  Front Genome Ed       Date:  2022-02-09

8.  Competitive dCas9 binding as a mechanism for transcriptional control.

Authors:  Daniel A Anderson; Christopher A Voigt
Journal:  Mol Syst Biol       Date:  2021-11       Impact factor: 11.429

Review 9.  Cell and Gene Therapy for Anemia: Hematopoietic Stem Cells and Gene Editing.

Authors:  Dito Anurogo; Nova Yuli Prasetyo Budi; Mai-Huong Thi Ngo; Yen-Hua Huang; Jeanne Adiwinata Pawitan
Journal:  Int J Mol Sci       Date:  2021-06-10       Impact factor: 5.923

Review 10.  Advances in Editing Silkworms (Bombyx mori) Genome by Using the CRISPR-Cas System.

Authors:  Gabriela-Maria Baci; Alexandra-Antonia Cucu; Alexandru-Ioan Giurgiu; Adriana-Sebastiana Muscă; Lilla Bagameri; Adela Ramona Moise; Otilia Bobiș; Attila Cristian Rațiu; Daniel Severus Dezmirean
Journal:  Insects       Date:  2021-12-27       Impact factor: 2.769

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