CRISPR-Cas9/Cas12a biotechnology and application in bacteria

Yao, Ruilian; Liu, Di; Jia, Xiao; Zheng, Yuan; Liu, Wei; Xiao, Yi

doi:10.1016/j.synbio.2018.09.004

Title: CRISPR-Cas9/Cas12a biotechnology and application in bacteria

Journal Article · 02 October 2018 · Synthetic and Systems Biotechnology

DOI: https://doi.org/10.1016/j.synbio.2018.09.004 · OSTI ID:1629058

Yao, Ruilian ^[1]; Liu, Di ^[2]; Jia, Xiao ^[3]; Zheng, Yuan ^[3]; Liu, Wei ^[3]; Xiao, Yi ^[3]

Shanghai Jiao Tong Univ. (China). State Key Lab. of Microbial Metabolism; Shanghai Jiao Tong University
Sandia National Laboratories, Livermore, CA (United States). Dept. of Biomass Science and Conversion Technology
Shanghai Jiao Tong Univ. (China). State Key Lab. of Microbial Metabolism

CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nucleasedependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.

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Research Organization:: Sandia National Laboratories (SNL), Livermore, CA (United States)

Sponsoring Organization:: China Postdoctoral Science Foundation; Natural Science Foundation of Shanghai; Science and Technology Commission of Shanghai Municipality; USDOE

Grant/Contract Number:: NA0003525

OSTI ID:: 1629058

Journal Information:: Synthetic and Systems Biotechnology, Journal Name: Synthetic and Systems Biotechnology Journal Issue: 3 Vol. 3; ISSN 2405-805X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Applications of CRISPR/Cas System to Bacterial Metabolic Engineering Cho, Suhyung; Shin, Jongoh; Cho, Byung-Kwan International Journal of Molecular Sciences, Vol. 19, Issue 4 https://doi.org/10.3390/ijms19041089	journal	April 2018
Natural Products from Mangrove Actinomycetes Xu, Dong-Bo; Ye, Wan-Wan; Han, Ying Marine Drugs, Vol. 12, Issue 5 https://doi.org/10.3390/md12052590	journal	May 2014
Genome editing of Clostridium autoethanogenum using CRISPR/Cas9 Nagaraju, Shilpa; Davies, Naomi; Walker, David Figshare https://doi.org/10.6084/m9.figshare.c.3596099	collection	January 2016
Bio-based 3-hydroxypropionic- and acrylic acid production from biodiesel glycerol via integrated microbial and chemical catalysis Dishisha, Tarek; Pyo, Sang-Hyun; Hatti-Kaul, Rajni Figshare https://doi.org/10.6084/m9.figshare.c.3607055.v1	collection	January 2015
CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973 [Supplemental Data] Wendt, Kristen; Ungerer, Justin; Cobb, Ryan figshare-Supplementary information for journal article at DOI: 10.1186/s12934-016-0514-7, 1 DOCX file (70.56 kB) https://doi.org/10.6084/m9.figshare.c.3611978	preprint	June 2016
Utilising the native plasmid, pCA2.4, from the cyanobacterium Synechocystis sp. strain PCC6803 as a cloning site for enhanced product production Armshaw, Patricia; Carey, Dawn; Sheahan, Con Figshare https://doi.org/10.6084/m9.figshare.c.3612665	collection	January 2015
WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system Wong, Nathan; Liu, Weijun; Wang, Xiaowei figshare https://doi.org/10.6084/m9.figshare.c.3635516	collection	January 2015
Efficient gene editing in Corynebacterium glutamicum using the CRISPR/Cas9 system Peng, Feng; Wang, Xinyue; Sun, Yang figshare https://doi.org/10.6084/m9.figshare.c.3930493.v1	collection	January 2017
Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum Liu, Jiao; Wang, Yu; Lu, Yujiao figshare https://doi.org/10.6084/m9.figshare.c.3933031.v1	collection	January 2017
RNA-guided single/double gene repressions in Corynebacterium glutamicum using an efficient CRISPR interference and its application to industrial strain Park, Jaehyun; Shin, Hyojung; Lee, Sun-Mi figshare https://doi.org/10.6084/m9.figshare.c.3972612	collection	January 2018
CRISPR/dCas9-mediated transcriptional improvement of the biosynthetic gene cluster for the epothilone production in Myxococcus xanthus Peng, Ran; Wang, Ye; Feng, Wan-wan figshare https://doi.org/10.6084/m9.figshare.c.3990012.v1	collection	January 2018
Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system Sun, Jun; Wang, Qingzhuo; Jiang, Yu figshare https://doi.org/10.6084/m9.figshare.c.4030942	collection	January 2018
Engineering CRISPR interference system in Klebsiella pneumoniae for attenuating lactic acid synthesis Wang, Jingxuan; Zhao, Peng; Li, Ying figshare https://doi.org/10.6084/m9.figshare.c.4061291.v1	collection	January 2018
A RecET-assisted CRISPR–Cas9 genome editing in Corynebacterium glutamicum Wang, Bo; Hu, Qitiao; Zhang, Yu figshare https://doi.org/10.6084/m9.figshare.c.4078625.v1	collection	January 2018

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Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology Zhang, Shangjie; Guo, Feng; Yan, Wei Frontiers in Bioengineering and Biotechnology, Vol. 7 https://doi.org/10.3389/fbioe.2019.00459	journal	January 2020
Endogenous Type I CRISPR-Cas: From Foreign DNA Defense to Prokaryotic Engineering Zheng, Yanli; Li, Jie; Wang, Baiyang Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00062	journal	March 2020
CRISPR, Prime Editing, Optogenetics, and DREADDs: New Therapeutic Approaches Provided by Emerging Technologies in the Treatment of Spinal Cord Injury Paschon, Vera; Correia, Felipe Fernandes; Morena, Beatriz Cintra Molecular Neurobiology, Vol. 57, Issue 4 https://doi.org/10.1007/s12035-019-01861-w	journal	January 2020
Listeria Phages Induce Cas9 Degradation to Protect Lysogenic Genomes Osuna, Beatriz A.; Karambelkar, Shweta; Mahendra, Caroline Cell Host & Microbe, Vol. 28, Issue 1 https://doi.org/10.1016/j.chom.2020.04.001	journal	July 2020
Rewiring cellular metabolism for heterologous biosynthesis of Taxol Nazhand, Amirhossein; Durazzo, Alessandra; Lucarini, Massimo Natural Product Research, Vol. 34, Issue 1 https://doi.org/10.1080/14786419.2019.1630122	journal	July 2019
Characterization and repurposing of the endogenous Type I-F CRISPR–Cas system of Zymomonas mobilis for genome engineering Zheng, Yanli; Han, Jiamei; Wang, Baiyang Nucleic Acids Research, Vol. 47, Issue 21 https://doi.org/10.1093/nar/gkz940	journal	October 2019
Establishment and application of a CRISPR–Cas12a assisted genome-editing system in Zymomonas mobilis Shen, Wei; Zhang, Jun; Geng, Binan Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1219-5	journal	October 2019

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