CRISPR-derived genome editing technologies for metabolic engineering

Developing a base‐editing system to expand the carbon source utilization spectra of Shewanella oneidensis MR‐1 for enhanced pollutant degradation

(2020) Lei Cheng et al.   BIOTECHNOLOGY AND BIOENGINEERING

CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1

(2020) Yufeng Luo et al.   Microbial Cell Factories

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Perturbing proteomes at single residue resolution using base editing

(2020) Philippe C. Després et al.   Nature Communications

Pooled CRISPRi screening of the cyanobacterium Synechocystis sp PCC 6803 for enhanced industrial phenotypes

(2020) Lun Yao et al.   Nature Communications

Multiplex design of metabolic network for production of L-homoserine in Escherichia coli

(2020) Peng Liu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Reprogramming Acetogenic Bacteria with CRISPR-Targeted Base Editing via Deamination

(2020) Peng-Fei Xia et al.   ACS Synthetic Biology

Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing

(2020) Muhammad Naeem et al.   Cells

Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria

(2020) Philip M. Nussenzweig et al.   Annual Review of Genetics

Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli

(2019) Tian Tian et al.   ACS Synthetic Biology

Highly efficient single base editing in Aspergillus niger with CRISPR/Cas9 cytidine deaminase fusion

(2019) Lianggang Huang et al.   MICROBIOLOGICAL RESEARCH

CRISPR-Cas9D10A nickase-assisted base editing in the solvent producer Clostridium beijerinckii

(2019) Qi Li et al.   BIOTECHNOLOGY AND BIOENGINEERING

CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications

(2019) Peng Cai et al.   Microbial Cell Factories

CRISPR-Cas9 genome editing approaches in filamentous fungi and oomycetes

(2019) Mariana Schuster et al.   FUNGAL GENETICS AND BIOLOGY

Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST

(2019) Yaojun Tong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reshuffling yeast chromosomes with CRISPR/Cas9

(2019) Aubin Fleiss et al.   PLoS Genetics

Multiplex Gene Disruption by Targeted Base Editing of Yarrowia lipolytica Genome Using Cytidine Deaminase Combined with the CRISPR/Cas9 System

(2019) Sang‐Jeong Bae et al.   Biotechnology Journal

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Characterization and repurposing of the endogenous Type I-F CRISPR–Cas system of Zymomonas mobilis for genome engineering

(2019) Yanli Zheng et al.   NUCLEIC ACIDS RESEARCH

Reprogramming AA catabolism in CHO cells with CRISPR/Cas9 genome editing improves cell growth and reduces byproduct secretion

(2019) Daniel Ley et al.   METABOLIC ENGINEERING

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

Exploiting endogenous CRISPR-Cas system for multiplex genome editing in Clostridium tyrobutyricum and engineer the strain for high-level butanol production

(2018) Jie Zhang et al.   METABOLIC ENGINEERING

MACBETH: Multiplex automated Corynebacterium glutamicum base editing method

(2018) Yu Wang et al.   METABOLIC ENGINEERING

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision

(2018) Zehua Bao et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

(2018) Janice S. Chen et al.   SCIENCE

Deaminase-mediated multiplex genome editing in Escherichia coli

(2018) Satomi Banno et al.   Nature Microbiology

In Silico Processing of the Complete CRISPR-Cas Spacer Space for Identification of PAM Sequences

(2018) Brian J. Mendoza et al.   Biotechnology Journal

Engineered CRISPR-Cas9 nuclease with expanded targeting space

(2018) Hiroshi Nishimasu et al.   SCIENCE

CRISPR/Cas9 gene editing for the creation of an MGAT1-deficient CHO cell line to control HIV-1 vaccine glycosylation

(2018) Gabriel Byrne et al.   PLOS BIOLOGY

Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity

(2018) Stefano Stella et al.   CELL

Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae

(2017) Matthew Deaner et al.   METABOLIC ENGINEERING

Methods for decoding Cas9 protospacer adjacent motif (PAM) sequences: A brief overview

(2017) Tautvydas Karvelis et al.   METHODS

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Efficient targeted DNA editing and replacement inChlamydomonas reinhardtiiusing Cpf1 ribonucleoproteins and single-stranded DNA

(2017) Aron Ferenczi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Beyond Native Cas9: Manipulating Genomic Information and Function

(2017) Hitoshi Mitsunobu et al.   TRENDS IN BIOTECHNOLOGY

Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system

(2017) Jiazhang Lian et al.   Nature Communications

Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae

(2017) Matthew Deaner et al.   ACS Synthetic Biology

Efficient increase of ɣ-aminobutyric acid (GABA) content in tomato fruits by targeted mutagenesis

(2017) Satoko Nonaka et al.   Scientific Reports

Development of a comprehensive set of tools for genome engineering in a cold- and thermo-tolerant Kluyveromyces marxianus yeast strain

(2017) Yumiko Nambu-Nishida et al.   Scientific Reports

Enhanced protein and biochemical production using CRISPRi-based growth switches

(2016) Songyuan Li et al.   METABOLIC ENGINEERING

A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae

(2016) Shuobo Shi et al.   METABOLIC ENGINEERING

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

Manipulating the Biosynthesis of Bioactive Compound Alkaloids for Next-Generation Metabolic Engineering in Opium Poppy Using CRISPR-Cas 9 Genome Editing Technology

(2016) Yagiz Alagoz et al.   Scientific Reports

Harnessing heterologous and endogenous CRISPR-Cas machineries for efficient markerless genome editing in Clostridium

(2016) Michael E. Pyne et al.   Scientific Reports

Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase

(2015) Tao Xu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing

(2015) Yifan Li et al.   METABOLIC ENGINEERING

Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae

(2015) Tadas Jakočiūnas et al.   METABOLIC ENGINEERING

Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway

(2015) Jae Seong Lee et al.   Scientific Reports

CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae

(2015) Tadas Jakočiu̅nas et al.   ACS Synthetic Biology

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

(2014) Ryan E. Cobb et al.   ACS Synthetic Biology

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems

(2013) James E. DiCarlo et al.   NUCLEIC ACIDS RESEARCH