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Chapter 7 - CRISPR-Based Tools for Microbial Cell Factories

Book ·

The development of microbial chassis for the production of a variety of biochemicals and biofuels is a growing area of research. How to efficiently manipulate genetic information to achieve optimal production of these compounds is a key area of focus in the field. In recent years, clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) have become a popular strategy for gene editing and regulation in many organisms due to its versatility and efficacy. Here, we describe methods developed utilizing CRISPR-Cas systems for engineering microbial cell factories (e.g., bacteria and yeast) at the single gene to genome scale for mutagenesis and transcriptional regulation of target genes. Finally, we provide a perspective on the challenges and opportunities for the applications of advanced CRISPR-Cas-based tools for engineering microbial cell factories.

Research Organization:
National Renewable Energy Laboratory (NREL), Golden, CO (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
DOE Contract Number:
AC36-08GO28308
OSTI ID:
1862943
Report Number(s):
NREL/CH-2700-76795; MainId:9456; UUID:9276b7cc-e4f2-4954-bcb6-764820858de6; MainAdminID:19875
Country of Publication:
United States
Language:
English

References (156)

A Robust CRISPR Interference Gene Repression System in Pseudomonas journal January 2018
A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity journal June 2012
RNA-guided editing of bacterial genomes using CRISPR-Cas systems journal January 2013
CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives journal June 2015
Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production journal January 2019
Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing journal February 2019
CRISPR interference (CRISPRi) for gene regulation and succinate production in cyanobacterium S. elongatus PCC 7942 journal November 2016
CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production journal November 2016
Synergies between synthetic biology and metabolic engineering journal August 2011
Defining synonymous codon compression schemes by genome recoding journal October 2016
CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae journal March 2015
Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria journal September 2012
Combinatorial pathway engineering using type I-E CRISPR interference journal March 2018
Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase journal November 2016
Engineering Cellular Metabolism journal March 2016
The CRISPR tool kit for genome editing and beyond journal May 2018
Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering journal December 2016
CRISPR Interference Directs Strand Specific Spacer Acquisition journal April 2012
Genome Engineering with CRISPR-Cas9 in the Mosquito Aedes aegypti journal April 2015
Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli journal April 2016
Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System journal January 2015
Multiplex Engineering of Industrial Yeast Genomes Using CRISPRm book January 2014
Bio-based production of C2-C6 platform chemicals journal July 2012
Programming cells by multiplex genome engineering and accelerated evolution journal July 2009
Central pathway engineering for enhanced succinate biosynthesis from acetate in Escherichia coli journal January 2018
Highly efficient base editing in bacteria using a Cas9-cytidine deaminase fusion journal April 2018
Simultaneously down-regulation of multiplex branch pathways using CRISPRi and fermentation optimization for enhancing β-amyrin production in Saccharomyces cerevisiae journal June 2019
Diversity, classification and evolution of CRISPR-Cas systems journal June 2017
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria journal June 2016
Establishment and application of a CRISPR–Cas12a assisted genome-editing system in Zymomonas mobilis journal October 2019
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes journal March 2007
CRISPRi engineering E. coli for morphology diversification journal November 2016
Synthetic RNA Polymerase III Promoters Facilitate High-Efficiency CRISPR–Cas9-Mediated Genome Editing in Yarrowia lipolytica journal January 2016
Automated multiplex genome-scale engineering in yeast journal May 2017
Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies journal March 2017
Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes journal March 2018
CRISPR interference‐mediated gene regulation in Pseudomonas putida KT 2440 journal January 2020
Engineering cell wall synthesis mechanism for enhanced PHB accumulation in E. coli journal January 2018
Directed evolution of CRISPR-Cas9 to increase its specificity journal August 2018
Mechanism of spacer integration links the CRISPR/Cas system to transposition as a form of mobile DNA journal May 2015
Impact of CRISPR interference on strain development in biotechnology journal January 2020
Metabolic engineering of an acid-tolerant yeast strain Pichia kudriavzevii for itaconic acid production journal June 2020
Combinatorial metabolic pathway assembly in the yeast genome with RNA-guided Cas9 journal July 2016
Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity journal April 2018
Development of both type I–B and type II CRISPR/Cas genome editing systems in the cellulolytic bacterium Clostridium thermocellum journal June 2020
Yeast Oligo-Mediated Genome Engineering (YOGE) journal November 2013
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression journal February 2013
Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System journal October 2015
CRISPR-Cas12a/Cpf1-assisted precise, efficient and multiplexed genome-editing in Yarrowia lipolytica journal June 2020
Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system journal March 2018
CRISPR–Cas12a system in fission yeast for multiplex genomic editing and CRISPR interference journal May 2020
Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae journal March 2017
Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches journal March 2020
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system journal November 2017
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes journal July 2013
Multiplexed precision genome editing with trackable genomic barcodes in yeast journal May 2018
CRISPR-Cas12a-Assisted Recombineering in Bacteria journal June 2017
Multiplex gene regulation by CRISPR-ddCpf1 journal June 2017
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol journal May 2011
Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas journal June 2013
Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes journal August 2008
CRISPR–Cas9 D10A nickase‐assisted base editing in the solvent producer Clostridium beijerinckii journal February 2019
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems journal March 2013
CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum journal May 2017
Reducing phenolic off-flavors through CRISPR-based gene editing of the FDC1 gene in Saccharomyces cerevisiae x Saccharomyces eubayanus hybrid lager beer yeasts journal January 2019
High-yield and plasmid-free biocatalytic production of 5-methylpyrazine-2-carboxylic acid by combinatorial genetic elements engineering and genome engineering of Escherichia coli journal March 2020
Enhanced solvent production by metabolic engineering of a twin-clostridial consortium journal January 2017
Engineering Escherichia coli for malate production by integrating modular pathway characterization with CRISPRi-guided multiplexed metabolic tuning journal November 2017
Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping journal December 2019
CRISPR-Cpf1-Assisted Multiplex Genome Editing and Transcriptional Repression in Streptomyces journal September 2018
Method for Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas9 book October 2019
Genome scale engineering techniques for metabolic engineering journal November 2015
Escherichia coli as a model organism for systems metabolic engineering journal December 2017
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism journal September 2018
Advances in Industrial Biotechnology Using CRISPR-Cas Systems journal February 2018
A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9 journal May 2018
Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi journal January 2019
Metabolic engineering of Pichia pastoris for production of isopentanol (3-Methyl-1-butanol) journal August 2020
Regulation of ATP levels in Escherichia coli using CRISPR interference for enhanced pinocembrin production journal September 2018
Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae journal March 2015
Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli journal January 2019
High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast journal May 2018
Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution journal June 2015
CRISPR–Cas9-enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in Kluyveromyces marxianus journal June 2017
High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects journal January 2016
Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica journal September 2019
Systems metabolic engineering of microorganisms for natural and non-natural chemicals journal May 2012
Controlling microbial PHB synthesis via CRISPRi journal June 2017
Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing journal September 2015
CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli journal May 2017
Comparison and optimization of CRISPR/dCas9/gRNA genome-labeling systems for live cell imaging journal March 2018
Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris journal October 2016
Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae journal September 2014
The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA journal April 2016
Total synthesis of Escherichia coli with a recoded genome journal May 2019
Combining CRISPR and CRISPRi Systems for Metabolic Engineering of E. coli and 1,4-BDO Biosynthesis journal September 2017
Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system journal June 2013
Highly Multiplexed CRISPRi Repression of Respiratory Functions Enhances Mitochondrial Localized Ethyl Acetate Biosynthesis in Kluyveromyces marxianus journal October 2018
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems journal April 2016
Development of an Efficient Genome Editing Tool in Bacillus licheniformis Using CRISPR-Cas9 Nickase journal January 2018
Improvement of cis , cis -Muconic Acid Production in Saccharomyces cerevisiae through Biosensor-Aided Genome Engineering journal February 2020
MACBETH: Multiplex automated Corynebacterium glutamicum base editing method journal May 2018
Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds journal January 2015
Enhanced proofreading governs CRISPR–Cas9 targeting accuracy journal September 2017
CRISPR interference-guided multiplex repression of endogenous competing pathway genes for redirecting metabolic flux in Escherichia coli journal November 2017
Candida albicans Gene Deletion with a Transient CRISPR-Cas9 System journal June 2016
Short motif sequences determine the targets of the prokaryotic CRISPR defence system journal March 2009
CRISPRi and CRISPRa Screens in Mammalian Cells for Precision Biology and Medicine journal September 2017
Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination journal September 2013
Yeast as a cell factory: current state and perspectives journal June 2015
Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision journal May 2018
Efficient Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas journal July 2015
Multiplexed CRISPR Activation of Cryptic Sugar Metabolism Enables Yarrowia Lipolytica Growth on Cellobiose journal May 2018
CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae journal March 2015
Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli journal April 2020
Toward tunable dynamic repression using CRISPRi journal May 2018
Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi) journal July 2018
Selection of chromosomal DNA libraries using a multiplex CRISPR system journal August 2014
High-throughput functional genomics using CRISPR–Cas9 journal April 2015
Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production journal May 2018
A highly efficient single-step, markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae journal January 2016
Bacterial DNA repair by non-homologous end joining journal November 2007
A light-inducible CRISPR-Cas9 system for control of endogenous gene activation journal February 2015
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases journal December 2014
The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli journal October 2015
Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n -Butanol Production in Escherichia coli journal October 2016
Engineering tolerance to industrially relevant stress factors in yeast cell factories journal June 2017
How adaptive evolution reshapes metabolism to improve fitness: recent advances and future outlook journal December 2018
CRMAGE: CRISPR Optimized MAGE Recombineering journal January 2016
CRISPR/Cas9-mediated engineering of Escherichia coli for n-butanol production from xylose in defined medium journal April 2019
CRISPR/Cas9-Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L. journal February 2014
Efficient Genome Editing in Clostridium cellulolyticum via CRISPR-Cas9 Nickase journal April 2015
Directed evolution and synthetic biology applications to microbial systems journal June 2016
Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering journal May 2018
Re-engineered RNA-Guided FokI-Nucleases for Improved Genome Editing in Human Cells journal February 2017
Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation journal June 2017
Development of a CRISPR/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion journal March 2020
Modulating Pathogenesis with Mobile-CRISPRi journal September 2019
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing journal September 2013
Increasing n-butanol production with Saccharomyces cerevisiae by optimizing acetyl-CoA synthesis, NADH levels and trans-2-enoyl-CoA reductase expression journal November 2016
Implementation of the CRISPR-Cas9 system in fission yeast journal October 2014
Partial DNA-guided Cas9 enables genome editing with reduced off-target activity journal January 2018
Reconstitution of TCA cycle involving l-isoleucine dioxygenase for hydroxylation of l-isoleucine in Escherichia coli using CRISPR-Cas9 journal March 2020
Diversity and evolution of class 2 CRISPR–Cas systems journal January 2017
Lambda Red Recombineering in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate journal September 2010
Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli journal December 2003
Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation journal December 2015
Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria journal December 2016
CRISPR /Cas‐based screening of a gene activation library in Saccharomyces cerevisiae identifies a crucial role of OLE 1 in thermotolerance journal November 2018
CRISPR-Cas: New Tools for Genetic Manipulations from Bacterial Immunity Systems journal October 2015
Furfural and hydroxymethylfurfural tolerance in Escherichia coli Δ acrR regulatory mutants: Furfural and HMF Tolerance in E. coli Δ acrR Mutants journal July 2014
Transcription control engineering and applications in synthetic biology journal September 2017
Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria journal June 2018
CRISPR-Cas systems for editing, regulating and targeting genomes journal March 2014
Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design journal March 2016
Genome engineering of E. coli for improved styrene production journal January 2020

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