CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications

Burbano, Diego Alba; Kiattisewee, Cholpisit; Karanjia, Ava V.; Cardiff, Ryan A.L.; Faulkner, Ian D.; Sugianto, Widianti; Carothers, James M.

doi:10.1146/annurev-chembioeng-100522-114706

CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications

Journal Article · Wed Apr 10 00:00:00 EDT 2024 · Annual Review of Chemical and Biomolecular Engineering

DOI:https://doi.org/10.1146/annurev-chembioeng-100522-114706· OSTI ID:2530757

Burbano, Diego Alba ^[1]; Kiattisewee, Cholpisit ^[1]; Karanjia, Ava V. ^[1]; Cardiff, Ryan A.L. ^[1]; Faulkner, Ian D. ^[1]; Sugianto, Widianti ^[1]; Carothers, James M. ^[1]

University of Washington, Seattle, WA (United States)

In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.

View Accepted Manuscript (DOE)

Research Organization:: University of Washington, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO); USDOE Advanced Research Projects Agency - Energy (ARPA-E); US National Science Foundation (NSF)

Grant/Contract Number:: EE0008927; SC0023091

OSTI ID:: 2530757

Journal Information:: Annual Review of Chemical and Biomolecular Engineering, Journal Name: Annual Review of Chemical and Biomolecular Engineering Journal Issue: 1 Vol. 15; ISSN 1947-5438

Publisher:: Annual ReviewsCopyright Statement

Country of Publication:: United States

Language:: English

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CRISPR/dCas9-mediated transcriptional improvement of the biosynthetic gene cluster for the epothilone production in Myxococcus xanthus Peng, Ran; Wang, Ye; Feng, Wan-wan Microbial Cell Factories, Vol. 17, Issue 1 https://doi.org/10.1186/s12934-018-0867-1	journal	January 2018
Efficient Cas9-based genome editing of Rhodobacter sphaeroides for metabolic engineering Mougiakos, Ioannis; Orsi, Enrico; Ghiffary, Mohammad Rifqi Microbial Cell Factories, Vol. 18, Issue 1 https://doi.org/10.1186/s12934-019-1255-1	journal	November 2019
CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1 Luo, Yufeng; Ge, Mei; Wang, Bolun Microbial Cell Factories, Vol. 19, Issue 1 https://doi.org/10.1186/s12934-020-01345-w	journal	April 2020
Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage Kulcsár, Péter István; Tálas, András; Huszár, Krisztina Genome Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s13059-017-1318-8	journal	October 2017
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration Yu, Yanying; Gawlitt, Sandra; de Andrade e. Sousa, Lisa Barros Genome Biology, Vol. 25, Issue 1 https://doi.org/10.1186/s13059-023-03153-y	journal	January 2024
Genome editing of Ralstonia eutropha using an electroporation-based CRISPR-Cas9 technique Xiong, Bin; Li, Zhongkang; Liu, Li Biotechnology for Biofuels, Vol. 11, Issue 1 https://doi.org/10.1186/s13068-018-1170-4	journal	June 2018
Aptamer-based CRISPR-Cas powered diagnostics of diverse biomarkers and small molecule targets Kadam, Ulhas Sopanrao; Cho, Yuhan; Park, Tae Yoon Applied Biological Chemistry, Vol. 66, Issue 1 https://doi.org/10.1186/s13765-023-00771-9	journal	February 2023
A compact Cas9 ortholog from Staphylococcus Auricularis (SauriCas9) expands the DNA targeting scope Hu, Ziying; Wang, Shuai; Zhang, Chengdong PLOS Biology, Vol. 18, Issue 3 https://doi.org/10.1371/journal.pbio.3000686	journal	March 2020
Optimal number of spacers in CRISPR arrays Martynov, Alexander; Severinov, Konstantin; Ispolatov, Iaroslav PLOS Computational Biology, Vol. 13, Issue 12 https://doi.org/10.1371/journal.pcbi.1005891	journal	December 2017
Evidence of Selection upon Genomic GC-Content in Bacteria Hildebrand, Falk; Meyer, Axel; Eyre-Walker, Adam PLoS Genetics, Vol. 6, Issue 9 https://doi.org/10.1371/journal.pgen.1001107	journal	September 2010
Nonlinear Fitness Landscape of a Molecular Pathway Perfeito, Lilia; Ghozzi, Stéphane; Berg, Johannes PLoS Genetics, Vol. 7, Issue 7 https://doi.org/10.1371/journal.pgen.1002160	journal	July 2011
Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands Vercoe, Reuben B.; Chang, James T.; Dy, Ron L. PLoS Genetics, Vol. 9, Issue 4 https://doi.org/10.1371/journal.pgen.1003454	journal	April 2013
CRISPR-Cas9 modified bacteriophage for treatment of Staphylococcus aureus induced osteomyelitis and soft tissue infection Cobb, Leah H.; Park, JooYoun; Swanson, Elizabeth A. PLOS ONE, Vol. 14, Issue 11 https://doi.org/10.1371/journal.pone.0220421	journal	November 2019
Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms Flores-Bautista, Emanuel; Hernandez-Guerrero, Rafael; Huerta-Saquero, Alejandro PLOS ONE, Vol. 15, Issue 8 https://doi.org/10.1371/journal.pone.0237135	journal	August 2020
A new family of CRISPR ‐type V nucleases with C‐rich PAM recognition Urbaitis, Tomas; Gasiunas, Giedrius; Young, Joshua K. EMBO reports, Vol. 23, Issue 12 https://doi.org/10.15252/embr.202255481	journal	October 2022
Multi‐input CRISPR / C as genetic circuits that interface host regulatory networks Nielsen, Alec AK; Voigt, Christopher A. Molecular Systems Biology, Vol. 10, Issue 11 https://doi.org/10.15252/msb.20145735	journal	November 2014
Dynamic control of endogenous metabolism with combinatorial logic circuits Moser, Felix; Espah Borujeni, Amin; Ghodasara, Amar N. Molecular Systems Biology, Vol. 14, Issue 11 https://doi.org/10.15252/msb.20188605	journal	November 2018
Programmable CRISPR‐Cas transcriptional activation in bacteria Ho, Hsing‐I; Fang, Jennifer R.; Cheung, Jacky Molecular Systems Biology, Vol. 16, Issue 7 https://doi.org/10.15252/msb.20199427	journal	July 2020
High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing Neil, Kevin; Allard, Nancy; Roy, Patricia Molecular Systems Biology, Vol. 17, Issue 10 https://doi.org/10.15252/msb.202110335	journal	October 2021
beditor: A Computational Workflow for Designing Libraries of Guide RNAs for CRISPR-Mediated Base Editing Dandage, Rohan; Després, Philippe C.; Yachie, Nozomu Genetics, Vol. 212, Issue 2 https://doi.org/10.1534/genetics.119.302089	journal	April 2019
Biological Materials: The Next Frontier for Cell-Free Synthetic Biology Kelwick, Richard J. R.; Webb, Alexander J.; Freemont, Paul S. Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00399	journal	May 2020
CRISPR-Assisted Multiplex Base Editing System in Pseudomonas putida KT2440 Sun, Jun; Lu, Li-Bing; Liang, Tian-Xin Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.00905	journal	July 2020
CRISPR Interference Modules as Low-Burden Logic Inverters in Synthetic Circuits Bellato, Massimo; Frusteri Chiacchiera, Angelica; Salibi, Elia Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.743950	journal	January 2022
Internal Promoters and Their Effects on the Transcription of Operon Genes for Epothilone Production in Myxococcus xanthus Wang, Ye; Yue, Xin-jing; Yuan, Shu-fei Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.758561	journal	October 2021
Engineered Bacteria-Based Living Materials for Biotherapeutic Applications Omer, Rabia; Mohsin, Muhammad Zubair; Mohsin, Ali Frontiers in Bioengineering and Biotechnology, Vol. 10 https://doi.org/10.3389/fbioe.2022.870675	journal	April 2022
Research progress of CRISPR-based biosensors and bioassays for molecular diagnosis Chen, Kun; Shen, Ziyi; Wang, Guanzhen Frontiers in Bioengineering and Biotechnology, Vol. 10 https://doi.org/10.3389/fbioe.2022.986233	journal	September 2022
CRISPR/Cas System and Factors Affecting Its Precision and Efficiency Javaid, Nasir; Choi, Sangdun Frontiers in Cell and Developmental Biology, Vol. 9 https://doi.org/10.3389/fcell.2021.761709	journal	November 2021
CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria Call, Stephanie N.; Andrews, Lauren B. Frontiers in Genome Editing, Vol. 4 https://doi.org/10.3389/fgeed.2022.892304	journal	June 2022
Challenges and Advances for Genetic Engineering of Non-model Bacteria and Uses in Consolidated Bioprocessing Yan, Qiang; Fong, Stephen S. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02060	journal	October 2017
Simulation Modeling to Compare High-Throughput, Low-Iteration Optimization Strategies for Metabolic Engineering Heinsch, Stephen C.; Das, Siba R.; Smanski, Michael J. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00313	journal	February 2018
Cytosine Base Editor-Mediated Multiplex Genome Editing to Accelerate Discovery of Novel Antibiotics in Bacillus subtilis and Paenibacillus polymyxa Kim, Man Su; Kim, Ha-Rim; Jeong, Da-Eun Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.691839	journal	May 2021
From DNA-protein interactions to the genetic circuit design using CRISPR-dCas systems Shaytan, A. K.; Novikov, R. V.; Vinnikov, R. S. Frontiers in Molecular Biosciences, Vol. 9 https://doi.org/10.3389/fmolb.2022.1070526	journal	December 2022
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
In Vivo Rapid Investigation of CRISPR-Based Base Editing Components in Escherichia coli (IRI-CCE): A Platform for Evaluating Base Editing Tools and Their Components Shelake, Rahul Mahadev; Pramanik, Dibyajyoti; Kim, Jae-Yean International Journal of Molecular Sciences, Vol. 23, Issue 3 https://doi.org/10.3390/ijms23031145	journal	January 2022
Genome Editing in Bacteria: CRISPR-Cas and Beyond Arroyo-Olarte, Ruben D.; Bravo Rodríguez, Ricardo; Morales-Ríos, Edgar Microorganisms, Vol. 9, Issue 4 https://doi.org/10.3390/microorganisms9040844	journal	April 2021
Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems Jeong, Dohyun; Klocke, Melissa; Agarwal, Siddharth Methods and Protocols, Vol. 2, Issue 2 https://doi.org/10.3390/mps2020039	journal	May 2019
Cell-Free PURE System: Evolution and Achievements Cui, Yi; Chen, Xinjie; Wang, Ze BioDesign Research, Vol. 2022 https://doi.org/10.34133/2022/9847014	journal	January 2022
The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems Chylinski, Krzysztof; Le Rhun, Anaïs; Charpentier, Emmanuelle RNA Biology, Vol. 10, Issue 5 https://doi.org/10.4161/rna.24321	journal	February 2013

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