1
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Nawab S, Zhang Y, Ullah MW, Lodhi AF, Shah SB, Rahman MU, Yong YC. Microbial host engineering for sustainable isobutanol production from renewable resources. Appl Microbiol Biotechnol 2024; 108:33. [PMID: 38175234 DOI: 10.1007/s00253-023-12821-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Due to the limited resources and environmental problems associated with fossil fuels, there is a growing interest in utilizing renewable resources for the production of biofuels through microbial fermentation. Isobutanol is a promising biofuel that could potentially replace gasoline. However, its production efficiency is currently limited by the use of naturally isolated microorganisms. These naturally isolated microorganisms often encounter problems such as a limited range of substrates, low tolerance to solvents or inhibitors, feedback inhibition, and an imbalanced redox state. This makes it difficult to improve their production efficiency through traditional process optimization methods. Fortunately, recent advancements in genetic engineering technologies have made it possible to enhance microbial hosts for the increased production of isobutanol from renewable resources. This review provides a summary of the strategies and synthetic biology approaches that have been employed in the past few years to improve naturally isolated or non-natural microbial hosts for the enhanced production of isobutanol by utilizing different renewable resources. Furthermore, it also discusses the challenges that are faced by engineered microbial hosts and presents future perspectives to enhancing isobutanol production. KEY POINTS: • Promising potential of isobutanol to replace gasoline • Engineering of native and non-native microbial host for isobutanol production • Challenges and opportunities for enhanced isobutanol production.
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Affiliation(s)
- Said Nawab
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - YaFei Zhang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Muhammad Wajid Ullah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Adil Farooq Lodhi
- Department of Microbiology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Syed Bilal Shah
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Mujeeb Ur Rahman
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
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2
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González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. Simultaneous multi-site editing of individual genomes using retron arrays. Nat Chem Biol 2024:10.1038/s41589-024-01665-7. [PMID: 38982310 DOI: 10.1038/s41589-024-01665-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/06/2024] [Indexed: 07/11/2024]
Abstract
During recent years, the use of libraries-scale genomic manipulations scaffolded on CRISPR guide RNAs have been transformative. However, these existing approaches are typically multiplexed across genomes. Unfortunately, building cells with multiple, nonadjacent precise mutations remains a laborious cycle of editing, isolating an edited cell and editing again. The use of bacterial retrons can overcome this limitation. Retrons are genetic systems composed of a reverse transcriptase and a noncoding RNA that contains an multicopy single-stranded DNA, which is reverse transcribed to produce multiple copies of single-stranded DNA. Here we describe a technology-termed a multitron-for precisely modifying multiple sites on a single genome simultaneously using retron arrays, in which multiple donor-encoding DNAs are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization and metabolic engineering.
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Affiliation(s)
| | - Santiago C Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, San Francisco, CA, USA
| | | | - Chloe B Fishman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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3
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
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.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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4
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Widney KA, Yang DD, Rusch LM, Copley SD. CRISPR-Cas9-assisted genome editing in E. coli elevates the frequency of unintended mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.584922. [PMID: 38562785 PMCID: PMC10983943 DOI: 10.1101/2024.03.19.584922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cas-assisted lambda Red recombineering techniques have rapidly become a mainstay of bacterial genome editing. Such techniques have been used to construct both individual mutants and massive libraries to assess the effects of genomic changes. We have found that a commonly used Cas9-assisted editing method results in unintended mutations elsewhere in the genome in 26% of edited clones. The unintended mutations are frequently found over 200 kb from the intended edit site and even over 10 kb from potential off-target sites. We attribute the high frequency of unintended mutations to error-prone polymerases expressed in response to dsDNA breaks introduced at the edit site. Most unintended mutations occur in regulatory or coding regions and thus may have phenotypic effects. Our findings highlight the risks associated with genome editing techniques involving dsDNA breaks in E. coli and likely other bacteria and emphasize the importance of sequencing the genomes of edited cells to ensure the absence of unintended mutations.
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Affiliation(s)
- Karl A. Widney
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Dong-Dong Yang
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Leo M. Rusch
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, 80205, USA
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5
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Zou Z, Ji Y, Schwaneberg U. Empowering Site-Specific Bioconjugations In Vitro and In Vivo: Advances in Sortase Engineering and Sortase-Mediated Ligation. Angew Chem Int Ed Engl 2024; 63:e202310910. [PMID: 38081121 DOI: 10.1002/anie.202310910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Indexed: 12/23/2023]
Abstract
Sortase-mediated ligation (SML) has emerged as a powerful and versatile methodology for site-specific protein conjugation, functionalization/labeling, immobilization, and design of biohybrid molecules and systems. However, the broader application of SML faces several challenges, such as limited activity and stability, dependence on calcium ions, and reversible reactions caused by nucleophilic side-products. Over the past decade, protein engineering campaigns and particularly directed evolution, have been extensively employed to overcome sortase limitations, thereby expanding the potential application of SML in multiple directions, including therapeutics, biorthogonal chemistry, biomaterials, and biosensors. This review provides an overview of achieved advancements in sortase engineering and highlights recent progress in utilizing SML in combination with other state-of-the-art chemical and biological methodologies. The aim is to encourage scientists to employ sortases in their conjugation experiments.
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Affiliation(s)
- Zhi Zou
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Yu Ji
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
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6
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Wang Z, Pan H, Ni S, Li Z, Lian J. Establishing CRISPRi for Programmable Gene Repression and Genome Evolution in Cupriavidus necator. ACS Synth Biol 2024; 13:851-861. [PMID: 38350870 DOI: 10.1021/acssynbio.3c00664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Cupriavidus necator H16 is a "Knallgas" bacterium with the ability to utilize various carbon sources and has been employed as a versatile microbial cell factory to produce a wide range of value-added compounds. However, limited genome engineering, especially gene regulation methods, has constrained its full potential as a microbial production platform. The advent of CRISPR/Cas9 technology has shown promise in addressing this limitation. Here, we developed an optimized CRISPR interference (CRISPRi) system for gene repression in C. necator by expressing a codon-optimized deactivated Cas9 (dCas9) and appropriate single guide RNAs (sgRNAs). CRISPRi was proven to be a programmable and controllable tool and could successfully repress both exogenous and endogenous genes. As a case study, we decreased the accumulation of polyhydroxyalkanoate (PHB) via CRISPRi and rewired the carbon fluxes to the synthesis of lycopene. Additionally, by disturbing the expression of DNA mismatch repair gene mutS with CRISPRi, we established CRISPRi-Mutator for genome evolution, rapidly generating mutant strains with enhanced hydrogen peroxide tolerance and robustness in microbial electrosynthesis (MES) system. Our work provides an efficient CRISPRi toolkit for advanced genetic manipulation and optimization of C. necator cell factories for diverse biotechnology applications.
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Affiliation(s)
- Zhijiao Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310000, China
| | - Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310000, China
| | - Sulin Ni
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310000, China
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7
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Montagud‐Martínez R, Márquez‐Costa R, Heras‐Hernández M, Dolcemascolo R, Rodrigo G. On the ever-growing functional versatility of the CRISPR-Cas13 system. Microb Biotechnol 2024; 17:e14418. [PMID: 38381083 PMCID: PMC10880580 DOI: 10.1111/1751-7915.14418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024] Open
Abstract
CRISPR-Cas systems evolved in prokaryotes to implement a powerful antiviral immune response as a result of sequence-specific targeting by ribonucleoproteins. One of such systems consists of an RNA-guided RNA endonuclease, known as CRISPR-Cas13. In very recent years, this system is being repurposed in different ways in order to decipher and engineer gene expression programmes. Here, we discuss the functional versatility of the CRISPR-Cas13 system, which includes the ability for RNA silencing, RNA editing, RNA tracking, nucleic acid detection and translation regulation. This functional palette makes the CRISPR-Cas13 system a relevant tool in the broad field of systems and synthetic biology.
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Affiliation(s)
- Roser Montagud‐Martínez
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Rosa Márquez‐Costa
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - María Heras‐Hernández
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio)CSIC – University of ValenciaPaternaSpain
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8
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Yang DD, Rusch LM, Widney KA, Morgenthaler AB, Copley SD. Synonymous edits in the Escherichia coli genome have substantial and condition-dependent effects on fitness. Proc Natl Acad Sci U S A 2024; 121:e2316834121. [PMID: 38252823 PMCID: PMC10835057 DOI: 10.1073/pnas.2316834121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
CRISPR-Cas-based genome editing is widely used in bacteria at scales ranging from construction of individual mutants to massively parallel libraries. This procedure relies on guide RNA-directed cleavage of the genome followed by repair with a template that introduces a desired mutation along with synonymous "immunizing" mutations to prevent re-cleavage of the genome after editing. Because the immunizing mutations do not change the protein sequence, they are often assumed to be neutral. However, synonymous mutations can change mRNA structures in ways that alter levels of the encoded proteins. We have tested the assumption that immunizing mutations are neutral by constructing a library of over 50,000 edits that consist of only synonymous mutations in Escherichia coli. Thousands of edits had substantial effects on fitness during growth of E. coli on acetate, a poor carbon source that is toxic at high concentrations. The percentage of high-impact edits varied considerably between genes and at different positions within genes. We reconstructed clones with high-impact edits and found that 69% indeed had significant effects on growth in acetate. Interestingly, fewer edits affected fitness during growth in glucose, a preferred carbon source, suggesting that changes in protein expression caused by synonymous mutations may be most important when an organism encounters challenging conditions. Finally, we showed that synonymous edits can have widespread effects; a synonymous edit at the 5' end of ptsI altered expression of hundreds of genes. Our results suggest that the synonymous immunizing edits introduced during CRISPR-Cas-based genome editing should not be assumed to be innocuous.
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Affiliation(s)
- Dong-Dong Yang
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Leo M. Rusch
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Karl A. Widney
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
| | - Andrew B. Morgenthaler
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
- Amyris, Inc., Emeryville, CA94608
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO80309
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9
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Zhang H, Ma J, Wu Z, Chen X, Qian Y, Chen W, Wang Z, Zhang Y, Zhu H, Huang X, Ji Q. BacPE: a versatile prime-editing platform in bacteria by inhibiting DNA exonucleases. Nat Commun 2024; 15:825. [PMID: 38280845 PMCID: PMC10821919 DOI: 10.1038/s41467-024-45114-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
Prime editing allows precise installation of any single base substitution and small insertions and deletions without requiring homologous recombination or double-strand DNA breaks in eukaryotic cells. However, the applications in bacteria are hindered and the underlying mechanisms that impede efficient prime editing remain enigmatic. Here, we report the determination of vital cellular factors that affect prime editing in bacteria. Genetic screening of 129 Escherichia coli transposon mutants identified sbcB, a 3'→5' DNA exonuclease, as a key genetic determinant in impeding prime editing in E. coli, combinational deletions of which with two additional 3'→5' DNA exonucleases, xseA and exoX, drastically enhanced the prime editing efficiency by up to 100-fold. Efficient prime editing in wild-type E. coli can be achieved by simultaneously inhibiting the DNA exonucleases via CRISPRi. Our results pave the way for versatile applications of prime editing for bacterial genome engineering.
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Affiliation(s)
- Hongyuan Zhang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Jiacheng Ma
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Zhaowei Wu
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaoyang Chen
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Yangyang Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Weizhong Chen
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315832, China
| | - Zhipeng Wang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Ya Zhang
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China
| | - Huanhu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xingxu Huang
- Zhejiang Lab, Hangzhou, Zhejiang, 311121, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Quanjiang Ji
- School of Physical Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech University, Shanghai, 201210, China.
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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10
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Noda S, Fujiwara R, Mori Y, Dainin M, Shirai T, Kondo A. Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture. BIOTECH 2024; 13:2. [PMID: 38247732 PMCID: PMC10801462 DOI: 10.3390/biotech13010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from Arabidopsis thaliana (AtPAL) and Brachypodium distachyon (BdPAL) for their ability to produce trans-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing E. coli produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an E. coli strain that co-expressed AtPAL2 and ferulic acid decarboxylase from Saccharomyces cerevisiae. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large-scale industrial production of styrene.
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Affiliation(s)
- Shuhei Noda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Saitama, Japan
| | - Ryosuke Fujiwara
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Yutaro Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
| | - Mayumi Dainin
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
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11
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Teng Y, Jiang T, Yan Y. The expanded CRISPR toolbox for constructing microbial cell factories. Trends Biotechnol 2024; 42:104-118. [PMID: 37500408 PMCID: PMC10808275 DOI: 10.1016/j.tibtech.2023.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
Microbial cell factories (MCFs) convert low-cost carbon sources into valuable compounds. The CRISPR/Cas9 system has revolutionized MCF construction as a remarkable genome editing tool with unprecedented programmability. Recently, the CRISPR toolbox has been significantly expanded through the exploration of new CRISPR systems, the engineering of Cas effectors, and the incorporation of other effectors, enabling multi-level regulation and gene editing free of double-strand breaks. This expanded CRISPR toolbox powerfully promotes MCF construction by facilitating pathway construction, enzyme engineering, flux redistribution, and metabolic burden control. In this article, we summarize different CRISPR tool designs and their applications in MCF construction for gene editing, transcriptional regulation, and enzyme modulation. Finally, we also discuss future perspectives for the development and application of the CRISPR toolbox.
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Affiliation(s)
- Yuxi Teng
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Tian Jiang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA.
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12
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Fooladi S, Rabiee N, Iravani S. Genetically engineered bacteria: a new frontier in targeted drug delivery. J Mater Chem B 2023; 11:10072-10087. [PMID: 37873584 DOI: 10.1039/d3tb01805a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genetically engineered bacteria (GEB) have shown significant promise to revolutionize modern medicine. These engineered bacteria with unique properties such as enhanced targeting, versatility, biofilm disruption, reduced drug resistance, self-amplification capabilities, and biodegradability represent a highly promising approach for targeted drug delivery and cancer theranostics. This innovative approach involves modifying bacterial strains to function as drug carriers, capable of delivering therapeutic agents directly to specific cells or tissues. Unlike synthetic drug delivery systems, GEB are inherently biodegradable and can be naturally eliminated from the body, reducing potential long-term side effects or complications associated with residual foreign constituents. However, several pivotal challenges such as safety and controllability need to be addressed. Researchers have explored novel tactics to improve their capabilities and overcome existing challenges, including synthetic biology tools (e.g., clustered regularly interspaced short palindromic repeats (CRISPR) and bioinformatics-driven design), microbiome engineering, combination therapies, immune system interaction, and biocontainment strategies. Because of the remarkable advantages and tangible progress in this field, GEB may emerge as vital tools in personalized medicine, providing precise and controlled drug delivery for various diseases (especially cancer). In this context, future directions include the integration of nanotechnology with GEB, the focus on microbiota-targeted therapies, the incorporation of programmable behaviors, the enhancement in immunotherapy treatments, and the discovery of non-medical applications. In this way, careful ethical considerations and regulatory frameworks are necessary for developing GEB-based systems for targeted drug delivery. By addressing safety concerns, ensuring informed consent, promoting equitable access, understanding long-term effects, mitigating dual-use risks, and fostering public engagement, these engineered bacteria can be employed as promising delivery vehicles in bio- and nanomedicine. In this review, recent advances related to the application of GEB in targeted drug delivery and cancer therapy are discussed, covering crucial challenging issues and future perspectives.
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Affiliation(s)
- Saba Fooladi
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06511, USA
| | - Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia.
- School of Engineering, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Siavash Iravani
- Independent Researcher, W Nazar ST, Boostan Ave, Isfahan, Iran.
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13
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van Schaik J, Li Z, Cheadle J, Crook N. Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions. ACS Synth Biol 2023; 12:3030-3040. [PMID: 37712562 DOI: 10.1021/acssynbio.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Sustainably enhancing crop production is a global necessity to meet the escalating demand for staple crops while sustainably managing their associated carbon/nitrogen inputs. Leveraging plant-associated microbiomes is a promising avenue for addressing this demand. However, studying these communities and engineering them for sustainable enhancement of crop production have remained a challenge due to limited genetic tools and methods. In this work, we detail the development of the Maize Root Microbiome ToolKit (MRMTK), a rapid Modular Cloning (MoClo) toolkit that only takes 2.5 h to generate desired constructs (5400 potential plasmids) that replicate and express heterologous genes in Enterobacter ludwigii strain AA4 (Elu), Pseudomonas putida strain AA7 (Ppu), Herbaspirillum robiniae strain AA6 (Hro), Stenotrophomonas maltophilia strain AA1 (Sma), and Brucella pituitosa strain AA2 (Bpi), which comprise a model maize root synthetic community (SynCom). In addition to these genetic tools, we describe a highly efficient transformation protocol (107-109 transformants/μg of DNA) 1 for each of these strains. Utilizing this highly efficient transformation protocol, we identified endogenous Expression Sequences (ES; promoter and ribosomal binding sites) for each strain via genomic promoter trapping. Overall, MRMTK is a scalable and adaptable platform that expands the genetic engineering toolbox while providing a standardized, high-efficiency transformation method across a diverse group of root commensals. These results unlock the ability to elucidate and engineer plant-microbe interactions promoting plant growth for each of the 5 bacterial strains in this study.
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Affiliation(s)
- John van Schaik
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - John Cheadle
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
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14
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Volke DC, Orsi E, Nikel PI. Emergent CRISPR-Cas-based technologies for engineering non-model bacteria. Curr Opin Microbiol 2023; 75:102353. [PMID: 37413959 DOI: 10.1016/j.mib.2023.102353] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) technologies brought a transformative change in the way bacterial genomes are edited, and a plethora of studies contributed to developing multiple tools based on these approaches. Prokaryotic biotechnology benefited from the implementation of such genome engineering strategies, with an increasing number of non-model bacterial species becoming genetically tractable. In this review, we summarize the recent trends in engineering non-model microbes using CRISPR-Cas technologies, discussing their potential in supporting cell factory design towards biotechnological applications. These efforts include, among other examples, genome modifications as well as tunable transcriptional regulation (both positive and negative). Moreover, we examine how CRISPR-Cas toolkits for engineering non-model organisms enabled the exploitation of emergent biotechnological processes (e.g. native and synthetic assimilation of one-carbon substrates). Finally, we discuss our slant on the future of bacterial genome engineering for domesticating non-model organisms in light of the most recent advances in the ever-expanding CRISPR-Cas field.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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15
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Yi J, Zhang M, Zhu L, Xu C, Li B, Wu P, Wu H, Zhang B. High-efficiency genetic engineering toolkit for virus based on lambda red-mediated recombination. Biotechnol Lett 2023; 45:1327-1337. [PMID: 37526868 DOI: 10.1007/s10529-023-03412-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/15/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
PURPOSE Viruses, such as Ebola virus (EBOV), evolve rapidly and threaten the human health. There is a great demand to exploit efficient gene-editing techniques for the identification of virus to probe virulence mechanism for drug development. METHODS Based on lambda Red recombination in Escherichia coli (E. coli), counter-selection, and in vitro annealing, a high-efficiency genetic method was utilized here for precisely engineering viruses. EBOV trVLPs assay and dual luciferase reporter assay were used to further test the effect of mutations on virus replication. RESULTS Considering the significance of matrix protein VP24 in EBOV replication, the types of mutations within vp24, including several single-base substitutions, one double-base substitution, two seamless deletions, and one targeted insertion, were generated on the multi-copy plasmid of E. coli. Further, the length of the homology arms for recombination and in vitro annealing, and the amount of DNA cassettes and linear plasmids were optimized to create a more elaborate and cost-efficient protocol than original approach. The effects of VP24 mutations on the expression of a reporter gene (luciferase) from the EBOV minigenome were determined, and results indicated that mutations of key sites within VP24 have significant impacts on EBOV replication. CONCLUSION This precise mutagenesis method will facilitate effective and simple editing of viral genes in E. coli.
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Affiliation(s)
- Jing Yi
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Maifei Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Lin Zhu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Changzhi Xu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Binglin Li
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Panpan Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Hang Wu
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China.
| | - Buchang Zhang
- School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei, 230601, Anhui, People's Republic of China
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16
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Frisch C, Kostes WW, Galyon B, Whitman B, Tekel SJ, Standage-Beier K, Srinivasan G, Wang X, Brafman DA. PINE-TREE enables highly efficient genetic modification of human cell lines. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:483-492. [PMID: 37588683 PMCID: PMC10425837 DOI: 10.1016/j.omtn.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
Prime editing technologies enable precise genome editing without the caveats of CRISPR nuclease-based methods. Nonetheless, current approaches to identify and isolate prime-edited cell populations are inefficient. Here, we established a fluorescence-based system, prime-induced nucleotide engineering using a transient reporter for editing enrichment (PINE-TREE), for real-time enrichment of prime-edited cell populations. We demonstrated the broad utility of PINE-TREE for highly efficient introduction of substitutions, insertions, and deletions at various genomic loci. Finally, we employ PINE-TREE to rapidly and efficiently generate clonal isogenic human pluripotent stem cell lines, a cell type recalcitrant to genome editing.
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Affiliation(s)
- Carlye Frisch
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - William W. Kostes
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Brooke Galyon
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Brycelyn Whitman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Stefan J. Tekel
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Kylie Standage-Beier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
- Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ 85287, USA
| | - Gayathri Srinivasan
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - David A. Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
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17
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Liu W, Zuo S, Shao Y, Bi K, Zhao J, Huang L, Xu Z, Lian J. Retron-mediated multiplex genome editing and continuous evolution in Escherichia coli. Nucleic Acids Res 2023; 51:8293-8307. [PMID: 37471041 PMCID: PMC10450171 DOI: 10.1093/nar/gkad607] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/02/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
While there are several genome editing techniques available, few are suitable for dynamic and simultaneous mutagenesis of arbitrary targeted sequences in prokaryotes. Here, to address these limitations, we present a versatile and multiplex retron-mediated genome editing system (REGES). First, through systematic optimization of REGES, we achieve efficiency of ∼100%, 85 ± 3%, 69 ± 14% and 25 ± 14% for single-, double-, triple- and quadruple-locus genome editing, respectively. In addition, we employ REGES to generate pooled and barcoded variant libraries with degenerate RBS sequences to fine-tune the expression level of endogenous and exogenous genes, such as transcriptional factors to improve ethanol tolerance and biotin biosynthesis. Finally, we demonstrate REGES-mediated continuous in vivo protein evolution, by combining retron, polymerase-mediated base editing and error-prone transcription. By these case studies, we demonstrate REGES as a powerful multiplex genome editing and continuous evolution tool with broad applications in synthetic biology and metabolic engineering.
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Affiliation(s)
- Wenqian Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Siqi Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Youran Shao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ke Bi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiarun Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
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18
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González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. Simultaneous multi-site editing of individual genomes using retron arrays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549397. [PMID: 37503029 PMCID: PMC10370050 DOI: 10.1101/2023.07.17.549397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Our understanding of genomics is limited by the scale of our genomic technologies. While libraries of genomic manipulations scaffolded on CRISPR gRNAs have been transformative, these existing approaches are typically multiplexed across genomes. Yet much of the complexity of real genomes is encoded within a genome across sites. Unfortunately, building cells with multiple, non-adjacent precise mutations remains a laborious cycle of editing, isolating an edited cell, and editing again. Here, we describe a technology for precisely modifying multiple sites on a single genome simultaneously. This technology - termed a multitron - is built from a heavily modified retron, in which multiple donor-encoding msds are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization, and metabolic engineering.
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Affiliation(s)
| | - Santiago C. Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | | | - Chloe B. Fishman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Seth L. Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA
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19
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Duan Y, Tan Y, Chen X, Pei X, Li M. Modular and Flexible Molecular Device for Simultaneous Cytosine and Adenine Base Editing at Random Genomic Loci in Filamentous Fungi. ACS Synth Biol 2023. [PMID: 37428865 DOI: 10.1021/acssynbio.3c00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Random base editing is regarded as a fundamental method for accelerating the genomic evolution in both scientific research and industrial applications. In this study, we designed a modular interaction-based dual base editor (MIDBE) that assembled a DNA helicase and various base editors through dockerin/cohesin-mediated protein-protein interactions, resulting in a self-assembled MIDBE complex capable of editing bases at any locus in the genome. The base editing type of MIDBE can be readily controlled by the induction of cytidine or/and adenine deaminase gene expression. MIDBE exhibited the highest editing efficiency 2.3 × 103 times greater than the native genomic mutation rate. To evaluate the potential of MIDBE in genomic evolution, we developed a removable plasmid-based MIDBE tool, which led to a remarkable 977.1% increase of lovastatin production in Monascus purpureus HJ11. MIDBE represents the first biological tool for generating and accumulating base mutations in Monascus chromosome and also offers a bottom-up strategy for designing the base editor.
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Affiliation(s)
- Yali Duan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Yingao Tan
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Xizhu Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
| | - Xiaolin Pei
- College of Material, Chemistry and Chemical Engineering, Hangzhou Normal University, Hangzhou 310012, China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province 430070, China
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20
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Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P, Rehm FBH, Sale JE, Chin JW. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 2023; 619:555-562. [PMID: 37380776 PMCID: PMC7614783 DOI: 10.1038/s41586-023-06268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.
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Affiliation(s)
- Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Askar A Kleefeldt
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jakob Birnbaum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Simona Grazioli
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pierre Murat
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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21
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Improved Dual Base Editor Systems (iACBEs) for Simultaneous Conversion of Adenine and Cytosine in the Bacterium Escherichia coli. mBio 2023; 14:e0229622. [PMID: 36625577 PMCID: PMC9973308 DOI: 10.1128/mbio.02296-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Genome-editing (GE) techniques like base editing are ideal for introducing novel gain-of-function mutations and in situ protein evolution. Features of base editors (BEs) such as higher efficacy, relaxed protospacer adjacent motif (PAM), and a broader editing window enables diversification of user-defined targeted locus. Cytosine (CBE) or adenine (ABE) BEs alone can only alter C-to-T or A-to-G in target sites. In contrast, dual BEs (ACBEs) can concurrently generate C-to-T and A-to-G modifications. Although BE tools have recently been applied in microbes, there is no report of ACBE for microbial GE. In this study, we engineered four improved ACBEs (iACBEs) tethering highly active CBE and ABE variants that can introduce synchronized C-to-T and A-to-G mutations in targeted loci. iACBE4 generated by evoCDA1-ABE9e fusion demonstrated a broader editing window (positions -6 to 15) and is also compatible with the multiplex editing approach in Escherichia coli. We further show that the iACBE4-NG containing PAM-relaxed nCas9-NG expands the targeting scope beyond NGG (N-A/G/C/T) PAM. As a proof-of-concept, iACBE was effectively utilized to identify previously unknown mutations in the rpoB gene, conferring gain-of-function, i.e., rifampicin resistance. The iACBE tool would expand the CRISPR-GE toolkit for microbial genome engineering and synthetic biology. IMPORTANCE Dual base editors are DSB-free CRISPR tools applied in eukaryotes but not yet in bacteria. We developed an improved ACBE toolset for bacteria, combining highly processive deaminases. We believe that the bacterial optimized iACBE toolset is a significant advancement in CRISPR-based E. coli genome editing and adaptable to other microbes.
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22
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Kolasinliler G, Aagre MM, Akkale C, Kaya HB. The use of CRISPR-Cas-based systems in bacterial cell factories. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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23
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Li C, Wang L, Cseke LJ, Vasconcelos F, Huguet-Tapia JC, Gassmann W, Pauwels L, White FF, Dong H, Yang B. Efficient CRISPR-Cas9 based cytosine base editors for phytopathogenic bacteria. Commun Biol 2023; 6:56. [PMID: 36646768 PMCID: PMC9842757 DOI: 10.1038/s42003-023-04451-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Phytopathogenic bacteria play important roles in plant productivity, and developments in gene editing have potential for enhancing the genetic tools for the identification of critical genes in the pathogenesis process. CRISPR-based genome editing variants have been developed for a wide range of applications in eukaryotes and prokaryotes. However, the unique mechanisms of different hosts restrict the wide adaptation for specific applications. Here, CRISPR-dCas9 (dead Cas9) and nCas9 (Cas9 nickase) deaminase vectors were developed for a broad range of phytopathogenic bacteria. A gene for a dCas9 or nCas9, cytosine deaminase CDA1, and glycosylase inhibitor fusion protein (cytosine base editor, or CBE) was applied to base editing under the control of different promoters. Results showed that the RecA promoter led to nearly 100% modification of the target region. When residing on the broad host range plasmid pHM1, CBERecAp is efficient in creating base edits in strains of Xanthomonas, Pseudomonas, Erwinia and Agrobacterium. CBE based on nCas9 extended the editing window and produced a significantly higher editing rate in Pseudomonas. Strains with nonsynonymous mutations in test genes displayed expected phenotypes. By multiplexing guide RNA genes, the vectors can modify up to four genes in a single round of editing. Whole-genome sequencing of base-edited isolates of Xanthomonas oryzae pv. oryzae revealed guide RNA-independent off-target mutations. Further modifications of the CBE, using a CDA1 variant (CBERecAp-A) reduced off-target effects, providing an improved editing tool for a broad group of phytopathogenic bacteria.
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Affiliation(s)
- Chenhao Li
- grid.134936.a0000 0001 2162 3504Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri USA ,grid.27871.3b0000 0000 9750 7019Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu P. R. China
| | - Longfei Wang
- grid.134936.a0000 0001 2162 3504Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri USA
| | - Leland J. Cseke
- grid.134936.a0000 0001 2162 3504Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri USA
| | - Fernanda Vasconcelos
- grid.134936.a0000 0001 2162 3504Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri USA
| | - Jose Carlos Huguet-Tapia
- grid.15276.370000 0004 1936 8091Department of Plant Pathology, University of Florida, Gainesville, Florida USA
| | - Walter Gassmann
- grid.134936.a0000 0001 2162 3504Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri USA
| | - Laurens Pauwels
- grid.5342.00000 0001 2069 7798Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium ,grid.511033.5Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Frank F. White
- grid.15276.370000 0004 1936 8091Department of Plant Pathology, University of Florida, Gainesville, Florida USA
| | - Hansong Dong
- grid.27871.3b0000 0000 9750 7019Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu P. R. China
| | - Bing Yang
- grid.134936.a0000 0001 2162 3504Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, Missouri USA ,grid.34424.350000 0004 0466 6352Donald Danforth Plant Science Center, St. Louis, Missouri USA
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Yan F, Wang J, Zhang S, Lu Z, Li S, Ji Z, Song C, Chen G, Xu J, Feng J, Zhou X, Zhou H. CRISPR/FnCas12a-mediated efficient multiplex and iterative genome editing in bacterial plant pathogens without donor DNA templates. PLoS Pathog 2023; 19:e1010961. [PMID: 36626407 PMCID: PMC9870152 DOI: 10.1371/journal.ppat.1010961] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/23/2023] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
CRISPR-based genome editing technology is revolutionizing prokaryotic research, but it has been rarely studied in bacterial plant pathogens. Here, we have developed a targeted genome editing method with no requirement of donor templates for convenient and efficient gene knockout in Xanthomonas oryzae pv. oryzae (Xoo), one of the most important bacterial pathogens on rice, by employing the heterologous CRISPR/Cas12a from Francisella novicida and NHEJ proteins from Mycobacterium tuberculosis. FnCas12a nuclease generated both small and large DNA deletions at the target sites as well as it enabled multiplex genome editing, gene cluster deletion, and plasmid curing in the Xoo PXO99A strain. Accordingly, a non-TAL effector-free polymutant strain PXO99AD25E, which lacks all 25 xop genes involved in Xoo pathogenesis, has been engineered through iterative genome editing. Whole-genome sequencing analysis indicated that FnCas12a did not have a noticeable off-target effect. In addition, we revealed that these strategies are also suitable for targeted genome editing in another bacterial plant pathogen Pseudomonas syringae pv. tomato (Pst). We believe that our bacterial genome editing method will greatly expand the CRISPR study on microorganisms and advance our understanding of the physiology and pathogenesis of Xoo.
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Affiliation(s)
- Fang Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingwen Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sujie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Zhenwan Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China
| | - Shaofang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Congfeng Song
- Key Laboratory of Monitoring and Management of Plant Diseases and Insects, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Gongyou Chen
- State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China,Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, China,* E-mail:
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Jeong SH, Lee HJ, Lee SJ. Recent Advances in CRISPR-Cas Technologies for Synthetic Biology. J Microbiol 2023; 61:13-36. [PMID: 36723794 PMCID: PMC9890466 DOI: 10.1007/s12275-022-00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 02/02/2023]
Abstract
With developments in synthetic biology, "engineering biology" has emerged through standardization and platformization based on hierarchical, orthogonal, and modularized biological systems. Genome engineering is necessary to manufacture and design synthetic cells with desired functions by using bioparts obtained from sequence databases. Among various tools, the CRISPR-Cas system is modularly composed of guide RNA and Cas nuclease; therefore, it is convenient for editing the genome freely. Recently, various strategies have been developed to accurately edit the genome at a single nucleotide level. Furthermore, CRISPR-Cas technology has been extended to molecular diagnostics for nucleic acids and detection of pathogens, including disease-causing viruses. Moreover, CRISPR technology, which can precisely control the expression of specific genes in cells, is evolving to find the target of metabolic biotechnology. In this review, we summarize the status of various CRISPR technologies that can be applied to synthetic biology and discuss the development of synthetic biology combined with CRISPR technology in microbiology.
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Affiliation(s)
- Song Hee Jeong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ho Joung Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Huang Z, Liu G. Current advancement in the application of prime editing. Front Bioeng Biotechnol 2023; 11:1039315. [PMID: 36873365 PMCID: PMC9978821 DOI: 10.3389/fbioe.2023.1039315] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023] Open
Abstract
Prime editing (PE) is a precise genome manipulation technology based on the "search and replace" approach of the CRISPR-Cas9 system, while it does not require the exogenous donor DNA and the DNA double-strand breaks (DSBs). Comparing the base editing technology, the editing scope of prime editing has been widely expanded. Prime editing has been successfully applied in a variety of plant cells, animal cells and the model microorganism Escherichia coli so far, and it has shown a good application potential in breeding and genomic functional study of animals and plants, disease treatment, and modification of the microbial strains. In this paper, the basic strategies of prime editing are briefly described, and its research progress is summarized and prospected from the application of multiple species. In addition, a variety of optimization strategies for improving its efficiency and specificity of prime editing are outlined.
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Affiliation(s)
- Zhangrao Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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Gawlitt S, Liao C, Achmedov T, Beisel CL. Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint. RNA Biol 2023; 20:666-680. [PMID: 37654098 PMCID: PMC10478742 DOI: 10.1080/15476286.2023.2247247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
CRISPR technologies comprising a Cas nuclease and a guide RNA (gRNA) can utilize multiple gRNAs to enact multi-site editing or regulation in the same cell. Nature devised a highly compact means of encoding gRNAs in the form of CRISPR arrays composed of conserved repeats separated by targeting spacers. However, the capacity to acquire new spacers keeps the arrays longer than necessary for CRISPR technologies. Here, we show that CRISPR arrays utilized by the Cas9 nuclease can be shortened without compromising and sometimes even enhancing targeting activity. Using multiplexed gene repression in E. coli, we found that each region could be systematically shortened to varying degrees before severely compromising targeting activity. Surprisingly, shortening some spacers yielded enhanced targeting activity, which was linked to folding of the transcribed array prior to processing. Overall, shortened CRISPR-Cas9 arrays can facilitate multiplexed editing and gene regulation from a smaller DNA footprint across many bacterial applications of CRISPR technologies.
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Affiliation(s)
- Sandra Gawlitt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Chunyu Liao
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Tatjana Achmedov
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Chase L. Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Medical Faculty, University of Würzburg, Würzburg, Germany
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28
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Kim GY, Kim J, Park G, Kim HJ, Yang J, Seo SW. Synthetic biology tools for engineering Corynebacterium glutamicum. Comput Struct Biotechnol J 2023; 21:1955-1965. [PMID: 36942105 PMCID: PMC10024154 DOI: 10.1016/j.csbj.2023.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Corynebacterium glutamicum is a promising organism for the industrial production of amino acids, fuels, and various value-added chemicals. From the whole genome sequence release, C. glutamicum has been valuable in the field of industrial microbiology and biotechnology. Continuous discovery of genetic manipulations and regulation mechanisms has developed C. glutamicum as a synthetic biology platform chassis. This review summarized diverse genomic manipulation technologies and gene expression tools for static, dynamic, and multiplex control at transcription and translation levels. Moreover, we discussed the current challenges and applicable tools to C. glutamicum for future advancements.
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Affiliation(s)
- Gi Yeon Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jinyoung Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Geunyung Park
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hyeon Jin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jina Yang
- Department of Chemical Engineering, Jeju National University, 102, Jejudaehak-ro, Jeju-si, Jeju-do 63243, South Korea
- Corresponding author.
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Chemical Processes, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Bio-MAX Institute, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Institute of Engineering Research Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
- Corresponding author at: School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea.
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29
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Heo YB, Hwang GH, Kang SW, Bae S, Woo HM. High-Fidelity Cytosine Base Editing in a GC-Rich Corynebacterium glutamicum with Reduced DNA Off-Target Editing Effects. Microbiol Spectr 2022; 10:e0376022. [PMID: 36374037 PMCID: PMC9769817 DOI: 10.1128/spectrum.03760-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Genome editing technology is a powerful tool for programming microbial cell factories. However, rat APOBEC1-derived cytosine base editor (CBE) that converts C•G to T•A at target genes induced DNA off-targets, regardless of single-guide RNA (sgRNA) sequences. Although the high efficiencies of the bacterial CBEs have been developed, a risk of unidentified off-targets impeded genome editing for microbial cell factories. To address the issues, we demonstrate the genome engineering of Corynebacterium glutamicum as a GC-rich model industrial bacterium by generating premature termination codons (PTCs) in desired genes using high-fidelity cytosine base editors (CBEs). Through this CBE-STOP approach of introducing specific cytosine conversions, we constructed several single-gene-inactivated strains for three genes (ldh, idsA, and pyc) with high base editing efficiencies of average 95.6% (n = 45, C6 position) and the highest success rate of up to 100% for PTCs and ultimately developed a strain with five genes (ldh, actA, ackA, pqo, and pta) that were inactivated sequentially for enhancing succinate production. Although these mutant strains showed the desired phenotypes, whole-genome sequencing (WGS) data revealed that genome-wide point mutations occurred in each strain and further accumulated according to the duration of CBE plasmids. To lower the undesirable mutations, high-fidelity CBEs (pCoryne-YE1-BE3 and pCoryne-BE3-R132E) was employed for single or multiplexed genome editing in C. glutamicum, resulting in drastically reduced sgRNA-independent off-targets. Thus, we provide a CRISPR-assisted bacterial genome engineering tool with an average high efficiency of 90.5% (n = 76, C5 or C6 position) at the desired targets. IMPORTANCE Rat APOBEC1-derived cytosine base editor (CBE) that converts C•G to T•A at target genes induced DNA off-targets, regardless of single-guide RNA (sgRNA) sequences. Although the high efficiencies of bacterial CBEs have been developed, a risk of unidentified off-targets impeded genome editing for microbial cell factories. To address the issues, we identified the DNA off-targets for single and multiple genome engineering of the industrial bacterium Corynebacterium glutamicum using whole-genome sequencing. Further, we developed the high-fidelity (HF)-CBE with significantly reduced off-targets with comparable efficiency and precision. We believe that our DNA off-target analysis and the HF-CBE can promote CRISPR-assisted genome engineering over conventional gene manipulation tools by providing a markerless genetic tool without need for a foreign DNA donor.
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Affiliation(s)
- Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Gue-Ho Hwang
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, Republic of Korea
| | - Seok Won Kang
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sangsu Bae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Jongno-gu, Seoul, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, Republic of Korea
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30
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Wang D, Fan X, Li M, Liu T, Lu P, Wang G, Li Y, Han J, Zhao J. Prime Editing in Mammals: The Next Generation of Precision Genome Editing. CRISPR J 2022; 5:746-768. [PMID: 36512351 DOI: 10.1089/crispr.2022.0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The recently established prime editor (PE) system is regarded as next-generation gene-editing technology. This methodology can install any base-to-base change as well as insertions and deletions without the requirement for double-stranded break formation or donor DNA templates; thus, it offers more targeting flexibility and greater editing precision than conventional CRISPR-Cas systems or base editors. In this study, we introduce the basic principles of PE and then review its most recent progress in terms of editing versatility, specificity, and efficiency in mammals. Next, we summarize key considerations regarding the selection of PE variants, prime editing guide RNA (pegRNA) design rules, and the efficiency and accuracy evaluation of PE. Finally, we highlight and discuss how PE can assist in a wide range of biological studies and how it can be applied to make precise genomic corrections in animal models, which paves the way for curing human diseases.
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Affiliation(s)
- Dawei Wang
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xiude Fan
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Mengzhu Li
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Tianbo Liu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Peng Lu
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Guangxin Wang
- Shandong Innovation Center of Intelligent Diagnosis, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yuan Li
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JunMing Han
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - JiaJun Zhao
- Department of Endocrinology, Shandong Provincial Hospital, Shandong University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Engineering Research Center of Stem Cell and Gene Therapy for Endocrine and Metabolic Diseases, Jinan, China; Central Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China; and Central Hospital Affiliated to Shandong First Medical University, Jinan, China
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Yilmaz S, Nyerges A, van der Oost J, Church GM, Claassens NJ. Towards next-generation cell factories by rational genome-scale engineering. Nat Catal 2022. [DOI: 10.1038/s41929-022-00836-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Bourgade B, Stensjö K. Synthetic biology in marine cyanobacteria: Advances and challenges. Front Microbiol 2022; 13:994365. [PMID: 36188008 PMCID: PMC9522894 DOI: 10.3389/fmicb.2022.994365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022] Open
Abstract
The current economic and environmental context requests an accelerating development of sustainable alternatives for the production of various target compounds. Biological processes offer viable solutions and have gained renewed interest in the recent years. For example, photosynthetic chassis organisms are particularly promising for bioprocesses, as they do not require biomass-derived carbon sources and contribute to atmospheric CO2 fixation, therefore supporting climate change mitigation. Marine cyanobacteria are of particular interest for biotechnology applications, thanks to their rich diversity, their robustness to environmental changes, and their metabolic capabilities with potential for therapeutics and chemicals production without requiring freshwater. The additional cyanobacterial properties, such as efficient photosynthesis, are also highly beneficial for biotechnological processes. Due to their capabilities, research efforts have developed several genetic tools for direct metabolic engineering applications. While progress toward a robust genetic toolkit is continuously achieved, further work is still needed to routinely modify these species and unlock their full potential for industrial applications. In contrast to the understudied marine cyanobacteria, genetic engineering and synthetic biology in freshwater cyanobacteria are currently more advanced with a variety of tools already optimized. This mini-review will explore the opportunities provided by marine cyanobacteria for a greener future. A short discussion will cover the advances and challenges regarding genetic engineering and synthetic biology in marine cyanobacteria, followed by a parallel with freshwater cyanobacteria and their current genetic availability to guide the prospect for marine species.
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Affiliation(s)
- Barbara Bourgade
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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Past, Present, and Future of Genome Modification in Escherichia coli. Microorganisms 2022; 10:microorganisms10091835. [PMID: 36144436 PMCID: PMC9504249 DOI: 10.3390/microorganisms10091835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 12/04/2022] Open
Abstract
Escherichia coli K-12 is one of the most well-studied species of bacteria. This species, however, is much more difficult to modify by homologous recombination (HR) than other model microorganisms. Research on HR in E. coli has led to a better understanding of the molecular mechanisms of HR, resulting in technical improvements and rapid progress in genome research, and allowing whole-genome mutagenesis and large-scale genome modifications. Developments using λ Red (exo, bet, and gam) and CRISPR-Cas have made E. coli as amenable to genome modification as other model microorganisms, such as Saccharomyces cerevisiae and Bacillus subtilis. This review describes the history of recombination research in E. coli, as well as improvements in techniques for genome modification by HR. This review also describes the results of large-scale genome modification of E. coli using these technologies, including DNA synthesis and assembly. In addition, this article reviews recent advances in genome modification, considers future directions, and describes problems associated with the creation of cells by design.
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34
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Maliga P. Engineering the plastid and mitochondrial genomes of flowering plants. NATURE PLANTS 2022; 8:996-1006. [PMID: 36038655 DOI: 10.1038/s41477-022-01227-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Engineering the plastid genome based on homologous recombination is well developed in a few model species. Homologous recombination is also the rule in mitochondria, but transformation of the mitochondrial genome has not been realized in the absence of selective markers. The application of transcription activator-like (TAL) effector-based tools brought about a dramatic change because they can be deployed from nuclear genes and targeted to plastids or mitochondria by an N-terminal targeting sequence. Recognition of the target site in the organellar genomes is ensured by the modular assembly of TALE repeats. In this paper, I review the applications of TAL effector nucleases and TAL effector cytidine deaminases for gene deletion, base editing and mutagenesis in plastids and mitochondria. I also review emerging technologies such as post-transcriptional RNA modification to regulate gene expression, Agrobacterium- and nanoparticle-mediated organellar genome transformation, and self-replicating organellar vectors as production platforms.
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Affiliation(s)
- Pal Maliga
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA.
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA.
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35
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Prime Editing: An All-Rounder for Genome Editing. Int J Mol Sci 2022; 23:ijms23179862. [PMID: 36077252 PMCID: PMC9456398 DOI: 10.3390/ijms23179862] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Prime editing (PE), as a "search-and-replace" genome editing technology, has shown the attractive potential of versatile genome editing ability, which is, in principle, currently superior to other well-established genome-editing technologies in the all-in-one operation scope. However, essential technological solutions of PE technology, such as the improvement of genome editing efficiency, the inhibition of potential off-targets and intended edits accounting for unexpected side-effects, and the development of effective delivery systems, are necessary to broaden its application. Since the advent of PE, many optimizations have been performed on PE systems to improve their performance, resulting in bright prospects for application in many fields. This review briefly discusses the development of PE technology, including its functional principle, noteworthy barriers restraining its application, current efforts in technical optimization, and its application directions and potential risks. This review may provide a concise and informative insight into the burgeoning field of PE, highlight the exciting prospects for this powerful tool, and provide clues for questions that may propel the field forward.
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36
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Li W, Huang C, Chen J. The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations. Front Bioeng Biotechnol 2022; 10:890155. [PMID: 36091445 PMCID: PMC9452635 DOI: 10.3389/fbioe.2022.890155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated enzymes (Cas) is a simple and convenient genome editing tool that has been used in various cell factories and emerging synthetic biology in the recent past. However, several problems, including off-target effects, cytotoxicity, and low efficiency of multi-gene editing, are associated with the CRISPR/Cas system, which have limited its application in new species. In this review, we briefly describe the mechanisms of CRISPR/Cas engineering and propose strategies to optimize the system based on its defects, including, but not limited to, enhancing targeted specificity, reducing toxicity related to Cas protein, and improving multi-point editing efficiency. In addition, some examples of improvements in synthetic biology are also highlighted. Finally, future perspectives of system optimization are discussed, providing a reference for developing safe genome-editing tools for new species.
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Affiliation(s)
- Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
- *Correspondence: Jingyu Chen,
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Li X, Liao L, Jiang B, Yuan R, Xiang Y. Invader assay-induced catalytic assembly of multi-DNAzyme junctions for sensitive detection of single nucleotide polymorphisms. Anal Chim Acta 2022; 1224:340225. [DOI: 10.1016/j.aca.2022.340225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/21/2022] [Accepted: 07/31/2022] [Indexed: 01/07/2023]
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Alfaro T, Elmore JR, Stromberg ZR, Hutchison JR, Hess BM. Engineering Citrobacter freundii using CRISPR/Cas9 system. METHODS IN MICROBIOLOGY 2022; 200:106533. [PMID: 35779647 DOI: 10.1016/j.mimet.2022.106533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 11/17/2022]
Abstract
The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) system is a useful tool to edit genomes quickly and efficiently. However, the use of CRISPR/Cas9 to edit bacterial genomes has been limited to select microbial chassis primarily used for bioproduction of high value products. Thus, expansion of CRISPR/Cas9 tools to other microbial organisms is needed. Here, our aim was to assess the suitability of CRISPR/Cas9 for genome editing of the Citrobacter freundii type strain ATCC 8090. We evaluated the commonly used two plasmid pCas/pTargetF system to enable gene deletions and insertions in C. freundii and determined editing efficiency. The CRISPR/Cas9 based method enabled high editing efficiency (~91%) for deletion of galactokinase (galk) and enabled deletion with various single guide RNA (sgRNA) sequences. To assess the ability of CRISPR/Cas9 tools to insert genes, we used the fluorescent reporter mNeonGreen, an endopeptidase (yebA), and a transcriptional regulator (xylS) and found successful insertion with high efficiency (81-100%) of each gene individually. These results strengthen and expand the use of CRISPR/Cas9 genome editing to C. freundii as an additional microbial chassis.
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Affiliation(s)
- Trinidad Alfaro
- Chemical and Biological Signatures Group, National Security Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Joshua R Elmore
- Synthetic Biology Group, Earth and Biological Science Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Zachary R Stromberg
- Chemical and Biological Signatures Group, National Security Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Janine R Hutchison
- Chemical and Biological Signatures Group, National Security Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Becky M Hess
- Chemical and Biological Signatures Group, National Security Directorate, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA.
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Yu HY, Wang SG, Xia PF. Reprogramming Microbial CO2-Metabolizing Chassis With CRISPR-Cas Systems. Front Bioeng Biotechnol 2022; 10:897204. [PMID: 35814004 PMCID: PMC9260013 DOI: 10.3389/fbioe.2022.897204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/07/2022] [Indexed: 02/03/2023] Open
Abstract
Global warming is approaching an alarming level due to the anthropogenic emission of carbon dioxide (CO2). To overcome the challenge, the reliance on fossil fuels needs to be alleviated, and a significant amount of CO2 needs to be sequestrated from the atmosphere. In this endeavor, carbon-neutral and carbon-negative biotechnologies are promising ways. Especially, carbon-negative bioprocesses, based on the microbial CO2-metabolizing chassis, possess unique advantages in fixing CO2 directly for the production of fuels and value-added chemicals. In order to fully uncover the potential of CO2-metabolizing chassis, synthetic biology tools, such as CRISPR-Cas systems, have been developed and applied to engineer these microorganisms, revolutionizing carbon-negative biotechnology. Herein, we review the recent advances in the adaption of CRISPR-Cas systems, including CRISPR-Cas based genome editing and CRISPR interference/activation, in cyanobacteria, acetogens, and methanogens. We also envision future innovations via the implementation of rising CRISPR-Cas systems, such as base editing, prime editing, and transposon-mediated genome editing.
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Affiliation(s)
- Hai-Yan Yu
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- *Correspondence: Peng-Fei Xia,
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Li M, Huo YX, Guo S. CRISPR-Mediated Base Editing: From Precise Point Mutation to Genome-Wide Engineering in Nonmodel Microbes. BIOLOGY 2022; 11:571. [PMID: 35453770 PMCID: PMC9024924 DOI: 10.3390/biology11040571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/27/2022] [Accepted: 04/02/2022] [Indexed: 12/23/2022]
Abstract
Nonmodel microbes with unique and diverse metabolisms have become rising stars in synthetic biology; however, the lack of efficient gene engineering techniques still hinders their development. Recently, the use of base editors has emerged as a versatile method for gene engineering in a wide range of organisms including nonmodel microbes. This method is a fusion of impaired CRISPR/Cas9 nuclease and base deaminase, enabling the precise point mutation at the target without inducing homologous recombination. This review updates the latest advancement of base editors in microbes, including the conclusion of all microbes that have been researched by base editors, the introduction of newly developed base editors, and their applications. We provide a list that comprehensively concludes specific applications of BEs in nonmodel microbes, which play important roles in industrial, agricultural, and clinical fields. We also present some microbes in which BEs have not been fully established, in the hope that they are explored further and so that other microbial species can achieve arbitrary base conversions. The current obstacles facing BEs and solutions are put forward. Lastly, the highly efficient BEs and other developed versions for genome-wide reprogramming of cells are discussed, showing great potential for future engineering of nonmodel microbes.
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Affiliation(s)
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China;
| | - Shuyuan Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing 100081, China;
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Shelake RM, Pramanik D, Kim JY. 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. Int J Mol Sci 2022; 23:ijms23031145. [PMID: 35163069 PMCID: PMC8834901 DOI: 10.3390/ijms23031145] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid assessment of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing (GE) tools and their components is a critical aspect for successful GE applications in different organisms. In many bacteria, double-strand breaks (DSBs) generated by CRISPR/Cas tool generally cause cell death due to the lack of an efficient nonhomologous end-joining pathway and restricts its use. CRISPR-based DSB-free base editors (BEs) have been applied for precise nucleotide (nt) editing in bacteria, which does not need to make DSBs. However, optimization of newer BE tools in bacteria is challenging owing to the toxic effects of BE reagents expressed using strong promoters. Improved variants of two main BEs, cytidine base editor (CBE) and adenine base editor (ABE), capable of converting C to T and A to G, respectively, have been recently developed but yet to be tested for editing characteristics in bacteria. Here, we report a platform for in vivo rapid investigation of CRISPR-BE components in Escherichia coli (IRI-CCE) comprising a combination of promoters and terminators enabling the expression of nCas9-based BE and sgRNA to nontoxic levels, eventually leading to successful base editing. We demonstrate the use of IRI-CCE to characterize different variants of CBEs (PmCDA1, evoCDA1, APOBEC3A) and ABEs (ABE8e, ABE9e) for bacteria, exhibiting that each independent BE has its specific editing pattern for a given target site depending on protospacer length. In summary, CRISPR-BE components expressed without lethal effects on cell survival in the IRI-CCE allow an analysis of various BE tools, including cloned biopart modules and sgRNAs.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Correspondence: (R.M.S.); (J.-Y.K.)
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
- Correspondence: (R.M.S.); (J.-Y.K.)
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Nambiar TS, Baudrier L, Billon P, Ciccia A. CRISPR-based genome editing through the lens of DNA repair. Mol Cell 2022; 82:348-388. [PMID: 35063100 PMCID: PMC8887926 DOI: 10.1016/j.molcel.2021.12.026] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Genome editing technologies operate by inducing site-specific DNA perturbations that are resolved by cellular DNA repair pathways. Products of genome editors include DNA breaks generated by CRISPR-associated nucleases, base modifications induced by base editors, DNA flaps created by prime editors, and integration intermediates formed by site-specific recombinases and transposases associated with CRISPR systems. Here, we discuss the cellular processes that repair CRISPR-generated DNA lesions and describe strategies to obtain desirable genomic changes through modulation of DNA repair pathways. Advances in our understanding of the DNA repair circuitry, in conjunction with the rapid development of innovative genome editing technologies, promise to greatly enhance our ability to improve food production, combat environmental pollution, develop cell-based therapies, and cure genetic and infectious diseases.
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Affiliation(s)
- Tarun S. Nambiar
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032
| | - Lou Baudrier
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada
| | - Pierre Billon
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive N. W., Calgary, Alberta T2N 4N1, Canada,Corresponding authors: ,
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032,Lead Contact,Corresponding authors: ,
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