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Ma S, Su T, Lu X, Qi Q. Bacterial genome reduction for optimal chassis of synthetic biology: a review. Crit Rev Biotechnol 2024; 44:660-673. [PMID: 37380345 DOI: 10.1080/07388551.2023.2208285] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/13/2022] [Accepted: 02/20/2023] [Indexed: 06/30/2023]
Abstract
Bacteria with streamlined genomes, that harbor full functional genes for essential metabolic networks, are able to synthesize the desired products more effectively and thus have advantages as production platforms in industrial applications. To obtain streamlined chassis genomes, a large amount of effort has been made to reduce existing bacterial genomes. This work falls into two categories: rational and random reduction. The identification of essential gene sets and the emergence of various genome-deletion techniques have greatly promoted genome reduction in many bacteria over the past few decades. Some of the constructed genomes possessed desirable properties for industrial applications, such as: increased genome stability, transformation capacity, cell growth, and biomaterial productivity. The decreased growth and perturbations in physiological phenotype of some genome-reduced strains may limit their applications as optimized cell factories. This review presents an assessment of the advancements made to date in bacterial genome reduction to construct optimal chassis for synthetic biology, including: the identification of essential gene sets, the genome-deletion techniques, the properties and industrial applications of artificially streamlined genomes, the obstacles encountered in constructing reduced genomes, and the future perspectives.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
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Ma S, Su T, Liu J, Lu X, Qi Q. Reduction of the Bacterial Genome by Transposon-Mediated Random Deletion. ACS Synth Biol 2022; 11:668-677. [PMID: 35104106 DOI: 10.1021/acssynbio.1c00353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genome reduction is an important strategy in synthetic biology for constructing functional chassis cells or minimal genomes. However, the limited knowledge of complex gene functions and interactions makes genome reduction by rational design encounter a bottleneck. Here, we present an iterative and random genome reduction method for Escherichia coli, named "transposon-mediated random deletion (TMRD)". TMRD generates random double-strand breaks (DSBs) in the genome by combining Tn5 transposition with the CRISPR/Cas9 system and allows genomic deletions of various sizes at random positions during DSB repair through the intracellular alternative end-joining mechanism. Using E. coli MG1655 as the original strain, a pool of cells with multiple random genomic deletions were obtained after five reduction cycles. The growth rates of the obtained cells were comparable to that of MG1655, while the electroporation efficiency increased by at least 2 magnitudes. TMRD can generate a small E. coli library carrying multiple and random genomic deletions while enriching the cells with environmental fitness in the population. TMRD has the potential to be widely applied in the construction of minimal genomes or chassis cells for metabolic engineering.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Jinming Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Xuemei Lu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
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Dong H, Cui Y, Zhang D. CRISPR/Cas Technologies and Their Applications in Escherichia coli. Front Bioeng Biotechnol 2021; 9:762676. [PMID: 34858961 PMCID: PMC8632213 DOI: 10.3389/fbioe.2021.762676] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems have revolutionized genome editing and greatly promoted the development of biotechnology. However, these systems unfortunately have not been developed and applied in bacteria as extensively as in eukaryotic organism. Here, the research progress on the most widely used CRISPR/Cas tools and their applications in Escherichia coli is summarized. Genome editing based on homologous recombination, non-homologous DNA end-joining, transposons, and base editors are discussed. Finally, the state of the art of transcriptional regulation using CRISPRi is briefly reviewed. This review provides a useful reference for the application of CRISPR/Cas systems in other bacterial species.
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Affiliation(s)
- Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
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Liang Y, Wei Y, Jiao S, Yu H. A CRISPR/Cas9-based single-stranded DNA recombineering system for genome editing of Rhodococcus opacus PD630. Synth Syst Biotechnol 2021; 6:200-208. [PMID: 34430726 PMCID: PMC8365321 DOI: 10.1016/j.synbio.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 12/01/2022] Open
Abstract
Genome engineering of Rhodococcus opacus PD630, an important microorganism used for the bioconversion of lignin, is currently dependent on inefficient homologous recombination. Although a CRISPR interference procedure for gene repression has previously been developed for R. opacus PD630, a CRISPR/Cas9 system for gene knockout has yet to be reported for the strain. In this study, we found that the cytotoxicity of Cas9 and the deficiency in pathways for repairing DNA double-strand breaks (DSBs) were the major causes of the failure of conventional CRISPR/Cas9 technologies in R. opacus, even when augmented with the recombinases Che9c60 and Che9c61. We successfully developed an efficient single-stranded DNA (ssDNA) recombineering system coupled with CRISPR/Cas9 counter-selection, which facilitated rapid and scarless editing of the R. opacus genome. A two-plasmid system, comprising Cas9 driven by a weak Rhodococcus promoter Pniami, designed to prevent cytotoxicity, and a single-guide RNA (sgRNA) under the control of a strong constitutive promoter, was proven to be appropriate with respect to cleavage function. A novel recombinase, RrRecT derived from a Rhodococcus ruber prophage, was identified for the first time, which facilitated recombination of short ssDNA donors (40–80 nt) targeted to the lagging strand and enabled us to obtain a recombination efficiency up to 103-fold higher than that of endogenous pathways. Finally, by incorporating RrRecT and Cas9 into a single plasmid and then co-transforming cells with sgRNA plasmids and short ssDNA donors, we efficiently achieved gene disruption and base mutation in R. opacus, with editing efficiencies ranging from 22 % to 100 %. Simultaneous disruption of double genes was also confirmed, although at a lower efficiency. This effective genome editing tool will accelerate the engineering of R. opacus metabolism.
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Affiliation(s)
- Youxiang Liang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Industrial Biocatalysis (Tsinghua University), The Ministry of Education, Beijing, 100084, China
| | - Yuwen Wei
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Industrial Biocatalysis (Tsinghua University), The Ministry of Education, Beijing, 100084, China
| | - Song Jiao
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.,Key Laboratory of Industrial Biocatalysis (Tsinghua University), The Ministry of Education, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
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Fenster JA, Eckert CA. High-Throughput Functional Genomics for Energy Production. Curr Opin Biotechnol 2020; 67:7-14. [PMID: 33152605 DOI: 10.1016/j.copbio.2020.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Functional genomics remains a foundational field for establishing genotype-phenotype relationships that enable strain engineering. High-throughput (HTP) methods accelerate the Design-Build-Test-Learn cycle that currently drives synthetic biology towards a forward engineering future. Trackable mutagenesis techniques including transposon insertion sequencing and CRISPR-Cas-mediated genome editing allow for rapid fitness profiling of a collection, or library, of mutants to discover beneficial mutations. Due to the relative speed of these experiments compared to adaptive evolution experiments, iterative rounds of mutagenesis can be implemented for next-generation metabolic engineering efforts to design complex production and tolerance phenotypes. Additionally, the expansion of these mutagenesis techniques to novel bacteria are opening up industrial microbes that show promise for establishing a bio-based economy.
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Affiliation(s)
- Jacob A Fenster
- Chemical and Biological Engineering, University of Colorado, Boulder CO, United States; Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States
| | - Carrie A Eckert
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder CO, United States; National Renewable Energy Laboratory, Golden CO, United States.
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Luo JM, Cui HL, Jia HC, Li F, Cheng HJ, Shen YB, Wang M. Identification, Biological Characteristics, and Active Site Residues of 3-Ketosteroid Δ 1-Dehydrogenase Homologues from Arthrobacter simplex. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9496-9512. [PMID: 32786835 DOI: 10.1021/acs.jafc.0c03360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
3-Ketosteroid Δ1-dehydrogenase (KsdD) is the key enzyme responsible for Δ1-dehydrogenation, which is one of the most valuable reactions for steroid catabolism. Arthrobacter simplex has been widely used in the industry due to its superior bioconversion efficiency, but KsdD information is not yet fully clear. Here, five KsdD homologues were identified in A. simplex CGMCC 14539. Bioinformatic analysis indicated their distinct properties and structures. Each KsdD was functionally confirmed by transcriptional response, overexpression, and heterologous expression. The substantial difference in substrate profiles might be related to the enzyme loop structure. Two promising enzymes (KsdD3 and KsdD5) were purified and characterized, exhibiting strong organic solvent tolerance and clear preference for 4-ene-3-oxosteroids. KsdD5 seemed to be more versatile due to good activity on substrates with or without a substituent at C11 and high optimal temperature and also possessed unique residues. It is the first time that KsdDs have been comprehensively disclosed in the A. simplex industrial strain.
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Affiliation(s)
- Jian-Mei Luo
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
- Ministry of Education Key Laboratory of Molecular Microbiology and Technology, Nankai University, Tianjin 300071, P. R. China
| | - Hui-Lin Cui
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Hong-Chen Jia
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Fang Li
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Hong-Jin Cheng
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Yan-Bing Shen
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
| | - Min Wang
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, 89 P.O. Box, No. 29, Street No. 13, Tianjin Economic-Technological Development Area (TEDA), Tianjin 30057, P. R. China
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Xu Z, Li Y, Li M, Xiang H, Yan A. Harnessing the type I CRISPR-Cas systems for genome editing in prokaryotes. Environ Microbiol 2020; 23:542-558. [PMID: 32510745 DOI: 10.1111/1462-2920.15116] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/26/2022]
Abstract
Genetic analysis is crucial to the understanding, exploitation, and control of microorganisms. The advent of CRISPR-Cas-based genome-editing techniques, particularly those mediated by the single-effector (Cas9 and Cas12a) class 2 CRISPR-Cas systems, has revolutionized the genetics in model eukaryotic organisms. However, their applications in prokaryotes are rather limited, largely owing to the exceptional diversity of DNA homeostasis in microorganisms and severe cytotoxicity of overexpressing these nuclease proteins in certain genotypes. Remarkably, CRISPR-Cas systems belonging to different classes and types are continuously identified in prokaryotic genomes and serve as a deep reservoir for expansion of the CRISPR-based genetic toolkits. ~90% of the CRISPR-Cas systems identified so far belong to the class 1 system which hinges on multi-protein effector complexes for DNA interference. Harnessing these widespread native CRISPR-Cas systems for 'built-in' genome editing represents an emerging and powerful genetic tool in prokaryotes, especially in the genetically recalcitrant non-model species and strains. In this progress review, we introduce the general workflow of this emerging editing platform and summarize its establishment in a growing number of prokaryotes by harnessing the most widespread, diverse type I CRISPR-Cas systems present in their genomes. We also discuss the various factors affecting the success and efficiency of this editing platform and the corresponding solutions.
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Affiliation(s)
- Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yanran Li
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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