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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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Wiles D, Shanbhag BK, O'Brien M, Doblin MS, Bacic A, Beddoe T. Heterologous production of Cannabis sativa-derived specialised metabolites of medicinal significance - Insights into engineering strategies. PHYTOCHEMISTRY 2022; 203:113380. [PMID: 36049526 DOI: 10.1016/j.phytochem.2022.113380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Cannabis sativa L. has been known for at least 2000 years as a source of important, medically significant specialised metabolites and several bio-active molecules have been enriched from multiple chemotypes. However, due to the many levels of complexity in both the commercial cultivation of cannabis and extraction of its specialised metabolites, several heterologous production approaches are being pursued in parallel. In this review, we outline the recent achievements in engineering strategies used for heterologous production of cannabinoids, terpenes and flavonoids along with their strength and weakness. We provide an overview of the specialised metabolism pathway in C. sativa and a comprehensive list of the specialised metabolites produced along with their medicinal significance. We highlight cannabinoid-like molecules produced by other species. We discuss the key biosynthetic enzymes and their heterologous production using various hosts such as microbial and eukaryotic systems. A brief discussion on complementary production strategies using co-culturing and cell-free systems is described. Various approaches to optimise specialised metabolite production through co-expression, enzyme engineering and pathway engineering are discussed. We derive insights from recent advances in metabolic engineering of hosts with improved precursor supply and suggest their application for the production of C. sativa speciality metabolites. We present a collation of non-conventional hosts with speciality traits that can improve the feasibility of commercial heterologous production of cannabis-based specialised metabolites. We provide a perspective of emerging research in synthetic biology, allied analytical techniques and plant heterologous platforms as focus areas for heterologous production of cannabis specialised metabolites in the future.
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Affiliation(s)
- Danielle Wiles
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Bhuvana K Shanbhag
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin O'Brien
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Monika S Doblin
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Travis Beddoe
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia.
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Yao C, Hu X, Wang X. Construction and application of a CRISPR/Cas9-assisted genomic editing system for Corynebacterium glutamicum. AMB Express 2021; 11:70. [PMID: 34009533 PMCID: PMC8134620 DOI: 10.1186/s13568-021-01231-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
Corynebacterium glutamicum is widely used as microbial cell factory for various bioproducts, but its genomic editing efficiency needs to be improved. In this study, a highly efficient CRISPR/Cas9-assisted genomic editing system for C. glutamicum was constructed. This system mainly involves a plasmid and can be used for both gene insertion and deletion in the chromosome of C. glutamicum. The recombinant plasmid for the target gene containing all the editing elements, and first constructed it in E. coli, then purified and transformed it into C. glutamicum. This temperature-sensitive plasmid was cured at high temperature after the genomic editing was completed in C. glutamicum. Using this genetic editing system, the genetic editing efficiency in C. glutamicum ATCC 13032 could reach 95%. The whole work of editing could be done in 8-9 days and showed most time-saving compared to the reported. Using this system, the native promoter of gdhA1 in ATCC 13032 has been replaced with the strong promoter PtacM, and more than 10 genes in ATCC 13032 have been deleted. The results demonstrate that this CRISPR/Cas9-assisted system is highly efficient and very suitable for genome editing in C. glutamicum.
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Genome Editing in Bacteria: CRISPR-Cas and Beyond. Microorganisms 2021; 9:microorganisms9040844. [PMID: 33920749 PMCID: PMC8071187 DOI: 10.3390/microorganisms9040844] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/11/2022] Open
Abstract
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids. The discovery and applications of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas based technologies have revolutionized genome editing in eukaryotic organisms due to its simplicity and programmability. Nevertheless, this system has not been as widely favored for bacterial genome editing. In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs. Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria. CRISPR-Cas still holds promise as a generalized genome-editing tool in bacteria and is developing further optimization for an expanded application in these organisms. This review provides a rarely offered comprehensive view of genome editing. It also aims to familiarize the microbiology community with an ever-growing genome-editing toolbox for bacteria.
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Wang Q, Zhang J, Al Makishah NH, Sun X, Wen Z, Jiang Y, Yang S. Advances and Perspectives for Genome Editing Tools of Corynebacterium glutamicum. Front Microbiol 2021; 12:654058. [PMID: 33897668 PMCID: PMC8058222 DOI: 10.3389/fmicb.2021.654058] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
Corynebacterium glutamicum has been considered a promising synthetic biological platform for biomanufacturing and bioremediation. However, there are still some challenges in genetic manipulation of C. glutamicum. Recently, more and more genetic parts or elements (replicons, promoters, reporter genes, and selectable markers) have been mined, characterized, and applied. In addition, continuous improvement of classic molecular genetic manipulation techniques, such as allelic exchange via single/double-crossover, nuclease-mediated site-specific recombination, RecT-mediated single-chain recombination, actinophages integrase-mediated integration, and transposition mutation, has accelerated the molecular study of C. glutamicum. More importantly, emerging gene editing tools based on the CRISPR/Cas system is revolutionarily rewriting the pattern of genetic manipulation technology development for C. glutamicum, which made gene reprogramming, such as insertion, deletion, replacement, and point mutation, much more efficient and simpler. This review summarized the recent progress in molecular genetic manipulation technology development of C. glutamicum and discussed the bottlenecks and perspectives for future research of C. glutamicum as a distinctive microbial chassis.
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Affiliation(s)
- Qingzhuo Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Jiao Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Naief H. Al Makishah
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- School of Environmental and Biological Engineering, Nanjing University of Science & Technology, Nanjing, China
| | - Yu Jiang
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Huzhou Center of Industrial Biotechnology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Marques F, Luzhetskyy A, Mendes MV. Engineering Corynebacterium glutamicum with a comprehensive genomic library and phage-based vectors. Metab Eng 2020; 62:221-234. [DOI: 10.1016/j.ymben.2020.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
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Kim HJ, Oh SY, Lee SJ. Single-Base Genome Editing in Corynebacterium glutamicum with the Help of Negative Selection by Target-Mismatched CRISPR/Cpf1. J Microbiol Biotechnol 2020; 30:1583-1591. [PMID: 32807756 PMCID: PMC9728170 DOI: 10.4014/jmb.2006.06036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022]
Abstract
CRISPR/Cpf1 has emerged as a new CRISPR-based genome editing tool because, in comparison with CRIPSR/Cas9, it has a different T-rich PAM sequence to expand the target DNA sequence. Single-base editing in the microbial genome can be facilitated by oligonucleotide-directed mutagenesis (ODM) followed by negative selection with the CRISPR/Cpf1 system. However, single point mutations aided by Cpf1 negative selection have been rarely reported in Corynebacterium glutamicum. This study aimed to introduce an amber stop codon in crtEb encoding lycopene hydratase, through ODM and Cpf1-mediated negative selection; deficiency of this enzyme causes pink coloration due to lycopene accumulation in C. glutamicum. Consequently, on using double-, triple-, and quadruple-basemutagenic oligonucleotides, 91.5-95.3% pink cells were obtained among the total live C. glutamicum cells. However, among the negatively selected live cells, 0.6% pink cells were obtained using single-base-mutagenic oligonucleotides, indicating that very few single-base mutations were introduced, possibly owing to mismatch tolerance. This led to the consideration of various targetmismatched crRNAs to prevent the death of single-base-edited cells. Consequently, we obtained 99.7% pink colonies after CRISPR/Cpf1-mediated negative selection using an appropriate singlemismatched crRNA. Furthermore, Sanger sequencing revealed that single-base mutations were successfully edited in the 99.7% of pink cells, while only two of nine among 0.6% of pink cells were correctly edited. The results indicate that the target-mismatched Cpf1 negative selection can assist in efficient and accurate single-base genome editing methods in C. glutamicum.
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Affiliation(s)
- Hyun Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Se Young Oh
- 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,Corresponding author Phone: +82-31-670-3356 E-mail:
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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Wendisch VF. Metabolic engineering advances and prospects for amino acid production. Metab Eng 2019; 58:17-34. [PMID: 30940506 DOI: 10.1016/j.ymben.2019.03.008] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 11/18/2022]
Abstract
Amino acid fermentation is one of the major pillars of industrial biotechnology. The multi-billion USD amino acid market is rising steadily and is diversifying. Metabolic engineering is no longer focused solely on strain development for the bulk amino acids L-glutamate and L-lysine that are produced at the million-ton scale, but targets specialty amino acids. These demands are met by the development and application of new metabolic engineering tools including CRISPR and biosensor technologies as well as production processes by enabling a flexible feedstock concept, co-production and co-cultivation schemes. Metabolic engineering advances are exemplified for specialty proteinogenic amino acids, cyclic amino acids, omega-amino acids, and amino acids functionalized by hydroxylation, halogenation and N-methylation.
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Affiliation(s)
- Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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