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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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2
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Lee SM, Jeong KJ. Advances in Synthetic Biology Tools and Engineering of Corynebacterium glutamicum as a Platform Host for Recombinant Protein Production. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0219-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022; 4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.
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Affiliation(s)
- Nicole LeBlanc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Nicole LeBlanc,
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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4
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Shekhar C, Maeda T. A simple approach for random genomic insertion-deletions using ambiguous sequences in Escherichia coli. J Basic Microbiol 2022; 62:948-962. [PMID: 35739617 DOI: 10.1002/jobm.202100636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/20/2022] [Accepted: 06/11/2022] [Indexed: 11/07/2022]
Abstract
Escherichia coli K-12, being one of the best understood and thoroughly analyzed organisms, is the preferred platform for genetic and biochemical research. Among all genetic engineering approaches applied on E. coli, the homologous recombination approach is versatile and precise, which allows engineering genes or large segments of the chromosome directly by using polymerase chain reaction (PCR) products or synthetic oligonucleotides. The previously explained approaches for random insertion and deletions were reported as technically not easy and laborious. This study, first, finds the minimum length of homology extension that is efficient and accurate for homologous recombination, as 30 nt. Second, proposes an approach utilizing PCR products flanking ambiguous NNN-sequence (30-nt) extensions, which facilitate the homologous recombination to recombine them at multiple regions on the genome and generate insertion-deletion mutations. Further analysis found that these mutations were varying in number, that is, multiple genomic regions were deleted. Moreover, evaluation of the phenotype of all the multiple random insertion-deletion mutants demonstrated no significant changes in the normal metabolism of bacteria. This study not only presents the efficiency of ambiguous sequences in making random deletion mutations, but also demonstrates their further applicability in genomics.
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Affiliation(s)
- Chandra Shekhar
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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Shaw D, Miravet‐Verde S, Piñero‐Lambea C, Serrano L, Lluch‐Senar M. LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions. Microb Biotechnol 2021; 14:2403-2419. [PMID: 33325626 PMCID: PMC8601177 DOI: 10.1111/1751-7915.13714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deepsequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via Cre recombinase, catalogued via deep sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from > 50 bp to 28 Kb, which represents 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions.
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Affiliation(s)
- Daniel Shaw
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Samuel Miravet‐Verde
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
| | - Carlos Piñero‐Lambea
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Present address:
Pulmobiotics ltdDr. Aiguader 88Barcelona08003Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Universitat Pompeu Fabra (UPF)Barcelona08002Spain
- ICREAPg. Lluís Companys 23Barcelona08010Spain
| | - Maria Lluch‐Senar
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88Barcelona08003Spain
- Basic Sciences DepartmentFaculty of Medicine and Health SciencesUniversitat Internacional de CatalunyaSant Cugat del Vallès08195Spain
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6
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Recent progress in metabolic engineering of Corynebacterium glutamicum for the production of C4, C5, and C6 chemicals. KOREAN J CHEM ENG 2021. [DOI: 10.1007/s11814-021-0788-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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8
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Zwiener T, Dziuba M, Mickoleit F, Rückert C, Busche T, Kalinowski J, Uebe R, Schüler D. Towards a 'chassis' for bacterial magnetosome biosynthesis: genome streamlining of Magnetospirillum gryphiswaldense by multiple deletions. Microb Cell Fact 2021; 20:35. [PMID: 33541381 PMCID: PMC7860042 DOI: 10.1186/s12934-021-01517-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/12/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Because of its tractability and straightforward cultivation, the magnetic bacterium Magnetospirillum gryphiswaldense has emerged as a model for the analysis of magnetosome biosynthesis and bioproduction. However, its future use as platform for synthetic biology and biotechnology will require methods for large-scale genome editing and streamlining. RESULTS We established an approach for combinatory genome reduction and generated a library of strains in which up to 16 regions including large gene clusters, mobile genetic elements and phage-related genes were sequentially removed, equivalent to ~ 227.6 kb and nearly 5.5% of the genome. Finally, the fragmented genomic magnetosome island was replaced by a compact cassette comprising all key magnetosome biosynthetic gene clusters. The prospective 'chassis' revealed wild type-like cell growth and magnetosome biosynthesis under optimal conditions, as well as slightly improved resilience and increased genetic stability. CONCLUSION We provide first proof-of-principle for the feasibility of multiple genome reduction and large-scale engineering of magnetotactic bacteria. The library of deletions will be valuable for turning M. gryphiswaldense into a microbial cell factory for synthetic biology and production of magnetic nanoparticles.
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Affiliation(s)
- Theresa Zwiener
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Marina Dziuba
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Frank Mickoleit
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Christian Rückert
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - René Uebe
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany.
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9
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Metabolic engineering of Corynebacterium glutamicum for fermentative production of chemicals in biorefinery. Appl Microbiol Biotechnol 2018; 102:3915-3937. [DOI: 10.1007/s00253-018-8896-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/22/2023]
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10
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Gorshkova NV, Lobanova JS, Tokmakova IL, Smirnov SV, Akhverdyan VZ, Krylov AA, Mashko SV. Mu-driven transposition of recombinant mini-Mu unit DNA in the Corynebacterium glutamicum chromosome. Appl Microbiol Biotechnol 2018; 102:2867-2884. [PMID: 29392386 PMCID: PMC5847225 DOI: 10.1007/s00253-018-8767-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 02/05/2023]
Abstract
A dual-component Mu-transposition system was modified for the integration/amplification of genes in Corynebacterium. The system consists of two types of plasmids: (i) a non-replicative integrative plasmid that contains the transposing mini-Mu(LR) unit bracketed by the L/R Mu ends or the mini-Mu(LER) unit, which additionally contains the enhancer element, E, and (ii) an integration helper plasmid that expresses the transposition factor genes for MuA and MuB. Efficient transposition in the C. glutamicum chromosome (≈ 2 × 10−4 per cell) occurred mainly through the replicative pathway via cointegrate formation followed by possible resolution. Optimizing the E location in the mini-Mu unit significantly increased the efficiency of Mu-driven intramolecular transposition–amplification in C. glutamicum as well as in gram-negative bacteria. The new C. glutamicum genome modification strategy that was developed allows the consequent independent integration/amplification/fixation of target genes at high copy numbers. After integration/amplification of the first mini-Mu(LER) unit in the C. glutamicum chromosome, the E-element, which is bracketed by lox-like sites, is excised by Cre-mediated fashion, thereby fixing the truncated mini-Mu(LR) unit in its position for the subsequent integration/amplification of new mini-Mu(LER) units. This strategy was demonstrated using the genes for the citrine and green fluorescent proteins, yECitrine and yEGFP, respectively.
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Affiliation(s)
- Natalya V Gorshkova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Juliya S Lobanova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Irina L Tokmakova
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Sergey V Smirnov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Valerii Z Akhverdyan
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Alexander A Krylov
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545
| | - Sergey V Mashko
- Ajinomoto-Genetika Research Institute, 1-st Dorozhny proezd, 1-1, Moscow, Russian Federation, 117545.
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11
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Construction of a minimal genome as a chassis for synthetic biology. Essays Biochem 2016; 60:337-346. [DOI: 10.1042/ebc20160024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 09/26/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022]
Abstract
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput ‘-omics’ research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300–500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis. Current size-reduced genomes are not perfect minimal genomes, but chemically synthesized genomes have just been constructed. Some minimal genomes provide various desirable functions for bioindustry, such as improved genome stability, increased transformation efficacy and improved production of biomaterials. The minimal genome as a chassis genome for synthetic biology can be used to construct custom-designed genomes for various practical and industrial applications.
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12
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Bott M, Eggeling L. Novel Technologies for Optimal Strain Breeding. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 159:227-254. [PMID: 27872965 DOI: 10.1007/10_2016_33] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The implementation of a knowledge-based bioeconomy requires the rapid development of highly efficient microbial production strains that are able to convert renewable carbon sources to value-added products, such as bulk and fine chemicals, pharmaceuticals, or proteins at industrial scale. Starting from classical strain breeding by random mutagenesis and screening in the 1950s via rational design by metabolic engineering initiated in the 1970s, a range of powerful new technologies have been developed in the past two decades that can revolutionize future strain engineering. In particular, next-generation sequencing technologies combined with new methods of genome engineering and high-throughput screening based on genetically encoded biosensors have allowed for new concepts. In this chapter, selected new technologies relevant for breeding microbial production strains with a special emphasis on amino acid producers will be summarized.
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Affiliation(s)
- Michael Bott
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany.
| | - Lothar Eggeling
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425, Jülich, Germany
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13
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Daniels W, Bouvin J, Busche T, Kalinowski J, Bernaerts K. Finding targets for genome reduction in Streptomyces lividans TK24 using flux balance analysis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.ifacol.2016.12.134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Mei J, Xu N, Ye C, Liu L, Wu J. Reconstruction and analysis of a genome-scale metabolic network of Corynebacterium glutamicum S9114. Gene 2015; 575:615-22. [PMID: 26392034 DOI: 10.1016/j.gene.2015.09.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 07/12/2015] [Accepted: 09/16/2015] [Indexed: 01/09/2023]
Abstract
Corynebacterium glutamicum S9114 is commonly used for industrial glutamate production. Therefore, a comprehensive understanding of the physiological and metabolic characteristics of C. glutamicum is important for developing its potential for industrial production. A genome-scale metabolic model, iJM658, was reconstructed based on genome annotation and literature mining. The model consists of 658 genes, 984 metabolites and 1065 reactions. The model quantitatively predicted C. glutamicum growth on different carbon and nitrogen sources and determined 129 genes to be essential for cell growth. The iJM658 model predicted that C. glutamicum had two glutamate biosynthesis pathways and lacked eight key genes in biotin synthesis. Robustness analysis indicated a relative low oxygen level (1.21mmol/gDW/h) would improve glutamate production rate. Potential metabolic engineering targets for improving γ-aminobutyrate and isoleucine production rate were predicted by in silico deletion or overexpression of some genes. The iJM658 model is a useful tool for understanding and optimizing the metabolism of C. glutamicum and a valuable resource for future metabolic and physiological research.
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Affiliation(s)
- Jie Mei
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Chao Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Laboratory of Food Microbial-Manufacturing Engineering, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Jianrong Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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15
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Liu X, Yang Y, Zhang W, Sun Y, Peng F, Jeffrey L, Harvey L, McNeil B, Bai Z. Expression of recombinant protein using Corynebacterium Glutamicum: progress, challenges and applications. Crit Rev Biotechnol 2015; 36:652-64. [PMID: 25714007 DOI: 10.3109/07388551.2015.1004519] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Corynebacterium glutamicum (C. glutamicum) is a highly promising alternative prokaryotic host for recombinant protein expression, as it possesses several significant advantages over Escherichia coli (E. coli), the currently leading bacterial protein expression system. During the past decades, several experimental techniques and vector components for genetic manipulation of C. glutamicum have been developed and validated, including strong promoters for tightly regulating target gene expression, various types of plasmid vectors, protein secretion systems and methods of genetically modifying the host strain genome to improve protein production potential. This review critically discusses current progress in establishing C. glutamicum as a host for recombinant protein expression, and examines, in depth, some successful case studies of actual application of this expression system. The established "expression tool box" for developing novel constructs based on C. glutamicum as a host are also evaluated. Finally, the existing issues and solutions in process development with C. glutamicum as a host are specifically addressed.
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Affiliation(s)
- Xiuxia Liu
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Yankun Yang
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Wei Zhang
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Yang Sun
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Feng Peng
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
| | - Laura Jeffrey
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Linda Harvey
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Brian McNeil
- b Institute of Pharmacy & Biomedical Sciences, Strathclyde University , Glasgow , UK
| | - Zhonghu Bai
- a National Engineering Laboratory of Cereal Fermentation Technology , School of Biotechnology, JiangNan University , Wuxi , China and
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16
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Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S. Chassis organism from Corynebacterium glutamicum--a top-down approach to identify and delete irrelevant gene clusters. Biotechnol J 2015; 10:290-301. [PMID: 25139579 PMCID: PMC4361050 DOI: 10.1002/biot.201400041] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/25/2014] [Accepted: 08/19/2014] [Indexed: 01/05/2023]
Abstract
For synthetic biology applications, a robust structural basis is required, which can be constructed either from scratch or in a top-down approach starting from any existing organism. In this study, we initiated the top-down construction of a chassis organism from Corynebacterium glutamicum ATCC 13032, aiming for the relevant gene set to maintain its fast growth on defined medium. We evaluated each native gene for its essentiality considering expression levels, phylogenetic conservation, and knockout data. Based on this classification, we determined 41 gene clusters ranging from 3.7 to 49.7 kbp as target sites for deletion. 36 deletions were successful and 10 genome-reduced strains showed impaired growth rates, indicating that genes were hit, which are relevant to maintain biological fitness at wild-type level. In contrast, 26 deleted clusters were found to include exclusively irrelevant genes for growth on defined medium. A combinatory deletion of all irrelevant gene clusters would, in a prophage-free strain, decrease the size of the native genome by about 722 kbp (22%) to 2561 kbp. Finally, five combinatory deletions of irrelevant gene clusters were investigated. The study introduces the novel concept of relevant genes and demonstrates general strategies to construct a chassis suitable for biotechnological application.
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Affiliation(s)
- Simon Unthan
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Andreas Radek
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Marius Herbst
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Daniel Siebert
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Natalie Brühl
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Anna Bartsch
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
| | - Kay Marin
- Evonik Degussa GmbHHalle/Westphalia, Germany
| | | | - Reinhard Krämer
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Gerd Seibold
- Institute of Biochemistry, University of CologneCologne, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systemic MicrobiologyForschungszentrum Jülich, Jülich, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - Volker F Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld UniversityBielefeld, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Systems BiotechnologyForschungszentrum Jülich, Jülich, Germany
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Hu J, Tan Y, Li Y, Hu X, Xu D, Wang X. Construction and application of an efficient multiple-gene-deletion system in Corynebacterium glutamicum. Plasmid 2013; 70:303-13. [DOI: 10.1016/j.plasmid.2013.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/03/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
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18
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Tsuge Y, Yamamoto S, Suda M, Inui M, Yukawa H. Reactions upstream of glycerate-1,3-bisphosphate drive Corynebacterium glutamicum (D)-lactate productivity under oxygen deprivation. Appl Microbiol Biotechnol 2013; 97:6693-703. [PMID: 23712891 DOI: 10.1007/s00253-013-4986-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/25/2022]
Abstract
We previously demonstrated the simplicity of oxygen-deprived Corynebacterium glutamicum to produce D-lactate, a primary building block of next-generation biodegradable plastics, at very high optical purity by introducing heterologous D-ldhA gene from Lactobacillus delbrueckii. Here, we independently evaluated the effects of overexpressing each of genes encoding the ten glycolytic enzymes on D-lactate production in C. glutamicum. We consequently show that while the reactions catalyzed by glucokinase (GLK), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), phosphofructokinase (PFK), triosephosphate isomerase (TPI), and bisphosphate aldolase had positive effects on D-lactate productivity by increasing 98, 39, 15, 13, and 10 %, respectively, in 10 h reactions in minimal salts medium, the reaction catalyzed by pyruvate kinase had large negative effect by decreasing 70 %. The other glycolytic enzymes did not affect D-lactate productivity when each of encoding genes was overexpressed. It is noteworthy that all reactions associated with positive effects are located upstream of glycerate-1,3-bisphosphate in the glycolytic pathway. The D-lactate yield also increased by especially overexpressing TPI encoding gene up to 94.5 %. Interestingly, overexpression of PFK encoding gene reduced the yield of succinate, one of the main by-products of D-lactate production, by 52 %, whereas overexpression of GAPDH encoding gene increased succinate yield by 26 %. Overexpression of GLK encoding gene markedly increased the yield of dihydroxyacetone and glycerol by 10- and 5.8-fold in exchange with decreasing the D-lactate yield. The effect of overexpressing glycolytic genes was also evaluated in 80 h long-term reactions. The variety of effects of overexpressing each of genes encoding the ten glycolytic enzymes on D-lactate production is discussed.
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Affiliation(s)
- Yota Tsuge
- Research Institute of Innovative Technology for the Earth (RITE), 9-2, Kizugawadai, Kizugawa-shi, Kyoto, 619-0292, Japan
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19
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Suzuki N, Inui M. Genome Engineering of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Juhas M, Eberl L, Church GM. Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol 2012; 30:601-7. [DOI: 10.1016/j.tibtech.2012.08.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/02/2012] [Accepted: 08/02/2012] [Indexed: 11/15/2022]
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21
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Vertès AA, Inui M, Yukawa H. Postgenomic Approaches to Using Corynebacteria as Biocatalysts. Annu Rev Microbiol 2012; 66:521-50. [DOI: 10.1146/annurev-micro-010312-105506] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alain A. Vertès
- Research Institute of Innovative Technology for the Earth, Kizugawadai, Kizugawa, Kyoto 619-0292, Japan;
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kizugawadai, Kizugawa, Kyoto 619-0292, Japan;
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth, Kizugawadai, Kizugawa, Kyoto 619-0292, Japan;
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22
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Tools for genetic manipulations in Corynebacterium glutamicum and their applications. Appl Microbiol Biotechnol 2011; 90:1641-54. [DOI: 10.1007/s00253-011-3272-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 03/21/2011] [Accepted: 03/23/2011] [Indexed: 01/26/2023]
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23
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Deletion of cgR_1596 and cgR_2070, encoding NlpC/P60 proteins, causes a defect in cell separation in Corynebacterium glutamicum R. J Bacteriol 2008; 190:8204-14. [PMID: 18931118 DOI: 10.1128/jb.00752-08] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In previous work, random genome deletion mutants of Corynebacterium glutamicum R were generated using the insertion sequence (IS) element IS31831 and the Cre/loxP excision system. One of these mutants, C. glutamicum strain RD41, resulting from the deletion of a 10.1-kb genomic region (DeltacgR_1595 through cgR_1604) from the WT strain, showed cell elongation, and several lines appeared on the cell surface (bamboo shape). The morphological changes were suppressed by overexpression of cgR_1596. Single disruption of cgR_1596 in WT C. glutamicum R resulted in morphological changes similar to those observed in the RD41 strain. CgR_1596 has a predicted secretion signal peptide in the amino-terminal region and a predicted NlpC/P60 domain, which is conserved in cell wall hydrolases, in the carboxyl-terminal region. In C. glutamicum R, CgR_0802, CgR_1596, CgR_2069, and CgR_2070 have the NlpC/P60 domain; however, only simultaneous disruption of cgR_1596 and cgR_2070, and not cgR_2070 single disruption, resulted in cell growth delay and more severe morphological changes than disruption of cgR_1596. Transmission electron microscopy revealed multiple septa within individual cells of cgR_1596 single and cgR_1596-cgR_2070 double disruptants. Taken together, these results suggest that cgR_1596 and cgR_2070 are involved in cell separation and cell growth in C. glutamicum.
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Suzuki N, Inui M, Yukawa H. Random genome deletion methods applicable to prokaryotes. Appl Microbiol Biotechnol 2008; 79:519-26. [PMID: 18491037 DOI: 10.1007/s00253-008-1512-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 04/16/2008] [Accepted: 04/19/2008] [Indexed: 11/28/2022]
Abstract
Through their enabling of simultaneous identification of multiple non-essential genes in a genome, large-segment genome deletion methods are an increasingly popular approach to minimize and tailor microbial genomes for specific functions. At present, difficulties in identifying target regions for deletion are a result of inadequate knowledge to define gene essentiality. Furthermore, with the majority of predicted open reading frames of completely sequenced genomes still annotated as putative genes, essential or important genes are found scattered throughout the genomes, limiting the size of non-essential segments that can be safely deleted in a single sweep. Recently described large-segment random genome deletion methods that utilize transposons enable the generation of random deletion strains, analysis of which makes identification of non-essential genes less tedious. Such and other efforts to determine the minimum genome content necessary for cell survival continue to accumulate important information that should help improve our understanding of genome function and evolution. This review presents an assessment of technological advancements of random genome deletion methods in prokaryotes to date.
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Affiliation(s)
- Nobuaki Suzuki
- Microbiology Research Group, Research Institute of Innovative Technology for the Earth (RITE), Kizugawa, Kyoto, Japan
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