1
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Champie A, Lachance JC, Sastry A, Matteau D, Lloyd CJ, Grenier F, Lamoureux CR, Jeanneau S, Feist AM, Jacques PÉ, Palsson BO, Rodrigue S. Diagnosis and mitigation of the systemic impact of genome reduction in Escherichia coli DGF-298. mBio 2024; 15:e0087324. [PMID: 39207109 PMCID: PMC11481515 DOI: 10.1128/mbio.00873-24] [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: 03/26/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Microorganisms with simplified genomes represent interesting cell chassis for systems and synthetic biology. However, genome reduction can lead to undesired traits, such as decreased growth rate and metabolic imbalances. To investigate the impact of genome reduction on Escherichia coli strain DGF-298, a strain in which ~ 36% of the genome has been removed, we reconstructed a strain-specific metabolic model (iAC1061), investigated the regulation of gene expression using iModulon-based transcriptome analysis, and performed adaptive laboratory evolution to let the strain correct potential imbalances that arose during its simplification. The model notably predicted that the removal of all three key pathways for glycolaldehyde disposal in this microorganism would lead to a metabolic bottleneck through folate starvation. Glycolaldehyde is also known to cause self-generation of reactive oxygen species, as evidenced by the increased expression of oxidative stress resistance genes in the SoxS iModulon. The reintroduction of the aldA gene, responsible for one native glycolaldehyde disposal route, alleviated the constitutive oxidative stress response. Our results suggest that systems-level approaches and adaptive laboratory evolution have additive benefits when trying to repair and optimize genome-engineered strains. IMPORTANCE Genomic streamlining can be employed in model organisms to reduce complexity and enhance strain predictability. One of the most striking examples is the bacterial strain Escherichia coli DGF-298, notable for having over one-third of its genome deleted. However, such extensive genome modifications raise the question of how similar this simplified cell remains when compared with its parent, and what are the possible unintended consequences of this simplification. In this study, we used metabolic modeling along with iModulon-based transcriptomic analysis in different growth conditions to assess the impact of genome reduction on metabolism and gene regulation. We observed little impact of genomic reduction on the regulatory network of E. coli DGF-298 and identified a potential metabolic bottleneck leading to the constitutive activity of the SoxS iModulon. We then leveraged the model's predictions to successfully restore SoxS activity to the basal level.
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Affiliation(s)
- Antoine Champie
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | - Anand Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Dominick Matteau
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Colton J. Lloyd
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Frédéric Grenier
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Cameron R. Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Simon Jeanneau
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Adam M. Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | | | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Sébastien Rodrigue
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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2
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Kim K, Choe D, Cho S, Palsson B, Cho BK. Reduction-to-synthesis: the dominant approach to genome-scale synthetic biology. Trends Biotechnol 2024; 42:1048-1063. [PMID: 38423803 DOI: 10.1016/j.tibtech.2024.02.008] [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: 12/14/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Advances in systems and synthetic biology have propelled the construction of reduced bacterial genomes. Genome reduction was initially focused on exploring properties of minimal genomes, but more recently it has been deployed as an engineering strategy to enhance strain performance. This review provides the latest updates on reduced genomes, focusing on dual-track approaches of top-down reduction and bottom-up synthesis for their construction. Using cases from studies that are based on established industrial workhorse strains, we discuss the construction of a series of synthetic phenotypes that are candidates for biotechnological applications. Finally, we address the possible uses of reduced genomes for biotechnological applications and the needed future research directions that may ultimately lead to the total synthesis of rationally designed genomes.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghui Choe
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Suhyung Cho
- KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kongens, Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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3
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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: 8] [Impact Index Per Article: 8.0] [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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4
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Amendola CR, Cordell WT, Kneucker CM, Szostkiewicz CJ, Ingraham MA, Monninger M, Wilton R, Pfleger BF, Salvachúa D, Johnson CW, Beckham GT. Comparison of wild-type KT2440 and genome-reduced EM42 Pseudomonas putida strains for muconate production from aromatic compounds and glucose. Metab Eng 2024; 81:88-99. [PMID: 38000549 DOI: 10.1016/j.ymben.2023.11.004] [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: 08/02/2023] [Revised: 11/12/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Pseudomonas putida KT2440 is a robust, aromatic catabolic bacterium that has been widely engineered to convert bio-based and waste-based feedstocks to target products. Towards industrial domestication of P. putida KT2440, rational genome reduction has been previously conducted, resulting in P. putida strain EM42, which exhibited characteristics that could be advantageous for production strains. Here, we compared P. putida KT2440- and EM42-derived strains for cis,cis-muconic acid production from an aromatic compound, p-coumarate, and in separate strains, from glucose. To our surprise, the EM42-derived strains did not outperform the KT2440-derived strains in muconate production from either substrate. In bioreactor cultivations, KT2440- and EM42-derived strains produced muconate from p-coumarate at titers of 45 g/L and 37 g/L, respectively, and from glucose at 20 g/L and 13 g/L, respectively. To provide additional insights about the differences in the parent strains, we analyzed growth profiles of KT2440 and EM42 on aromatic compounds as the sole carbon and energy sources. In general, the EM42 strain exhibited reduced growth rates but shorter growth lags than KT2440. We also observed that EM42-derived strains resulted in higher growth rates on glucose compared to KT2440-derived strains, but only at the lowest glucose concentrations tested. Transcriptomics revealed that genome reduction in EM42 had global effects on transcript levels and showed that the EM42-derived strains that produce muconate from glucose exhibit reduced modulation of gene expression in response to changes in glucose concentrations. Overall, our results highlight that additional studies are warranted to understand the effects of genome reduction on microbial metabolism and physiology, especially when intended for use in production strains.
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Affiliation(s)
- Caroline R Amendola
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - William T Cordell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Colin M Kneucker
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Caralyn J Szostkiewicz
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Morgan A Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Michela Monninger
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Rosemarie Wilton
- Agile BioFoundry, Emeryville, CA, 94608, USA; Biosciences Division Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Davinia Salvachúa
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher W Johnson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA.
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA; Agile BioFoundry, Emeryville, CA, 94608, USA.
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5
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Li J, Li P, Liu Q, Li J, Qi H. Translation initiation consistency between in vivo and in vitro bacterial protein expression systems. Front Bioeng Biotechnol 2023; 11:1201580. [PMID: 37304134 PMCID: PMC10248181 DOI: 10.3389/fbioe.2023.1201580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/17/2023] [Indexed: 06/13/2023] Open
Abstract
Strict on-demand control of protein synthesis is a crucial aspect of synthetic biology. The 5'-terminal untranslated region (5'-UTR) is an essential bacterial genetic element that can be designed for the regulation of translation initiation. However, there is insufficient systematical data on the consistency of 5'-UTR function among various bacterial cells and in vitro protein synthesis systems, which is crucial for the standardization and modularization of genetic elements in synthetic biology. Here, more than 400 expression cassettes comprising the GFP gene under the regulation of various 5'-UTRs were systematically characterized to evaluate the protein translation consistency in the two popular Escherichia coli strains of JM109 and BL21, as well as an in vitro protein expression system based on cell lysate. In contrast to the very strong correlation between the two cellular systems, the consistency between in vivo and in vitro protein translation was lost, whereby both in vivo and in vitro translation evidently deviated from the estimation of the standard statistical thermodynamic model. Finally, we found that the absence of nucleotide C and complex secondary structure in the 5'-UTR significantly improve the efficiency of protein translation, both in vitro and in vivo.
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Affiliation(s)
- Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Peixian Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Qian Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Jinjin Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Zhejiang Shaoxing Research Institute of Tianjin University, Shaoxing, China
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6
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Xu X, Meier F, Blount BA, Pretorius IS, Ellis T, Paulsen IT, Williams TC. Trimming the genomic fat: minimising and re-functionalising genomes using synthetic biology. Nat Commun 2023; 14:1984. [PMID: 37031253 PMCID: PMC10082837 DOI: 10.1038/s41467-023-37748-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
Naturally evolved organisms typically have large genomes that enable their survival and growth under various conditions. However, the complexity of genomes often precludes our complete understanding of them, and limits the success of biotechnological designs. In contrast, minimal genomes have reduced complexity and therefore improved engineerability, increased biosynthetic capacity through the removal of unnecessary genetic elements, and less recalcitrance to complete characterisation. Here, we review the past and current genome minimisation and re-functionalisation efforts, with an emphasis on the latest advances facilitated by synthetic genomics, and provide a critical appraisal of their potential for industrial applications.
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Affiliation(s)
- Xin Xu
- ARC Centre of Excellence in Synthetic Biology and School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Felix Meier
- ARC Centre of Excellence in Synthetic Biology and School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Benjamin A Blount
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology and School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
- Wellcome Trust Sanger Institute, Cambridgeshire, CB10 1SA, UK
| | - Ian T Paulsen
- ARC Centre of Excellence in Synthetic Biology and School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Thomas C Williams
- ARC Centre of Excellence in Synthetic Biology and School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
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7
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Yuan S, Shi J, Jiang J, Ma Y. Genome-scale top-down strategy to generate viable genome-reduced phages. Nucleic Acids Res 2022; 50:13183-13197. [PMID: 36511873 PMCID: PMC9825161 DOI: 10.1093/nar/gkac1168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Efforts have been made to reduce the genomes of living cells, but phage genome reduction remains challenging. It is of great interest to investigate whether genome reduction can make phages obtain new infectious properties. We developed a CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach and applied this to four distinct phages, thereby obtaining heterogeneous genome-reduced mutants. We isolated and sequenced 200 mutants with loss of up to 8-23% (3.3-35 kbp) of the original sequences. This allowed the identification of non-essential genes for phage propagation, although loss of these genes is mostly detrimental to phage fitness to various degrees. Notwithstanding this, mutants with higher infectious efficiency than their parental strains were characterized, indicating a trade-off between genome reduction and infectious fitness for phages. In conclusion, this study provides a foundation for future work to leverage the information generated by CiPGr in phage synthetic biology research.
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Affiliation(s)
- Shengjian Yuan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Shi
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianrong Jiang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingfei Ma
- To whom correspondence should be addressed. Tel: +86 755 8639 2674;
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8
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Bayer C, Sepulchro AGV, Rennig M, Nørholm MH. Efficient Bacterial Genome Engineering throughout the Central Dogma Using the Dual-Selection Marker tetAOPT. ACS Synth Biol 2022; 11:3440-3450. [PMID: 36206506 PMCID: PMC9594774 DOI: 10.1021/acssynbio.2c00345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Indexed: 01/24/2023]
Abstract
Engineering of bacterial genomes is a fundamental craft in contemporary biotechnology. The ability to precisely edit chromosomes allows for the development of cells with specific phenotypes for metabolic engineering and for the creation of minimized genomes. Genetic tools are needed to select for cells that underwent editing, and dual-selection markers that enable both positive and negative selection are highly useful. Here, we present an optimized and easy-to-use version of the tetA dual-selection marker and demonstrate how this tetAOPT can be used efficiently to engineer at different stages of the central dogma of molecular biology. On the DNA level, tetAOPT can be used to create scarless knockouts across the Escherichia coli genome with efficiency above 90%, whereas recombinant gene integrations can be achieved with approximately 50% efficiency. On the RNA and protein level, we show that tetAOPT enables advanced genome engineering of both gene translation and transcription by introducing sequence variation in the translation initiation region or by exchanging promoters. Finally, we demonstrate the use of tetAOPT for genome engineering in the industrially relevant probiotic strain E. coli Nissle.
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Affiliation(s)
- Carolyn
N. Bayer
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ana G. V. Sepulchro
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Maja Rennig
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Morten H.H. Nørholm
- Novo Nordisk Foundation Center for
Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
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9
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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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10
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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: 13] [Impact Index Per Article: 6.5] [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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11
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Liu S, Xu JZ, Zhang WG. Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production. World J Microbiol Biotechnol 2022; 38:22. [PMID: 34989926 DOI: 10.1007/s11274-021-03212-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
As an important raw material for pharmaceutical, food and feed industry, highly efficient production of L-tryptophan by Escherichia coli has attracted a considerable attention. However, there are complicated and multiple layers of regulation networks in L-tryptophan biosynthetic pathway and thus have difficulty to rewrite the biosynthetic pathway for producing L-tryptophan with high efficiency in E. coli. This review summarizes the biosynthetic pathway of L-tryptophan and highlights the main regulatory mechanisms in E. coli. In addition, we discussed the latest metabolic engineering strategies achieved in E. coli to reconstruct the L-tryptophan biosynthetic pathway. Moreover, we also review a few strategies that can be used in E. coli to improve robustness and streamline of L-tryptophan high-producing strains. Lastly, we also propose the potential strategies to further increase L-tryptophan production by systematic metabolic engineering and synthetic biology techniques.
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Affiliation(s)
- Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
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12
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Zhou S, Wu Y, Xie ZX, Jia B, Yuan YJ. Directed genome evolution driven by structural rearrangement techniques. Chem Soc Rev 2021; 50:12788-12807. [PMID: 34651628 DOI: 10.1039/d1cs00722j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Directed genome evolution simulates the process of natural evolution at the genomic level in the laboratory to generate desired phenotypes. Here we review the applications of recent technological advances in genome writing and editing to directed genome evolution, with a focus on structural rearrangement techniques. We highlight how these techniques can be used to generate diverse genotypes, and to accelerate the evolution of phenotypic traits. We also discuss the perspectives of directed genome evolution.
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Affiliation(s)
- Sijie Zhou
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yi Wu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Ze-Xiong Xie
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
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13
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Abstract
DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , , .,Department of Biomedical Engineering, New York University Tandon School of Engineering, New York, NY 11201, USA
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14
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Liang Y, Yu H. Genetic toolkits for engineering Rhodococcus species with versatile applications. Biotechnol Adv 2021; 49:107748. [PMID: 33823269 DOI: 10.1016/j.biotechadv.2021.107748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/31/2021] [Accepted: 03/31/2021] [Indexed: 02/09/2023]
Abstract
Rhodococcus spp. are a group of non-model gram-positive bacteria with diverse catabolic activities and strong adaptive capabilities, which enable their wide application in whole-cell biocatalysis, environmental bioremediation, and lignocellulosic biomass conversion. Compared with model microorganisms, the engineering of Rhodococcus is challenging because of the lack of universal molecular tools, high genome GC content (61% ~ 71%), and low transformation and recombination efficiencies. Nevertheless, because of the high interest in Rhodococcus species for bioproduction, various genetic elements and engineering tools have been recently developed for Rhodococcus spp., including R. opacus, R. jostii, R. ruber, and R. erythropolis, leading to the expansion of the genetic toolkits for Rhodococcus engineering. In this article, we provide a comprehensive review of the important developed genetic elements for Rhodococcus, including shuttle vectors, promoters, antibiotic markers, ribosome binding sites, and reporter genes. In addition, we also summarize gene transfer techniques and strategies to improve transformation efficiency, as well as random and precise genome editing tools available for Rhodococcus, including transposition, homologous recombination, recombineering, and CRISPR/Cas9. We conclude by discussing future trends in Rhodococcus engineering. We expect that more synthetic and systems biology tools (such as multiplex genome editing, dynamic regulation, and genome-scale metabolic models) will be adapted and optimized for Rhodococcus.
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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
| | - 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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15
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Wang J, Ma W, Wang X. Insights into the structure of Escherichia coli outer membrane as the target for engineering microbial cell factories. Microb Cell Fact 2021; 20:73. [PMID: 33743682 PMCID: PMC7980664 DOI: 10.1186/s12934-021-01565-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/12/2021] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is generally used as model bacteria to define microbial cell factories for many products and to investigate regulation mechanisms. E. coli exhibits phospholipids, lipopolysaccharides, colanic acid, flagella and type I fimbriae on the outer membrane which is a self-protective barrier and closely related to cellular morphology, growth, phenotypes and stress adaptation. However, these outer membrane associated molecules could also lead to potential contamination and insecurity for fermentation products and consume lots of nutrients and energy sources. Therefore, understanding critical insights of these membrane associated molecules is necessary for building better microbial producers. Here the biosynthesis, function, influences, and current membrane engineering applications of these outer membrane associated molecules were reviewed from the perspective of synthetic biology, and the potential and effective engineering strategies on the outer membrane to improve fermentation features for microbial cell factories were suggested.
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Affiliation(s)
- Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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16
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Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. J Proteome Res 2021; 20:1178-1189. [PMID: 33393786 PMCID: PMC7867644 DOI: 10.1021/acs.jproteome.0c00359] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
When the JCVI-syn3.0 genome was designed and implemented in 2016 as the minimal genome of a free-living organism, approximately one-third of the 438 protein-coding genes had no known function. Subsequent refinement into JCVI-syn3A led to inclusion of 16 additional protein-coding genes, including several unknown functions, resulting in an improved growth phenotype. Here, we seek to unveil the biological roles and protein-protein interaction (PPI) networks for these poorly characterized proteins using state-of-the-art deep learning contact-assisted structure prediction, followed by structure-based annotation of functions and PPI predictions. Our pipeline is able to confidently assign functions for many previously unannotated proteins such as putative vitamin transporters, which suggest the importance of nutrient uptake even in a minimized genome. Remarkably, despite the artificial selection of genes in the minimal syn3 genome, our reconstructed PPI network still shows a power law distribution of node degrees typical of naturally evolved bacterial PPI networks. Making use of our framework for combined structure/function/interaction modeling, we are able to identify both fundamental aspects of network biology that are retained in a minimal proteome and additional essential functions not yet recognized among the poorly annotated components of the syn3.0 and syn3A proteomes.
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Micah Cheng
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Internal Medicine and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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17
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Huang C, Guo L, Wang J, Wang N, Huo YX. Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering. Appl Microbiol Biotechnol 2020; 104:7943-7956. [PMID: 32794018 DOI: 10.1007/s00253-020-10819-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering. KEY POINTS: • This article reports an efficient genome engineering tool for E. coli. • The tool is advantageous for the manipulations of long DNA fragments. • The tool has been successfully applied for genome simplification. • The tool has been successfully applied for metabolic engineering.
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Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China. .,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China.
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18
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Exploring the fitness benefits of genome reduction in Escherichia coli by a selection-driven approach. Sci Rep 2020; 10:7345. [PMID: 32355292 PMCID: PMC7193553 DOI: 10.1038/s41598-020-64074-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/08/2020] [Indexed: 11/26/2022] Open
Abstract
Artificial simplification of bacterial genomes is thought to have the potential to yield cells with reduced complexity, enhanced genetic stability, and improved cellular economy. Of these goals, economical gains, supposedly due to the elimination of superfluous genetic material, and manifested in elevated growth parameters in selected niches, have not yet been convincingly achieved. This failure might stem from limitations of the targeted genome reduction approach that assumes full knowledge of gene functions and interactions, and allows only a limited number of reduction trajectories to interrogate. To explore the potential fitness benefits of genome reduction, we generated successive random deletions in E. coli by a novel, selection-driven, iterative streamlining process. The approach allows the exploration of multiple streamlining trajectories, and growth periods inherent in the procedure ensure selection of the fittest variants of the population. By generating single- and multiple-deletion strains and reconstructing the deletions in the parental genetic background, we showed that favourable deletions can be obtained and accumulated by the procedure. The most reduced multiple-deletion strain, obtained in five deletion cycles (2.5% genome reduction), outcompeted the wild-type, and showed elevated biomass yield. The spectrum of advantageous deletions, however, affecting only a few genomic regions, appears to be limited.
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19
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Expression and purification of codon-optimized cre recombinase in E. coli. Protein Expr Purif 2020; 167:105546. [DOI: 10.1016/j.pep.2019.105546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/15/2019] [Accepted: 11/24/2019] [Indexed: 12/31/2022]
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20
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Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins. Int J Mol Sci 2020; 21:ijms21030990. [PMID: 32024292 PMCID: PMC7037952 DOI: 10.3390/ijms21030990] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
A large proportion of the recombinant proteins manufactured today rely on microbe-based expression systems owing to their relatively simple and cost-effective production schemes. However, several issues in microbial protein expression, including formation of insoluble aggregates, low protein yield, and cell death are still highly recursive and tricky to optimize. These obstacles are usually rooted in the metabolic capacity of the expression host, limitation of cellular translational machineries, or genetic instability. To this end, several microbial strains having precisely designed genomes have been suggested as a way around the recurrent problems in recombinant protein expression. Already, a growing number of prokaryotic chassis strains have been genome-streamlined to attain superior cellular fitness, recombinant protein yield, and stability of the exogenous expression pathways. In this review, we outline challenges associated with heterologous protein expression, some examples of microbial chassis engineered for the production of recombinant proteins, and emerging tools to optimize the expression of heterologous proteins. In particular, we discuss the synthetic biology approaches to design and build and test genome-reduced microbial chassis that carry desirable characteristics for heterologous protein expression.
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21
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Kurokawa M, Ying BW. Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli. Microorganisms 2019; 8:E3. [PMID: 31861355 PMCID: PMC7022904 DOI: 10.3390/microorganisms8010003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
Genome reduction, as a top-down approach to obtain the minimal genetic information essential for a living organism, has been conducted with bacterial cells for decades. The most popular and well-studied cell models for genome reduction are Escherichia coli strains. As the previous literature intensively introduced the genetic construction and application of the genome-reduced Escherichia coli strains, the present review focuses the design principles and compares the reduced genome collections from the specific viewpoint of growth, which represents a fundamental property of living cells and is an important feature for their biotechnological application. For the extended simplification of the genomic sequences, the approach of experimental evolution and concern for medium optimization are newly proposed. The combination of the current techniques of genomic construction and the newly proposed methodologies could allow us to acquire growing Escherichia coli cells carrying the extensively reduced genome and to address the question of what the minimal genome essential for life is.
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Affiliation(s)
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 305-8572 Ibaraki, Japan;
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22
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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23
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Chi H, Wang X, Shao Y, Qin Y, Deng Z, Wang L, Chen S. Engineering and modification of microbial chassis for systems and synthetic biology. Synth Syst Biotechnol 2019; 4:25-33. [PMID: 30560208 PMCID: PMC6290258 DOI: 10.1016/j.synbio.2018.12.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/14/2018] [Accepted: 12/05/2018] [Indexed: 12/14/2022] Open
Abstract
Engineering and modifying synthetic microbial chassis is one of the best ways not only to unravel the fundamental principles of life but also to enhance applications in the health, medicine, agricultural, veterinary, and food industries. The two primary strategies for constructing a microbial chassis are the top-down approach (genome reduction) and the bottom-up approach (genome synthesis). Research programs on this topic have been funded in several countries. The 'Minimum genome factory' (MGF) project was launched in 2001 in Japan with the goal of constructing microorganisms with smaller genomes for industrial use. One of the best examples of the results of this project is E. coli MGF-01, which has a reduced-genome size and exhibits better growth and higher threonine production characteristics than the parental strain [1]. The 'cell factory' project was carried out from 1998 to 2002 in the Fifth Framework Program of the EU (European Union), which tried to comprehensively understand microorganisms used in the application field. One of the outstanding results of this project was the elucidation of proteins secreted by Bacillus subtilis, which was summarized as the 'secretome' [2]. The GTL (Genomes to Life) program began in 2002 in the United States. In this program, researchers aimed to create artificial cells both in silico and in vitro, such as the successful design and synthesis of a minimal bacterial genome by John Craig Venter's group [3]. This review provides an update on recent advances in engineering, modification and application of synthetic microbial chassis, with particular emphasis on the value of learning about chassis as a way to better understand life and improve applications.
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Affiliation(s)
- Haotian Chi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xiaoli Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Yue Shao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Ying Qin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan, 430071, China
- Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
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24
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Adaptive laboratory evolution of a genome-reduced Escherichia coli. Nat Commun 2019; 10:935. [PMID: 30804335 PMCID: PMC6389913 DOI: 10.1038/s41467-019-08888-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 01/31/2019] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. The unexpected phenotypes highlight our limited understanding of bacterial genomes. Here, we deploy adaptive laboratory evolution (ALE) to re-optimize growth performance of a genome-reduced strain. The basis for suboptimal growth is the imbalanced metabolism that is rewired during ALE. The metabolic rewiring is globally orchestrated by mutations in rpoD altering promoter binding of RNA polymerase. Lastly, the evolved strain has no translational buffering capacity, enabling effective translation of abundant mRNAs. Multi-omic analysis of the evolved strain reveals transcriptome- and translatome-wide remodeling that orchestrate metabolism and growth. These results reveal that failure of prediction may not be associated with understanding individual genes, but rather from insufficient understanding of the strain's systems biology.
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25
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Selectable marker recycling in the nonconventional yeast Xanthophyllomyces dendrorhous by transient expression of Cre on a genetically unstable vector. Appl Microbiol Biotechnol 2018; 103:963-971. [DOI: 10.1007/s00253-018-9496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
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26
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Transposase-Mediated Chromosomal Integration of Exogenous Genes in Acidithiobacillus ferrooxidans. Appl Environ Microbiol 2018; 84:AEM.01381-18. [PMID: 30143507 DOI: 10.1128/aem.01381-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/20/2018] [Indexed: 01/21/2023] Open
Abstract
The development of Acidithiobacillus ferrooxidans as a non-model host organism for synthetic biology is hampered by a lack of genetic tools and techniques. New plating and liquid-based selection methods were developed to improve the identification of transformed cell lines. Enabled by these methods, a hyperactive transposase was used to generate mutants with integrated genes for the expression of the superfolder green fluorescent protein (sfGFP) gene or a 2-keto decarboxylase (KDC) gene, which enabled the production and secretion of isobutyric acid (IBA). An inverse PCR method was used to identify the insertion sites of the KDC gene in several mutants, leading to the identification of a region on the chromosome that may be suitable for future genetic insertions. These results demonstrate that functional exogenous metabolic genes have been chromosomally integrated into A. ferrooxidans, and this advance will facilitate the future development of these cells for new biotechnology applications.IMPORTANCE Acidithiobacillus ferrooxidans is an iron- and sulfur-oxidizing chemolithoautotroph and is a key member of the microbial consortia used in industrial biomining applications. There is interest in exploiting these cells for other metal recovery applications as well as in developing them as unique nonmodel microbial cell factories. Plasmid-driven expression of exogenous genes has been reported, and homologous recombination has been used to knock out some gene expression. Here, new selection protocols facilitated the development of a transposition method for chromosomal integration of exogenous genes into A. ferrooxidans This greatly expands the available genetic toolbox, which will open the door to greater metabolic engineering efforts for these cells.
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27
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Whitford CM, Dymek S, Kerkhoff D, März C, Schmidt O, Edich M, Droste J, Pucker B, Rückert C, Kalinowski J. Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. J Biol Eng 2018; 12:13. [PMID: 30123321 PMCID: PMC6090650 DOI: 10.1186/s13036-018-0105-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer. MAIN BODY Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system. CONCLUSION Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.
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Affiliation(s)
| | - Saskia Dymek
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Denise Kerkhoff
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Camilla März
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Olga Schmidt
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Maximilian Edich
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
| | - Julian Droste
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Boas Pucker
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
- Present address: Evolution and Diversity, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Christian Rückert
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, 33615 Bielefeld, Germany
- Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Balikó G, Vernyik V, Karcagi I, Györfy Z, Draskovits G, Fehér T, Pósfai G. Rational Efforts to Streamline the Escherichia coliGenome. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gabriella Balikó
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Viktor Vernyik
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Ildikó Karcagi
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Zsuzsanna Györfy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Gábor Draskovits
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Tamás Fehér
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - György Pósfai
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
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Xin Y, Guo T, Mu Y, Kong J. Coupling the recombineering to Cre-lox system enables simplified large-scale genome deletion in Lactobacillus casei. Microb Cell Fact 2018; 17:21. [PMID: 29433512 PMCID: PMC5808424 DOI: 10.1186/s12934-018-0872-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
Background Lactobacillus casei is widely used in the dairy and pharmaceutical industries and a promising candidate for use as cell factories. Recently, genome sequencing and functional genomics provide the possibility for reducing L. casei genome. However, it was still limited by the inefficient and laborious genome deletion methods. Results Here, we proposed a genome minimization strategy based on LCABL_13040-50-60 recombineering and Cre-lox site-specific recombination system in L. casei. The LCABL_13040-50-60 recombineering system was used to introduce two lox sites (lox66 and lox71) into 5′ and 3′ ends of the targeted region. Subsequently, the targeted region was excised by Cre recombinase. The robustness of the strategy was demonstrated by single-deletion of a nonessential ~ 39.3 kb or an important ~ 12.8 kb region and simultaneous deletion of two non-continuous genome regions (5.2 and 6.6 kb) with 100% efficiency. Furthermore, a cyclical application of this strategy generated a double-deletion mutant of which 1.68% of the chromosome was sequentially excised. Moreover, biological features (including growth rate, electroporation efficiency, cell morphology or heterologous protein productivity) of these mutants were characterized. Conclusions To our knowledge, this strategy is the first instance of sequential deletion of large-scale genome regions in L. casei. We expected this efficient and inexpensive tool can help for rapid genome streamlining and generation restructured L. casei strains used as cell factories. Electronic supplementary material The online version of this article (10.1186/s12934-018-0872-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China
| | - Yingli Mu
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan, 250100, People's Republic of China.
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diCenzo GC, Finan TM. Techniques for Large-Scale Bacterial Genome Manipulation and Characterization of the Mutants with Respect to In Silico Metabolic Reconstructions. Methods Mol Biol 2018; 1716:291-314. [PMID: 29222759 DOI: 10.1007/978-1-4939-7528-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The rate at which all genes within a bacterial genome can be identified far exceeds the ability to characterize these genes. To assist in associating genes with cellular functions, a large-scale bacterial genome deletion approach can be employed to rapidly screen tens to thousands of genes for desired phenotypes. Here, we provide a detailed protocol for the generation of deletions of large segments of bacterial genomes that relies on the activity of a site-specific recombinase. In this procedure, two recombinase recognition target sequences are introduced into known positions of a bacterial genome through single cross-over plasmid integration. Subsequent expression of the site-specific recombinase mediates recombination between the two target sequences, resulting in the excision of the intervening region and its loss from the genome. We further illustrate how this deletion system can be readily adapted to function as a large-scale in vivo cloning procedure, in which the region excised from the genome is captured as a replicative plasmid. We next provide a procedure for the metabolic analysis of bacterial large-scale genome deletion mutants using the Biolog Phenotype MicroArray™ system. Finally, a pipeline is described, and a sample Matlab script is provided, for the integration of the obtained data with a draft metabolic reconstruction for the refinement of the reactions and gene-protein-reaction relationships in a metabolic reconstruction.
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Affiliation(s)
- George C diCenzo
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Turlough M Finan
- Department of Biology, McMaster University, Hamilton, ON, Canada.
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31
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Glass JI, Merryman C, Wise KS, Hutchison CA, Smith HO. Minimal Cells-Real and Imagined. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a023861. [PMID: 28348033 DOI: 10.1101/cshperspect.a023861] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A minimal cell is one whose genome only encodes the minimal set of genes necessary for the cell to survive. Scientific reductionism postulates the best way to learn the first principles of cellular biology would be to use a minimal cell in which the functions of all genes and components are understood. The genes in a minimal cell are, by definition, essential. In 2016, synthesis of a genome comprised of only the set of essential and quasi-essential genes encoded by the bacterium Mycoplasma mycoides created a near-minimal bacterial cell. This organism performs the cellular functions common to all organisms. It replicates DNA, transcribes RNA, translates proteins, undergoes cell division, and little else. In this review, we examine this organism and contrast it with other bacteria that have been used as surrogates for a minimal cell.
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Affiliation(s)
- John I Glass
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Chuck Merryman
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Kim S Wise
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Clyde A Hutchison
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
| | - Hamilton O Smith
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, California 92037
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Shen X, Wang Z, Huang X, Hu H, Wang W, Zhang X. Developing genome-reduced Pseudomonas chlororaphis strains for the production of secondary metabolites. BMC Genomics 2017; 18:715. [PMID: 28893188 PMCID: PMC5594592 DOI: 10.1186/s12864-017-4127-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The current chassis organisms or various types of cell factories have considerable advantages and disadvantages. Therefore, it is necessary to develop various chassis for an efficient production of different bioproducts from renewable resources. In this context, synthetic biology offers unique potentialities to produce value-added products of interests. Microbial genome reduction and modification are important strategies for constructing cellular chassis and cell factories. Many genome-reduced strains from Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum and Streptomyces, have been widely used for the production of amino acids, organic acids, and some enzymes. Some Pseudomonas strains could serve as good candidates for ideal chassis cells since they grow fast and can produce many valuable metabolites with low nutritional requirements and strong environmental adaptability. Pseudomonas chlororaphis GP72 is a non-pathogenic plant growth-promoting rhizobacterium that possesses capacities of tolerating various environmental stresses and synthesizing many kinds of bioactive compounds with high yield. These include phenazine-1-carboxylic acid (PCA) and 2-hydroxyphenazine (2-OH-PHZ), which exhibit strong bacteriostatic and antifungal activity toward some microbial pathogens. RESULTS We depleted 685 kb (10.3% of the genomic sequence) from the chromosome of P. chlororaphis GP72(rpeA-) by a markerless deletion method, which included five secondary metabolic gene clusters and 17 strain-specific regions (525 non-essential genes). Then we characterized the 22 multiple-deletion series (MDS) strains. Growth characteristics, production of phenazines and morphologies were changed greatly in mutants with large-fragment deletions. Some of the genome-reduced P. chlororaphis mutants exhibited more productivity than the parental strain GP72(rpeA-). For example, strain MDS22 had 4.4 times higher production of 2-OH-PHZ (99.1 mg/L) than strain GP72(rpeA-), and the specific 2-OH-PHZ production rate (mmol/g/h) increased 11.5-fold. Also and MDS10 had the highest phenazine production (852.0 mg/L) among all the studied strains with a relatively high specific total phenazine production rate (0.0056 g/g/h). CONCLUSIONS In conclusion, P. chlororaphis strains with reduced genome performed better in production of secondary metabolites than the parent strain. The newly developed mutants can be used for the further genetic manipulation to construct chassis cells with the less complex metabolic network, better regulation and more efficient productivity for diverse biotechnological applications.
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Affiliation(s)
- Xuemei Shen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.,Beijing Key Laboratory of Nutrition, Health and Food Safety, Nutrition and Health Research Institute, COFCO Corporation, No.4 Road, Future Science and Technology Park South, Beijing, 102209, People's Republic of China
| | - Zheng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, People's Republic of China.
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Mol M, Kabra R, Singh S. Genome modularity and synthetic biology: Engineering systems. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 132:43-51. [PMID: 28801037 DOI: 10.1016/j.pbiomolbio.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/05/2017] [Indexed: 12/15/2022]
Abstract
Whole genome sequencing projects running in various laboratories around the world has generated immense data. A systematic phylogenetic analysis of this data shows that genome complexity goes on decreasing as it evolves, due to its modular nature. This modularity can be harnessed to minimize the genome further to reduce it with the bare minimum essential genes. A reduced modular genome, can fuel progress in the area of synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health.
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Affiliation(s)
- Milsee Mol
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India
| | - Ritika Kabra
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, SP Pune University Campus, Pune 411007, India.
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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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Döhlemann J, Brennecke M, Becker A. Cloning-free genome engineering in Sinorhizobium meliloti advances applications of Cre/loxP site-specific recombination. J Biotechnol 2016; 233:160-70. [PMID: 27393468 DOI: 10.1016/j.jbiotec.2016.06.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/26/2016] [Accepted: 06/30/2016] [Indexed: 10/21/2022]
Abstract
The soil-dwelling α-proteobacterium Sinorhizobium meliloti serves as model for studies of symbiotic nitrogen fixation, a highly important process in sustainable agriculture. Here, we report advancements of the genetic toolbox accelerating genome editing in S. meliloti. The hsdMSR operon encodes a type-I restriction-modification (R-M) system. Transformation of S. meliloti is counteracted by the restriction endonuclease HsdR degrading DNA which lacks the appropriate methylation pattern. We provide a stable S. meliloti hsdR deletion mutant showing enhanced transformation with Escherichia coli-derived plasmid DNA and demonstrate that using an E. coli plasmid donor, expressing S. meliloti methyl transferase genes, is an alternative strategy of increasing the transformation efficiency of S. meliloti. Furthermore, we devise a novel cloning-free genome editing (CFGE) method for S. meliloti, Agrobacterium tumefaciens and Xanthomonas campestris, and demonstrate the applicability of this method for intricate applications of the Cre/lox recombination system in S. meliloti. An enhanced Cre/lox system, allowing for serial deletions of large genomic regions, was established. An assay of lox spacer mutants identified a set of lox sites mediating specific recombination. The availability of several non-promiscuous Cre recognition sites enables simultaneous specific Cre/lox recombination events. CFGE combined with Cre/lox recombination is put forward as powerful approach for targeted genome editing, involving serial steps of manipulation to expedite the genetic accessibility of S. meliloti as chassis.
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Affiliation(s)
- Johannes Döhlemann
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Meike Brennecke
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany.
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Kurokawa M, Seno S, Matsuda H, Ying BW. Correlation between genome reduction and bacterial growth. DNA Res 2016; 23:517-525. [PMID: 27374613 PMCID: PMC5144675 DOI: 10.1093/dnares/dsw035] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/08/2016] [Indexed: 11/13/2022] Open
Abstract
Genome reduction by removing dispensable genomic sequences in bacteria is commonly used in both fundamental and applied studies to determine the minimal genetic requirements for a living system or to develop highly efficient bioreactors. Nevertheless, whether and how the accumulative loss of dispensable genomic sequences disturbs bacterial growth remains unclear. To investigate the relationship between genome reduction and growth, a series of Escherichia coli strains carrying genomes reduced in a stepwise manner were used. Intensive growth analyses revealed that the accumulation of multiple genomic deletions caused decreases in the exponential growth rate and the saturated cell density in a deletion-length-dependent manner as well as gradual changes in the patterns of growth dynamics, regardless of the growth media. Accordingly, a perspective growth model linking genome evolution to genome engineering was proposed. This study provides the first demonstration of a quantitative connection between genomic sequence and bacterial growth, indicating that growth rate is potentially associated with dispensable genomic sequences.
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Affiliation(s)
- Masaomi Kurokawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
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Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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Liu Y, Yang M, Chen J, Yan D, Cheng W, Wang Y, Thygesen A, Chen R, Xing J, Wang Q, Ma Y. PCR-Based Seamless Genome Editing with High Efficiency and Fidelity in Escherichia coli. PLoS One 2016; 11:e0149762. [PMID: 27019283 PMCID: PMC4809717 DOI: 10.1371/journal.pone.0149762] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/04/2016] [Indexed: 11/18/2022] Open
Abstract
Efficiency and fidelity are the key obstacles for genome editing toolboxes. In the present study, a PCR-based tandem repeat assisted genome editing (TRAGE) method with high efficiency and fidelity was developed. The design of TRAGE is based on the mechanism of repair of spontaneous double-strand breakage (DSB) via replication fork reactivation. First, cat-sacB cassette flanked by tandem repeat sequence was integrated into target site in chromosome assisted by Red enzymes. Then, for the excision of the cat-sacB cassette, only subculturing is needed. The developed method was successfully applied for seamlessly deleting, substituting and inserting targeted genes using PCR products. The effects of different manipulations including sucrose addition time, subculture times in LB with sucrose and stages of inoculation on the efficiency were investigated. With our recommended procedure, seamless excision of cat-sacB cassette can be realized in 48 h efficiently. We believe that the developed method has great potential for seamless genome editing in E. coli.
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Affiliation(s)
- Yilan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Maohua Yang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Jinjin Chen
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Daojiang Yan
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Wanwan Cheng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Yanyan Wang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Anders Thygesen
- Center of Bioprocess Engineering, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Ruonan Chen
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Jianmin Xing
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, PR China
- * E-mail: (JX); (QW)
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
- * E-mail: (JX); (QW)
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Area, Tianjin, 300308, China
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Juhas M, Ajioka JW. High molecular weight DNA assembly in vivo for synthetic biology applications. Crit Rev Biotechnol 2016; 37:277-286. [PMID: 26863154 DOI: 10.3109/07388551.2016.1141394] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.
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Affiliation(s)
- Mario Juhas
- a Department of Pathology , University of Cambridge , Tennis Court Road , Cambridge , UK
| | - James W Ajioka
- a Department of Pathology , University of Cambridge , Tennis Court Road , Cambridge , UK
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Choi JW, Yim SS, Kim MJ, Jeong KJ. Enhanced production of recombinant proteins with Corynebacterium glutamicum by deletion of insertion sequences (IS elements). Microb Cell Fact 2015; 14:207. [PMID: 26715464 PMCID: PMC4696348 DOI: 10.1186/s12934-015-0401-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In most bacteria, various jumping genetic elements including insertion sequences elements (IS elements) cause a variety of genetic rearrangements resulting in harmful effects such as genome and recombinant plasmid instability. The genetic stability of a plasmid in a host is critical for high-level production of recombinant proteins, and in this regard, the development of an IS element-free strain could be a useful strategy for the enhanced production of recombinant proteins. Corynebacterium glutamicum, which is a workhorse in the industrial-scale production of various biomolecules including recombinant proteins, also has several IS elements, and it is necessary to identify the critical IS elements and to develop IS element deleted strain. RESULTS From the cultivation of C. glutamicum harboring a plasmid for green fluorescent protein (GFP) gene expression, non-fluorescent clones were isolated by FACS (fluorescent activated cell sorting). All the isolated clones had insertions of IS elements in the GFP coding region, and two major IS elements (ISCg1 and ISCg2 families) were identified. By co-cultivating cells harboring either the isolated IS element-inserted plasmid or intact plasmid, it was clearly confirmed that cells harboring the IS element-inserted plasmids became dominant during the cultivation due to their growth advantage over cells containing intact plasmids, which can cause a significant reduction in recombinant protein production during cultivation. To minimize the harmful effects of IS elements on the expression of heterologous genes in C. glutamicum, two IS element free C. glutamicum strains were developed in which each major IS element was deleted, and enhanced productivity in the engineered C. glutamicum strain was successfully demonstrated with three models: GFP, poly(3-hydroxybutyrate) [P(3HB)] and γ-aminobutyrate (GABA). CONCLUSIONS Our findings clearly indicate that the hopping of IS elements could be detrimental to the production of recombinant proteins in C. glutamicum, emphasizing the importance of developing IS element free host strains.
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Affiliation(s)
- Jae Woong Choi
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Sung Sun Yim
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Min Jeong Kim
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering (BK Plus program), KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea. .,Institute for the BioCentury, KAIST, 291 Daehakro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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42
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Choe D, Cho S, Kim SC, Cho BK. Minimal genome: Worthwhile or worthless efforts toward being smaller? Biotechnol J 2015; 11:199-211. [DOI: 10.1002/biot.201400838] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/08/2015] [Accepted: 07/27/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Donghui Choe
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- Intelligent Synthetic Biology Center; Daejeon Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
- Intelligent Synthetic Biology Center; Daejeon Republic of Korea
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Xue X, Wang T, Jiang P, Shao Y, Zhou M, Zhong L, Wu R, Zhou J, Xia H, Zhao G, Qin Z. MEGA (Multiple Essential Genes Assembling) deletion and replacement method for genome reduction in Escherichia coli. ACS Synth Biol 2015; 4:700-6. [PMID: 25494410 DOI: 10.1021/sb500324p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Top-down reduction of the bacterial genome to construct desired chassis cells is important for synthetic biology. However, the current progress in the field of genome reduction is greatly hindered by indispensable life-essential genes that are interspersed throughout the chromosomal loci. Here, we described a new method designated as "MEGA (Multiple Essential Genes Assembling) deletion and replacement" that functions by assembling multiple essential genes in an E. coli-S. cerevisiae shuttle vector, removing targeted chromosomal regions containing essential and nonessential genes using a one-round deletion, and then integrating the cloned essential genes into the in situ chromosomal loci via I-SceI endonuclease cleavage. As a proof of concept, we separately generated three large deletions (80-205 kbp) in the E. coli MDS42 chromosome. We believe that the MEGA deletion and replacement method has potential to become widely used in large-scale genome reductions in other sequenced organisms in addition to E. coli.
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Affiliation(s)
- Xiaoli Xue
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Wang
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Jiang
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yangyang Shao
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Min Zhou
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Li Zhong
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ronghai Wu
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jianting Zhou
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haiyang Xia
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guoping Zhao
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhongjun Qin
- Key Laboratory of Synthetic
Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Bao Z, Xiao H, Liang J, Zhang L, Xiong X, Sun N, Si T, Zhao H. Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae. ACS Synth Biol 2015; 4:585-94. [PMID: 25207793 DOI: 10.1021/sb500255k] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
One-step multiple gene disruption in the model organism Saccharomyces cerevisiae is a highly useful tool for both basic and applied research, but it remains a challenge. Here, we report a rapid, efficient, and potentially scalable strategy based on the type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated proteins (Cas) system to generate multiple gene disruptions simultaneously in S. cerevisiae. A 100 bp dsDNA mutagenizing homologous recombination donor is inserted between two direct repeats for each target gene in a CRISPR array consisting of multiple donor and guide sequence pairs. An ultrahigh copy number plasmid carrying iCas9, a variant of wild-type Cas9, trans-encoded RNA (tracrRNA), and a homology-integrated crRNA cassette is designed to greatly increase the gene disruption efficiency. As proof of concept, three genes, CAN1, ADE2, and LYP1, were simultaneously disrupted in 4 days with an efficiency ranging from 27 to 87%. Another three genes involved in an artificial hydrocortisone biosynthetic pathway, ATF2, GCY1, and YPR1, were simultaneously disrupted in 6 days with 100% efficiency. This homology-integrated CRISPR (HI-CRISPR) strategy represents a powerful tool for creating yeast strains with multiple gene knockouts.
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Affiliation(s)
- Zehua Bao
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Han Xiao
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jing Liang
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lu Zhang
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Xiong Xiong
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ning Sun
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Tong Si
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Biochemistry, ‡Department of Chemical and Biomolecular
Engineering, §Departments of Chemistry,
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Abstract
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
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Abstract
Synthetic biology employs rational engineering principles to build biological systems from the libraries of standard, well characterized biological parts. Biological systems designed and built by synthetic biologists fulfill a plethora of useful purposes, ranging from better healthcare and energy production to biomanufacturing. Recent advancements in the synthesis, assembly and "booting-up" of synthetic genomes and in low and high-throughput genome engineering have paved the way for engineering on the genome-wide scale. One of the key goals of genome engineering is the construction of minimal genomes consisting solely of essential genes (genes indispensable for survival of living organisms). Besides serving as a toolbox to understand the universal principles of life, the cell encoded by minimal genome could be used to build a stringently controlled "cell factory" with a desired phenotype. This review provides an update on recent advances in the genome-scale engineering with particular emphasis on the engineering of minimal genomes. Furthermore, it presents an ongoing discussion to the scientific community for better suitability of minimal or robust cells for industrial applications.
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Affiliation(s)
- Mario Juhas
- a Department of Pathology , University of Cambridge , Cambridge , UK
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Juhas M, Reuß DR, Zhu B, Commichau FM. Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering. Microbiology (Reading) 2014; 160:2341-2351. [DOI: 10.1099/mic.0.079376-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Investigation of essential genes, besides contributing to understanding the fundamental principles of life, has numerous practical applications. Essential genes can be exploited as building blocks of a tightly controlled cell ‘chassis’. Bacillus subtilis and Escherichia coli K-12 are both well-characterized model bacteria used as hosts for a plethora of biotechnological applications. Determination of the essential genes that constitute the B. subtilis and E. coli minimal genomes is therefore of the highest importance. Recent advances have led to the modification of the original B. subtilis and E. coli essential gene sets identified 10 years ago. Furthermore, significant progress has been made in the area of genome minimization of both model bacteria. This review provides an update, with particular emphasis on the current essential gene sets and their comparison with the original gene sets identified 10 years ago. Special attention is focused on the genome reduction analyses in B. subtilis and E. coli and the construction of minimal cell factories for industrial applications.
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Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Daniel R. Reuß
- Department of General Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Fabian M. Commichau
- Department of General Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
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O'Brien SP, DeLisa MP. Split-Cre recombinase effectively monitors protein-protein interactions in living bacteria. Biotechnol J 2014; 9:355-61. [DOI: 10.1002/biot.201300462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/13/2013] [Accepted: 12/31/2013] [Indexed: 01/15/2023]
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Srinivasan R, Chandraprakash D, Krishnamurthi R, Singh P, Scolari VF, Krishna S, Seshasayee ASN. Genomic analysis reveals epistatic silencing of "expensive" genes in Escherichia coli K-12. MOLECULAR BIOSYSTEMS 2013; 9:2021-33. [PMID: 23661089 DOI: 10.1039/c3mb70035f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system - involving the homologous H-NS and StpA - operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed "epistatic" and "unilateral". In the absence of H-NS, the expression of "epistatically controlled genes" is repressed by StpA, whereas that of "unilaterally controlled genes" is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.
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Affiliation(s)
- Rajalakshmi Srinivasan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India
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50
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Lee BR, Cho S, Song Y, Kim SC, Cho BK. Emerging tools for synthetic genome design. Mol Cells 2013; 35:359-70. [PMID: 23708771 PMCID: PMC3887862 DOI: 10.1007/s10059-013-0127-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/26/2013] [Indexed: 12/29/2022] Open
Abstract
Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives.
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Affiliation(s)
- Bo-Rahm Lee
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
| | - Suhyung Cho
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Yoseb Song
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Sun Chang Kim
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Byung-Kwan Cho
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
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