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Wang L, Hu J, Li K, Zhao Y, Zhu M. Advancements in gene editing technologies for probiotic-enabled disease therapy. iScience 2024; 27:110791. [PMID: 39286511 PMCID: PMC11403445 DOI: 10.1016/j.isci.2024.110791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Probiotics typically refer to microorganisms that have been identified for their health benefits, and they are added to foods or supplements to promote the health of the host. A growing number of probiotic strains have been identified lately and developed into valuable regulatory pharmaceuticals for nutritional and medical applications. Gene editing technologies play a crucial role in addressing the need for safe and therapeutic probiotics in disease treatment. These technologies offer valuable assistance in comprehending the underlying mechanisms of probiotic bioactivity and in the development of advanced probiotics. This review aims to offer a comprehensive overview of gene editing technologies applied in the engineering of both traditional and next-generation probiotics. It further explores the potential for on-demand production of customized products derived from enhanced probiotics, with a particular emphasis on the future of gene editing in the development of live biotherapeutics.
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Affiliation(s)
- Lixuan Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Motao Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Noda S, Fujiwara R, Mori Y, Dainin M, Shirai T, Kondo A. Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture. BIOTECH 2024; 13:2. [PMID: 38247732 PMCID: PMC10801462 DOI: 10.3390/biotech13010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from Arabidopsis thaliana (AtPAL) and Brachypodium distachyon (BdPAL) for their ability to produce trans-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing E. coli produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an E. coli strain that co-expressed AtPAL2 and ferulic acid decarboxylase from Saccharomyces cerevisiae. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large-scale industrial production of styrene.
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Affiliation(s)
- Shuhei Noda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Saitama, Japan
| | - Ryosuke Fujiwara
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Yutaro Mori
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
| | - Mayumi Dainin
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; (R.F.); (T.S.)
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3
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Metabolic engineering of Escherichia coli to enhance protein production by coupling ShCAST-based optimized transposon system and CRISPR interference. J Taiwan Inst Chem Eng 2023. [DOI: 10.1016/j.jtice.2023.104746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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4
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Hao M, Tang J, Ge S, Li T, Xia N. Bacterial-Artificial-Chromosome-Based Genome Editing Methods and the Applications in Herpesvirus Research. Microorganisms 2023; 11:589. [PMID: 36985163 PMCID: PMC10056367 DOI: 10.3390/microorganisms11030589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Herpesviruses are major pathogens that infect humans and animals. Manipulating the large genome is critical for exploring the function of specific genes and studying the pathogenesis of herpesviruses and developing novel anti-viral vaccines and therapeutics. Bacterial artificial chromosome (BAC) technology significantly advanced the capacity of herpesviruses researchers to manipulate the virus genomes. In the past years, advancements in BAC-based genome manipulating and screening strategies of recombinant BACs have been achieved, which has promoted the study of the herpes virus. This review summarizes the advances in BAC-based gene editing technology and selection strategies. The merits and drawbacks of BAC-based herpesvirus genome editing methods and the application of BAC-based genome manipulation in viral research are also discussed. This review provides references relevant for researchers in selecting gene editing methods in herpes virus research. Despite the achievements in the genome manipulation of the herpes viruses, the efficiency of BAC-based genome manipulation is still not satisfactory. This review also highlights the need for developing more efficient genome-manipulating methods for herpes viruses.
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Affiliation(s)
- Mengling Hao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jiabao Tang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Shengxiang Ge
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Tingdong Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
- Xiang An Biomedicine Laboratory, Xiamen 361102, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, Xiamen 361102, China
- The Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical Sciences, Xiamen 361102, China
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5
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Shekhar C, Maeda T. A simple approach for random genomic insertion-deletions using ambiguous sequences in Escherichia coli. J Basic Microbiol 2022; 62:948-962. [PMID: 35739617 DOI: 10.1002/jobm.202100636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/20/2022] [Accepted: 06/11/2022] [Indexed: 11/07/2022]
Abstract
Escherichia coli K-12, being one of the best understood and thoroughly analyzed organisms, is the preferred platform for genetic and biochemical research. Among all genetic engineering approaches applied on E. coli, the homologous recombination approach is versatile and precise, which allows engineering genes or large segments of the chromosome directly by using polymerase chain reaction (PCR) products or synthetic oligonucleotides. The previously explained approaches for random insertion and deletions were reported as technically not easy and laborious. This study, first, finds the minimum length of homology extension that is efficient and accurate for homologous recombination, as 30 nt. Second, proposes an approach utilizing PCR products flanking ambiguous NNN-sequence (30-nt) extensions, which facilitate the homologous recombination to recombine them at multiple regions on the genome and generate insertion-deletion mutations. Further analysis found that these mutations were varying in number, that is, multiple genomic regions were deleted. Moreover, evaluation of the phenotype of all the multiple random insertion-deletion mutants demonstrated no significant changes in the normal metabolism of bacteria. This study not only presents the efficiency of ambiguous sequences in making random deletion mutations, but also demonstrates their further applicability in genomics.
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Affiliation(s)
- Chandra Shekhar
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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6
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Tang H, Zhang P, Luo X. Recent Technologies for Genetic Code Expansion and their Implications on Synthetic Biology Applications. J Mol Biol 2021; 434:167382. [PMID: 34863778 DOI: 10.1016/j.jmb.2021.167382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 02/03/2023]
Abstract
Genetic code expansion (GCE) enables the site-specific incorporation of non-canonical amino acids as novel building blocks for the investigation and manipulation of proteins. The advancement of genetic code expansion has been benefited from the development of synthetic biology, while genetic code expansion also helps to create more synthetic biology tools. In this review, we summarize recent advances in genetic code expansion brought by synthetic biology progresses, including engineering of the translation machinery, genome-wide codon reassignment, and the biosynthesis of non-canonical amino acids. We highlight the emerging application of this technology in construction of new synthetic biology parts, circuits, chassis, and products.
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Affiliation(s)
- Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Pan Zhang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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7
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Du Y, Wang X, Han Z, Hua Y, Yan K, Zhang B, Zhao W, Wan C. Polyphosphate Kinase 1 Is a Pathogenesis Determinant in Enterohemorrhagic Escherichia coli O157:H7. Front Microbiol 2021; 12:762171. [PMID: 34777317 PMCID: PMC8578739 DOI: 10.3389/fmicb.2021.762171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
The ppk1 gene encodes polyphosphate kinase (PPK1), which is the major catalytic enzyme that Escherichia coli utilizes to synthesize inorganic polyphosphate (polyP). The aim of this study was to explore the role of PPK1 in the pathogenesis of Enterohemorrhagic E. coli O157:H7 (EHEC O157:H7). An isogenic in-frame ppk1 deletion mutant (Δppk1) and ppk1 complemented mutant (Cppk1) were constructed and characterized in comparison to wild-type (WT) EHEC O157:H7 strain EDL933w by microscope observation and growth curve analysis. Survival rates under heat stress and acid tolerance, both of which the bacteria would face during pathogenesis, were compared among the three strains. LoVo cells and a murine model of intestinal colitis were used as the in vitro and in vivo models, respectively, to evaluate the effect of PPK1 on adhesion and invasion during the process of pathogenesis. Real-time reverse-transcription PCR of regulatory gene rpoS, adhesion gene eae, and toxin genes stx1 and stx2 was carried out to corroborate the results from the in vitro and in vivo models. The ppk1 deletion mutant exhibited disrupted polyP levels, but not morphology and growth characteristics. The survival rate of the Δppk1 strain under stringent environmental conditions was lower as compared with WT and Cppk1. The in vitro assays showed that deletion of the ppk1 gene reduced the adhesion, formation of attaching and effacing (A/E) lesions, and invasive ability of EHEC O157:H7. Moreover, the virulence of the Δppk1 in BALB/c mice was weaker as compared with the other two strains. Additionally, mRNA expression of rpoS, eae, stx1 and stx2 were consistent with the in vitro and in vivo results. In conclusion: EHEC O157:H7 requires PPK1 for both survival under harsh environmental conditions and virulence in vivo.
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Affiliation(s)
- Yanli Du
- School of Medical Technology and Nursing, Shenzhen Polytechnic, Shenzhen, China
| | - Xiangyu Wang
- Department of Gastroenterology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, China.,Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zongli Han
- Department of Neurosurgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Ying Hua
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Kaina Yan
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Bao Zhang
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wei Zhao
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Chengsong Wan
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, China.,Key Laboratory of Tropical Disease Research of Guangdong Province, Guangzhou, China
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8
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Wang J, Huang C, Guo K, Ma L, Meng X, Wang N, Huo YX. Converting Escherichia coli MG1655 into a chemical overproducer through inactivating defense system against exogenous DNA. Synth Syst Biotechnol 2020; 5:333-342. [PMID: 33102829 PMCID: PMC7568196 DOI: 10.1016/j.synbio.2020.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 01/05/2023] Open
Abstract
Escherichia coli strain K-12 MG1655 has been proposed as an appropriate host strain for industrial production. However, the direct application of this strain suffers from the transformation inefficiency and plasmid instability. Herein, we conducted genetic modifications at a serial of loci of MG1655 genome, generating a robust and universal host strain JW128 with higher transformation efficiency and plasmid stability that can be used to efficiently produce desired chemicals after introducing the corresponding synthetic pathways. Using JW128 as the host, the titer of isobutanol reached 5.76 g/L in shake-flask fermentation, and the titer of lycopene reached 1.91 g/L in test-tube fermentation, 40-fold and 5-fold higher than that of original MG1655, respectively. These results demonstrated JW128 is a promising chassis for high-level production of value-added chemicals.
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Affiliation(s)
- Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- SIP-UCLA Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Kai Guo
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Xiangyu Meng
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- Corresponding author.
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
- SIP-UCLA Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
- Corresponding author. Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China.
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9
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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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10
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Zou X, Guo L, Huang L, Li M, Zhang S, Yang A, Zhang Y, Zhu L, Zhang H, Zhang J, Feng Z. Pathway construction and metabolic engineering for fermentative production of β-alanine in Escherichia coli. Appl Microbiol Biotechnol 2020; 104:2545-2559. [PMID: 31989219 DOI: 10.1007/s00253-020-10359-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/03/2019] [Accepted: 01/05/2020] [Indexed: 12/29/2022]
Abstract
β-Alanine is a naturally occurring β-amino acid that has been widely applied in the life and health field. Although microbial fermentation is a promising method for industrial production of β-alanine, an efficient microbial cell factory is still lacking. In this study, a new metabolically engineered Escherichia coli strain for β-alanine production was developed through a series of introduction, deletion, and overexpression of genes involved in its biosynthesis pathway. First, the L-aspartate a-decarboxylase gene, BtADC, from Bacillus tequilensis, with higher catalytic activity to produce β-alanine from aspartate, was constitutively expressed in E. coli, leading to an increased production of β-alanine up to 2.76 g/L. Second, three native aspartate kinase genes, akI, akII, and akIII, were knocked out to promote the production of β-alanine to a higher concentration of 4.43 g/L by preventing from bypass loss of aspartate. To increase the amount of aspartate, the native AspC gene was replaced with PaeAspDH, a L-aspartate dehydrogenase gene from Pseudomonas aeruginosa, accompanied with the overexpression of the native AspA gene, to further improve the production level of β-alanine to 9.27 g/L. Last, increased biosynthesis of oxaloacetic acid (OAA) was achieved by a combination of overexpression of the native PPC, introduction of CgPC, a pyruvate decarboxylase from Corynebacterium glutamicum, and deletion of ldhA, pflB, pta, and adhE in E. coli, to further enhance the production of β-alanine. Finally, the engineered E. coli strain produced 43.12 g/L β-alanine in fed-batch fermentation. Our study will lay a solid foundation for the promising application of β-alanine in the life and health field. KEY POINTS: • Overexpression of BtADC resulted in substantial accumulation of β-alanine. • The native AspC was replaced with PaeAspDH to catalyze the transamination of OAA. • Deletion of gluDH prevented from losing carbon flux in TCA recycle. • A 43.12-g/L β-alanine production in fed-batch fermentation was achieved. Graphical abstract.
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Affiliation(s)
- Xinyu Zou
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Laixian Guo
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Lilong Huang
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Miao Li
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Sheng Zhang
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Anren Yang
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Yu Zhang
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Luying Zhu
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Hongxia Zhang
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China.,Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China
| | - Juan Zhang
- School of Agriculture, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China. .,Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China.
| | - Zhibin Feng
- School of Life Sciences, Ludong University, 186 Hongqizhong Road, Yantai, 264025, Shandong Province, China.
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11
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Ren J, Lee J, Na D. Recent advances in genetic engineering tools based on synthetic biology. J Microbiol 2020; 58:1-10. [PMID: 31898252 DOI: 10.1007/s12275-020-9334-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/19/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022]
Abstract
Genome-scale engineering is a crucial methodology to rationally regulate microbiological system operations, leading to expected biological behaviors or enhanced bioproduct yields. Over the past decade, innovative genome modification technologies have been developed for effectively regulating and manipulating genes at the genome level. Here, we discuss the current genome-scale engineering technologies used for microbial engineering. Recently developed strategies, such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, multiplex automated genome engineering (MAGE), promoter engineering, CRISPR-based regulations, and synthetic small regulatory RNA (sRNA)-based knockdown, are considered as powerful tools for genome-scale engineering in microbiological systems. MAGE, which modifies specific nucleotides of the genome sequence, is utilized as a genome-editing tool. Contrastingly, synthetic sRNA, CRISPRi, and CRISPRa are mainly used to regulate gene expression without modifying the genome sequence. This review introduces the recent genome-scale editing and regulating technologies and their applications in metabolic engineering.
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Affiliation(s)
- Jun Ren
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jingyu Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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12
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Advances in engineered trans-acting regulatory RNAs and their application in bacterial genome engineering. J Ind Microbiol Biotechnol 2019; 46:819-830. [PMID: 30887255 DOI: 10.1007/s10295-019-02160-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022]
Abstract
Small noncoding RNAs, a large class of ancient posttranscriptional regulators, are increasingly recognized and utilized as key modulators of gene expression in a broad range of microorganisms. Owing to their small molecular size and the central role of Watson-Crick base pairing in defining their interactions, structure and function, numerous diverse types of trans-acting RNA regulators that are functional at the DNA, mRNA and protein levels have been experimentally characterized. It has become increasingly clear that most small RNAs play critical regulatory roles in many processes and are, therefore, considered to be powerful tools for genetic engineering and synthetic biology. The trans-acting regulatory RNAs accelerate this ability to establish potential framework for genetic engineering and genome-scale engineering, which allows RNA structure characterization, easier to design and model compared to DNA or protein-based systems. In this review, we summarize recent advances in engineered trans-acting regulatory RNAs that are used in bacterial genome-scale engineering and in novel cellular capabilities as well as their implementation in wide range of biotechnological, biological and medical applications.
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13
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Sung L, Wu M, Lin M, Hsu M, Truong VA, Shen C, Tu Y, Hwang K, Tu A, Chang Y, Hu Y. Combining orthogonal CRISPR and CRISPRi systems for genome engineering and metabolic pathway modulation in
Escherichia coli. Biotechnol Bioeng 2019; 116:1066-1079. [DOI: 10.1002/bit.26915] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/07/2018] [Accepted: 01/06/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Li‐Yu Sung
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu Taiwan
| | - Meng‐Ying Wu
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu Taiwan
| | - Mei‐Wei Lin
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu Taiwan
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research InstituteHsinchu Taiwan
| | - Mu‐Nung Hsu
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu Taiwan
| | - Vu Anh Truong
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu Taiwan
| | - Chih‐Che Shen
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu Taiwan
| | - Yi Tu
- Department of Life ScienceNational Taiwan UniversityTaipei Taiwan
| | | | - An‐Pang Tu
- Chang Chun Petrochemical GroupTaipei Taiwan
| | - Yu‐Han Chang
- College of Medicine, Chang Gung UniversityTaoyuan Taiwan
- Department of Orthopaedic SurgeryChang Gung Memorial HospitalLinkou Taiwan
| | - Yu‐Chen Hu
- Department of Chemical EngineeringNational Tsing Hua UniversityHsinchu Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua UniversityHsinchu Taiwan
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14
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Li Y, Yan F, Wu H, Li G, Han Y, Ma Q, Fan X, Zhang C, Xu Q, Xie X, Chen N. Multiple-step chromosomal integration of divided segments from a large DNA fragment via CRISPR/Cas9 in Escherichia coli. J Ind Microbiol Biotechnol 2019; 46:81-90. [PMID: 30470963 DOI: 10.1007/s10295-018-2114-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022]
Abstract
Although CRISPR/Cas9-mediated gene editing technology has developed vastly in Escherichia coli, the chromosomal integration of large DNA fragment is still challenging compared with gene deletion and small fragment integration. Moreover, to guarantee sufficient Cas9-induced double-strand breaks, it is usually necessary to design several gRNAs to select the appropriate one. Accordingly, we established a practical daily routine in the laboratory work, involving multiple-step chromosomal integration of the divided segments from a large DNA fragment. First, we introduced and optimized the protospacers from Streptococcus pyogenes in E. coli W3110. Next, the appropriate fragment size for each round of integration was optimized to be within 3-4 kb. Taking advantage of the optimized protospacer/gRNA pairs, a DNA fragment with a total size of 15.4 kb, containing several key genes for uridine biosynthesis, was integrated into W3110 chromosome, which produced 5.6 g/L uridine in shake flask fermentation. Using this strategy, DNA fragments of virtually any length can be integrated into a suitable genomic site, and two gRNAs can be alternatively used, avoiding the tedious construction of gRNA-expressing plasmids. This study thus presents a useful strategy for large DNA fragment integration into the E. coli chromosome, which can be easily adapted for use in other bacteria.
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Affiliation(s)
- Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Fangqing Yan
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Heyun Wu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Guoliang Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yakun Han
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qian Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xiaoguang Fan
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Chenglin Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Qingyang Xu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Xixian Xie
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, 300457, China.
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin, 300457, China.
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, China.
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15
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Wu H, Li Y, Ma Q, Li Q, Jia Z, Yang B, Xu Q, Fan X, Zhang C, Chen N, Xie X. Metabolic engineering of Escherichia coli for high-yield uridine production. Metab Eng 2018; 49:248-256. [PMID: 30189293 DOI: 10.1016/j.ymben.2018.09.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/22/2018] [Accepted: 09/01/2018] [Indexed: 01/14/2023]
Abstract
Uridine is a kind of pyrimidine nucleoside that has been widely applied in the pharmaceutical industry. Although microbial fermentation is a promising method for industrial production of uridine, an efficient microbial cell factory is still lacking. In this study, we constructed a metabolically engineered Escherichia coli capable of high-yield uridine production. First, we developed a CRISPR/Cas9-mediated chromosomal integration strategy to integrate large DNA into the E. coli chromosome, and a 9.7 kb DNA fragment including eight genes in the pyrimidine operon of Bacillus subtilis F126 was integrated into the yghX locus of E. coli W3110. The resultant strain produced 3.3 g/L uridine and 4.5 g/L uracil in shake flask culture for 32 h. Subsequently, five genes involved in uridine catabolism were knocked out, and the uridine titer increased to 7.8 g/L. As carbamyl phosphate, aspartate, and 5'-phosphoribosyl pyrophosphate are important precursors for uridine synthesis, we further modified several metabolism-related genes and synergistically improved the supply of these precursors, leading to a 76.9% increase in uridine production. Finally, nupC and nupG encoding nucleoside transport proteins were deleted, and the extracellular uridine accumulation increased to 14.5 g/L. After 64 h of fed-batch fermentation, the final engineered strain UR6 produced 70.3 g/L uridine with a yield and productivity of 0.259 g/g glucose and 1.1 g/L/h, respectively. To the best of our knowledge, this is the highest uridine titer and productivity ever reported for the fermentative production of uridine.
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Affiliation(s)
- Heyun Wu
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanjun Li
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qian Ma
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qiang Li
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zifan Jia
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Bo Yang
- The Institute of Seawater Desalination and Multipurpose Utilization, SOA, Tianjin 300192, China
| | - Qingyang Xu
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaoguang Fan
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chenglin Zhang
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Xixian Xie
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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16
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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17
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Alonso‐Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS. Toward industrial production of isoprenoids in
Escherichia coli
: Lessons learned from CRISPR‐Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng 2018; 115:1000-1013. [DOI: 10.1002/bit.26530] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jorge Alonso‐Gutierrez
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Daisuke Koma
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- Osaka Municipal Technical Research InstituteOsakaJapan
| | - Qijun Hu
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Yuchen Yang
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Leanne J. G. Chan
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Paul D. Adams
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkHorsholmDenmark
- Department of Chemical and Biomolecular EngineeringUniversity of CaliforniaBerkeleyCalifornia
- Department of BioengineeringUniversity of CaliforniaBerkeleyCalifornia
| | - Taek S. Lee
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
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18
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Ryu YS, Chandran SP, Kim K, Lee SK. Oligo- and dsDNA-mediated genome editing using a tetA dual selection system in Escherichia coli. PLoS One 2017; 12:e0181501. [PMID: 28719630 PMCID: PMC5515457 DOI: 10.1371/journal.pone.0181501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/03/2017] [Indexed: 12/26/2022] Open
Abstract
The ability to precisely and seamlessly modify a target genome is needed for metabolic engineering and synthetic biology techniques aimed at creating potent biosystems. Herein, we report on a promising method in Escherichia coli that relies on the insertion of an optimized tetA dual selection cassette followed by replacement of the same cassette with short, single-stranded DNA (oligos) or long, double-stranded DNA and the isolation of recombinant strains by negative selection using NiCl2. This method could be rapidly and successfully used for genome engineering, including deletions, insertions, replacements, and point mutations, without inactivation of the methyl-directed mismatch repair (MMR) system and plasmid cloning. The method we describe here facilitates positive genome-edited recombinants with selection efficiencies ranging from 57 to 92%. Using our method, we increased lycopene production (3.4-fold) by replacing the ribosome binding site (RBS) of the rate-limiting gene (dxs) in the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway with a strong RBS. Thus, this method could be used to achieve scarless, proficient, and targeted genome editing for engineering E. coli strains.
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Affiliation(s)
- Young Shin Ryu
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sathesh-Prabu Chandran
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Kyungchul Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sung Kuk Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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19
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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20
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Mechanism of salinomycin overproduction in Streptomyces albus as revealed by comparative functional genomics. Appl Microbiol Biotechnol 2017; 101:4635-4644. [DOI: 10.1007/s00253-017-8278-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/26/2017] [Accepted: 03/29/2017] [Indexed: 12/11/2022]
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21
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Oesterle S, Wuethrich I, Panke S. Toward Genome-Based Metabolic Engineering in Bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2017; 101:49-82. [PMID: 29050667 DOI: 10.1016/bs.aambs.2017.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Prokaryotes modified stably on the genome are of great importance for production of fine and commodity chemicals. Traditional methods for genome engineering have long suffered from imprecision and low efficiencies, making construction of suitable high-producer strains laborious. Here, we review the recent advances in discovery and refinement of molecular precision engineering tools for genome-based metabolic engineering in bacteria for chemical production, with focus on the λ-Red recombineering and the clustered regularly interspaced short palindromic repeats/Cas9 nuclease systems. In conjunction, they enable the integration of in vitro-synthesized DNA segments into specified locations on the chromosome and allow for enrichment of rare mutants by elimination of unmodified wild-type cells. Combination with concurrently developing improvements in important accessory technologies such as DNA synthesis, high-throughput screening methods, regulatory element design, and metabolic pathway optimization tools has resulted in novel efficient microbial producer strains and given access to new metabolic products. These new tools have made and will likely continue to make a big impact on the bioengineering strategies that transform the chemical industry.
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22
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Green DW, Watson GS, Watson JA, Lee DJ, Lee JM, Jung HS. Diversification and enrichment of clinical biomaterials inspired by Darwinian evolution. Acta Biomater 2016; 42:33-45. [PMID: 27381524 DOI: 10.1016/j.actbio.2016.06.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 06/11/2016] [Accepted: 06/21/2016] [Indexed: 02/06/2023]
Abstract
UNLABELLED Regenerative medicine and biomaterials design are driven by biomimicry. There is the essential requirement to emulate human cell, tissue, organ and physiological complexity to ensure long-lasting clinical success. Biomimicry projects for biomaterials innovation can be re-invigorated with evolutionary insights and perspectives, since Darwinian evolution is the original dynamic process for biological organisation and complexity. Many existing human inspired regenerative biomaterials (defined as a nature generated, nature derived and nature mimicking structure, produced within a biological system, which can deputise for, or replace human tissues for which it closely matches) are without important elements of biological complexity such as, hierarchy and autonomous actions. It is possible to engineer these essential elements into clinical biomaterials via bioinspired implementation of concepts, processes and mechanisms played out during Darwinian evolution; mechanisms such as, directed, computational, accelerated evolutions and artificial selection contrived in the laboratory. These dynamos for innovation can be used during biomaterials fabrication, but also to choose optimal designs in the regeneration process. Further evolutionary information can help at the design stage; gleaned from the historical evolution of material adaptations compared across phylogenies to changes in their environment and habitats. Taken together, harnessing evolutionary mechanisms and evolutionary pathways, leading to ideal adaptations, will eventually provide a new class of Darwinian and evolutionary biomaterials. This will provide bioengineers with a more diversified and more efficient innovation tool for biomaterial design, synthesis and function than currently achieved with synthetic materials chemistry programmes and rational based materials design approach, which require reasoned logic. It will also inject further creativity, diversity and richness into the biomedical technologies that we make. All of which are based on biological principles. Such evolution-inspired biomaterials have the potential to generate innovative solutions, which match with existing bioengineering problems, in vital areas of clinical materials translation that include tissue engineering, gene delivery, drug delivery, immunity modulation, and scar-less wound healing. STATEMENT OF SIGNIFICANCE Evolution by natural selection is a powerful generator of innovations in molecular, materials and structures. Man has influenced evolution for thousands of years, to create new breeds of farm animals and crop plants, but now molecular and materials can be molded in the same way. Biological molecules and simple structures can be evolved, literally in the laboratory. Furthermore, they are re-designed via lessons learnt from evolutionary history. Through a 3-step process to (1) create variants in material building blocks, (2) screen the variants with beneficial traits/properties and (3) select and support their self-assembly into usable materials, improvements in design and performance can emerge. By introducing biological molecules and small organisms into this process, it is possible to make increasingly diversified, sophisticated and clinically relevant materials for multiple roles in biomedicine.
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Affiliation(s)
- D W Green
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Republic of Korea; Oral Biosciences, Faculty of Dentistry, The University of Hong Kong, 34, Hospital Road, Hong Kong SAR
| | - G S Watson
- School of Science & Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - J A Watson
- School of Science & Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - D-J Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Republic of Korea
| | - J-M Lee
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Republic of Korea
| | - H-S Jung
- Division in Anatomy and Developmental Biology, Department of Oral Biology, Oral Science Research Center, BK21 PLUS Project, Yonsei University College of Dentistry, Seoul, Republic of Korea; Oral Biosciences, Faculty of Dentistry, The University of Hong Kong, 34, Hospital Road, Hong Kong SAR.
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23
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Chung ME, Yeh IH, Sung LY, Wu MY, Chao YP, Ng IS, Hu YC. Enhanced integration of large DNA intoE. colichromosome by CRISPR/Cas9. Biotechnol Bioeng 2016; 114:172-183. [DOI: 10.1002/bit.26056] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Mu-En Chung
- Department of Chemical Engineering; National Tsing Hua University; 101, Sec 2, Kuang Fu Rd. Hsinchu 300 Taiwan
| | - I-Hsin Yeh
- Department of Chemical Engineering; National Tsing Hua University; 101, Sec 2, Kuang Fu Rd. Hsinchu 300 Taiwan
| | - Li-Yu Sung
- Department of Chemical Engineering; National Tsing Hua University; 101, Sec 2, Kuang Fu Rd. Hsinchu 300 Taiwan
| | - Meng-Ying Wu
- Department of Chemical Engineering; National Tsing Hua University; 101, Sec 2, Kuang Fu Rd. Hsinchu 300 Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering; Feng Chia University; Taichung Taiwan
| | - I-Son Ng
- Department of Chemical Engineering; National Cheng Kung University; Tainan Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering; National Tsing Hua University; 101, Sec 2, Kuang Fu Rd. Hsinchu 300 Taiwan
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24
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Regulatory RNA-assisted genome engineering in microorganisms. Curr Opin Biotechnol 2015; 36:85-90. [DOI: 10.1016/j.copbio.2015.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/18/2015] [Accepted: 08/09/2015] [Indexed: 01/05/2023]
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25
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Singh V, Braddick D. Recent advances and versatility of MAGE towards industrial applications. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:1-9. [PMID: 26702302 DOI: 10.1007/s11693-015-9184-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/31/2015] [Accepted: 11/04/2015] [Indexed: 01/11/2023]
Abstract
The genome engineering toolkit has expanded significantly in recent years, allowing us to study the functions of genes in cellular networks and assist in over-production of proteins, drugs, chemicals and biofuels. Multiplex automated genome engineering (MAGE) has been recently developed and gained more scientific interest towards strain engineering. MAGE is a simple, rapid and efficient tool for manipulating genes simultaneously in multiple loci, assigning genetic codes and integrating non-natural amino acids. MAGE can be further expanded towards the engineering of fast, robust and over-producing strains for chemicals, drugs and biofuels at industrial scales.
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Affiliation(s)
- Vijai Singh
- Institute of Systems and Synthetic Biology, Université d'Évry Val d'Essonne, Genopole Campus 1, Batiment Genavenir 6, 5 rue Henri Desbruères, 91030 Évry, France
| | - Darren Braddick
- Institute of Systems and Synthetic Biology, Université d'Évry Val d'Essonne, Genopole Campus 1, Batiment Genavenir 6, 5 rue Henri Desbruères, 91030 Évry, France
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Chaudhary AK, Na D, Lee EY. Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs. Biotechnol Adv 2015; 33:914-30. [PMID: 26027891 DOI: 10.1016/j.biotechadv.2015.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/27/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022]
Abstract
Due to global crises such as pollution and depletion of fossil fuels, sustainable technologies based on microbial cell-factories have been garnering great interest as an alternative to chemical factories. The development of microbial cell-factories is imperative in cutting down the overall manufacturing cost. Thus, diverse metabolic engineering strategies and engineering tools have been established to obtain a preferred genotype and phenotype displaying superior productivity. However, these tools are limited to only a handful of genes with permanent modification of a genome and significant labor costs, and this is one of the bottlenecks associated with biofactory construction. Therefore, a groundbreaking rapid and high-throughput engineering tool is needed for efficient construction of microbial cell-factories. During the last decade, copious small noncoding RNAs (ncRNAs) have been discovered in bacteria. These are involved in substantial regulatory roles like transcriptional and post-transcriptional gene regulation by modulating mRNA elongation, stability, or translational efficiency. Because of their vulnerability, ncRNAs can be used as another layer of conditional control over gene expression without modifying chromosomal sequences, and hence would be a promising high-throughput tool for metabolic engineering. Here, we review successful design principles and applications of ncRNAs for high-throughput metabolic engineering or physiological studies of diverse industrially important microorganisms.
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Affiliation(s)
- Amit Kumar Chaudhary
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Gyeonggi-do 446-701, Republic of Korea.
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Mahalik S, Sharma AK, Mukherjee KJ. Genome engineering for improved recombinant protein expression in Escherichia coli. Microb Cell Fact 2014; 13:177. [PMID: 25523647 PMCID: PMC4300154 DOI: 10.1186/s12934-014-0177-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/05/2014] [Indexed: 01/09/2023] Open
Abstract
A metabolic engineering perspective which views recombinant protein
expression as a multistep pathway allows us to move beyond vector design and
identify the downstream rate limiting steps in expression. In E.coli these are typically at the translational level
and the supply of precursors in the form of energy, amino acids and nucleotides.
Further recombinant protein production triggers a global cellular stress response
which feedback inhibits both growth and product formation. Countering this requires
a system level analysis followed by a rational host cell engineering to sustain
expression for longer time periods. Another strategy to increase protein yields
could be to divert the metabolic flux away from biomass formation and towards
recombinant protein production. This would require a growth stoppage mechanism which
does not affect the metabolic activity of the cell or the transcriptional or
translational efficiencies. Finally cells have to be designed for efficient export
to prevent buildup of proteins inside the cytoplasm and also simplify downstream
processing. The rational and the high throughput strategies that can be used for the
construction of such improved host cell platforms for recombinant protein expression
is the focus of this review.
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Affiliation(s)
- Shubhashree Mahalik
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ashish K Sharma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Krishna J Mukherjee
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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Si T, Xiao H, Zhao H. Rapid prototyping of microbial cell factories via genome-scale engineering. Biotechnol Adv 2014; 33:1420-32. [PMID: 25450192 DOI: 10.1016/j.biotechadv.2014.11.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/13/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Abstract
Advances in reading, writing and editing genetic materials have greatly expanded our ability to reprogram biological systems at the resolution of a single nucleotide and on the scale of a whole genome. Such capacity has greatly accelerated the cycles of design, build and test to engineer microbes for efficient synthesis of fuels, chemicals and drugs. In this review, we summarize the emerging technologies that have been applied, or are potentially useful for genome-scale engineering in microbial systems. We will focus on the development of high-throughput methodologies, which may accelerate the prototyping of microbial cell factories.
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Affiliation(s)
- Tong Si
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Han Xiao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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29
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Tools for developing tolerance to toxic chemicals in microbial systems and perspectives on moving the field forward and into the industrial setting. Curr Opin Chem Eng 2014. [DOI: 10.1016/j.coche.2014.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Rodriguez A, Martínez JA, Flores N, Escalante A, Gosset G, Bolivar F. Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds. Microb Cell Fact 2014; 13:126. [PMID: 25200799 PMCID: PMC4174253 DOI: 10.1186/s12934-014-0126-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/17/2014] [Indexed: 11/10/2022] Open
Abstract
The production of aromatic amino acids using fermentation processes with recombinant microorganisms can be an advantageous approach to reach their global demands. In addition, a large array of compounds with alimentary and pharmaceutical applications can potentially be synthesized from intermediates of this metabolic pathway. However, contrary to other amino acids and primary metabolites, the artificial channelling of building blocks from central metabolism towards the aromatic amino acid pathway is complicated to achieve in an efficient manner. The length and complex regulation of this pathway have progressively called for the employment of more integral approaches, promoting the merge of complementary tools and techniques in order to surpass metabolic and regulatory bottlenecks. As a result, relevant insights on the subject have been obtained during the last years, especially with genetically modified strains of Escherichia coli. By combining metabolic engineering strategies with developments in synthetic biology, systems biology and bioprocess engineering, notable advances were achieved regarding the generation, characterization and optimization of E. coli strains for the overproduction of aromatic amino acids, some of their precursors and related compounds. In this paper we review and compare recent successful reports dealing with the modification of metabolic traits to attain these objectives.
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31
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Song CW, Lee J, Lee SY. Genome engineering and gene expression control for bacterial strain development. Biotechnol J 2014; 10:56-68. [PMID: 25155412 DOI: 10.1002/biot.201400057] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 07/26/2014] [Accepted: 07/30/2014] [Indexed: 12/21/2022]
Abstract
In recent years, a number of techniques and tools have been developed for genome engineering and gene expression control to achieve desired phenotypes of various bacteria. Here we review and discuss the recent advances in bacterial genome manipulation and gene expression control techniques, and their actual uses with accompanying examples. Genome engineering has been commonly performed based on homologous recombination. During such genome manipulation, the counterselection systems employing SacB or nucleases have mainly been used for the efficient selection of desired engineered strains. The recombineering technology enables simple and more rapid manipulation of the bacterial genome. The group II intron-mediated genome engineering technology is another option for some bacteria that are difficult to be engineered by homologous recombination. Due to the increasing demands on high-throughput screening of bacterial strains having the desired phenotypes, several multiplex genome engineering techniques have recently been developed and validated in some bacteria. Another approach to achieve desired bacterial phenotypes is the repression of target gene expression without the modification of genome sequences. This can be performed by expressing antisense RNA, small regulatory RNA, or CRISPR RNA to repress target gene expression at the transcriptional or translational level. All of these techniques allow efficient and rapid development and screening of bacterial strains having desired phenotypes, and more advanced techniques are expected to be seen.
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Affiliation(s)
- Chan Woo Song
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea; BioProcess Engineering Research Center, KAIST, Daejeon, Republic of Korea
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Current advances of integrated processes combining chemical absorption and biological reduction for NO x removal from flue gas. Appl Microbiol Biotechnol 2014; 98:8497-512. [PMID: 25149446 DOI: 10.1007/s00253-014-6016-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 01/09/2023]
Abstract
Anthropogenic nitrogen oxides (NO x ) emitted from the fossil-fuel-fired power plants cause adverse environmental issues such as acid rain, urban ozone smoke, and photochemical smog. A novel chemical absorption-biological reduction (CABR) integrated process under development is regarded as a promising alternative to the conventional selective catalytic reduction processes for NO x removal from the flue gas because it is economic and environmentally friendly. CABR process employs ferrous ethylenediaminetetraacetate [Fe(II)EDTA] as a solvent to absorb the NO x following microbial denitrification of NO x to harmless nitrogen gas. Meanwhile, the absorbent Fe(II)EDTA is biologically regenerated to sustain the adequate NO x removal. Compared with conventional denitrification process, CABR not only enhances the mass transfer of NO from gas to liquid phase but also minimize the impact of oxygen on the microorganisms. This review provides the current advances of the development of the CABR process for NO x removal from the flue gas.
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