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Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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2
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Semkum P, Thangthamniyom N, Chankeeree P, Keawborisuth C, Theerawatanasirikul S, Lekcharoensuk P. The Application of the Gibson Assembly Method in the Production of Two pKLS3 Vector-Derived Infectious Clones of Foot-and-Mouth Disease Virus. Vaccines (Basel) 2023; 11:1111. [PMID: 37376500 DOI: 10.3390/vaccines11061111] [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: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The construction of a full-length infectious clone, essential for molecular virological study and vaccine development, is quite a challenge for viruses with long genomes or possessing complex nucleotide sequence structures. Herein, we have constructed infectious clones of foot-and-mouth disease virus (FMDV) types O and A by joining each viral coding region with our pKLS3 vector in a single isothermal reaction using Gibson Assembly (GA). pKLS3 is a 4.3-kb FMDV minigenome. To achieve optimal conditions for the DNA joining, each FMDV coding sequence was divided into two overlapping fragments of approximately 3.8 and 3.2 kb, respectively. Both DNA fragments contain the introduced linker sequences for assembly with the linearized pKLS3 vector. FMDV infectious clones were produced upon directly transfecting the GA reaction into baby hamster kidney-21 (BHK-21) cells. After passing in BHK-21 cells, both rescued FMDVs (rO189 and rNP05) demonstrated growth kinetics and antigenicity similar to their parental viruses. Thus far, this is the first report on GA-derived, full-length infectious FMDV cDNA clones. This simple DNA assembly method and the FMDV minigenome would facilitate the construction of FMDV infectious clones and enable genetic manipulation for FMDV research and custom-made FMDV vaccine production.
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Affiliation(s)
- Ploypailin Semkum
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies in Agriculture and Food, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
| | - Nattarat Thangthamniyom
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Penpitcha Chankeeree
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Challika Keawborisuth
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sirin Theerawatanasirikul
- Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies in Agriculture and Food, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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3
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Chen M, Wang M, Zhang Y, Zhag H, Du Q, Jin P. Biosynthesis of hyaluronan in engineered Escherichia coli via the secretion of thermophilic exo-mannanase using palm kernel cake as the carbon source. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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4
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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5
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Wang W, Zheng G, Lu Y. Recent Advances in Strategies for the Cloning of Natural Product Biosynthetic Gene Clusters. Front Bioeng Biotechnol 2021; 9:692797. [PMID: 34327194 PMCID: PMC8314000 DOI: 10.3389/fbioe.2021.692797] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial natural products (NPs) are a major source of pharmacological agents. Most NPs are synthesized from specific biosynthetic gene clusters (BGCs). With the rapid increase of sequenced microbial genomes, large numbers of NP BGCs have been discovered, regarded as a treasure trove of novel bioactive compounds. However, many NP BGCs are silent in native hosts under laboratory conditions. In order to explore their therapeutic potential, a main route is to activate these silent NP BGCs in heterologous hosts. To this end, the first step is to accurately and efficiently capture these BGCs. In the past decades, a large number of effective technologies for cloning NP BGCs have been established, which has greatly promoted drug discovery research. Herein, we describe recent advances in strategies for BGC cloning, with a focus on the preparation of high-molecular-weight DNA fragment, selection and optimization of vectors used for carrying large-size DNA, and methods for assembling targeted DNA fragment and appropriate vector. The future direction into novel, universal, and high-efficiency methods for cloning NP BGCs is also prospected.
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Affiliation(s)
- Wenfang Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guosong Zheng
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, China.,Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
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6
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Zhao W, Ruan J, Wang Q, Du G, Zhou J, Liu S. Metabolic pathway optimization through fusion with self-assembling amphipathic peptides. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Jin P, Liang Z, Li H, Chen C, Xue Y, Du Q. Biosynthesis of low-molecular-weight mannan using metabolically engineered Bacillus subtilis 168. Carbohydr Polym 2021; 251:117115. [PMID: 33142650 DOI: 10.1016/j.carbpol.2020.117115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/19/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023]
Abstract
Mannans are functional polysaccharides with unique biological activities that have been employed widely in food, medicine and pharmaceutics. Recent breakthroughs in plant polysaccharide metabolism identified numerous genes involved in the biosynthesis of mannans. However, constructing highly efficient low-cost microbial cell factories to produce low-molecular-weight (LMW) mannans remains challenging. In this work, we designed a de novo mannan synthetic pathway in food-grade Bacillus subtilis, resulting in mannan accumulation of 0.97 g/L. By co-expressing the identified committed genes (manC, manB, manA and pgi), mannan production was significantly increased to 2.5 g/L. Furthermore, by redirecting the carbon flux using a glucose-repressed promoter to control pfkA expression, mannan production was substantially increased to 4.1 g/L. Production was further enhanced to 12.6 g/L (average MW 6370 Da) in 3-L fed-batch fermentation. This work provides alternative synthetic pathways for metabolic engineering of LMW mannans in B. subtilis, and a useful, optimisable approach to enhance mannans production.
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Affiliation(s)
- Peng Jin
- College of Agricultural and Food Sciences, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Zhengang Liang
- Technology Center of Haikou Customs District China, Haikou 570311, China
| | - Hua Li
- Institute of Microbial Engineering, Henan University, Kaifeng, China
| | - Chunxiao Chen
- College of Agricultural and Food Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Yang Xue
- College of Agricultural and Food Sciences, Zhejiang A & F University, Hangzhou, 311300, China
| | - Qizhen Du
- College of Agricultural and Food Sciences, Zhejiang A & F University, Hangzhou, 311300, China.
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8
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Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
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Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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9
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Lammens EM, Nikel PI, Lavigne R. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, DK, Denmark
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium.
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10
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Combinatorial-Hierarchical DNA Library Design Using the TeselaGen DESIGN Module with j5. Methods Mol Biol 2020. [PMID: 32809191 DOI: 10.1007/978-1-0716-0908-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Modern DNA assembly techniques are known for their potential to link multiple large DNA fragments together into even larger constructs in single pot reactions that are easier to automate and work more reliably than traditional cloning methods. The simplicity of the chemistry is in contrast to the increased work needed to design optimal reactions that maximize DNA fragment reuse, minimize cost, and organize thousands of potential chemical reactions. Here we examine available DNA assembly methods and describe through example, the construction of a complex but not atypical combinatorial and hierarchical library using protocols that are generated automatically with the assistance of modern synthetic biology software.
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11
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Wang J, Zhu J, Wang C, Zhou G, Yu X, Fan H, An R, Komiyama M, Liang X. Thermus thermophilus DNA Ligase Connects Two Fragments Having Exceptionally Short Complementary Termini at High Temperatures. Biochemistry 2020; 59:400-406. [PMID: 31887028 DOI: 10.1021/acs.biochem.9b00866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermus thermophilus DNA ligase (Tth DNA ligase) is widely employed for cloning, enzymatic synthesis, and molecular diagnostics at high temperatures (e.g., 65 °C). It has been long believed that the complementary ends must be very long (e.g., >30 bp) to place two DNA fragments nearby for the ligation. In the current study, the length of the complementary portion was systematically varied, and the ligation efficiency was evaluated using the high resolution melting (HRM) method. Unexpectedly, very short oligonucleotides (7-10 nt) were successfully ligated on the complementary overhang attached to a dsDNA at 70 °C. Furthermore, sticky ends with the overhang of only 4 nt long, available after scission with many restriction enzymes, were also efficiently ligated at 45-70 °C. The ligation yield for the 6-nt-long sticky ends was as high as 80%. It was concluded that Tth DNA ligase can be used as a unique tool for DNA manipulation that cannot be otherwise easily accomplished.
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Affiliation(s)
- Jing Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,CAS Key laboratory of Marine Ecology and Environmental Sciences , Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 , China
| | - Jianming Zhu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Chenru Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Guangqing Zhou
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xin Yu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Huijun Fan
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
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12
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Guo W, Xie B, Jiang M, Zhu XJ, Qiu M, Dai ZM. An improved overlap extension PCR for simultaneous multiple sites large fragments insertion, deletion and substitution. Sci Rep 2019; 9:15637. [PMID: 31666610 PMCID: PMC6821815 DOI: 10.1038/s41598-019-52122-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 10/14/2019] [Indexed: 11/30/2022] Open
Abstract
The existing molecular cloning methods are often limited by the availability of suitable restriction sites. It is still a challenge for simultaneous cloning of multiple fragments into different sites of a single vector. Here we developed a novel method named improved overlap extension PCR (IOEP) for restriction enzyme independent cloning of large fragments. The addition of primers enables IOEP to exponentially amplify the overlap extension product, thus greatly improves the amplification efficiency of large fragments. Moreover, coupled with the benefit of T4 DNA polymerase to improve cloning efficiency, our method can be used to simultaneously insert, delete and replace multiple DNA fragments at different sites.
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Affiliation(s)
- Wei Guo
- College of Life Sciences, Zhejiang University, 388 Yuhangtang Road, Hangzhou, Zhejiang, 310058, P.R. China.,Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou, Zhejiang, 310036, P.R. China
| | - Binhua Xie
- Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou, Zhejiang, 310036, P.R. China
| | - Min Jiang
- Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou, Zhejiang, 310036, P.R. China
| | - Xiao-Jing Zhu
- Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou, Zhejiang, 310036, P.R. China
| | - Mengsheng Qiu
- College of Life Sciences, Zhejiang University, 388 Yuhangtang Road, Hangzhou, Zhejiang, 310058, P.R. China. .,Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou, Zhejiang, 310036, P.R. China.
| | - Zhong-Min Dai
- Institute of Life Sciences, Key Laboratory of Organ Development and Regeneration of Zhejiang Province, College of Life and Environmental Sciences, Hangzhou Normal University, 16 Xuelin Street, Hangzhou, Zhejiang, 310036, P.R. China.
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13
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Xia Y, Li K, Li J, Wang T, Gu L, Xun L. T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis. Nucleic Acids Res 2019; 47:e15. [PMID: 30462336 PMCID: PMC6379645 DOI: 10.1093/nar/gky1169] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/31/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
The assembly of DNA fragments with homologous arms is becoming popular in routine cloning. For an in vitro assembly reaction, a DNA polymerase is often used either alone for its 3'-5' exonuclease activity or together with a 5'-3' exonuclease for its DNA polymerase activity. Here, we present a 'T5 exonuclease DNA assembly' (TEDA) method that only uses a 5'-3' exonuclease. DNA fragments with short homologous ends were treated by T5 exonuclease and then transformed into Escherichia coli to produce clone colonies. The cloning efficiency was similar to that of the commercial In-Fusion method employing a proprietary DNA polymerase, but higher than that of the Gibson method utilizing T5 exonuclease, Phusion DNA polymerase, and DNA ligase. It also assembled multiple DNA fragments and did simultaneous site-directed mutagenesis at multiple sites. The reaction mixture was simple, and each reaction used 0.04 U of T5 exonuclease that cost 0.25 US cents. The simplicity, cost effectiveness, and cloning efficiency should promote its routine use, especially for labs with a budget constraint. TEDA may trigger further development of DNA assembly methods that employ single exonucleases.
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Affiliation(s)
- Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Kai Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Jingjing Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, P.R. China.,School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
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14
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Liu S, Xiao H, Zhang F, Lu Z, Zhang Y, Deng A, Li Z, Yang C, Wen T. A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:180. [PMID: 31338122 PMCID: PMC6628500 DOI: 10.1186/s13068-019-1520-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND DNA assembly is an essential technique enabling metabolic engineering and synthetic biology. Combining novel DNA assembly technologies with rational metabolic engineering can facilitate the construction of microbial cell factories. Amino acids and derived biochemicals are important products in industrial biotechnology with wide application and huge markets. DNA assembly scenarios encountered in metabolic engineering for the construction of amino acid and related compound producers, such as design-build-test-learn cycles, construction of precise genetic circuits and repetitive DNA molecules, usually require for iterative, scarless and repetitive sequence assembly methods, respectively. RESULTS Restriction endonuclease (RE)-assisted strategies constitute one of the major categories of DNA assembly. Here, we developed a Type IIP and IIS RE-assisted method named PS-Brick that comprehensively takes advantage of the properties of PCR fragments and REs for iterative, seamless and repetitive sequence assembly. One round of PS-Brick reaction using purified plasmids and PCR fragments was accomplished within several hours, and transformation of the resultant reaction product from this PS-Brick assembly reaction exhibited high efficiency (104-105 CFUs/µg DNA) and high accuracy (~ 90%). An application of metabolic engineering to threonine production, including the release of feedback regulation, elimination of metabolic bottlenecks, intensification of threonine export and inactivation of threonine catabolism, was stepwise resolved in E. coli by rounds of "design-build-test-learn" cycles through the iterative PS-Brick paradigm, and 45.71 g/L threonine was obtained through fed-batch fermentation. In addition to the value of the iterative character of PS-Brick for sequential strain engineering, seamless cloning enabled precise in-frame fusion for codon saturation mutagenesis and bicistronic design, and the repetitive sequence cloning ability of PS-Brick enabled construction of tandem CRISPR sgRNA arrays for genome editing. Moreover, the heterologous pathway deriving 1-propanol pathway from threonine, composed of Lactococcus lactis kivD and Saccharomyces cerevisiae ADH2, was assembled by one cycle of PS-Brick, resulting in 1.35 g/L 1-propanol in fed-batch fermentation. CONCLUSIONS To the best of our knowledge, the PS-Brick framework is the first RE-assisted DNA assembly method using the strengths of both Type IIP and IIS REs. In this study, PS-Brick was demonstrated to be an efficient DNA assembly method for pathway construction and genome editing and was successfully applied in design-build-test-learn (DBTL) cycles of metabolic engineering for the production of threonine and threonine-derived 1-propanol. The PS-Brick presents a valuable addition to the current toolbox of synthetic biology and metabolic engineering.
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Affiliation(s)
- Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Haihan Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230039 China
| | - Zheng Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhongcai Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Cui Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
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15
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Seamless assembly of DNA parts into functional devices and higher order multi-device systems. PLoS One 2019; 14:e0199653. [PMID: 31251741 PMCID: PMC6599225 DOI: 10.1371/journal.pone.0199653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 06/07/2019] [Indexed: 11/19/2022] Open
Abstract
A new method is introduced allowing seamless assembly of independent, functionally tested, blunt-end double strand nucleic acid parts (DNA fragments not supplied in vectors such as plasmids) into more complex biological devices (e.g. protein expression vectors) and higher order multi-device systems (e.g. biochemical pathways). Individual parts include bacterial selection markers and origins of replication, promoters useful in a variety of species, transcription terminators, shuttle sequences and a variety of “N” and “C” terminal solubility/affinity protein tags. Parts are not subjected to pre-assembly manipulation with nucleic acid modifying enzymes. Instead, they are simply mixed in appropriate pre-defined combinations and concentrations and then seamlessly linked into devices employing a specialized thermostable enzyme blend. Combinatorial assembly of parts is an inherent time-saving feature of the new method, in contrast to hierarchical binary assembly (“one part at a time”) methods. This feature substantially simplifies and speeds optimization of device and system development. The versatility and functionality of the new method was shown by combinatorial assembly of parts into vector devices, one of which optimally expressed protein from a model gene. Also, a four-enzyme biosynthetic pathway system was re-created by combinatorial construction from parts and devices. Concepts discussed in this paper provide synthetic biologists, chemists and bio-engineers with improved and expanded capability to create novel biological molecules and systems.
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16
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Pollak B, Cerda A, Delmans M, Álamos S, Moyano T, West A, Gutiérrez RA, Patron NJ, Federici F, Haseloff J. Loop assembly: a simple and open system for recursive fabrication of DNA circuits. THE NEW PHYTOLOGIST 2019; 222:628-640. [PMID: 30521109 DOI: 10.1111/nph.15625] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 09/20/2018] [Indexed: 06/09/2023]
Abstract
High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing. Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Ariel Cerda
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Mihails Delmans
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Simón Álamos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Tomás Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Anthony West
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Nicola J Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Fernán Federici
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331150, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Millennium Institute for Integrative Biology (iBio), 8331150, Santiago, Chile
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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17
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Kang Z, Ding W, Jin P, Du G, Chen J. DNA Assembly with the DATEL Method. Methods Mol Biol 2018; 1772:421-428. [PMID: 29754243 DOI: 10.1007/978-1-4939-7795-6_24] [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] [Indexed: 06/08/2023]
Abstract
Simple and reliable DNA assembly methods have become a critical technique in synthetic biology. Here, we present a protocol of the recently developed DATEL (scarless and sequence-independent DNA assembly method using thermostable exonuclease and ligase) method for the construction of genetic circuits and biological pathways from multiple DNA parts in one tube. DATEL is expected to be an applicable choice for both manual and automated high-throughput assembly of DNA fragments, which will greatly facilitate the rapid progress of synthetic biology and metabolic engineering.
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Affiliation(s)
- Zhen Kang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China.
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
| | - Wenwen Ding
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Peng Jin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guocheng Du
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu, China
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18
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Zeng F, Zang J, Zhang S, Hao Z, Dong J, Lin Y. AFEAP cloning: a precise and efficient method for large DNA sequence assembly. BMC Biotechnol 2017; 17:81. [PMID: 29137618 PMCID: PMC5686892 DOI: 10.1186/s12896-017-0394-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
Background Recent development of DNA assembly technologies has spurred myriad advances in synthetic biology, but new tools are always required for complicated scenarios. Here, we have developed an alternative DNA assembly method named AFEAP cloning (Assembly of Fragment Ends After PCR), which allows scarless, modular, and reliable construction of biological pathways and circuits from basic genetic parts. Methods The AFEAP method requires two-round of PCRs followed by ligation of the sticky ends of DNA fragments. The first PCR yields linear DNA fragments and is followed by a second asymmetric (one primer) PCR and subsequent annealing that inserts overlapping overhangs at both sides of each DNA fragment. The overlapping overhangs of the neighboring DNA fragments annealed and the nick was sealed by T4 DNA ligase, followed by bacterial transformation to yield the desired plasmids. Results We characterized the capability and limitations of new developed AFEAP cloning and demonstrated its application to assemble DNA with varying scenarios. Under the optimized conditions, AFEAP cloning allows assembly of an 8 kb plasmid from 1-13 fragments with high accuracy (between 80 and 100%), and 8.0, 11.6, 19.6, 28, and 35.6 kb plasmids from five fragments at 91.67, 91.67, 88.33, 86.33, and 81.67% fidelity, respectively. AFEAP cloning also is capable to construct bacterial artificial chromosome (BAC, 200 kb) with a fidelity of 46.7%. Conclusions AFEAP cloning provides a powerful, efficient, seamless, and sequence-independent DNA assembly tool for multiple fragments up to 13 and large DNA up to 200 kb that expands synthetic biologist’s toolbox. Electronic supplementary material The online version of this article (doi: 10.1186/s12896-017-0394-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Jinping Zang
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Suhua Zhang
- Institute of Biophysics, Hebei University of Technology, Tianjin, 300401, People's Republic of China
| | - Zhimin Hao
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Jingao Dong
- College of Life Sciences, Hebei Agricultural University, Baoding, 071001, People's Republic of China.
| | - Yibin Lin
- McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, 77030, USA.
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19
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Ding W, Weng H, Jin P, Du G, Chen J, Kang Z. Scarless assembly of unphosphorylated DNA fragments with a simplified DATEL method. Bioengineered 2017; 8:296-301. [PMID: 28384080 DOI: 10.1080/21655979.2017.1308986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Efficient assembly of multiple DNA fragments is a pivotal technology for synthetic biology. A scarless and sequence-independent DNA assembly method (DATEL) using thermal exonucleases has been developed recently. Here, we present a simplified DATEL (sDATEL) for efficient assembly of unphosphorylated DNA fragments with low cost. The sDATEL method is only dependent on Taq DNA polymerase and Taq DNA ligase. After optimizing the committed parameters of the reaction system such as pH and the concentration of Mg2+ and NAD+, the assembly efficiency was increased by 32-fold. To further improve the assembly capacity, the number of thermal cycles was optimized, resulting in successful assembly 4 unphosphorylated DNA fragments with an accuracy of 75%. sDATEL could be a desirable method for routine manual and automated assembly.
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Affiliation(s)
- Wenwen Ding
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China.,b Synergetic Innovation Center of Food Safety and Nutrition , Jiangnan University, Wuxi, Jiangsu, China Jiangnan University , Wuxi , China
| | - Huanjiao Weng
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China.,b Synergetic Innovation Center of Food Safety and Nutrition , Jiangnan University, Wuxi, Jiangsu, China Jiangnan University , Wuxi , China
| | - Peng Jin
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China.,b Synergetic Innovation Center of Food Safety and Nutrition , Jiangnan University, Wuxi, Jiangsu, China Jiangnan University , Wuxi , China
| | - Guocheng Du
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China.,b Synergetic Innovation Center of Food Safety and Nutrition , Jiangnan University, Wuxi, Jiangsu, China Jiangnan University , Wuxi , China
| | - Jian Chen
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China.,b Synergetic Innovation Center of Food Safety and Nutrition , Jiangnan University, Wuxi, Jiangsu, China Jiangnan University , Wuxi , China
| | - Zhen Kang
- a The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China.,b Synergetic Innovation Center of Food Safety and Nutrition , Jiangnan University, Wuxi, Jiangsu, China Jiangnan University , Wuxi , China.,c The Key Laboratory of Carbohydrate Chemistry and Biotechnology , Ministry of Education, Jiangnan University , Wuxi , P. R. China
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20
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Decoene T, De Paepe B, Maertens J, Coussement P, Peters G, De Maeseneire SL, De Mey M. Standardization in synthetic biology: an engineering discipline coming of age. Crit Rev Biotechnol 2017; 38:647-656. [PMID: 28954542 DOI: 10.1080/07388551.2017.1380600] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. PURPOSE In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. CONCLUSION Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.
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Affiliation(s)
- Thomas Decoene
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Brecht De Paepe
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Jo Maertens
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | | | - Gert Peters
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
| | - Sofie L De Maeseneire
- b InBio.be, Centre for Industrial Biotechnology and Biocatalysis, Ghent University , Ghent , Belgium
| | - Marjan De Mey
- a Centre for Synthetic Biology, Ghent University , Ghent , Belgium
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21
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Recent advances of molecular toolbox construction expand Pichia pastoris in synthetic biology applications. World J Microbiol Biotechnol 2016; 33:19. [PMID: 27905091 DOI: 10.1007/s11274-016-2185-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 11/24/2016] [Indexed: 10/20/2022]
Abstract
Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P. pastoris. Furthermore, the applications of P. pastoris towards synthetic biology were also discussed and prospected especially in the context of genome-scale metabolic pathway analysis.
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