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Zhang J, Su X, Wang Y, Wang X, Zhou S, Jia H, Jing X, Gong Y, Wang J, Xu J. Improved single-cell genome amplification by a high-efficiency phi29 DNA polymerase. Front Bioeng Biotechnol 2023; 11:1233856. [PMID: 37456715 PMCID: PMC10347390 DOI: 10.3389/fbioe.2023.1233856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Single-cell genomic whole genome amplification (WGA) is a crucial step in single-cell sequencing, yet its low amplification efficiency, incomplete and uneven genome amplification still hinder the throughput and efficiency of single-cell sequencing workflows. Here we introduce a process called Improved Single-cell Genome Amplification (iSGA), in which the whole single-cell sequencing cycle is completed in a high-efficient and high-coverage manner, through phi29 DNA polymerase engineering and process engineering. By establishing a disulfide bond of F137C-A377C, the amplification ability of the enzyme was improved to that of single-cell. By further protein engineering and process engineering, a supreme enzyme named HotJa Phi29 DNA Polymerase was developed and showed significantly better coverage (99.75%) at a higher temperature (40°C). High single-cell genome amplification ability and high coverage (93.59%) were also achieved for commercial probiotic samples. iSGA is more efficient and robust than the wild-type phi29 DNA polymerase, and it is 2.03-fold more efficient and 10.89-fold cheaper than the commercial Thermo Scientific EquiPhi29 DNA Polymerase. These advantages promise its broad applications in large-scale single-cell sequencing.
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Affiliation(s)
- Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolu Su
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yefei Wang
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Xiaohang Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shiqi Zhou
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Jia
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jichao Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
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Zhang J, Xu T, Wang X, Jing X, Zhang J, Hong J, Xu J, Wang J. Lignocellulosic xylitol production from corncob using engineered Kluyveromycesmarxianus. Front Bioeng Biotechnol 2022; 10:1029203. [PMID: 36338133 PMCID: PMC9633946 DOI: 10.3389/fbioe.2022.1029203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/07/2022] [Indexed: 11/21/2022] Open
Abstract
Xylitol production from lignocellulose hydrolysate is a sustainable and environment-friendly process. In this study, a systematic process of converting corncob waste into xylitol is described. First, the corncobs are hydrolyzed with acid to a hydrolysate. Second, Kluyveromyces marxianus YZJQ016 derived from K. marxianus YZJ074, constructed by overexpressing ScGAL2-N376F from Saccharomyces cerevisiae, CtXYL1 from Candida tropicalis, and KmZWF1 from K. marxianus, produces xylitol from the hydrolysate. A total of ten xylose reductase genes were evaluated, and CtXYL1 proved best by showing the highest catalytic activity under the control of the KmGAPDH promoter. A 5 L fermenter at 42°C produced 105.22 g/L xylitol using K. marxianus YZJQ016—the highest production reported to date from corncob hydrolysate. Finally, for crystallization of the xylitol, the best conditions were 50% (v/v) methanol as an antisolvent, at 25°C, with purity and yield of 99%–100% and 74%, respectively—the highest yield reported to date.
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Affiliation(s)
- Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohang Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jichao Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Jichao Wang,
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Choi H, Choi Y, Choi J, Lee AC, Yeom H, Hyun J, Ryu T, Kwon S. Purification of multiplex oligonucleotide libraries by synthesis and selection. Nat Biotechnol 2022; 40:47-53. [PMID: 34326548 DOI: 10.1038/s41587-021-00988-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023]
Abstract
Complex oligonucleotide (oligo) libraries are essential materials for diverse applications in synthetic biology, pharmaceutical production, nanotechnology and DNA-based data storage. However, the error rates in synthesizing complex oligo libraries can be substantial, leading to increment in cost and labor for the applications. As most synthesis errors arise from faulty insertions and deletions, we developed a length-based method with single-base resolution for purification of complex libraries containing oligos of identical or different lengths. Our method-purification of multiplex oligonucleotide libraries by synthesis and selection-can be performed either step-by-step manually or using a next-generation sequencer. When applied to a digital data-encoded library containing oligos of identical length, the method increased the purity of full-length oligos from 83% to 97%. We also show that libraries encoding the complementarity-determining region H3 with three different lengths (with an empirically achieved diversity >106) can be simultaneously purified in one pot, increasing the in-frame oligo fraction from 49.6% to 83.5%.
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Affiliation(s)
- Hansol Choi
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yeongjae Choi
- Nano Systems Institute, Seoul National University, Seoul, Republic of Korea.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Jaewon Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.,Integrated Major in Innovative Medical Science, Seoul National University, Seoul, Republic of Korea
| | - Amos Chungwon Lee
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Huiran Yeom
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Jinwoo Hyun
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea. .,Nano Systems Institute, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea. .,Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea.
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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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