1
|
Zhang J, Wang Y, Chai B, Wang J, Li L, Liu M, Zhao G, Yao L, Gao X, Yin Y, Xu J. Efficient and Low-Cost Error Removal in DNA Synthesis by a High-Durability MutS. ACS Synth Biol 2020; 9:940-952. [PMID: 32135061 DOI: 10.1021/acssynbio.0c00079] [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] [Indexed: 02/08/2023]
Abstract
Enzyme-based error correction is a key step in de novo DNA synthesis, yet the inherent instability of error-correction enzymes such as MutS has hindered the throughput and efficiency of DNA synthesis workflows. Here we introduce a process called Improved MICC (iMICC), in which all error-correction steps of oligos and fragments within a complete gene-synthesis cycle are completed in a simple, efficient, and low-cost manner via a MutS protein engineered for high durability. By establishing a disulfide bond of L157C-G233C, full-activity shelf life of E. coli MutS (eMutS) was prolonged from 7 to 49 days and was further extended to 63 days via cellulose-bound 4 °C storage. In synthesis of 10 Cas9 homologues in-solution and 10 xylose reductase (XR) homologues on-chip, iMICC reduced error frequency to 0.64/Kb and 0.41/Kb, respectively, with 72.1% and 86.4% of assembled fragments being error-free. By elevating base accuracy by 37.6-fold while avoiding repetitive preparation of fresh enzymes, iMICC is more efficient and robust than the wild-type eMutS, and it is 6.6-fold more accurate and 26.7-fold cheaper than CorrectASE. These advantages promise its broad applications in industrial DNA synthesis.
Collapse
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, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yefei Wang
- 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 266101, China
| | - Baihui Chai
- 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, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichao Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Li
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
| | - Min Liu
- 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, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishan Yao
- 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 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolian Gao
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004-5001, United States
| | - Yifeng Yin
- 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, Shandong 266101, 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, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
2
|
Chong SL, Cardoso V, Brás JLA, Gomes MZDV, Fontes CMGA, Olsson L. Immobilization of bacterial feruloyl esterase on mesoporous silica particles and enhancement of synthetic activity by hydrophobic-modified surface. BIORESOURCE TECHNOLOGY 2019; 293:122009. [PMID: 31493730 DOI: 10.1016/j.biortech.2019.122009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
Here, we demonstrated the immobilization of bacterial feruloyl esterase (FAE) from Butyrivibrio sp. XPD2006, Lactobacillus crispatus, Butyrivibrio sp. AE2015, Ruminococcus albus, Cellulosilyticum ruminicola and Clostridium cellulovorans on SBA-15 and their ability to synthesize butyl ferulate (BFA). The BFae2 from Butyrivibrio sp. XPD2006 showed the best catalytic efficiency. High BFA yield was produced when the immobilization of BFae2 took place with a high protein loading and narrow pore sized SBA-15, suggesting alteration of enzyme behavior due to the crowding environment in SBA-15. Grafting of SBA-15 with octyl moieties led to shrinking pore size and resulted in 2.5-fold increment of BFA activity compared to the free enzyme and 70%mol BFA was achieved. The BFae2 encapsulated in hydrophobic-modified SBA-15 endured up to seven reaction cycles while the BFA activity remained above 60%. This is the first report showing the superior performance of hydrophobic-modified surface to entrap FAE to produce fatty phenolic esters.
Collapse
Affiliation(s)
- Sun Li Chong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300 Hangzhou, China; Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Vânia Cardoso
- NZYTech Genes & Enzymes, Campus do Lumiar, 1649-038 Lisbon, Portugal; CIISA - Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal
| | - Joana L A Brás
- NZYTech Genes & Enzymes, Campus do Lumiar, 1649-038 Lisbon, Portugal
| | - Milene Zezzi do Valle Gomes
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Applied Chemistry, SE 412 96 Gothenburg, Sweden
| | - Carlos M G A Fontes
- NZYTech Genes & Enzymes, Campus do Lumiar, 1649-038 Lisbon, Portugal; CIISA - Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal
| | - Lisbeth Olsson
- Chalmers University of Technology, Department of Biology and Biological Engineering, Division of Industrial Biotechnology, Kemivägen 10, SE-412 96 Göteborg, Sweden.
| |
Collapse
|
3
|
Shevelev GY, Pyshnyi DV. Modern approaches to artificial gene synthesis: aspects of oligonucleotide synthesis, enzymatic assembly, sequence verification and error correction. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
4
|
Khilko Y, Weyman PD, Glass JI, Adams MD, McNeil MA, Griffin PB. DNA assembly with error correction on a droplet digital microfluidics platform. BMC Biotechnol 2018; 18:37. [PMID: 29859085 PMCID: PMC5984785 DOI: 10.1186/s12896-018-0439-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 04/24/2018] [Indexed: 12/02/2022] Open
Abstract
Background Custom synthesized DNA is in high demand for synthetic biology applications. However, current technologies to produce these sequences using assembly from DNA oligonucleotides are costly and labor-intensive. The automation and reduced sample volumes afforded by microfluidic technologies could significantly decrease materials and labor costs associated with DNA synthesis. The purpose of this study was to develop a gene assembly protocol utilizing a digital microfluidic device. Toward this goal, we adapted bench-scale oligonucleotide assembly methods followed by enzymatic error correction to the Mondrian™ digital microfluidic platform. Results We optimized Gibson assembly, polymerase chain reaction (PCR), and enzymatic error correction reactions in a single protocol to assemble 12 oligonucleotides into a 339-bp double- stranded DNA sequence encoding part of the human influenza virus hemagglutinin (HA) gene. The reactions were scaled down to 0.6-1.2 μL. Initial microfluidic assembly methods were successful and had an error frequency of approximately 4 errors/kb with errors originating from the original oligonucleotide synthesis. Relative to conventional benchtop procedures, PCR optimization required additional amounts of MgCl2, Phusion polymerase, and PEG 8000 to achieve amplification of the assembly and error correction products. After one round of error correction, error frequency was reduced to an average of 1.8 errors kb− 1. Conclusion We demonstrated that DNA assembly from oligonucleotides and error correction could be completely automated on a digital microfluidic (DMF) platform. The results demonstrate that enzymatic reactions in droplets show a strong dependence on surface interactions, and successful on-chip implementation required supplementation with surfactants, molecular crowding agents, and an excess of enzyme. Enzymatic error correction of assembled fragments improved sequence fidelity by 2-fold, which was a significant improvement but somewhat lower than expected compared to bench-top assays, suggesting an additional capacity for optimization. Electronic supplementary material The online version of this article (10.1186/s12896-018-0439-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yuliya Khilko
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, CA, 94304, USA.,Department of Biomedical, Chemical and Materials Engineering, San Jose State University, 1 Washington Sq, San Jose, CA, 95192, USA
| | - Philip D Weyman
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - John I Glass
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Mark D Adams
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Melanie A McNeil
- Department of Biomedical, Chemical and Materials Engineering, San Jose State University, 1 Washington Sq, San Jose, CA, 95192, USA
| | - Peter B Griffin
- Stanford Genome Technology Center, Stanford University, 3165 Porter Drive, Palo Alto, CA, 94304, USA.
| |
Collapse
|
5
|
Sequeira AF, Brás JLA, Fernandes VO, Guerreiro CIPD, Vincentelli R, Fontes CMGA. A Novel Platform for High-Throughput Gene Synthesis to Maximize Recombinant Expression in Escherichia coli. Methods Mol Biol 2018; 1620:113-128. [PMID: 28540703 DOI: 10.1007/978-1-4939-7060-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. Here, we describe a high-throughput platform to design and produce multiple synthetic genes (<500 bp) for recombinant expression in Escherichia coli. This pipeline includes an innovative codon optimization algorithm that designs DNA sequences to maximize heterologous protein production in different hosts. The platform is based on a simple gene synthesis method that uses a PCR-based protocol to assemble synthetic DNA from pools of overlapping oligonucleotides. This technology incorporates an accurate, automated and cost-effective ligase-independent cloning step to directly integrate the synthetic genes into an effective E. coli expression vector. High-throughput production of synthetic genes is of increasing relevance to allow exploring the biological function of the extensive genomic and meta-genomic information currently available from various sources.
Collapse
Affiliation(s)
- Ana Filipa Sequeira
- Faculdade de Medicina Veterinária, Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA), Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal. .,NZYTech Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E, r/c, 1649-038, Lisbon, Portugal.
| | - Joana L A Brás
- Faculdade de Medicina Veterinária, Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA), Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal.,NZYTech Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E, r/c, 1649-038, Lisbon, Portugal
| | - Vânia O Fernandes
- Faculdade de Medicina Veterinária, Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA), Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal.,NZYTech Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E, r/c, 1649-038, Lisbon, Portugal
| | - Catarina I P D Guerreiro
- NZYTech Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E, r/c, 1649-038, Lisbon, Portugal
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS) - Aix-Marseille Université, Campus de Luminy, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Carlos M G A Fontes
- Faculdade de Medicina Veterinária, Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA), Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Lisbon, Portugal.,NZYTech Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E, r/c, 1649-038, Lisbon, Portugal
| |
Collapse
|
6
|
Lubock NB, Zhang D, Sidore AM, Church GM, Kosuri S. A systematic comparison of error correction enzymes by next-generation sequencing. Nucleic Acids Res 2017; 45:9206-9217. [PMID: 28911123 PMCID: PMC5587813 DOI: 10.1093/nar/gkx691] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/14/2017] [Accepted: 07/31/2017] [Indexed: 11/13/2022] Open
Abstract
Gene synthesis, the process of assembling gene-length fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared six different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.
Collapse
Affiliation(s)
- Nathan B. Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Di Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Angus M. Sidore
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
7
|
Pires VMR, Pereira PMM, Brás JLA, Correia M, Cardoso V, Bule P, Alves VD, Najmudin S, Venditto I, Ferreira LMA, Romão MJ, Carvalho AL, Fontes CMGA, Prazeres DM. Stability and Ligand Promiscuity of Type A Carbohydrate-binding Modules Are Illustrated by the Structure of Spirochaeta thermophila StCBM64C. J Biol Chem 2017; 292:4847-4860. [PMID: 28179427 DOI: 10.1074/jbc.m116.767541] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/07/2017] [Indexed: 11/06/2022] Open
Abstract
Deconstruction of cellulose, the most abundant plant cell wall polysaccharide, requires the cooperative activity of a large repertoire of microbial enzymes. Modular cellulases contain non-catalytic type A carbohydrate-binding modules (CBMs) that specifically bind to the crystalline regions of cellulose, thus promoting enzyme efficacy through proximity and targeting effects. Although type A CBMs play a critical role in cellulose recycling, their mechanism of action remains poorly understood. Here we produced a library of recombinant CBMs representative of the known diversity of type A modules. The binding properties of 40 CBMs, in fusion with an N-terminal GFP domain, revealed that type A CBMs possess the ability to recognize different crystalline forms of cellulose and chitin over a wide range of temperatures, pH levels, and ionic strengths. A Spirochaeta thermophila CBM64, in particular, displayed plasticity in its capacity to bind both crystalline and soluble carbohydrates under a wide range of extreme conditions. The structure of S. thermophila StCBM64C revealed an untwisted, flat, carbohydrate-binding interface comprising the side chains of four tryptophan residues in a co-planar linear arrangement. Significantly, two highly conserved asparagine side chains, each one located between two tryptophan residues, are critical to insoluble and soluble glucan recognition but not to bind xyloglucan. Thus, CBM64 compact structure and its extended and versatile ligand interacting platform illustrate how type A CBMs target their appended plant cell wall-degrading enzymes to a diversity of recalcitrant carbohydrates under a wide range of environmental conditions.
Collapse
Affiliation(s)
- Virgínia M R Pires
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Pedro M M Pereira
- the Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Joana L A Brás
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Márcia Correia
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Vânia Cardoso
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Pedro Bule
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Victor D Alves
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Shabir Najmudin
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Immacolata Venditto
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal
| | - Luís M A Ferreira
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal.,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Maria João Romão
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Luísa Carvalho
- the UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carlos M G A Fontes
- From the CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Pólo Universitário da Ajuda, 1300-477 Lisboa, Portugal, .,NZYTech Genes Enzymes, 1649-038 Lisboa, Portugal, and
| | - Duarte Miguel Prazeres
- the Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal,
| |
Collapse
|