1
|
Nam H, Kim T, Moon S, Ji Y, Lee JB. Self-assembly of a multimeric genomic hydrogel via multi-primed chain reaction of dual single-stranded circular plasmids for cell-free protein production. iScience 2023; 26:107089. [PMID: 37416467 PMCID: PMC10319821 DOI: 10.1016/j.isci.2023.107089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/20/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
Recent technical advances in cell-free protein synthesis (CFPS) offer several advantages over cell-based expression systems, including the application of cellular machinery, such as transcription and translation, in the test tube. Inspired by the advantages of CFPS, we have fabricated a multimeric genomic DNA hydrogel (mGD-gel) via rolling circle chain amplification (RCCA) using dual single-stranded circular plasmids with multiple primers. The mGD-gel exhibited significantly enhanced protein yield. In addition, mGD-gel can be reused at least five times, and the shape of the mGD-gel can be easily manipulated without losing the feasibility of protein expression. The mGD-gel platform based on the self-assembly of multimeric genomic DNA strands (mGD strands) has the potential to be used in CFPS systems for a variety of biotechnological applications.
Collapse
Affiliation(s)
- Hyangsu Nam
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Taehyeon Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Sunghyun Moon
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Yoonbin Ji
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, Republic of Korea
| |
Collapse
|
2
|
Shi J, Oger PM, Cao P, Zhang L. Thermostable DNA ligases from hyperthermophiles in biotechnology. Front Microbiol 2023; 14:1198784. [PMID: 37293226 PMCID: PMC10244674 DOI: 10.3389/fmicb.2023.1198784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
DNA ligase is an important enzyme ubiquitous in all three kingdoms of life that can ligate DNA strands, thus playing essential roles in DNA replication, repair and recombination in vivo. In vitro, DNA ligase is also used in biotechnological applications requiring in DNA manipulation, including molecular cloning, mutation detection, DNA assembly, DNA sequencing, and other aspects. Thermophilic and thermostable enzymes from hyperthermophiles that thrive in the high-temperature (above 80°C) environments have provided an important pool of useful enzymes as biotechnological reagents. Similar to other organisms, each hyperthermophile harbors at least one DNA ligase. In this review, we summarize recent progress on structural and biochemical properties of thermostable DNA ligases from hyperthermophiles, focusing on similarities and differences between DNA ligases from hyperthermophilic bacteria and archaea, and between these thermostable DNA ligases and non-thermostable homologs. Additionally, altered thermostable DNA ligases are discussed. Possessing improved fidelity or thermostability compared to the wild-type enzymes, they could be potential DNA ligases for biotechnology in the future. Importantly, we also describe current applications of thermostable DNA ligases from hyperthermophiles in biotechnology.
Collapse
Affiliation(s)
- Jingru Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Philippe M. Oger
- University of Lyon, INSA de Lyon, CNRS UMR, Villeurbanne, France
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| |
Collapse
|
3
|
Shao W, Ma K, Le Y, Wang H, Sha C. Development and Use of a Novel Random Mutagenesis Method: In Situ Error-Prone PCR (is-epPCR). Methods Mol Biol 2017; 1498:497-506. [PMID: 27709598 DOI: 10.1007/978-1-4939-6472-7_34] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Directed evolution methods are increasingly needed to improve gene and protein properties. Error-prone PCR is the most efficient method to introduce random mutations by reducing the fidelity of the DNA polymerase. However, a highly efficient process is required for constructing and screening a diverse mutagenesis library since a large pool of transformants is needed to generate a desired mutant. We developed a method called in situ error-prone PCR (is-epPCR) to improve the efficiency of constructing a mutation library for directed evolution. This method offers the following advantages: (1) closed-circular PCR products can be directly transformed into competent E. coli cells and easily selected by using an alternative antibiotic; (2) a mutant library can be created and screened by one-step error-prone amplification of a variable DNA region in an expression plasmid; and (3) accumulation of desired mutations in one sequence can be obtained by multiple rounds of is-epPCR. Is-epPCR offers a novel, convenient, and efficient approach for improving genes and proteins through directed evolution.
Collapse
Affiliation(s)
- Weilan Shao
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Kesen Ma
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Yilin Le
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Hongcheng Wang
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Chong Sha
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| |
Collapse
|
4
|
Kumar S, Arumugam N, Permaul K, Singh S. Chapter 5 Thermostable Enzymes and Their Industrial Applications. Microb Biotechnol 2016. [DOI: 10.1201/9781315367880-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
|
5
|
Pezeshgi Modarres H, Dorokhov BD, Popov VO, Ravin NV, Skryabin KG, Dal Peraro M. Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp. 1519. Biochemistry 2015; 54:3076-85. [DOI: 10.1021/bi501227b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hassan Pezeshgi Modarres
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Boris D. Dorokhov
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
| | - Vladimir O. Popov
- Bach
Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia
- RSC “Kurchatov Institute”, Moscow 123182, Russia
| | - Nikolai V. Ravin
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
| | - Konstantin G. Skryabin
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
- RSC “Kurchatov Institute”, Moscow 123182, Russia
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| |
Collapse
|
6
|
Killelea T, Ralec C, Bossé A, Henneke G. PCR performance of a thermostable heterodimeric archaeal DNA polymerase. Front Microbiol 2014; 5:195. [PMID: 24847315 PMCID: PMC4019886 DOI: 10.3389/fmicb.2014.00195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/12/2014] [Indexed: 11/17/2022] Open
Abstract
DNA polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (PCR), cDNA cloning, genome sequencing, and nucleic acid based diagnostics. Taking into account the multiple DNA amplification techniques in use, different DNA polymerases must be optimized for each type of application. One of the current tendencies is to reengineer or to discover new DNA polymerases with increased performance and broadened substrate spectra. At present, there is a great demand for such enzymes in applications, e.g., forensics or paleogenomics. Current major limitations hinge on the inability of conventional PCR enzymes, such as Taq, to amplify degraded or low amounts of template DNA. Besides, a wide range of PCR inhibitors can also impede reactions of nucleic acid amplification. Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. Proficient proof-reading Pab-polD enzyme could also extend a primer containing up to two mismatches at the 3' primer termini. Overall, we found valuable biochemical properties in Pab-polD compared to the conventional Taq, which makes the enzyme ideally suited for cutting-edge PCR-applications.
Collapse
Affiliation(s)
- Tom Killelea
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Céline Ralec
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Audrey Bossé
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| | - Ghislaine Henneke
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France ; CNRS, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes Plouzané, France
| |
Collapse
|
7
|
Tee KL, Wong TS. Polishing the craft of genetic diversity creation in directed evolution. Biotechnol Adv 2013; 31:1707-21. [PMID: 24012599 DOI: 10.1016/j.biotechadv.2013.08.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/31/2013] [Accepted: 08/31/2013] [Indexed: 12/25/2022]
Abstract
Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.
Collapse
Affiliation(s)
- Kang Lan Tee
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, England, United Kingdom
| | | |
Collapse
|