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Sun Y, Ko DH, Gao J, Fu K, Gao Y, Zhang Q, Baldi S, Hong T, Ivanov I, He Y, Tian H. Unraveling the salt tolerance of Phi29 DNA polymerase using compartmentalized self-replication and microfluidics platform. Front Microbiol 2023; 14:1267196. [PMID: 38029082 PMCID: PMC10661337 DOI: 10.3389/fmicb.2023.1267196] [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: 07/26/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
In Phi29-α-hemolysin (α-HL) nanopore sequencing systems, a strong electrochemical signal is dependent on a high concentration of salt. However, high salt concentrations adversely affect polymerase activity. Sequencing by synthesis (SBS) requires the use of phi29 polymerase without exonuclease activity to prevent the degradation of modified nucleotide tags; however, the lack of exonuclease activity also affects polymerase processivity. This study aimed to optimize phi29 polymerase for improved salt tolerance and processivity while maintaining its lack of exonuclease activity to meet the requirements of nanopore sequencing. Using salt tolerance compartmentalized self-replication (stCSR) and a microfluidic platform, we obtained 11 mutant sites with enhanced salt tolerance attributes. Sequencing and biochemical analyses revealed that the substitution of conserved amino acids such as G197D, Y369E, T372N, and I378R plays a critical role in maintaining the processivity of exonuclease-deficient phi29 polymerase under high salt conditions. Furthermore, Y369E and T372N have been identified as important determinants of DNA polymerase binding affinity. This study provides insights into optimizing polymerase processability under high-salt conditions for real-time polymerase nanopore sequencing, paving the way for improved performance and applications in nanopore sequencing technologies.
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Affiliation(s)
- Yaping Sun
- Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Danny Hsu Ko
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Jie Gao
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Kang Fu
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Yaping Gao
- Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Qiwen Zhang
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Salem Baldi
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Tao Hong
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Igor Ivanov
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
| | - Yun He
- Research Center of Molecular Diagnostics and Sequencing, Research Institute of Tsinghua University in Shenzhen, Shenzhen, China
| | - Hui Tian
- Research Center of Molecular Diagnostics and Sequencing, Axbio Biotechnology (Shenzhen) Co., Ltd., Shenzhen, China
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Gao Y, He Y, Chen L, Liu X, Ivanov I, Yang X, Tian H. Chimeric Phi29 DNA polymerase with helix-hairpin-helix motifs shows enhanced salt tolerance and replication performance. Microb Biotechnol 2021; 14:1642-1656. [PMID: 34009743 PMCID: PMC8313265 DOI: 10.1111/1751-7915.13830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 11/29/2022] Open
Abstract
Phi29 DNA polymerase (Phi29 Pol) has been successfully applied in DNA nanoball-based sequencing, real-time DNA sequencing from single polymerase molecules and nanopore sequencing employing the sequencing by synthesis (SBS) method. Among these, polymerase-assisted nanopore sequencing technology analyses nucleotide sequences as a function of changes in electrical current. This ionic, current-based sequencing technology requires polymerases to perform replication at high salt concentrations, for example 0.3 M KCl. Nonetheless, the salt tolerance of wild-type Phi29 Pol is relatively low. Here, we fused helix-hairpin-helix (HhH)2 domains E-L (eight repeats in total) of topoisomerase V (Topo V) from the hyperthermophile Methanopyrus kandleri to the Phi29 Pol COOH terminus, designated Phi29EL DNA polymerase (Phi29EL Pol). Domain fusion increased the overall enzyme replication efficiency by fourfold. Phi29EL Pol catalysed rolling circle replication in a broader range of salt concentrations than did Phi29 Pol, extending the KCl concentration range for activity up to 0.3 M. In addition, the mutation of Glu375 to Ser or Gln increased Phi29EL Pol activity in the presence of KCl. In this work, we produced a salt-tolerant Phi29 Pol derivative by means of (HhH)2 domain insertion. The multiple advantages of this insertion make it a good substitute for Phi29 Pol, especially for use in nanopore sequencing or other circumstances that require high salt concentrations.
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Affiliation(s)
- Yaping Gao
- Research Center of Molecular Diagnostics and SequencingResearch Institute of Tsinghua University in ShenzhenShenzhenGuangdong518057China
| | - Yun He
- Research Center of Molecular Diagnostics and SequencingResearch Institute of Tsinghua University in ShenzhenShenzhenGuangdong518057China
| | - Liyi Chen
- Research Center of Molecular Diagnostics and SequencingResearch Institute of Tsinghua University in ShenzhenShenzhenGuangdong518057China
| | - Xing Liu
- Research Center of Molecular Diagnostics and SequencingResearch Institute of Tsinghua University in ShenzhenShenzhenGuangdong518057China
| | - Igor Ivanov
- Research Center of Molecular Diagnostics and SequencingResearch Institute of Tsinghua University in ShenzhenShenzhenGuangdong518057China
| | - Xuerui Yang
- MOE Key Lab of BioinformaticsSchool of Life SciencesTsinghua UniversityBeijing100101China
| | - Hui Tian
- Research Center of Molecular Diagnostics and SequencingResearch Institute of Tsinghua University in ShenzhenShenzhenGuangdong518057China
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