Systematic functional comparative analysis of four single-stranded DNA-binding proteins and their affection on viral RNA metabolism

Haiyan Shi; Yonghui Zhang; Guohui Zhang; Jinlei Guo; Xun Zhang; Haiyan Song; Jianxin Lv; Jimin Gao; Yuepeng Wang; Litian Chen; Yue Wang

doi:10.1371/journal.pone.0055076

Systematic functional comparative analysis of four single-stranded DNA-binding proteins and their affection on viral RNA metabolism

PLoS One. 2013;8(1):e55076. doi: 10.1371/journal.pone.0055076. Epub 2013 Jan 24.

Authors

Haiyan Shi¹, Yonghui Zhang, Guohui Zhang, Jinlei Guo, Xun Zhang, Haiyan Song, Jianxin Lv, Jimin Gao, Yuepeng Wang, Litian Chen, Yue Wang

Affiliation

¹ National Institute for Viral Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China.

Abstract

The accumulation of single-stranded DNA-binding (SSB) proteins is essential for organisms and has various applications. However, no study has simultaneously and systematically compared the characteristics of SSB proteins. In addition, SSB proteins may bind RNA and play an unknown biological role in RNA metabolism. Here, we expressed a novel species of SSB protein derived from Thermococcus kodakarensis KOD1 (KOD), as well as SSB proteins from Thermus thermophilus (TTH), Escherichia coli, and Sulfolobus Solfataricus P2 (SSOB), abbreviated kod, tth, bl21, and ssob, respectively. These SSB proteins could bind ssDNA and viral RNA. bl21 resisted heat treatment for more than 9 h, Ssob and kod could withstand 95°C for 10 h and retain its ssDNA- and RNA-binding ability. Four SSB proteins promoted the specificity of the DNA polymerase in PCR-based 5- and 9-kb genome fragment amplification. kod also increased the amplification of a 13-kb PCR product, and SSB protein-bound RNA resisted Benzonase digestion. The SSB proteins could also enter the host cell bound to RNA, which resulted in modulation of viral RNA metabolism, particularly ssob and bl21.

Publication types

Comparative Study
Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / genetics
Bacterial Proteins / metabolism*
Bacterial Proteins / pharmacology
Cell Line, Tumor
DNA, Single-Stranded / chemistry*
DNA, Single-Stranded / genetics
DNA, Single-Stranded / metabolism
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism*
DNA-Binding Proteins / pharmacology
Endodeoxyribonucleases
Endoribonucleases
Escherichia coli / chemistry*
Hepacivirus / drug effects*
Hepacivirus / metabolism
Hepatocytes / drug effects
Hepatocytes / virology
Hot Temperature
Humans
Protein Binding
Protein Stability
RNA, Viral / chemistry*
RNA, Viral / genetics
RNA, Viral / metabolism
Recombinant Proteins / genetics
Recombinant Proteins / metabolism
Recombinant Proteins / pharmacology
Sulfolobus solfataricus / chemistry
Thermococcus / chemistry
Thermus thermophilus / chemistry

Substances

Bacterial Proteins
DNA, Single-Stranded
DNA-Binding Proteins
RNA, Viral
Recombinant Proteins
Endodeoxyribonucleases
Endoribonucleases
Serratia marcescens nuclease

Grants and funding

This work was supported by the Natural Science Foundation of Zhejiang Province (Y2101159). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.