A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea
The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA bin...
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MDPI AG
2022-03-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/7/3455 |
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| author | Can Huang Xuehui Liu Yuanyuan Chen Junshi Zhou Wenqian Li Niannian Ding Li Huang Jingyu Chen Zhenfeng Zhang |
| author_facet | Can Huang Xuehui Liu Yuanyuan Chen Junshi Zhou Wenqian Li Niannian Ding Li Huang Jingyu Chen Zhenfeng Zhang |
| author_sort | Can Huang |
| collection | DOAJ |
| description | The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in <i>Sulfolobaceae</i>. Sul7s from <i>Sulfolobus islandicus</i> binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)<sub>30</sub> over oligo(dC)<sub>30</sub> or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)<sub>30</sub>. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution. |
| first_indexed | 2024-03-09T11:49:32Z |
| format | Article |
| id | doaj.art-77fb54e3693b47b7a31eb878148f675f |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T11:49:32Z |
| publishDate | 2022-03-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-77fb54e3693b47b7a31eb878148f675f2023-11-30T23:17:09ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-03-01237345510.3390/ijms23073455A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from ArchaeaCan Huang0Xuehui Liu1Yuanyuan Chen2Junshi Zhou3Wenqian Li4Niannian Ding5Li Huang6Jingyu Chen7Zhenfeng Zhang8MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaThe Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, ChinaThe Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, ChinaState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, ChinaMOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, ChinaState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, ChinaMOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, ChinaState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, ChinaThe winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in <i>Sulfolobaceae</i>. Sul7s from <i>Sulfolobus islandicus</i> binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)<sub>30</sub> over oligo(dC)<sub>30</sub> or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)<sub>30</sub>. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution.https://www.mdpi.com/1422-0067/23/7/3455winged-helix proteinsingle-stranded DNA-binding proteinhyperthermophilic archaeaNMR |
| spellingShingle | Can Huang Xuehui Liu Yuanyuan Chen Junshi Zhou Wenqian Li Niannian Ding Li Huang Jingyu Chen Zhenfeng Zhang A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea International Journal of Molecular Sciences winged-helix protein single-stranded DNA-binding protein hyperthermophilic archaea NMR |
| title | A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea |
| title_full | A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea |
| title_fullStr | A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea |
| title_full_unstemmed | A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea |
| title_short | A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea |
| title_sort | novel family of winged helix single stranded dna binding proteins from archaea |
| topic | winged-helix protein single-stranded DNA-binding protein hyperthermophilic archaea NMR |
| url | https://www.mdpi.com/1422-0067/23/7/3455 |
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