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Kalichuk V, Béhar G, Renodon-Cornière A, Danovski G, Obal G, Barbet J, Mouratou B, Pecorari F. The archaeal "7 kDa DNA-binding" proteins: extended characterization of an old gifted family. Sci Rep 2016; 6:37274. [PMID: 27853299 PMCID: PMC5112516 DOI: 10.1038/srep37274] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/27/2016] [Indexed: 01/06/2023] Open
Abstract
The “7 kDa DNA-binding” family, also known as the Sul7d family, is composed of chromatin proteins from the Sulfolobales archaeal order. Among them, Sac7d and Sso7d have been the focus of several studies with some characterization of their properties. Here, we studied eleven other proteins alongside Sac7d and Sso7d under the same conditions. The dissociation constants of the purified proteins for binding to double-stranded DNA (dsDNA) were determined in phosphate-buffered saline at 25 °C and were in the range from 11 μM to 22 μM with a preference for G/C rich sequences. In accordance with the extremophilic origin of their hosts, the proteins were found highly stable from pH 0 to pH 12 and at temperatures from 85.5 °C to 100 °C. Thus, these results validate eight putative “7 kDa DNA-binding” family proteins and show that they behave similarly regarding both their function and their stability among various genera and species. As Sac7d and Sso7d have found numerous uses as molecular biology reagents and artificial affinity proteins, this study also sheds light on even more attractive proteins that will facilitate engineering of novel highly robust reagents.
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Affiliation(s)
- Valentina Kalichuk
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,Université catholique de Louvain, Louvain Drug Research Institute, Advanced Drug Delivery and Biomaterials, Brussels, Belgium
| | - Ghislaine Béhar
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | - Georgi Danovski
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Gonzalo Obal
- Institut Pasteur de Montevideo, Protein Biophysics Unit, Montevideo, Uruguay
| | - Jacques Barbet
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Barbara Mouratou
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Frédéric Pecorari
- CRCNA, Inserm, CNRS, Université d'Angers, Université de Nantes, Nantes, France
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Guo L, Feng Y, Zhang Z, Yao H, Luo Y, Wang J, Huang L. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea. Nucleic Acids Res 2008; 36:1129-37. [PMID: 18096617 PMCID: PMC2275093 DOI: 10.1093/nar/gkm1128] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 12/03/2007] [Accepted: 12/04/2007] [Indexed: 11/13/2022] Open
Abstract
Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.
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Affiliation(s)
- Li Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Yingang Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Hongwei Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Jinfeng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 3A Datun Road, Beijing 100101, P. R. China and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, P.R. China
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