Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales

ssDNA-binding proteins (SSBs) based on the oligonucleotide-binding fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination, and repair. We demonstrate that the Thermoproteales, a clade of hyperthermophilic Crenarchaea, lack a can...

Full description

Saved in:
Bibliographic Details
Published inProceedings of the National Academy of Sciences - PNAS Vol. 109; no. 7; pp. E398 - E405
Main Authors Paytubi, Sonia, McMahon, Stephen A, Graham, Shirley, Liu, Huanting, Botting, Catherine H, Makarova, Kira S, Koonin, Eugene V, Naismith, James H, White, Malcolm F
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 14.02.2012
National Acad Sciences
SeriesPNAS Plus
Subjects
Amino acids
Binding sites
Biological Sciences
Cloning, Molecular
Crystal structure
Crystallography, X-Ray
DNA biosynthesis
DNA repair
DNA-binding proteins
DNA-Binding Proteins - chemistry
DNA-Binding Proteins - genetics
DNA-Binding Proteins - metabolism
Evolution
Hydrophobicity
leucine zipper
Leucine zipper proteins
Molecular structure
Phenylalanine
PNAS Plus
Protein Binding
Protein Folding
Proteins
Recombination
Replication
single-stranded DNA
single-stranded DNA-binding protein
Thermoproteales
Thermoproteales - metabolism
Thermoproteus tenax
Online AccessGet full text

Cover

More Information
Summary:ssDNA-binding proteins (SSBs) based on the oligonucleotide-binding fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination, and repair. We demonstrate that the Thermoproteales, a clade of hyperthermophilic Crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term "ThermoDBP," exemplified by the protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and a mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the Thermoproteales, a highly unusual example of the loss of a "ubiquitous" protein during evolution.
Bibliography:ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
content type line 23
ObjectType-Article-1
ObjectType-Feature-2
2S.P. and S.A.M. contributed equally to this work.
Author contributions: J.H.N. and M.F.W. designed research; S.P., S.A.M., S.G., H.L., C.H.B., and K.S.M. performed research; S.P., S.A.M., C.H.B., E.V.K., J.H.N., and M.F.W. analyzed data; and S.P., S.A.M., K.S.M., E.V.K., J.H.N., and M.F.W. wrote the paper.
1Present address: Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain.
Edited by Stephen C. Kowalczykowski, University of California, Davis, CA, and approved October 25, 2011 (received for review August 12, 2011)
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1113277108