The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins

J Biol Chem. 2005 Apr 15;280(15):15325-39. doi: 10.1074/jbc.M412870200. Epub 2005 Jan 24.

Abstract

The architecture of single-stranded DNA-binding proteins, which play key roles in DNA metabolism, is based on different combinations of the oligonucleotide/oligosaccharide binding (OB) fold. Whereas the polypeptide serving this function in bacteria contains one OB fold, the eukaryotic functional homolog comprises a complex of three proteins, each harboring at least one OB fold. Here we show that unlike these groups of organisms, the Euryarchaeota has exploited the potential in the OB fold to re-invent single-stranded DNA-binding proteins many times. However, the most common form is a protein with two OB folds and one zinc finger domain. We created several deletion mutants of this protein based on its conserved motifs, and from these structures functional chimeras were synthesized, supporting the hypothesis that gene duplication and recombination could lead to novel functional forms of single-stranded DNA-binding proteins. Biophysical studies showed that the orthologs of the two OB fold/one zinc finger replication protein A in Methanosarcina acetivorans and Methanopyrus kandleri exhibit two binding modes, wrapping and stretching of DNA. However, the ortholog in Ferroplasma acidarmanus possessed only the stretching mode. Most interestingly, a second single-stranded DNA-binding protein, FacRPA2, in this archaeon exhibited the wrapping mode. Domain analysis of this protein, which contains a single OB fold, showed that its architecture is similar to the functional homologs thought to be unique to the Crenarchaeotes. Most unexpectedly, genes coding for similar proteins were found in the genomes of eukaryotes, including humans. Although the diversity shown by archaeal single-stranded DNA-binding proteins is unparalleled, the presence of their simplest form in many organisms across all domains of life is of greater evolutionary consequence.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Anisotropy
  • Binding, Competitive
  • Biophysical Phenomena
  • Biophysics
  • Chromatography, Gel
  • DNA / metabolism
  • DNA Primers / chemistry
  • DNA, Single-Stranded / metabolism*
  • Dose-Response Relationship, Drug
  • Electrophoresis, Polyacrylamide Gel
  • Euryarchaeota / genetics*
  • Euryarchaeota / metabolism*
  • Fluorescence Resonance Energy Transfer
  • Gene Deletion
  • Humans
  • Kinetics
  • Methanosarcina / metabolism
  • Microscopy, Fluorescence
  • Models, Biological
  • Molecular Sequence Data
  • Mutation
  • Phylogeny
  • Protein Binding
  • Protein Folding
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Sequence Homology, Amino Acid
  • Temperature
  • Zinc Fingers

Substances

  • DNA Primers
  • DNA, Single-Stranded
  • Recombinant Proteins
  • DNA