Remote Homology Detection Identifies a Eukaryotic RPA DBD-C-like DNA Binding Domain as a Conserved Feature of...

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Biochemistry

Background:

• Replication protein A (RPA) is a vital eukaryotic protein complex involved in DNA replication, repair, and recombination.
• Eukaryotic RPA is a heterotrimer with six OB folds (DBD-A to DBD-F) and a winged helix-turn-helix (wH) domain, with DBD-A to DBD-D binding single-stranded DNA.
• Archaeal RPA proteins exhibit diverse structures, with some possessing a zinc finger followed by a C-terminal region of unknown similarity.

Purpose of the Study:

• To investigate the structural and evolutionary relationship between archaeal and eukaryotic RPA proteins.
• To identify previously unrecognized structural domains in archaeal RPA proteins.
• To clarify the oligomeric state and evolutionary connections of archaeal RPA complexes.

Main Methods:

• Sequence analysis of archaeal RPA proteins.
• Structural comparison of archaeal and eukaryotic RPA domains.
• Bioinformatic analysis to infer evolutionary relationships.

Main Results:

• The C-terminal region following the zinc finger in a widespread class of archaeal RPA proteins constitutes a previously unrecognized DBD-C-like OB fold.
• This DBD-C-like OB fold confirms the evolutionary relatedness of these archaeal RPA proteins to eukaryotic RPA1.
• Archaeal RPA2-like proteins containing an OB fold and a C-terminal wH domain were identified, suggesting that previously characterized monomeric archaeal RPA proteins are likely RPA1-RPA2 heterodimers.

Conclusions:

• Archaeal RPA proteins share significant evolutionary links with their eukaryotic counterparts, particularly RPA1.
• The identification of a DBD-C-like OB fold in archaea provides crucial evidence for this evolutionary connection.
• The findings suggest a conserved RPA1-RPA2 heterodimer structure in archaea, challenging previous assumptions about their quaternary structure.