The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Area of Science:

• Biochemistry
• Molecular Biology
• Bioinformatics

Background:

• The Ribonuclease H-like (RNHL) superfamily, also known as the retroviral integrase superfamily, encompasses diverse enzymes vital for nucleic acid metabolism.
• These enzymes play roles in critical biological processes such as DNA replication, repair, recombination, transposition, and RNA interference.
• RNHL superfamily proteins exhibit significant divergence in both sequence and structure.

Purpose of the Study:

• To comprehensively identify and classify members of the RNHL superfamily.
• To elucidate the evolutionary relationships and structural-functional correlations within the RNHL superfamily.
• To provide a framework for understanding the diverse functions of RNHL proteins.

Main Methods:

• Extensive database searches were performed to identify RNHL superfamily domain sequences.
• Clustering analysis was employed to group identified sequences into families.
• Phylogenetic and structural analyses were conducted to investigate evolutionary history and structure-function relationships.

Main Results:

• Over 60,000 unique RNHL domain sequences were identified, leading to the discovery of new members.
• The identified sequences were classified into 152 distinct families based on clustering.
• Phylogenetic analysis revealed evolutionary relationships and suggested a history of the RNHL fold and active site.
• A clear division between exonucleases and endonucleases within the superfamily was established.
• Structural features, particularly the C-terminal helix orientation, correlated with exonuclease/endonuclease function and active site architecture.

Conclusions:

• This study provides a comprehensive classification of the RNHL superfamily, revealing significant sequence and structural diversity.
• The findings clarify the evolutionary trajectory of the RNHL fold and its active site.
• The identified structure-function relationships, especially the correlation between C-terminal helix orientation and enzymatic activity, offer insights into RNHL protein mechanisms.
• This work serves as a valuable resource for future functional studies of uncharacterized RNHL protein families.