Structural insights into nanoRNA degradation by human Rexo2

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Human RNA exoribonuclease 2 (Rexo2) is a mitochondrial DEDDh-family exonuclease.
• Rexo2 degrades small RNA oligonucleotides (<5 nucleotides, nanoRNA), similar to E. coli ORN, suggesting a role in mitochondrial RNA turnover.
• The precise mechanism of Rexo2's preferential binding and degradation of nanoRNA was previously unknown.

Purpose of the Study:

• To elucidate the molecular mechanism by which human Rexo2 binds and degrades nanoRNA.
• To determine the structural basis for Rexo2's substrate preference and catalytic activity.
• To understand Rexo2's role in mitochondrial RNA salvage pathways.

Main Methods:

• X-ray crystallography to determine the structures of Rexo2 in complex with RNA or DNA substrates.
• Biochemical assays to assess Rexo2's degradation activity and substrate binding affinity.
• Comparative structural analysis with related enzymes like E. coli ORN.

Main Results:

• Rexo2 exhibits highest affinity for small RNA and DNA oligonucleotides.
• Degradation of nanoRNA into mononucleotides is most efficient in the presence of magnesium ions.
• Crystal structures reveal Rexo2 as a homodimer that binds substrates via hydrophobic and π-π stacking interactions at the 3'-end, without sequence specificity.
• The structure of Rexo2 is highly similar to ORN, indicating a conserved two-magnesium-ion-dependent hydrolysis mechanism.

Conclusions:

• The study provides the molecular basis for human Rexo2 function, detailing its binding and degradation of nanoRNA.
• Rexo2 plays a critical role in RNA salvage pathways within mammalian mitochondria by processing nanoRNA into nucleoside monophosphates.
• Structural insights highlight Rexo2's preference for short oligonucleotides and its conserved catalytic mechanism.