Solution structure of the HIV-1 exon splicing silencer 3

Area of Science:

• Structural Biology
• Virology
• Molecular Biology

Background:

• HIV-1 replication relies on alternative splicing of its genomic RNA.
• Host factors, like heterogeneous nuclear ribonucleoprotein (hnRNP) A1, regulate HIV-1 splicing by binding specific RNA elements.
• The precise molecular mechanisms of hnRNP A1 binding to HIV-1 splicing sites are not fully understood.

Purpose of the Study:

• To determine the three-dimensional structure of the HIV-1 exon splicing silencer 3 (ESS3).
• To investigate the binding interactions between hnRNP A1 subdomains and ESS3.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy was used to determine the ESS3 structure.
• Isothermal titration calorimetry and NMR titrations were employed to study hnRNP A1 subdomain binding to ESS3.

Main Results:

• ESS3 forms a 27-nucleotide hairpin structure with a pH-sensitive wobble pair in its stem.
• The hairpin loop contains the hnRNP A1-binding site (5'-UAGU-3') and a proximal 5'-GAU-3' motif.
• The UP1 domain of hnRNP A1 binds ESS3 with high affinity (Kd = 37.8 ± 1.1 nM) through specific loop interactions.

Conclusions:

• The determined structure of ESS3 provides insights into its RNA conformation and regulatory elements.
• The UP1 domain of hnRNP A1 is identified as the primary binding component for ESS3.
• These findings contribute to understanding the molecular basis of HIV-1 alternative splicing regulation.