Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• The target of rapamycin (TOR) pathway is crucial for cellular homeostasis and ribosome biogenesis.
• La-related protein 1 (LARP1) is a key mediator, binding terminal oligopyrimidine (TOP) mRNAs in a TOR-dependent manner.
• The evolutionary conservation and precise mechanism of LARP1-TOP mRNA interaction in diverse species are not fully understood.

Purpose of the Study:

• To investigate the conservation and function of the LARP1-DM15 module and its interaction with 5' TOP motifs in evolutionarily divergent animals.
• To elucidate the structural basis for LARP1 DM15 binding to TOP mRNAs.
• To explore the role of RNA structure in regulating this interaction.

Main Methods:

• Comparative structural analysis of LARP1-DM15 domains across species (human, fruit fly, zebrafish).
• Molecular dynamics simulations to predict structural stability.
• In vitro binding assays to assess affinity of LARP1 orthologs for TOP sequences.
• Bioinformatic analysis of RNA secondary structures.

Main Results:

• The overall architecture of the LARP1-DM15 module is conserved in fruit flies and zebrafish, adopting similar curved arrangements.
• Molecular dynamics simulations indicate potential instability in the fruit fly LARP1-DM15 N-terminal fold.
• Orthologs exhibit varying affinities for TOP sequences, suggesting context-dependent binding.
• The binding specificity appears to be influenced by RNA secondary structure rather than solely sequence recognition.

Conclusions:

• The LARP1-DM15 module's conserved structure facilitates TOP mRNA binding across species.
• RNA secondary structure plays a significant role in regulating LARP1 DM15 recognition of TOP mRNAs.
• This suggests a conserved mechanism for controlling ribosome biogenesis through TOP mRNA regulation in diverse animals.