Eukaryotic nuclear structure explains the evolutionary rate difference of ribosome export factors

Area of Science:

• Evolutionary Biology
• Cell Biology
• Molecular Evolution

Background:

• The formation of the nucleus is a defining event in eukaryotic evolution.
• Efficient nucleocytoplasmic transport, especially ribosome export, was essential for early eukaryotes.
• Ribosome export factors (REFs) facilitate nucleocytoplasmic transport but their evolution is poorly understood.

Purpose of the Study:

• To investigate the evolutionary features and rates of amino acid substitutions in REFs.
• To compare the evolutionary rates of REFs with ribosomal components and other proteins.
• To understand the functional constraints on different classes of REFs during eukaryotic evolution.

Main Methods:

• Estimated rates of amino acid substitutions for REFs in two yeast species (Saccharomyces cerevisiae and Saccharomyces paradoxus).
• Compared REF substitution rates with those of ribosomal components.
• Analyzed evolutionary rates of 112 REFs across 16 eukaryotic species, classifying them into membranous (mREFs) and non-membranous (non-mREFs).

Main Results:

• Average amino acid substitution rate for REFs was higher than ribosomal components but lower than the average of other proteins.
• REFs were classified into slowly evolving (mREFs) and rapidly evolving (non-mREFs) groups.
• mREFs showed significantly stronger functional constraints than non-mREFs, consistent with their roles in nuclear export.

Conclusions:

• The evolutionary divergence of REFs, particularly the slower evolution of mREFs, played a critical role in establishing nuclear transport systems.
• The distinct evolutionary rates of mREFs and non-mREFs highlight their specialized functions in nucleocytoplasmic transport.
• The evolution of mREFs likely contributed to the successful establishment of the nucleus in early eukaryotic cells.