Lineage-specific retention of the plastid tilS-trnI(CAU) module and its variable relationship with codon usage...

Area of Science:

• Evolutionary biology
• Molecular biology
• Genomics

Background:

• Plastid genomes retain essential translation machinery from cyanobacteria.
• The tRNAIle-lysidine synthetase (TilS) system is crucial for accurate decoding of the isoleucine AUA codon.
• Evolutionary pressures on plastid genome diversification, particularly translation systems, are not fully understood.

Purpose of the Study:

• To characterize the complete plastid genome of Micractinium simplicissimum.
• To investigate the evolutionary distribution of the tilS-trnI(CAU) module in green algal plastomes.
• To explore the relationship between codon usage, TilS evolution, and potential nuclear relocation of decoding functions.

Main Methods:

• Whole plastid genome sequencing and characterization.
• Phylogenomic analyses of 35 green algal plastomes.
• Comparative analyses of codon usage and protein domain structures.
• Identification of nuclear-encoded TilS homologs.

Main Results:

• The tilS-trnI(CAU) module is consistently retained in Chlorellales but shows partial loss or fragmentation in Trebouxiophyceae.
• AUA codon frequencies vary independently of tilS retention, indicating evolutionary decoupling.
• Plastid TilS proteins exhibit lineage-specific structural variations compared to cyanobacterial homologs.
• Nuclear-encoded TilS homologs were found in taxa lacking plastid tilS, suggesting functional relocation.

Conclusions:

• Plastid decoding systems evolve via modular, lineage-specific pathways, allowing structural plasticity.
• The evolution of translational fidelity in plastids involves complex trajectories, including potential nuclear gene transfer.
• This study offers novel insights into the evolutionary dynamics of gene expression in endosymbiotic organelles.