The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling

Area of Science:

• Molecular Biology
• Genomics
• Plant Science

Background:

• Translational control is key for crop improvement, but its conservation across species and crop translatomes are understudied.
• Arabidopsis translational studies show potential, yet tomato's translational landscape remains largely unexplored.

Purpose of the Study:

• To investigate global mRNA translation in tomato (Solanum lycopersicum) roots using advanced techniques.
• To identify unannotated translation events, including upstream open reading frames (uORFs) and small open reading frames (sORFs).
• To understand conserved and species-specific translational regulation in crops.

Main Methods:

• Combined de novo transcriptome assembly with ribosome profiling for high-throughput analysis.
• Analyzed features indicative of active mRNA translation in tomato root tissues.
• Utilized proteomic analysis to validate the existence of proteins from unannotated ORFs.

Main Results:

• Discovered 1,329 unannotated upstream open reading frames (uORFs) and 354 small open reading frames (sORFs) in tomato.
• Identified 96 Solanaceae-specific sORFs, highlighting crop-specific translational elements.
• Confirmed protein production from unannotated ORFs via proteomics.
• Revealed global translational regulation by uORFs and microRNAs.

Conclusions:

• The study defines the tomato root translatome, uncovering significant unannotated translational activity.
• Many translational features are conserved between Arabidopsis and tomato, despite long evolutionary divergence.
• The developed approach offers a high-throughput method for discovering ORFs and regulatory mechanisms in crop genomes, crucial for crop improvement.