Unveiling the Hidden: Exploring Translating Genes in Plants and Plant Viruses

By Ming-Jung Liu

Abstract : The translation of mRNA into protein is at the heart of gene expression. Essential to this process is the precise identification of translation initiation sites (TISs) by ribosomes, which in turn govern the protein-coding potential of mRNA and is critical for ensuring timely and accurate protein production in plants. Our laboratory is dedicated to the study of translational control, with a particular focus on uncovering novel TISs and exploring hidden genes. These investigations are aimed at unraveling the intricacies of plant defense responses and the pathogenesis of plant viruses.
To achieve this, we employ a multidisciplinary approach integrating molecular techniques, data mining, and predictive biology. So far, our study revealed that more than 30% of plant genes have novel TISs (i.e., the TISs occur at AUG and non-AUG codons and differ from the annotated AUG sites). These unanticipated TIS-initiated open-reading frames (ORFs) encode small peptides or play a regulatory role in protein diversity or subcellular localization. In addition, we found multiple initiation sites that were previously uncharacterized and encode new viral factors required for disease symptom development in begomoviruses.

These findings bring the next question of how plant ribosomes recognize these novel AUG and non-AUG TIS ?
In this seminar, I will talk about our recent findings of the mechanistic and evolutionary basis of TIS recognition across plants. By integrating machine-learning, computational, and experimental techniques, we characterized the hidden cis-regulatory sequences features of these novel TISs that are critical and conserved across plant species and also in viruses. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across plant species, human and viruses suggests their broad and critical roles in reprogramming the translational landscape.

21 may, 11am, Lynn Margulis Hall - PABS, INRAE Occitanie-Toulouse
https://inrae-fr.zoom.us/j/92215899092?pwd=VTJQMW9WZnFvY0VHeFJjRlNRNmVzZz09 
ID meeting : 922 1589 9092 
Code : MingLiu24! 

Key publication :

T.-Y. Wu*, Y.-R. Li, K.-J. Chang, J.-C. Fang, D. Urano and M.-J. Liu*. Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes. (in press; Genome Research; https://doi.org/10.1101/2023.10.20.563379)

J.-C. Fang and M.-J. Liu*. (2023) Translation initiation at AUG and non-AUG triplets in plants. Plant Science 335 (2023) 111822

C.-W. Chiu, Y.-R. Li, C.-Y. Lin, H.-H. Yeh and M.-J. Liu*. (2022) Translation initiation landscape profiling reveals hidden open reading frames required for tomato yellow leaf curl Thailand virus pathogenesis. Plant Cell, 34, 1804–1821.

Y.-R. Li and M.-J. Liu*. (2020) Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants. Genome Research 30, 1418-1433.

Contact :

Ming-Jung Liu : mjliu@gate.sinica.edu.tw
Chercheur d'accueil : jean-marc.deragon@univ-perp.fr