May 4th, 2025

Recent Publications Harnessing the Power of Translatomics

Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.

In this week’s Sunday papers,

  • Hang et al. used ribosome profiling to mechanistically define how plants optimize chloroplast biogenesis and photosynthesis.
  • Liboy-Lugo et al. used ribosome profiling to reveal the effect of isoform-specific translation regulation on stress granule formation.
  • Arribas et al. used ribosome profiling to explore how transcriptional element exonization serves as a reservoir of alternative protein variants.

HOT3/eIF5B1 confers Kozak motif-dependent translational control of photosynthesis-associated nuclear genes for chloroplast biogenesis

Nature Communications, 2024

Runlai Hang, Hao Li, Wenjing Liu, Runyu Wang, Hao Hu, Meng Chen, Chenjiang You and Xuemei Chen

This study reveals the mechanism that mediates Kozak motif-dependent translational control in the model plant species Arabidopsis. The translation initiation factor in plants, HOT3/eIF5B1, facilitates the ribosomal transition from initiation to elongation (I-E), particularly in photosynthesis-associated nuclear genes (PhANGs). HOT3 translational regulation primarily influences PhANGs, and through ribosome profiling (ribo-seq), the study establishes a genome-wide link between specific Kozak motifs and improved translation. Ribosome profiling was used in tandem with a defective HOT3 to reveal ribosome stalling at translation initiation sites, impairing the initiation-to-elongation transition. The authors quantified this genome-wide defect and discovered that transcripts with the A/GC-type (-3A/+4G/+5C) Kozak motif exhibit the most efficient I-E transition. Additionally, it was observed that these motifs are enriched in photosynthesis-associated nuclear genes (PhANGs), encoding crucial components of the chloroplast thylakoid membranes.

This result implies that HOT3 selectively enhances translation of PhANGs essential for chloroplast development and photosynthetic function in Arabidopsis. By linking cis-regulatory sequence regulatory elements to efficient translation through HOT3/eIF5B1, the work reveals an evolutionarily conserved strategy for optimizing chloroplast biogenesis and photosynthesis. These findings provide new insights into translational control in plants and suggest potential molecular targets for engineering improved photosynthetic efficiency and stress tolerance in crops.

Learn more about EIRNA Bio’s ribosome profiling service here.

G3BP isoforms differentially affect stress granule assembly and gene expression during cellular stress

Molecular Biology of the Cell, 2024

José M. Liboy-Lugo, Carla A. Espinoza, Jessica Sheu-Gruttadauria, Jesslyn E. Park, Albert Xu, Ziad Jowhar, Angela L. Gao, José A. Carmona-Negrón, Torsten Wittmann, Natalia Jura, and Stephen N. Floor

This study explores how isoforms of the RNA-binding protein G3BP regulate stress granule (SG) formation and gene expression during the integrated stress response (ISR), uncovering isoform-specific roles in SG dynamics and mRNA regulation. Three vertebrate G3BP isoforms—G3BP1, G3BP2A, and G3BP2B—differentially regulate stress granule assembly and gene expression in response to cellular stress. A valine at position 11 (V11) in the NTF2L domain is critical for SG assembly, mediating interactions with Caprin-1. This was determined by observing how a V11A mutant impaired SG formation without disrupting dimerization, leading to altered expression of stress-responsive mRNAs.

Ribosome profiling (Ribo-seq) and RNA-seq were used to evaluate gene expression changes at steady state and under stress. Ribo-seq determined that the G3BP1-V11A mutation had a minimal impact on translation at steady state, but altered the expression of SG-associated mRNAs under oxidative stress. Under ER stress, Ribo-seq of G3BP1/2 knockout cells reconstituted with different G3BP isoforms revealed isoform-specific translation regulation. G3BP2B altered translation efficiency and RNA levels of more transcripts than G3BP1 or G3BP2A, with a distinct profile of SG-associated mRNA repression. These mechanistic insights of SG formation could inform therapeutic strategies targeting SG pathways in diseases such as cancer, neurodegeneration, and viral infections.

Learn more about EIRNA Bio’s ribosome profiling service here.

Transposable element exonization generates a reservoir of evolving and functional protein isoforms

Cell, 2024

Yago A. Arribas, Blandine Baudon, Maxime Rotival, Guadalupe Suárez, Pierre-Emmanuel Bonté, Vanessa Casas, Apollinaire Roubert, Paul Klein, Elisa Bonnin, Basma Mchich, Patricia Legoix, Sylvain Baulande, Benjamin Sadacca, Julien Diharce, Joshua J. Waterfall, Catherine Etchebest, Montserrat Carrascal, Christel Goudot, Lluís Quintana-Murci, Marianne Burbage, Antonela Merlotti, Sebastian Amigorena

This study explores how transposable elements (TEs), through exonization, contribute to protein diversity in humans. Using transcriptomics, ribosome profiling (ribo-seq), and proteomics, the authors identify over 1,200 previously unannotated isoforms created by TE exonization. While often shorter with low levels of expression, they are efficiently translated, functionally stable, and some are recurrent across individuals, leading to the conclusion that TE-derived exons can create a reservoir of evolving protein variants.

Ribo-seq was key in identifying 1,227 translated protein isoforms derived from transposable element (TE) exonization, termed JET-ORFs. These isoforms were supported by clear ribosome P-site signals and showed efficient translation despite generally lower mRNA abundance compared to canonical isoforms. Through combined use of ribo-seq and proteomics, it was demonstrated that TE-exonized sequences contribute to protein folding—frequently adopting alpha helices—and subcellular localization in addition to functional modifications. By serving as a reservoir of alternative protein variants, TE exonization offers a mechanism for evolutionary innovation without compromising core gene function. The findings open new avenues for understanding gene regulation, evolutionary biology, and potential therapeutic targeting of isoform-specific functions in health and disease.

Learn more about EIRNA Bio’s ribosome profiling services here.

Scroll to Top