Monitoring the translation initiation process in prokaryotes via large-scale examination using optimized SSU-seq technique
- 1Tel Aviv University
Abstract
Translation initiation is a critical stage of protein synthesis in prokaryotes, where ribosomes assemble on mRNA to begin decoding genetic information. The interactions between ribosomal RNA (rRNA) and mRNA significantly influence this process, with features like ribosomal binding site (RBS) affecting ribosomal dynamics. However, direct experimental validation of these types of interaction is yet to be provided. In this study, we developed an optimized small sub-unit sequencing (SSU-seq) protocol for Escherichia coli, enabling the detailed examination of ribosomal complexes and subunits dynamics. Unlike Ribo-seq, which primarily maps fully assembled ribosomes, SSU-seq captures both ribosomal subunits and intact ribosomes, offering a comprehensive view of translation initiation and elongation events. By integrating experimental data with predictive models, our study advances the understanding of translation regulation in prokaryotes and underscores the utility of SSU-seq in decoding the complexities of ribosome-mRNA interactions. Our analysis reveals distinct patterns of small subunit distribution across the entire mRNAs with higher density near positions with stronger rRNA-mRNA hybridization. The results may suggest that rRNA-mRNA hybridization positions along the entire transcript facilitate efficient start codon recognition by maintaining proximity between the small subunit and the mRNA.
Related
- Structural basis for the CsrA-dependent modulation of translation initiation by an ancient regulatory protein.
- Mechanistic modeling of bacterial translation initiation across growth conditions
- 16S rRNA Modifications Are Dispensable for Viability but Collectively Optimize Ribosome Biogenesis and Translation Initiation in Escherichia coli
- Pangenome-wide insights into eukaryotic translation initiation factors (eIF) genes uncover targets for sterility mosaic disease resistance engineering in pigeonpea.
- Initiation codon context governs translation-coupled mRNA decay and coordinated expression in the human parasite Leishmania
BibTeX
@misc{fine2026monitoring,
title = {{Monitoring the translation initiation process in prokaryotes via large-scale examination using optimized SSU-seq technique}},
author = {L. Fine and A. Diament and R. Cohen-Kupiec and T. Tuller},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.04.756509},
url = {https://www.biorxiv.org/content/10.64898/2026.10.04.756509v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Monitoring the translation initiation process in prokaryotes via large-scale examination using optimized SSU-seq technique
AU - L. Fine
AU - A. Diament
AU - R. Cohen-Kupiec
AU - T. Tuller
PY - 2026
DA - 2026/10/04
PB - bioRxiv
DO - 10.64898/2026.10.04.756509
UR - https://www.biorxiv.org/content/10.64898/2026.10.04.756509v1
AB - Translation initiation is a critical stage of protein synthesis in prokaryotes, where ribosomes assemble on mRNA to begin decoding genetic information. The interactions between ribosomal RNA (rRNA) and mRNA significantly influence this process, with features like ribosomal binding site (RBS) affecting ribosomal dynamics. However, direct experimental validation of these types of interaction is yet to be provided. In this study, we developed an optimized small sub-unit sequencing (SSU-seq) protocol for Escherichia coli, enabling the detailed examination of ribosomal complexes and subunits dynamics. Unlike Ribo-seq, which primarily maps fully assembled ribosomes, SSU-seq captures both ribosomal subunits and intact ribosomes, offering a comprehensive view of translation initiation and elongation events. By integrating experimental data with predictive models, our study advances the understanding of translation regulation in prokaryotes and underscores the utility of SSU-seq in decoding the complexities of ribosome-mRNA interactions. Our analysis reveals distinct patterns of small subunit distribution across the entire mRNAs with higher density near positions with stronger rRNA-mRNA hybridization. The results may suggest that rRNA-mRNA hybridization positions along the entire transcript facilitate efficient start codon recognition by maintaining proximity between the small subunit and the mRNA.
ER -