February 25th, 2024
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, Li et al. characterise long non-coding RNAs derived from miRNA loci, Leblanc et al. present OpenProt 2.0, a new proteomics platform for functional characterisation of alternative proteins, and Bryant et al. delve into the differences in translational regulation between Salmonella and Listeria.
Deciphering the Functional Long Non-Coding RNAs Derived from MicroRNA Loci
Advanced Science, 2023
Weiqian Li, Yue Huo, Yue Ren, Chenxi Han, Shuo Li, Kangning Wang, Manman He, Yiying Chen, Yanran Wang, Lingjie Xu, Yuehong Guo, Yanmin Si, Yufeng Gao, Jiayue Xu, Xiaoshuang Wang, Yanni Ma, Jia Yu, Fang Wang
This study analyses the intricate mechanisms by which microRNA (miRNA) gene-originated long non-coding RNAs (molncRNAs) regulate hematopoietic processes. Employing several cutting-edge methodologies including PacBio Iso-seq, CRISPR-based screening, and single-cell RNA sequencing (scRNA-seq), over 860 molncRNAs were characterized. Among these, molnc-301b emerged as a central regulator, orchestrating protein synthesis and erythropoiesis. Through an antagonistic interaction with SMARCA5, molnc-301b downregulates translation-associated genes, impairing protein synthesis. Using Ribo-seq and polysome profiling coupled with qPCR, the authors showed molnc-301b-mediated translational inhibition of essential hematopoietic regulators like GATA1 and FOS, ultimately impeding erythroid differentiation.
CRISPR-based single-cell RNA-seq enabled the identification of a total of 29 functional molncRNAs, delineating their roles in modulating the expression of erythroid regulators. The study further classified molncRNAs into exonic and intronic categories based on their association with miRNA loci, indicating their diverse functions. Notably, molncRNAs exert distinct effects from their miRNA counterparts, highlighting the complexity of their regulatory roles. These findings underscore the importance of molncRNAs as crucial players in hematopoiesis, with implications for understanding gene regulation at both transcriptional and post-transcriptional levels. The comprehensive approach employed in this study provides valuable insights into the multifaceted roles of molncRNAs in cellular processes, paving the way for further exploration of their functional significance in other biological contexts and disease models.
OpenProt 2.0 builds a path to the functional characterization of alternative proteins
Nucleic
Acids Research, 2023
Sébastien Leblanc, Feriel Yala, Nicolas Provencher, Jean-François Lucier, Maxime Levesque, Xavier Lapointe, Jean-Francois Jacques, Isabelle Fournier, Michel Salzet, Aïda Ouangraoua, Michelle S Scott, François-Michel Boisvert, Marie A Brunet, Xavier Roucou
The authors introduce OpenProt 2.0, a comprehensive resource facilitating the exploration of noncanonical proteins encoded in alternative open reading frames (AltORFs) across various RNA biotypes. Traditional databases like NCBI RefSeq and Ensembl primarily annotate single, canonical open reading frames (ORFs) within mRNAs, overlooking AltORFs. OpenProt challenges this convention by annotating three types of proteins: RefProts (annotated in conventional databases), novel isoforms (unannotated proteins similar to RefProts), and AltProts (unannotated proteins lacking similarity to RefProts). The update incorporates transcript expression data, structural predictions, intrinsically disordered regions, and short linear motifs, enhancing functional annotations. Using these new annotations, OpenProt reanalyses Ribo-seq and MS-based proteomics studies to provide evidence of expression and display protein domains and conservation. Furthermore, a new mass spectrometry (MS) data analysis pipeline improves peptide identification rates, aiding in the discovery of AltProts.
OpenProt 2.0 introduces two new tools: OpenVar, a genomic variant annotator for multiple ORFs on single transcripts, and OpenCustomDB, which generates personalized RNAseq-derived protein sequence databases. These developments will allow researchers to expand their understanding of eukaryotic genes’ molecular function. The article emphasizes OpenProt’s unique approach to functional annotation, allowing for the presence of multiple ORFs on the same RNA, irrespective of its biotype.
Additionally, OpenProt enhances user experience with a new web interface, facilitating data exploration. The platform now includes a mass spectrum viewer, enabling users to visualize and download MS2 spectra directly. Links to other repositories enhance data sharing and accessibility.
Overall, OpenProt 2.0 represents a significant advancement in functional genomics, providing researchers with tools to identify and investigate novel proteins encoded by AltORFs, thereby expanding our understanding of eukaryotic gene function.
The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria
Nature Communications, 2023
This study uses Ribo-seq to thoroughly investigate the regulatory elements influencing translation efficiency in bacteria, specifically focusing on Salmonella and Listeria. It explores the interplay between the Shine-Dalgarno (SD) sequence, RNA secondary structure, and other cis-regulatory elements. In Salmonella, efficiently translated mRNAs exhibit weaker RNA secondary structures around the start codon, facilitating accessibility of the SD sequence to the 16S rRNA. Conversely, in Listeria, there is less structured RNA throughout the 5′ UTR and coding sequence, with a marginal difference in structure strength between efficiently and inefficiently translated mRNAs. Notably, a subset of efficiently translated Listeria genes contains out-of-frame upstream peaks (OUPs), which correlate with increased translation efficiency. These OUPs may represent a novel initiation mechanism in Listeria. Additionally, the presence of adenosine-rich sequences near the start codon and specific amino acid residues, particularly lysine, at certain positions within the coding sequence, positively influences translation efficiency in both bacteria. Furthermore, a luciferase reporter assay confirms the significance of lysine codons at specific positions in enhancing translation efficiency.
Overall, the study reveals distinct regulatory mechanisms governing translation in Salmonella and Listeria. While Salmonella relies on a strong SD sequence and reduced RNA secondary structure, Listeria demonstrates more variability in translation efficiency, with OUPs emerging as a unique feature. Understanding these differences not only sheds light on bacterial translational regulation but also provides potential targets for antibiotic development and advances our fundamental knowledge of bacterial molecular biology.