April 27th, 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,
- Tufail et al. used ribosome profiling to discover novel sORFs in Methanosarcina.
- Dolcemascolo et al. used ribosome profiling to establish Musashi-1 as an orthogonal tool for post-transcriptional gene regulation in E. coli.
- Fan et al. used ribosome profiling to identify novel antimicrobial peptides for potential therapeutic use.
Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions
Nature Communications, 2024
Muhammad Aammar Tufail, Britta Jordan, Lydia Hadjeras, Rick Gelhausen, Liam Cassidy, Tim Habenicht, Miriam Gutt, Lisa Hellwig, Rolf Backofen, Andreas Tholey, Cynthia M. Sharma and Ruth A. Schmitz
This study employs ribosome profiling (Ribo-seq) and peptidomics to identify and characterize the small proteome (<70 amino acids) in the archaeon Methanosarcina mazei—a methanogenic model species. The research found 314 previously unannotated and 93 annotated small open reading frames (sORFs), many of which were differentially regulated based on nitrogen availability. Under nitrogen stress, 29 unannotated sORFs were differentially expressed at the transcriptional level and 49 at the translational level. Additionally, the study revealed that several sRNAs act as dual-function RNAs—serving both regulatory roles and encoding small proteins, such as sRNA154, a key regulator in nitrogen metabolism.
Ribosome profiling in this study revealed extensive translation of small open reading frames (sORFs) in Methanosarcina mazei, and also corrected gene misannotations, revealing translation initiation shifts and providing improved genome annotation accuracy. The approach revealed that many small proteins were previously missed due to non-canonical start codons and short lengths. By integrating Ribo-seq with peptidomics, the research refines genome annotations and reveals regulatory complexity. This comprehensive multi-omic approach provides a valuable foundation for future functional studies on small proteins and regulatory RNAs in archaea.
Learn more about EIRNA Bio’s ribosome profiling service here.
Probing the orthogonality and robustness of the mammalian RNA-binding protein Musashi-1 in Escherichia coli
Journal of Biological Engineering, 2024
Roswitha Dolcemascolo, Raúl Ruiz, Sara Baldanta, Lucas Goiriz, María Heras‑Hernández, Roser Montagud‑Martínez and Guillermo Rodrigo
This study explored the functionality and consequences of expression of an engineered eukaryotic Musashi-1 (MSI-1) protein in a E. coli. Using RNA sequencing and ribosome sequencing, the study assesses how Musashi expression affects E. coli’s gene expression and translation. They investigate potential off-target interactions, metabolic stress responses, mutational robustness of protein variants, and the evolutionary stability of engineered circuits.
RNA-seq revealed over 1,200 differentially expressed genes upon engineered MSI-1 (MSI-1*) expression, indicating broad metabolic and stress responses. However, Ribo-seq showed that only two genes—lyxK and plsX—were translationally regulated, and likely not through direct RNA-protein interaction. Motif searches and indirect evidence suggest these effects stem from general expression burden rather than specific MSI-1-mediated control. The comprehensive profiling revealed that most observed changes in protein levels were attributable to altered mRNA abundance, not translation efficiency, supporting the conclusion that MSI-1* operates orthogonally with minimal direct influence on the host translatome. This study establishes Musashi-1 as a viable, orthogonal tool for post-transcriptional gene regulation in E. coli, broadening the synthetic biology toolkit for microbial engineering.
Learn more about EIRNA Bio’s ribosome profiling service here.
Bioprospecting of culturable marine biofilm bacteria for novel antimicrobial peptides
iMeta, Wiley, 2024
Shen Fan, Peng Qin, Jie Lu1, Shuaitao Wang, Jie Zhang, Yan Wang, Aifang Cheng, Yan Cao, Wei Ding, Weipeng Zhang
This study presents a comprehensive exploration of marine biofilm bacteria as a novel source for antimicrobial peptides (AMPs). Using ribosome profiling (Ribo-seq), genome sequencing of 713 culturable marine bacteria, and a novel deep learning pipeline, the study identifies 341 candidate AMPs. These peptides show low similarity to known AMPs and strong activity against drug-resistant pathogens. Using ribosome profiling (Ribo-seq), they identified over 150,000 expressed small open reading frames (sORFs), which were then screened with a custom-built deep learning model that included CNN, BiLSTM, and attention layers.
The model predicted 341 candidate AMPs with low sequence identity (<40%) to known peptides. Sixty top-ranked AMP candidates were chemically synthesized; 54 (90%) exhibited antibacterial activity, with several showing potent, broad-spectrum activity, including against multidrug-resistant Staphylococcus aureus. Importantly, many peptides displayed low cytotoxicity and hemolytic activity, indicating therapeutic potential. By integrating ribosome profiling with deep learning, the researchers established a powerful pipeline capable of predicting functionally active and structurally diverse AMPs with low toxicity and broad-spectrum antibacterial activity.
Learn more about EIRNA Bio’s ribosome profiling services here.