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,

  • El-Sharoud et al. investigate whether ribosome modulation factor promotes E. coli survival during milk fermentation and yogurt cold storage.
  • Kanodia et al. aimed to map the translational landscape during early and late stages of red clover necrotic mosaic virus infection.
  • Gao et al. determine the factors that set the pace of cell proliferation across changing nutrient environments in S. cerevisiae.

Ribosome modulation factor affects the antagonistic activity of lactic acid bacteria against Escherichia coli in milk and yogurt

International Dairy Journal, 2026

El-Sharoud, W.M. and Niven, G.W.

Sunday Paper 1

Lactic acid bacteria preserve fermented dairy products by lowering pH, yet acid-tolerant pathogens like Escherichia coli O157:H7 survive unexpectedly well under these conditions. Unlike mineral acids, lipophilic lactic acid permeates bacterial membranes in its undissociated form to acidify the cytoplasm directly. This study investigated whether ribosome modulation factor (RMF), a protein that dimerizes 70S ribosomes into stationary-phase 100S complexes, promotes E. coli survival during milk fermentation and yogurt cold storage by protecting the translation machinery. Ribosome profiling showed that the parent strain formed 30S, 50S, 70S, and 100S ribosomal units, whereas the rmf-deficient mutant lacked 100S dimers entirely. Under lactic acid stress (pH 4.2), the parent strain’s 100S dimers dissociated within 3 hours, serving as an initial buffer that shielded functional 70S ribosomes from breakdown.

Lacking this protection, the mutant’s 70S ribosomes dissociated directly into 30S and 50S subunits at 3 hours, followed by severe degradation across all subunits over 24 hours. Consequently, the mutant was undetectable in cold-stored yogurt after 7 days, whereas the parent persisted. RNA-seq and agarose gel electrophoresis confirmed intact 16S and 23S rRNA bands in the parent strain throughout 24 hours at pH 4.2. Conversely, the rmf mutant displayed a progressive loss of band intensity, indicating extensive rRNA degradation under organic acid stress. Overall, RMF promotes E. coli survival in fermented dairy by driving 100S dimer assembly, which shields 70S ribosomes and ribosomal RNA from acid-induced dissociation and degradation.

Learn more about EIRNABio’s ribosome profiling services here.

Changes in the translational landscape during red clover necrotic mosaic virus infection

Journal of Virology, 2026

Kanodia, P., Lozier, Z., Lastovka, F., Walker, D., Liu, P., Chung, B. and Miller, W.A.

Sunday Paper 2

Because positive-strand RNA viruses completely lack their own translation machinery, they must hijack host ribosomes to synthesize viral proteins. During infection, hosts regulate gene expression to restrict viral spread, while viruses simultaneously manipulate it to create a proviral environment. Recognizing the importance of this dynamic tug-of-war, the authors noted a lack of genome-wide assessments of translational control in plants infected by the large Tombusviridae virus family. Using an Arabidopsis thaliana model (with a DCL2/4-knockout to permit systemic infection), this study aimed to map the translational landscape during early and late stages of red clover necrotic mosaic virus (RCNMV) infection to uncover a new dimension of gene expression control in plant-virus interactions.

Transcriptomic profiling was conducted at an early, asymptomatic stage (5 days post-inoculation, or dpi) and a late, symptomatic stage (8 dpi). RNA-seq demonstrated a drastic shift in the host’s transcriptional landscape by 8 dpi, featuring a massive increase in differentially expressed genes compared to the early stage. By this late stage, viral replication was so profound that RCNMV RNAs overwhelmed the cellular environment, becoming the most abundant RNA species present. Through Ribo-Seq, the researchers discovered that many host genes experienced altered translational efficiency without corresponding changes in overall mRNA abundance. Profiling the viral genome itself revealed distinct translation strategies: the viral coat protein open reading frame (ORF) was translated with exceptional efficiency, while the p88 ORF was translated the least efficiently. The data also successfully mapped the viral ribosomal frameshifting rate and identified a strong ribosomal pause site within the viral movement protein ORF. In conclusion, the plant host’s translation landscape changes dramatically during RCNMV infection, and regulation at the translational level operates largely independently of changes in mRNA transcription.

Learn more about EIRNABio’s ribosome profiling services here.

The proportional scaling of mRNA and ribosome concentrations controls eukaryotic cell growth

Nature Cell Biology, 2026

Gao, X., Lanz, M., Grosely, R., Cremer, J., Puglisi, J. and Skotheim, J.M.

Sunday Paper 3

Bacterial growth models attribute rate control to charged tRNA abundance and varying peptide elongation rates, but the limiting biosynthetic factors in eukaryotes remain poorly defined. In Saccharomyces cerevisiae, it was unresolved whether ribosome activity, elongation speed, or global transcript abundance sets the pace of proliferation across changing nutrient environments. Using spike-in RNA sequencing, the authors found that total cellular mRNA concentration increases monotonically with growth rate, scaling in direct proportion to ribosome abundance. Gene-specific mRNA fractions closely matched relative protein levels. Coupled with SLAM-seq showing largely invariant mRNA decay rates across nutrients, the RNA-seq data revealed that elevated transcription—driven by higher RNA Polymerase II concentration and an increased DNA-bound fraction—drives the growth-dependent accumulation of mRNA rather than changes in transcript stability.

By integrating ribosome profiling with RNA sequencing, the researchers evaluated genome-wide translation efficiency, defined as normalized ribosome footprint density divided by normalized mRNA density. While translation efficiencies spanned roughly two orders of magnitude across different genes, each gene’s individual translation efficiency remained remarkably constant between fast-growth (glucose) and slow-growth (trehalose) conditions, demonstrating that cells do not tune growth through transcript-specific translational remodelling. Together with single-molecule tracking demonstrating an invariant elongation speed (~9 amino acids per second), these sequencing approaches overturn canonical bacterial growth paradigms. Instead of modulating the speed or translational efficiency of individual ribosomes, budding yeast govern proliferation through mass-action kinetics by co-ordinately scaling total mRNA and ribosome pools to expand the fraction of actively translating ribosomes.

Learn more about EIRNABio’s ribosome profiling services here.