March 9th, 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,
- Ramalho et al. use ribosome profiling to report that the nascent polypeptide–associated complex plays a crucial role in intestinal stem cell maintenance and differentiation.
- Han et al. use ribosome profiling to map genome-wide ribosome pausing sites in amylase producing Bacillus subtilis during long fermentation.
- Stevens et al. use RNA-Seq and 5PSeq to provide valuable insights into the early response to fluconazole in albicans.
NAC regulates metabolism and cell fate in intestinal stem cells
Science Advances, 2025
Ramalho, S., Alkan, F., Prekovic, S., Jastrzebski, K., Barberà, E.P., Hoekman, L., Altelaar, M., de Heus, C., Liv, N., Rodríguez-Colman, M.J., Yilmaz, M. et al.
The fate of intestinal stem cells (ISCs) is closely tied to their metabolic profile, which is typically marked by high mitochondrial respiration. Disruptions in ISC metabolism can lead to the loss of stem cells and contribute to disease development. Additionally, ISCs are the origin of intestinal cancer, and given the critical role of mitochondrial function in cancer maintenance, metastasis, and the development of chemotherapy resistance, gaining a deeper understanding of the metabolic processes that regulate ISCs could pave the way for potential therapeutic strategies. While studies have highlighted the complex relationship between metabolism and stem cell function, the regulatory mechanisms remain unclear.
Using ribosome profiling and CRISPR screening in intestinal organoids, the authors identify the nascent polypeptide–associated complex (NAC) as a crucial mediator of this process. Their findings show that NAC plays a key role in redistributing ribosomes to the mitochondria, thereby regulating ISC metabolism. When NAC is inhibited, intestinal cells exhibit reduced mitochondrial protein import, impairing oxidative phosphorylation and allowing the cells to retain their stem cell identity. Additionally, overexpressing NACα is sufficient to enhance mitochondrial respiration and promote ISC identity. In summary, their results highlight NAC’s central role in controlling ribosome localization, mitochondrial function, and ISC activity, offering new insights into the mechanisms that govern these processes.
Learn more about EIRNA Bio’s ribosome profiling service here.
Ribosome pausing in amylase producing Bacillus subtilis during long fermentation
Microbial Cell Factories, 2025
Han, Y., Wang, B., Agnolin, A., Dugar, G., van der Kloet, F., Sauer, C., Costea, P.I., Felle, M.F., Appelbaum, M. and Hamoen, L.W.
Ribosome pausing slows translation and affects protein synthesis, making the optimization of translation efficiency commercially valuable. This study investigated whether ribosome pausing occurs during the production of α-amylase AmyM in the industrial strain Bacillus subtilis under repeated batch fermentation. Ribosome profiling is a powerful tool for detecting translational pausing and stall sites. They validated their method using the antibiotic mupirocin, which halts translation at isoleucine codons. After confirming single-codon resolution, they mapped genome-wide ribosome pausing sites in B. subtilis at 16 and 64 hours of batch fermentation.
Several strong pausing sites were detected in the highly expressed amyM gene, persisting despite changes in nutrient availability. These pauses were not associated with proline residues, rare codons, or secondary protein structures. Notably, strong pausing sites were also observed in several toxin genes, potentially delaying translation to prevent premature cytosolic activity. The expression of amyM in B. subtilis involves multiple ribosome pausing events. Since these pauses cannot be explained by codon usage or protein structure, the researchers propose that secondary mRNA structures may be responsible. Mapping these sites provides valuable insights for future codon optimization strategies to enhance amylase production in B. subtilis.
Learn more about EIRNA Bio’s ribosome profiling service here.
The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans
Nature Scientific Reports, 2024
Stevens, I., Silao, F.G., Huch, S., Liu, H., Ryman, K., Carvajal-Jimenez, A., Ljungdahl, P.O. and Pelechano, V.
Candida albicans is a major cause of fungal infections in immunocompromised patients. Candidemia treatment relies on a limited number of antifungal agents, with fluconazole as the first-line therapy. However, the emergence of fluconazole-resistant strains underscores the urgent need to better understand the molecular mechanisms underlying drug response. In this study, by sequencing 5’P mRNA degradation intermediates, the authors demonstrate that co-translational mRNA decay occurs in C. albicans and show how in vivo 5′-3′ exonuclease degradation follows the last translating ribosome. This approach, known as 5’ Phosphorylated mRNA degradome sequencing (5PSeq), provides a simple and cost-effective method for analyzing ribosome dynamics and identifying codon-specific ribosome stalls in response to drugs and amino acid deprivation.
Building on this, they integrate RNA-Seq and 5PSeq to investigate the early response of fluconazole-sensitive and -resistant C. albicans isolates. The study reveals distinct transcriptional differences between fluconazole-sensitive and -resistant strains, even in the absence of drug treatment. Upon fluconazole exposure, they observe a strong upregulation of the ergosterol biosynthesis pathway and other related processes. In contrast, while global changes in ribosome dynamics occur across strains, the differences between them are relatively modest. Overall, these results provide valuable insights into the early response to fluconazole in C. albicans and highlight the utility of analyzing 5’P mRNA degradation intermediates to study ribosome dynamics.
Learn more about EIRNA Bio’s ribosome profiling services here.