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,

  • Zhao et al. show that Stuxnet regulates Uhg5 and parkin to balance mitochondrial translation, mitophagy, and sleep, with implications for neurodegeneration.
  • Choi et al. highlight that BipA coordinates ribosome assembly and surface biogenesis in Salmonella, linking translation defects to stress adaptation and virulence regulation.
  • Lee et al. reveal that Hda1C coordinates transcriptional and translational rewiring under nutrient starvation to support metabolic adaptation and cellular survival.

Stuxnet balances mitochondria homeostasis by regulating uhg5 and parkin.

Cell Reports. 2026.

Zhao, X., Yang, X., Huang, Y., Zhang, Y., Cui, X., Zhang, J. and Du, J.

Sunday Paper 1

The research group investigates the role of Stuxnet (Stx), a protein previously linked to proteasome-independent degradation, in regulating mitochondrial homeostasis and sleep in Drosophila. Ribo-seq was used to identify translation defects in mitochondrial transcripts caused by mitochondrial gene Uhg5 loss that disrupts sleep by impairing translation of mitochondrial genes. Uhg5 produces small nucleolar RNAs (snoRNAs) that directly regulate mitochondrial transcripts, linking noncoding RNA processing to mitochondrial biogenesis. Stx was found to bind both Uhg5 and parkin mRNAs, the latter encoding a key mitophagy regulator.

Using GoldCLIP and genetic interaction assays, the study demonstrates that Stx coordinates two complementary pathways: mitochondrial biogenesis via Uhg5 and mitochondrial quality control/mitophagy via Parkin. This balancing mechanism maintains mitochondrial homeostasis and normal sleep behaviour. The findings also suggest a molecular connection between Stx dysfunction and Parkinson’s disease-related pathways.

Learn more about EIRNABio’s ribosome profiling services here.

The dual functions of the GTPase BipA in ribosome assembly and surface structure biogenesis in Salmonella enterica serovar Typhimurium

PLoS Pathogens. 2025.

Choi, E., Ryu, E., Kim, D., Byun, J.W., Kim, K., Lee, M. and Hwang, J.

Sunday Paper 2

This study characterises the conserved GTPase BipA in Salmonella enterica serovar Typhimurium and shows it plays dual roles in ribosome assembly and surface structure biogenesis. BipA is required for efficient maturation of the 50S ribosomal subunit, particularly under stress conditions such as low temperature, and its loss leads to defects in ribosome assembly and impaired bacterial growth. Polysome profiling was used to connect ribosome biogenesis disruptions to altered protein synthesis under stress conditions.

Beyond translation machinery, BipA also regulates expression of genes involved in flagella production, motility, and outer membrane architecture, linking ribosome biogenesis with cell surface remodeling. This coordination suggests BipA acts as a molecular switch integrating environmental signals with both protein synthesis and virulence-related traits. Overall, the study reveals that BipA is essential for balancing translational capacity and bacterial adaptive responses, contributing to fitness and pathogenic potential.

Learn more about EIRNABio’s polysome profiling services here.

Nutrient starvation-induced Hda1C rewiring: coordinated regulation of transcription and translation

Nucleic Acids Research. 2025.

Lee, M.K., Kang, B., Shin, M.K., Kim, Y.K., Kim, H.Y., Lee, S.Y., Roh, T.Y. and Kim, T.

Sunday Paper 3

This study investigates how the Hda1C histone deacetylase complex in yeast is rewired under nutrient starvation to coordinate transcriptional and translational control. Under nutrient-rich conditions, Hda1C primarily represses gene expression through chromatin modification. However, during starvation, the complex undergoes functional reprogramming, leading to widespread changes in both mRNA production and translation efficiency. Ribosome profiling (Ribo-seq) was used to provide codon-level resolution of translational efficiency, uncovering gene-specific regulation and showing coordinated but distinct transcription–translation rewiring during nutrient stress.

The authors show that Hda1C interacts with stress-responsive regulatory networks to selectively activate genes involved in nutrient scavenging and metabolic adaptation while repressing growth-related programs. This dual regulation ensures efficient resource allocation during stress. Integrated multi-omics analyses reveal that transcriptional changes are tightly coupled with shifts in translation, indicating a coordinated gene expression response rather than independent regulation. Overall, the study demonstrates that Hda1C acts as a dynamic regulator that integrates chromatin remodeling with translational control to support cellular survival under nutrient-limited conditions.

Learn more about EIRNABio’s ribosome profiling services here.