January 12th, 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:
- Yun et al. used ribo-seq and m6A-seq to uncover how novel duck reovirus induces translational shutoff in Muscovy ducklings by recruiting m6A-modified RNA into stress granules.
- Lee et al. used ribo-seq and polysome profiling to investigate how DEAD-box RNA helicases Dbp1 and Ded1 modulate yeast cell survival under heat stress, highlighting distinct roles in translation and stress granule formation.
- Ishibashi et al. employed disome-seq to reveal that the translation of zinc finger domains in zebrafish leads to ribosome collisions, triggering Znf598-dependent mRNA decay, essential for regulating early development.
Infection with novel duck reovirus induces stress granule and methylation-mediated host translational shutoff in Muscovy ducklings
Communications Biology, 2024
Yun, T., Hua, J., Chen, L., Ye, W., Ni, Z., Zhu, Y. and Zhang, C.
This study investigates how novel duck reovirus (NDRV) affects protein synthesis in Muscovy ducklings. NDRV is known to cause significant disease in waterfowl, but its interaction with host cellular mechanisms was not fully understood.
Researchers analysed the global translation efficiency in the bursa of Fabricius—a lymphoid organ—in NDRV-infected Muscovy ducklings using mass spectrometry and ribosome profiling. They discovered that NDRV infection leads to a substantial reduction in host protein synthesis. m6A sequencing revealed an enrichment for m6A modifications in the downregulated mRNAs. This suppression is mediated by the viral structural protein σB, which decreases the translation efficiency of m6A-modified RNA.
Further investigations revealed that σB interacts with stress granule components CAPRIN1 and G3BP1, as well as with m6A reader proteins YTHDF1 and YTHDF3. This interaction suggests that σB facilitates the sequestration of m6A-modified RNA into stress granules, thereby hindering their translation. The study also found significant overlap between m6A-modified RNA and G3BP1-enriched RNA, indicating that stress granules capture these methylated RNAs during infection.
In summary, the study uncovers a novel mechanism by which NDRV induces host translational shutoff in Muscovy ducklings. The viral protein σB plays a crucial role by recruiting m6A-modified RNA into stress granules, effectively suppressing host protein synthesis. These findings enhance our understanding of NDRV pathogenesis and may inform future therapeutic strategies against reovirus infections in waterfowl.
Learn more about EIRNA Bio’s ribosome profiling service here.
Analyses of translation factors Dbp1 and Ded1 reveal the cellular response to heat stress to be separable from stress granule formation
Cell Reports, 2024
Kuwayama, N., Powers, E.N., Siketanc, M., Sousa, C.I., Reynaud, K., Jovanovic, M., Hondele, M., Ingolia, N.T. and Brar, G.A.
This paper investigates the roles of the DEAD-box RNA helicases Dbp1 and Ded1 in yeast cells under heat stress. These helicases are involved in mRNA metabolism and translation initiation.
Upon heat stress, cells typically undergo translational repression and form stress granules—cytoplasmic aggregates containing untranslated mRNAs and proteins. Polysome profiling of cells expressing Dbp1 and Ded1 showed a significant reduction in translation under heat stress. Both helicases relocalise to stress granules during heat stress. However, Ded1 rapidly accumulates in stress granules, while Dbp1 shows a delayed response.
Interestingly, the deletion of DBP1 led to enhanced survival rates after heat shock, suggesting that Dbp1 may have a role in modulating the cellular response to heat stress. In contrast, Ded1 is essential for cell viability, and its depletion resulted in increased sensitivity to heat stress.
Ribo-seq revealed that Ded1 enhances translation of mRNAs with structured 5′ leaders under heat stress, while Dbp1 is less effective, leading to poor growth at high temperatures. In contrast, Dbp1 showed reduced ability to translate these transcripts, particularly housekeeping genes, leading to impaired growth at high temperatures.
The study also found that stress granule formation is nonessential for survival under heat stress, as mutants lacking stress granules did not exhibit reduced viability, indicating that the cellular response to heat stress can be uncoupled from stress granule formation.
In summary, the research highlights distinct roles for Dbp1 and Ded1 in the heat stress response and suggests that stress granule formation is not essential for survival under such conditions.
Learn more about EIRNA Bio’s ribosome profiling and polysome profiling services here.
Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish
PLOS Biology, 2024
Ishibashi, K., Shichino, Y., Han, P., Wakabayashi, K., Mito, M., Inada, T., Kimura, S., Iwasaki, S. and Mishima, Y.
This study investigates how the translation of C2H2-type zinc finger (C2H2-ZF) domains affects mRNA stability during zebrafish embryogenesis.
Researchers found that mRNAs encoding C2H2-ZF domains are selectively degraded during the maternal-to-zygotic transition in zebrafish embryos. This degradation is mediated by Znf598, an E3 ubiquitin ligase known to play a role in ribosome-associated quality control. In embryos lacking functional Znf598, these mRNAs were stabilized, indicating Znf598’s essential role in their decay.
Further analysis revealed that the translation of C2H2-ZF sequences leads to ribosome stalling and collision. Disome profiling, which identifies collided ribosomes, showed increased ribosome collisions on C2H2-ZF sequences. Reporter assays confirmed that these sequences induce ribosome stalling, triggering Znf598-dependent mRNA decay.
The study also noted that C2H2-ZF sequences are enriched with positively charged amino acids and non-optimal codons, features that may contribute to ribosome stalling. This suggests that the intrinsic properties of C2H2-ZF domains make their mRNAs susceptible to ribosome collision and subsequent decay.
In summary, the research demonstrates that the translation of C2H2-ZF domains induces ribosome collisions, leading to Znf598-mediated mRNA decay in zebrafish embryos. This mechanism plays a crucial role in regulating mRNA stability during early development.