DCP2, encoding a major mRNA decapping enzyme, is identified as a previously unrecognized ISR-induced transcript and it is shown that translational induction of DCP2 depends on an overlapping ORF whose conserved 3′ region, corresponding to a ribosome pausing site, acts as a potent inhibitory element.
Abstract
The integrated stress response (ISR) globally suppresses protein synthesis while selectively permitting translation of a small subset of stress-responsive mRNAs, many of which contain upstream or overlapping open reading frames (uORFs/oORFs). Although translational induction of transcripts such as ATF4 has classically been attributed to delayed re-initiation caused by reduced ternary complex availability, the mechanisms by which uORFs and oORFs allow ISR-selective translation remain incompletely understood. Here, using ribosome profiling during early ISR activation combined with reporter assays, we identify DCP2, encoding a major mRNA decapping enzyme, as a previously unrecognized ISR-induced transcript. We show that translational induction of DCP2 depends on an overlapping ORF whose conserved 3′ region, corresponding to a ribosome pausing site, acts as a potent inhibitory element. Both the DCP2 oORF and main ORF increase in translation during stress, indicating that stress relieves repression by this inhibitory element. This reveals a mode of ISR- dependent gene regulation in which inhibition by a nascent peptide or stalling element embedded either in a uORF or an oORF is relieved upon stress to induce translation.
Together, the findings establish hY3 as a ribosome-bound regulator of translation and stress responses, positioning it as a determinant of cell fate under metabolic stress.
This study identifies the direct coordination of translation suppression and transcriptome reprogramming through m6A during the ISR, and shows that mRNA stabilization, not transcription activation, explains much of the transcriptome response during the ISR.
It is proposed that MraW modification of 16S rRNA enhances translation efficiency in general, and that specific transcripts have evolved structural features that fine-tune protein levels that may be prevalent in bacteria which exhibit uncoupled transcription and translation.
Zachory M. Park, Christina R. Savage, Amanda R. Decker-Farrell et al.· Cell Reports· 0 citations
Iron is an essential micronutrient for all eukaryotes, required as a cofactor for fundamental biological processes, including protein synthesis. Iron depletion causes extensive reprogramming of gene expression and a complex translational response. While global repression of translation under iron scarcity has largely been attributed to TORC1 inhibition and Gcn2 mediated phosphorylation of eIF2α, the involvement of additional post transcriptional regulators has remained unclear. In this report, we uncover that the DEAD box helicase Dhh1 and the decapping activator Pat1 are key regulators of the translational reprogramming that occurs during iron starvation. Polysome profiling shows that the deletion of
DHH1
or
PAT1
attenuates the reduction in translation after prolonged iron deficiency, and that both proteins act within the same pathway. In contrast, Dhh1 acts independently of the Gcn2 pathway. We further reveal an unexpected role of Dhh1 and Pat1 in the generation of 3′UTR derived translation products, a phenomenon associated with a reduced activity of the essential protein Rli1 during iron-limited conditions. Loss of either factor greatly diminishes the appearance of these reinitiation-derived peptides, while Gcn2 does not appear to be involved in this process. Notably,
RLI1
transcripts levels are elevated in a
dhh1Δ
mutant, suggesting that Dhh1 contributes to
RLI1
mRNA downregulation under iron deficiency. Altogether, our results situate Dhh1 and Pat1 as central regulators of the translational response to iron starvation, coordinating both repression of initiation and downstream reinitiation events.
Antonia María Romero Cuadrado, C. Gerez, Sara Sáiz-Baggetto et al.· Scientific Reports· 0 citations
A redox-sensitive mTOR-eIF4A signaling pathway that preferentially enhances ABCB1/P-gp translation and contributes to pulmonary detoxification is supported.
Peng Jin, Ming Jin, Luqiu Feng et al.· Free Radical Biology & Medic...· 0 citations
A quantitative live-cell imaging framework is developed that resolves distinct kinetic phases of SG assembly at single-cell resolution and combines these measurements with single-cell analysis of protein synthesis and identifies the conserved eIF4B RRM as a regulator of productive higher-order organization of the translation initiation machinery.
Jessica Bolivar, N. DeCuzzi, Elijah Kofke et al.· bioRxiv· 0 citations