A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress
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ABSTRACT: Shutoff of global protein synthesis is a conserved response to cellular stresses. This general phenomenon is accompanied by induction of distinct gene programs tailored to each stress condition. Although the mechanisms that lead to general repression of protein synthesis are well characterized, how cells reprogram the translation machinery for selective gene expression remains poorly understood. Here we show that the noncanonical 5′ cap-binding protein eIF3d is specifically activated in response to metabolic stress, due to loss of CK2-mediated phosphorylation near the eIF3d cap-binding pocket. Activated eIF3d controls a gene program enriched in factors important for glucose homeostasis, including members of the mTOR pathway, and eIF3d-mediated translation adaptation is essential for cell survival during chronic glucose deprivation. Our findings reveal a new mechanism of translation reprogramming engaged in response to metabolic stress.
Project description:All cells respond to intrinsic and extrinsic stresses by reducing global protein synthesis and activating select gene programs necessary for survival. Here, we show the fundamental integrated stress response (ISR) is driven by the non-canonical cap-binding protein eIF3d which acts as a master effector to control core stress response orchestrators, the translation factor eIF2ɑ and the transcription factor ATF4. We find that during persistent stress, eIF3d activates translation of the protein kinase GCN2, inducing eIF2ɑ phosphorylation and inhibiting global protein synthesis. In parallel, eIF3d upregulates the m6A demethylase enzyme ALKBH5 to drive 5′ UTR-specific demethylation of stress response genes, including ATF4. Ultimately, this cascade converges on ATF4 expression by increasing mRNA engagement of translation machinery and enhancing ribosome bypass of upstream open reading frames. Our results reveal that eIF3d acts as a critical life-or-death decision point during adaptation to chronic stress and uncover a synergistic signaling mechanism in which translational cascades dynamically complement transcriptional amplification to control essential cellular processes.
Project description:We study here how mRNAs are translated in an eIF4E1-independent manner by blocking eIF4E1 using a constitutively active version of eIF4E-binding protein (4E-BP). Via ribosome profiling we identify a subset of mRNAs that are still efficiently translated when eIF4E1 is inactive. We find that these mRNAs preferentially release eIF4E1 when eIF4E1 is inactive and bind instead to eIF3D via its cap-binding pocket. eIF3D then enables these mRNAs to be efficiently translated due to its cap-binding activity.
Project description:Pluripotent stem cell identities such as differentiation and infinite proliferation have long been decoded in the frameworks of transcription factor networks, epigenomes, and signal transduction, yet unclear and fragmented. However, directing attention toward translation regulation, the bridge between these events promises to provide new insights into previously unexplained mechanisms. Functional screening led to the discovery that EIF3D maintains primed pluripotency via selective translation regulation. The loss of EIF3D unbalanced the pluripotency-associated signaling pathways, disrupting primed pluripotency. Furthermore, we found that EIF3D safeguards robust proliferation by managing the translation of multiple p53 regulators that maintain low p53 activity in the undifferentiated state. Therefore, this study provides a paradigm for selective translation regulation that defines the primed pluripotent stem cell identity.
Project description:Pluripotent stem cell identities such as differentiation and infinite proliferation have long been decoded in the frameworks of transcription factor networks, epigenomes, and signal transduction, yet unclear and fragmented. However, directing attention toward translation regulation, the bridge between these events promises to provide new insights into previously unexplained mechanisms. Functional screening led to the discovery that EIF3D maintains primed pluripotency via selective translation regulation. The loss of EIF3D unbalanced the pluripotency-associated signaling pathways, disrupting primed pluripotency. Furthermore, we found that EIF3D safeguards robust proliferation by managing the translation of multiple p53 regulators that maintain low p53 activity in the undifferentiated state. Therefore, this study provides a paradigm for selective translation regulation that defines the primed pluripotent stem cell identity.
Project description:Pluripotent stem cell identities such as differentiation and infinite proliferation have long been decoded in the frameworks of transcription factor networks, epigenomes, and signal transduction, yet unclear and fragmented. However, directing attention toward translation regulation, the bridge between these events promises to provide new insights into previously unexplained mechanisms. Functional screening led to the discovery that EIF3D maintains primed pluripotency via selective translation regulation. The loss of EIF3D unbalanced the pluripotency-associated signaling pathways, disrupting primed pluripotency. Furthermore, we found that EIF3D safeguards robust proliferation by managing the translation of multiple p53 regulators that maintain low p53 activity in the undifferentiated state. Therefore, this study provides a paradigm for selective translation regulation that defines the primed pluripotent stem cell identity.
Project description:Pluripotent stem cell identities such as differentiation and infinite proliferation have long been decoded in the frameworks of transcription factor networks, epigenomes, and signal transduction, yet unclear and fragmented. However, directing attention toward translation regulation, the bridge between these events promises to provide new insights into previously unexplained mechanisms. Functional screening led to the discovery that EIF3D maintains primed pluripotency via selective translation regulation. The loss of EIF3D unbalanced the pluripotency-associated signaling pathways, disrupting primed pluripotency. Furthermore, we found that EIF3D safeguards robust proliferation by managing the translation of multiple p53 regulators that maintain low p53 activity in the undifferentiated state. Therefore, this study provides a paradigm for selective translation regulation that defines the primed pluripotent stem cell identity.
Project description:A prominent hallmark of cancer is deregulated protein synthesis. It is well established that various translation initiation factors (eIFs) are either overexpressed or under-expressed in numerous types of cancer. Recent studies suggest that rather than representing an indirect consequence of neoplasia, imbalanced expression of eIFs significantly contributes to cellular transformation, tumor development, cancer cell survival, metastasis and tumor angiogenesis. Among them, eIF3 stands out as the largest complex composed of 12 subunits with a modular assembly, where aberrant expression of one subunit leads to partially functional subcomplexes. Here we took advantage of well-established knockdowns of subunits d, e and h of human eIF3, all implicated in cancer, and investigated their impact on differential gene expression translatome-wide by Ribo-Seq. We demonstrate that eIF3e and eIF3d knock-downs result in reduced translation efficiency of numerous components of the MAPK signaling pathway, a pathway often upregulated in cancer, and pathways preventing genotoxic stress. Concurrently, depletion of eIF3d increased translation of proteins associated with membrane organelles, whereas eIF3e depletion increased expression of numerous ribosomal proteins, implicating eIF3e in controlling the balanced production of mature ribosomes. Overall, our data illustrate that individual eIF3 subunits exert specific translational control over a broad range of cellular transcripts.
Project description:Cellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in response to glucose starvation and heat shock. Each stress induced rapid remodeling of the RNA-protein interactome, without corresponding changes in RBP abundance. Consistent with general translation shutdown, ribosomal proteins contacting the mRNA showed decreased RNA-association. Among translation components, RNA-association was most reduced for initiation factors involved in 40S scanning (eIF4A, eIF4B, and Ded1), indicating a common mechanism of translational repression. In unstressed cells, eIF4A, eIF4B, and Ded1 primarily targeted the 5′-ends of mRNAs. Following glucose withdrawal, 5’-binding was abolished within 30sec, explaining the rapid translation shutdown, but mRNAs remained stable. Heat shock induced progressive loss of 5’ RNA-binding by initiation factors over ~16min. Translation shutoff provoked selective 5′-degradation of mRNAs encoding translation-related factors, mediated by Xrn1. These results reveal mechanisms underlying translational control of gene expression during stress.