Dataset Information

Oxygen-Sensitive Remodeling of Central Carbon Metabolism by Archaic eIF5B

ABSTRACT: The eukaryotic translation initiation factor 5B (eIF5B) is a homolog of the ancient IF2, a translation factor that facilitates initiator methionine-tRNAiMet (met-tRNAiMet) delivery to ribosomes in prokaryotes. IF2 evolved during early anaerobic cellular life and can be traced back to the last universal common ancestor. Here, we show that eIF5B is essential for eukaryotic hypoxia tolerance, reminiscent of how IF2 supports prokaryotic anaerobiosis. Global protein synthesis analyses identified eIF5B as a hypoxia-specific translation factor involved in translocating met-tRNAiMet to initiating ribosomes. Systemic translatome studies revealed that eIF5B-dependent mRNAs encode proteins of central carbon metabolism, fructolysis, and other pathways enhanced in organisms inhabiting hypoxic niches. These pathways rely preferentially on eIF5B rather than eIF2, the canonical initiation factor that delivers met-tRNAiMet during aerobic eukaryotic protein synthesis. We suggest that eIF5B/IF2 was retained during evolution of the aerobic eukaryotic lineage to cope with episodes of oxygen deprivation.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Jonathan Krieger

LAB HEAD: Stephen Lee

PROVIDER: PXD006799 | Pride | 2018-01-03

REPOSITORIES: Pride

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			Action	DRS
	David-HN-Fra1-2D1_170504093746.mgf	Mgf
	David-HN-Fra1-2D1_170504093746.pride.mgf.gz	Mgf
	David-HN-Fra1-2D1_170504093746.raw	Raw
	David-HN-Fra1-2D2_170504121031.mgf	Mgf
	David-HN-Fra1-2D2_170504121031.pride.mgf.gz	Mgf

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Oxygen-Sensitive Remodeling of Central Carbon Metabolism by Archaic eIF5B.

Ho J J David JJD Balukoff Nathan C NC Cervantes Grissel G Malcolm Petrice D PD Krieger Jonathan R JR Lee Stephen S

Cell reports 20180101 1

The eukaryotic translation initiation factor 5B (eIF5B) is a homolog of IF2, an ancient translation factor that enables initiator methionine-tRNAi<sup>Met</sup> (met-tRNAi<sup>Met</sup>) loading on prokaryotic ribosomes. While it can be traced back to the last universal common ancestor, eIF5B is curiously dispensable in modern aerobic yeast and mammalian cells. Here, we show that eIF5B is an essential element of the cellular hypoxic cap-dependent protein synthesis machinery. System-wide interrog ...[more]

PMID: 29298419

Publication: 1/2

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Project description:In eukaryotes, regulation of mRNA translation enables a fast, localized and finely tuned expression of gene products. Within the translation process, the first stage of translation initiation is most rigorously modulated by the actions of eukaryotic initiation factors (eIFs) and their associated proteins. These 11 eIFs catalyze the joining of the tRNA, mRNA and rRNA into a functional translation complex. Their activity is influenced by a wide variety of extra- and intracellular signals, ranging from global, such as hormone signaling and unfolded proteins, to specific, such as single amino acid imbalance and iron deficiency. Their action is correspondingly comprehensive, in increasing or decreasing recruitment and translation of most cellular mRNAs, and specialized, in targeting translation of mRNAs with regulatory features such as a 5’ terminal oligopyrimidine tract (TOP), upstream open reading frames (uORFs), or an internal ribosomal entry site (IRES). In mammals, two major pathways are linked to targeted mRNA translation. The target of rapamycin (TOR) kinase induces translation of TOP and perhaps other subsets of mRNAs, whereas a family of eIF2 kinases does so with mRNAs containing uORFs or an IRES. TOR targets translation of mRNAs that code for proteins involved in translation, an action compatible with its widely accepted role in regulating cellular growth. The four members of the eIF2 kinase family increase translation of mRNAs coding for stress response proteins such as transcription factors and chaperones. Though all four kinases act on one main substrate, eIF2, published literature demonstrates both common and unique effects by each kinase in response to its specific activating stress. This suggests that the activated eIF2 kinases regulate the translation of both a global and a specific set of mRNAs. Up to now, few studies have attempted to test such a hypothesis; none has been done in mammals. We use array analysis to determine the global mRNA shift into polysomes following a stress response, and to compare the translational response following activation of GCN2 versus PERK, two of the four eIF2alpha kinases. Experiment Overall Design: Gcn2 wild-type or knockout mouse liver were perfused with complete amino acids media or media lacking methionine for RNA extraction and hybridization of Affymetrix microarrays. RNA was extracted from unfractionated liver samples and polysome fraction of samples separated on sucrose density gradient. To minimize biological variations, we pooled RNA from two perfused liver samples to use in each array analysis. The conditions were total and polysome fraction of Gcn2+/+, +Met or -Met; total and polysome fraction of Gcn2-/-, +Met or -Met. Each array analysis was done in duplicate.