A translational program that suppresses metabolism to shield the genome

Nathan C Balukoff,Jonathan R Krieger,J J David Ho,Stephen Lee,Phaedra R Theodoridis,Lis M Llanio,Michael Bokros,Jonathan H Schatz,Miling Wang

doi:10.1038/s41467-020-19602-2

Abstract

Translatome reprogramming is a primary determinant of protein levels during stimuli adaptation. This raises the question: what are the translatome remodelers that reprogram protein output to activate biochemical adaptations. Here, we identify a translational pathway that represses metabolism to safeguard genome integrity. A system-wide MATRIX survey identified the ancient eIF5A as a pH-regulated translation factor that responds to fermentation-induced acidosis. TMT-pulse-SILAC analysis identified several pH-dependent proteins, including the mTORC1 suppressor Tsc2 and the longevity regulator Sirt1. Sirt1 operates as a pH-sensor that deacetylates nuclear eIF5A during anaerobiosis, enabling the cytoplasmic export of eIF5A/Tsc2 mRNA complexes for translational engagement. Tsc2 induction inhibits mTORC1 to suppress cellular metabolism and prevent acidosis-induced DNA damage. Depletion of eIF5A or Tsc2 leads to metabolic re-initiation and proliferation, but at the expense of incurring substantial DNA damage. We suggest that eIF5A operates as a translatome remodeler that suppresses metabolism to shield the genome.

Highlights

Translatome reprogramming is a primary determinant of protein levels during stimuli adaptation
Physiological anaerobic acidosis was modeled by allowing hypoxic (1% O2) cells to naturally acidify their extracellular milieu to pH 6.0, which recapitulates various in vivo conditions, e.g., ischemic tissues[36] and microenvironments of aggressive tumors[37,38]
We first performed an unbiased, high-throughput analysis of the translational architecture of cells adapting to hypoxia-induced acidosis using our recently developed MATRIX20 platform, which discriminates translation factors based on their distribution in sucrose gradients (Fig. 1a, Supplementary Fig. 2a)

Summary

Introduction

Translatome reprogramming is a primary determinant of protein levels during stimuli adaptation. Translation factors eIF3d31, eIF4E221,24, eIF4G321, eIF4E322, eIF5B20, and DAP532 have been demonstrated as critical components of specialized translation machineries in cells responding to various conditions These translation factors operate as translatome remodelers that control protein outputs at the translational level (i.e., TE of mRNAs) to activate biochemical pathways. Given a model of translational plasticity and the drastic effects of anaerobic acidosis on cellular physiology, we hypothesized that cells activate a unique translational program to produce key proteins required to suppress metabolism and preserve genomic integrity This hypothesis was tested using several system-level technologies, including our recently developed mass spectrometry analysis of translation factors using ribosomedensity fractionation and isotopic labeling experiments[20] (MATRIX) platform, which generates snapshots of translationfactor distribution in free, monosomes, light and heavy polysome fractions under different cellular conditions. We discuss a model by which eIF5A operates as a translatome remodeler that mediates metabolic depression to shield the genome

Methods

Results

Conclusion