Cotranslational N-degron masking by acetylation promotes proteome stability in plants

Eric Linster,Xiaodi Gong,Pavlina Miklankova,Johannes Mueller,Markus Wirtz,Thomas Ruppert,Laura Armbruster,Giovanna Serino,Matthias Mann,Francy L Forero Ruiz,Rüdiger Hell

doi:10.1038/s41467-022-28414-5

Abstract

N-terminal protein acetylation (NTA) is a prevalent protein modification essential for viability in animals and plants. The dominant executor of NTA is the ribosome tethered Nα-acetyltransferase A (NatA) complex. However, the impact of NatA on protein fate is still enigmatic. Here, we demonstrate that depletion of NatA activity leads to a 4-fold increase in global protein turnover via the ubiquitin-proteasome system in Arabidopsis. Surprisingly, a concomitant increase in translation, actioned via enhanced Target-of-Rapamycin activity, is also observed, implying that defective NTA triggers feedback mechanisms to maintain steady-state protein abundance. Quantitative analysis of the proteome, the translatome, and the ubiquitome reveals that NatA substrates account for the bulk of this enhanced turnover. A targeted analysis of NatA substrate stability uncovers that NTA absence triggers protein destabilization via a previously undescribed and widely conserved nonAc/N-degron in plants. Hence, the imprinting of the proteome with acetylation marks is essential for coordinating proteome stability.

Highlights

N-terminal protein acetylation (NTA) is a prevalent protein modification essential for viability in animals and plants
The accumulation of both subunits was not triggered by enhanced steady state transcript levels (Supplementary Fig. 2e), albeit, the pathways of ubiquitinmediated proteolysis is transcriptionally induced upon Nα-acetyltransferase A (NatA) depletion[10].The endogenous ubiquitination rate increased in NatA depleted plants and resulted in most significant accumulation of poly-ubiquitinated proteins in the transgenic line with the most substantial depletion of NatA activity
Enhanced neddylation of Cullin 1 demonstrated that Cullin-RING E3 ligases (CRLs20), contributed to the enhanced in vivo ubiquitination activity in NatA depleted plants (Fig. 1d, Supplementary Fig. 2g)

Summary

Introduction

N-terminal protein acetylation (NTA) is a prevalent protein modification essential for viability in animals and plants. Protein modifications have been identified as crucial determinants of protein stability in eukaryotes and are highly regulated upon diverse plant stress conditions. NTA occurs on 80-90% of human and Arabidopsis soluble proteins and is executed by up to five ribosome-associated N-terminal acetyltransferases (Nat) complexes, of which NatA, NatB and NatC are conserved in all eukaryotes[2]. NTA can create N-degrons recognized by the Ac/N-degron pathway and leading to the destruction of proteins by the UPS On the contrary, another set of proteins was stabilized by NTA13,14. A recent study demonstrated an overlap of substrates recognized by NatA and the IAP-type E3-ubiquitin ligases in vitro, suggesting that N-terminal acetylation is relevant for protein stabilization in metazoans[19]. We show that impairment of NatA-dependent NTA results in a global destabilization of the proteome in Arabidopsis and discover a novel degron that marks the majority of nonacetylated cytosolic proteins for degradation via the ubiquitin system

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Conclusion