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

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.

HYPK promotes the activity of the N α -acetyltransferase A complex to determine proteostasis of nonAc-X 2 /N-degron–containing proteins

“…The extractable proteasome activity was significantly enhanced in hypk lines compared to wild type and increased to similar levels as in NatA-depleted plants ( Fig. 4F ) ( 18 ).…”

“…Of these lower abundant proteins, 81 and 94% were canonical NatA substrates (table S4; Fisher’s exact test, P < 0.0001 for the enrichment of NatA substrates in the subset of lower abundant proteins in hypk lines), strongly suggesting that lowered NTA of these NatA substrates caused their destabilization. In a companion study ( 18 ), we demonstrated that decreased NatA activity resulted in a faster turnover of NatA substrates and identified the novel nonAc-X 2 /N-degron targeting nonacetylated NatA substrates for degradation. On the basis of the findings in hypk-3 and the knowledge of the NTA-mediated stabilization of NatA substrates, we suggested that the destabilization of many other NatA substrates is compensated by enhanced translation of these proteins to maintain their steady-state level in hypk plants.…”

“…The SPIS CCT1-tFT protein is not further destabilized in hypk-3 , demonstrating that CCT1 is destabilized in plants because of absent NTA. ( B ) Quantification of 10 selected NatA substrates (including CCT1) demonstrate that all previously identified nonAc-X 2 /N-degron containing proteins ( 18 ) are destabilized in hypk-3 . Data represent the means ± SE.…”

“…4E and 5, A and B ). In NatA-depleted plants, such an increased global protein turnover was also observed and caused by constitutively higher Target of Rapamycin (TOR) activity ( 18 ). Consequently, the increased protein turnover in hypk lines can be attributed to the NatA activity–promoting function of HYPK at the ribosome.…”

“…5 and figs. S11 to S18) ( 18 ). Because abscisic acid (ABA) dynamically down-regulates NatA transcription and NatA protein abundance, stimulus-induced increase of proteins harboring a free N terminus might help to replace stress-damaged proteins and add to protein surveillance as suggested earlier ( 16 ).…”