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Targeted protein degradation plays a wide range of important roles in plant growth and development, but analyzing protein turnover in vivo is technically challenging. Until recently, there has been no straightforward methodology for quantifying protein dynamics at subcellular resolution during cellular transitions in plants. A tandem fluorescent protein timer (tFT) is a fusion of two different fluorescent proteins with distinct fluorophore maturation kinetics, which allows estimation of relative protein age from the ratio of fluorescence intensities of the two fluorescent proteins. Here, we describe approaches to use this technology to report relative protein lifetime in both transient and stable plant transformation systems. tFTs enable in vivo, real-time protein lifetime assessment within subcellular compartments and across tissues, permitting the analysis of protein degradation dynamics in response to stresses or developmental cues and in different genetic backgrounds., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

In humans, the Huntingtin yeast partner K (HYPK) binds to the ribosome-associated N α -acetyltransferase A (NatA) complex that acetylates ~40% of the proteome in humans and Arabidopsis thaliana . However, the relevance of Hs HYPK for determining the human N-acetylome is unclear. Here, we identify the At HYPK protein as the first in vivo regulator of NatA activity in plants . At HYPK physically interacts with the ribosome-anchoring subunit of NatA and promotes N α -terminal acetylation of diverse NatA substrates. Loss-of- At HYPK mutants are remarkably resistant to drought stress and strongly resemble the phenotype of NatA-depleted plants. The ectopic expression of Hs HYPK rescues this phenotype. Combined transcriptomics, proteomics, and N-terminomics unravel that HYPK impairs plant metabolism and development, predominantly by regulating NatA activity. We demonstrate that HYPK is a critical regulator of global proteostasis by facilitating masking of the recently identified nonAc-X 2 /N-degron. This N-degron targets many nonacetylated NatA substrates for degradation by the ubiquitin-proteasome system.

N-terminal acetylation is one of the most common protein modifications in eukaryotes, and approximately 40% of human and plant proteomes are acetylated by ribosome-associated N-terminal acetyltransferase A (NatA) in a co-translational manner. However, the in vivo regulatory mechanism of NatA and the global impact of NatA-mediated N-terminal acetylation on protein fate remain unclear. Here, we identify Huntingtin Yeast partner K (HYPK), an evolutionarily conserved chaperone-like protein, as a positive regulator of NatA activity in rice. We found that loss of OsHYPK function leads to developmental defects in rice plant architecture but increased resistance to abiotic stresses, attributable to perturbation of the N-terminal acetylome and accelerated global protein turnover. Furthermore, we demonstrated that OsHYPK is also a substrate of NatA and that N-terminal acetylation of OsHYPK promotes its own degradation, probably through the Ac/N-degron pathway, which could be induced by abiotic stresses. Taken together, our findings suggest that the OsHYPK-NatA complex plays a critical role in coordinating plant development and stress responses by dynamically regulating NatA-mediated N-terminal acetylation and global protein turnover, which are essential for maintaining adaptive phenotypic plasticity in rice., (Copyright © 2022 The Author. Published by Elsevier Inc. All rights reserved.)

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 N α -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., (© 2022. The Author(s).)