Proteome-wide mapping of short-lived proteins in human cells

Li, Jiaming; Cai, Zhenying; Vaites, Laura Pontano; Shen, Ning; Mitchell, Dylan C.; Huttlin, Edward L.; Paulo, João A.; Harry, Brian L.; Gygi, Steven P.

doi:10.1016/j.molcel.2021.09.015

Cited by 76 publications

(76 citation statements)

References 84 publications

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“…[60][61][62] Interestingly, PRELID1 is a short-lived protein whose levels are highly sensitive to translational attenuation. 63 Consistent with this, PRELID1 levels are rapidly reduced in MEF mtGFP cells treated with CHX (Fig. S4C).…”

Section: Perk Signaling Leads To Reductions In the Intramitochondrial...supporting

confidence: 81%

PERK Signaling Promotes Mitochondrial Elongation By Remodeling Membrane Phosphatidic Acid

Perea

Cole

Lebeau

et al. 2022

Preprint

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Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are linked in the onset and pathogenesis of numerous diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria during ER stress. The PERK signaling arm of the unfolded protein response (UPR) has emerged as a prominent ER stress-responsive signaling pathway that regulates diverse aspects of mitochondrial biology. Here, we show that PERK activity also promotes adaptive remodeling of mitochondrial membrane phosphatidic acid (PA) to induce protective mitochondrial elongation during ER stress. We find that PERK activity is required for ER stress-dependent increases in both cellular PA and YME1L-dependent degradation of the intramitochondrial PA transporter PRELID1. Together, these processes lead to the accumulation of PA on the outer mitochondrial membrane where it induces mitochondrial elongation by inhibiting mitochondrial fission. Our results establish a new role for PERK in the adaptive remodeling of mitochondrial phospholipids and demonstrate that PERK-dependent PA regulation functions to adapt organellar shape in response to ER stress.

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Section: Perk Signaling Leads To Reductions In the Intramitochondrial...supporting

confidence: 81%

PERK Signaling Promotes Mitochondrial Elongation By Remodeling Membrane Phosphatidic Acid

Perea

Cole

Lebeau

et al. 2022

Preprint

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“…ATF6B, Sil1, APP, etc.) 53 demonstrate sharply decreased labeling by ER HRP following ML A/B treatment, consistent with their depletion from the ER (Figure S4).…”

Section: Orthogonality Of Cytosolic and Er Luminal Peroxidasessupporting

confidence: 63%

Monitoring Protein Import into the Endoplasmic Reticulum in Living Cells with Proximity Labeling

Lyu

Sycks

Espinoza

et al. 2021

Preprint

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The proper trafficking of eukaryotic proteins is essential to cellular function. Genetic, environmental, and other stresses can induce protein mistargeting, and in turn threaten cellular protein homeostasis. Current methods for measuring protein mistargeting are difficult to translate to living cells, and thus the role of cellular signaling networks in stress-dependent protein mistargeting processes, such as ER pre-emptive quality control (ER pQC), are difficult to parse. Herein, we use genetically encoded peroxidases to characterize protein import into the endoplasmic reticulum (ER). We show that the ERHRP/cytAPEX pair provides good selectivity and sensitivity for identifying protein mistargeting, using the known ER pQC substrate transthyretin (TTR). Although ERHRP labeling induces formation of detergent-resistant TTR aggregates, this is minimized by using low ERHRP expression, without loss of labeling efficiency. cytAPEX labeling recovers TTR that is mistargeted as a consequence of Sec61 inhibition or ER stress-induced ER pQC. Furthermore, we demonstrate that stress-free activation of the ER stress-associated transcription factor ATF6 recapitulates the TTR import deficiency of ER pQC. Hence, proximity labeling is an effective strategy for characterizing factors that influence ER protein import in living cells.

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“…For proteomics and phosphoproteomics analyses, the cells were treated for 10 min and 24 hours. The 10 min time point was chosen because rapid changes in the phosoproteome, and possibly the proteome, are expected to occur on this time scale 53 .…”

Section: Resultsmentioning

confidence: 99%

“…Protein half-lives in mammalian cells are generally in the order of hours on average, therefore at 10 min of exposure, little change would be expected in protein abundance. However, proteins can differ in turnover rates dramatically, across several orders of magnitude 77 , and many of them are shorted-lived 53 . Protein stability is also highly regulated, many with half-lives shorter than 20 min or even as short as a few minutes 78–81 .…”

Section: Discussionmentioning

confidence: 99%

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The phosphoproteome is a first responder in tiered cellular adaptation to chemical stress followed by proteomics and transcriptomics alteration

Chen

et al. 2022

Preprint

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Next-generation risk assessment for environmental chemicals and ingredients in consumer products involves a weight of evidence (WoE) framework integrating a suite of new approach methodologies (NAMs) based on points of departure (PoD) obtained from in vitro assays. Omics techniques provide broad coverages of the molecular toxicity pathway space. Transcriptomics assays especially play a leading role by providing relatively conservative PoDs in comparison with apical endpoints. However, it is unclear whether and how parameters measured using other omics technicquesparticipate in the cellular response to chemical perturbations, especially at exposure levels below the transcriptomically defined PoD. Multi-omics coverage may provide additional sensitive or confirmative biomarkers to complement and reduce the uncertainty in safety decisions made using targeted and transcriptomics assays. In the present study, we compared changes in transcriptomics, proteomics and phosphoproteomics with two prototype compounds, coumarin, as a main study and doxorubicin, as a complementary study to understand the sensitivity of the three omics techniques in response to chemically-induced changes in HepG2 and AC16 cells. With measurements obtained for multiple chemical concentrations and time points, we demonstrated that, compared with proteomics and transcriptomics, phosphoproteomics alterations occur not only earlier in time as expected, but also at much lower chemical concentrations and hence are proximal to the very early effects induced by chemical exposure. The phosphoproteomics changes appear to approach maximum when the transcriptomics alterations begin to be initiated. The results are consistent with a tiered framework of cellular response to chemical insults, where posttranslational modification of preexisting proteins is first seen before transcriptomics induction is engaged to launch a more energy-expensive defense that defines a useful PoD. We conclude that as the cost becomes more affordable, proteomics covering posttranslational modifications can be utilized to provide a more complete coverage of chemical-induced cellular alteration and supplement transcriptomics-based health safety decision making.

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Proteome-wide mapping of short-lived proteins in human cells

Cited by 76 publications

References 84 publications

PERK Signaling Promotes Mitochondrial Elongation By Remodeling Membrane Phosphatidic Acid

PERK Signaling Promotes Mitochondrial Elongation By Remodeling Membrane Phosphatidic Acid

Monitoring Protein Import into the Endoplasmic Reticulum in Living Cells with Proximity Labeling

The phosphoproteome is a first responder in tiered cellular adaptation to chemical stress followed by proteomics and transcriptomics alteration

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