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Proteome-wide modulation of degradation dynamics in response to growth arrest

  1. Sina Ghaemmaghamia,b,1
  1. aDepartment of Biology, University of Rochester, Rochester, NY 14627;
  2. bMass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY 14627
  1. Edited by David A. Baker, University of Washington, Seattle, WA, and approved October 18, 2017 (received for review June 6, 2017)

Significance

In dividing cells, long-lived proteins are continuously diluted by being partitioned into newly formed daughter cells. Conversely, short-lived proteins are cleared from a cell primarily by proteolysis rather than cell division. Thus, when a cell stops dividing, there is a natural tendency for long-lived proteins to accumulate relative to short-lived proteins. This effect is disruptive to cells and leads to the accumulation of aged and damaged proteins over time. Here, we analyzed the degradation of thousands of proteins in dividing and nondividing (quiescent) skin cells. Our results demonstrate that quiescent cells avoid the accumulation of long-lived proteins by enhancing their degradation through pathways involving the lysosome. This mechanism may be important for promotion of protein homeostasis in aged organisms.

Abstract

In dividing cells, cytoplasmic dilution is the dominant route of clearance for long-lived proteins whose inherent degradation is slower than the cellular growth rate. Thus, as cells transition from a dividing to a nondividing state, there is a propensity for long-lived proteins to become stabilized relative to short-lived proteins, leading to alterations in the abundance distribution of the proteome. However, it is not known if cells mount a compensatory response to counter this potentially deleterious proteostatic disruption. We used a proteomic approach to demonstrate that fibroblasts selectively increase degradation rates of long-lived proteins as they transition from a proliferating to a quiescent state. The selective degradation of long-lived proteins occurs by the concurrent activation of lysosomal biogenesis and up-regulation of macroautophagy. Through this mechanism, quiescent cells avoid the accumulation of aged long-lived proteins that would otherwise result from the absence of cytoplasmic dilution by cell division.

Footnotes

  • ?1To whom correspondence should be addressed. Email: sghaemma{at}bio.rochester.edu.
  • Author contributions: T.Z. and S.G. designed research; T.Z., C.W., A.P., K.A.W., and J.R.H. performed research; T.Z. and S.G. analyzed data; and T.Z., K.A.W., and S.G. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • Data deposition: The proteomic data reported in this paper have been deposited in the ProteomeXchange Consortium database (accession no. PXD004937). The RNA-seq data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, http://www.danielhellerman.com/geo (accession no. GSE86867).

  • This article contains supporting information online at www.danielhellerman.com/lookup/suppl/doi:10.1073/pnas.1710238114/-/DCSupplemental.

Online Impact

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