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Abstract Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studiedE. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200E. coliproteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway inE. coliremains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates inE. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.
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Alternative proteoforms and proteoform-dependent assemblies in humans and plants
Abstract The variability of proteins at the sequence level creates an enormous potential for proteome complexity. Exploring the depths and limits of this complexity is an ongoing goal in biology. Here, we systematically survey human and plant high-throughput bottom-up native proteomics data for protein truncation variants, where substantial regions of the full-length protein are missing from an observed protein product. In humans,Arabidopsis, and the green algaChlamydomonas, approximately one percent of observed proteins show a short form, which we can assign by comparison to RNA isoforms as either likely deriving from transcript-directed processes or limited proteolysis. While some detected protein fragments align with known splice forms and protein cleavage events, multiple examples are previously undescribed, such as our observation of fibrocystin proteolysis and nuclear translocation in a green alga. We find that truncations occur almost entirely between structured protein domains, even when short forms are derived from transcript variants. Intriguingly, multiple endogenous protein truncations of phase-separating translational proteins resemble cleaved proteoforms produced by enteroviruses during infection. Some truncated proteins are also observed in both humans and plants, suggesting that they date to the last eukaryotic common ancestor. Finally, we describe novel proteoform-specific protein complexes, where the loss of a domain may accompany complex formation.
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- Award ID(s):
- 2337141
- PAR ID:
- 10517334
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Molecular Systems Biology
- Volume:
- 20
- Issue:
- 8
- ISSN:
- 1744-4292
- Format(s):
- Medium: X Size: p. 933-951
- Size(s):
- p. 933-951
- Sponsoring Org:
- National Science Foundation
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