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Cited by 12RNA and protein synthesis mechanismsAdvanced Proteomics Techniques and ApplicationsPI3K/AKT/mTOR signaling in cancer

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pSNAP: Proteome-wide analysis of elongating nascent polypeptide chains

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Uchiyama, Junki, Roy, Rohini, Wang, Dan Ohtan, Morikawa, Kazuya, Kawahara, Yuka, Iwasaki, Mio, Yoshino, Chiaki, Mishima, Yuichiro, Ishihama, Yasushi, Imami, Koshi·2022·iScience
DOI 10.1016/j.isci.2022.104516PMC PMC9218386

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Abstract

Cellular global translation is often measured using ribosome profiling or quantitative mass spectrometry, but these methods do not provide direct information at the level of elongating nascent polypeptide chains (NPCs) and associated co-translational events. Here, we describe pSNAP, a method for proteome-wide profiling of NPCs by affinity enrichment of puromycin- and stable isotope-labeled polypeptides. pSNAP does not require ribosome purification and/or chemical labeling, and captures bona fide NPCs that characteristically exhibit protein N-terminus-biased positions. We applied pSNAP to evaluate the effect of silmitasertib, a potential molecular therapy for cancer, and revealed acute translational repression through casein kinase II and mTOR pathways. We also characterized modifications on NPCs and demonstrated that the combination of different types of modifications, such as acetylation and phosphorylation in the N-terminal region of histone H1.5, can modulate interactions with ribosome-associated factors. Thus, pSNAP provides a framework for dissecting co-translational regulations on a proteome-wide scale.

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Metadata

Authors
Uchiyama, J., Roy, R., Wang, D. O., Morikawa, K., Kawahara, Y., Iwasaki, M., Yoshino, C., Mishima, Y., Ishihama, Y., & Imami, K.
Affiliations
  • Kyoto University (JP)
  • Shenyang Pharmaceutical University (CN)
  • Center for iPS Cell Research and Application, Kyoto University (JP)
  • Kyoto Sangyo University (JP)
Corresponding author
  • Ishihama, Yasushi
  • Imami, Koshi
ORCID
Venue
iScience
Publisher
Elsevier BV
Published
2022-07
Volume
25
Issue
7
Pages
104516
ISSN
2589-0042 (ISSN-L)
DOI
10.1016/j.isci.2022.104516
PMC
PMC9218386
OpenAlex
W4281963797
Cited by
12
References
7
Citations by year
2026: 2 · 2025: 3 · 2024: 1 · 2023: 5 · 2022: 1
FWCI
0.82
Type
journal article
Language
en
Open access
Licence
Locations
  • iScience (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Institutional Repositories DataBase (IRDB) (submittedVersion)
  • Kyoto University Research Information Repository (Kyoto University) (submittedVersion, cc-by-nc-nd)
Funders
  • Dow Chemical Company
  • Harvard Medical School
  • Takeda Science Foundation
  • Exploratory Research for Advanced Technology (JPMJER2101)
  • Japan Science and Technology Agency
  • Tokyo Institute of Technology
  • Precursory Research for Embryonic Science and Technology (JPMJPR18H2)
  • Japan Agency for Medical Research and Development (18dm0307023h)
  • Japan Society for the Promotion of Science (17H05667, 18K14674, 20H03241, 20H04844, 21H05720)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › PI3K/AKT/mTOR signaling in cancer
Keywords
nascent polypeptide chains, co-translational modification, stable isotope labeling, silmitasertib, casein kinase 2, mTOR signaling, protein synthesis inhibition, acetylation, phosphorylation, ribosome-associated factors

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