Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor

  • Nat Chem Biol. 2022 Jun;18(6):643-651. doi: 10.1038/s41589-022-01003-9.
Xiongwen Cao  1  2 ,  Alexandra Khitun  1  2 ,  Cecelia M Harold  3 ,  Carson J Bryant  4 ,  Shu-Jian Zheng  1  2 ,  Susan J Baserga  3  4  5 ,  Sarah A Slavoff  6  7  8
Affiliations
  • 1. Department of Chemistry, Yale University, New Haven, CT, USA.
  • 2. Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA.
  • 3. Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
  • 4. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
  • 5. Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA.
  • 6. Department of Chemistry, Yale University, New Haven, CT, USA. [email protected].
  • 7. Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA. [email protected].
  • 8. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. [email protected].
PMID: 35393574 DOI: 10.1038/s41589-022-01003-9
Abstract

Many unannotated microproteins and alternative proteins (alt-proteins) are coencoded with canonical proteins, but few of their functions are known. Motivated by the hypothesis that alt-proteins undergoing regulated synthesis could play important cellular roles, we developed a chemoproteomic pipeline to identify nascent alt-proteins in human cells. We identified 22 actively translated alt-proteins or N-terminal extensions, one of which is post-transcriptionally upregulated by DNA damage stress. We further defined a nucleolar, cell-cycle-regulated alt-protein that negatively regulates assembly of the pre-60S ribosomal subunit (MINAS-60). Depletion of MINAS-60 increases the amount of cytoplasmic 60S ribosomal subunit, upregulating global protein synthesis and cell proliferation. Mechanistically, MINAS-60 represses the rate of late-stage pre-60S assembly and export to the cytoplasm. Together, these results implicate MINAS-60 as a potential checkpoint inhibitor of pre-60S assembly and demonstrate that chemoproteomics enables hypothesis generation for uncharacterized alt-proteins.