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

• Published in: Nature chemical biology Vol. 18; no. 6; pp. 643 - 651
• Main Authors: Cao, Xiongwen, Khitun, Alexandra, Harold, Cecelia M., Bryant, Carson J., Zheng, Shu-Jian, Baserga, Susan J., Slavoff, Sarah A.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.06.2022; Nature Publishing Group
• Subjects: 631/337/574; 631/92/475; Assembly; Biochemical Engineering; Biochemistry; Bioorganic Chemistry; Cell Biology; Cell Cycle Proteins - metabolism; Cell proliferation; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Cytoplasm; Depletion; DNA damage; Humans; Hypotheses; Immune checkpoint; Nucleoli; Post-transcription; Protein biosynthesis; Protein synthesis; Proteins; Ribosomal Proteins - metabolism; Ribosome Subunits, Large, Eukaryotic - genetics; Ribosome Subunits, Large, Eukaryotic - metabolism; RNA, Ribosomal; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - metabolism
• ISSN: 1552-4450; 1552-4469; 1552-4469
• DOI: 10.1038/s41589-022-01003-9

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. Cao et al. develop a chemoproteomic pipeline to identify nascent unannotated alt-proteins and show that cell-cycle-regulated alt-protein MINAS-60 is a checkpoint inhibitor of pre-60S assembly.