bims-micpro Biomed News
on Discovery and characterization of microproteins
Issue of 2021‒01‒31
three papers selected by
Thomas Martinez
Salk Institute for Biological Studies


  1. J Biol Chem. 2021 Jan 23. pii: S0021-9258(21)00100-9. [Epub ahead of print] 100329
    Gagnon M, Savard M, Jacques JF, Bkaily G, Geha S, Roucou X, Gobeil F.
      Recent functional and proteomic studies in eukaryotes (www.openprot.org) predict the translation of alternative open reading frames (AltORFs) in mature G protein-coupled receptor (GPCR) mRNAs, including that of bradykinin B2 receptor (B2R). Our main objective was to determine the implication of a newly discovered AltORF resulting-protein, termed AltB2R, in the known signaling properties of B2R using complementary methodological approaches. When ectopically expressed in HeLa cells, AltB2R presented predominant punctate cytoplasmic/perinuclear distribution and apparent co-interaction with B2R at plasma and endosomal/vesicular membranes. The presence of AltB2R increases intracellular [Ca2+] and ERK1/2-MAPK activation (via phosphorylation) following B2R stimulation. Moreover, HEK293A cells expressing mutant B2R lacking concomitant expression of AltB2R displayed significantly decreased maximal responses in agonist-stimulated Gαq- Gαi2/3-protein coupling, IP3 generation, and ERK1/2-MAPK activation as compared to wild-type controls. Conversely, there was no difference in cell-surface density as well as ligand-binding properties of B2R and in efficiencies of cognate agonists at promoting B2R internalization and β2-arrestin recruitment. Importantly, both AltB2R and B2R proteins were overexpressed in prostate and breast cancers, compared with their normal counterparts suggesting new associative roles of AltB2R in these diseases. Our study shows that BDKRB2 is a dual-coding gene and identifies AltB2R as a novel positive modulator of some B2R signaling pathways. More broadly, it also supports a new, unexpected alternative proteome for GPCRs, which opens new frontiers in fields of GPCR biology, diseases and drug discovery.
    Keywords:  Alternative open reading frames (AltORFs); B2 receptor (B2R); Bradykinin (BK); G protein-coupled receptors (GPCRs); coding DNA sequence (CDS); mitogen-activated protein kinases (MAPK); signal transduction
    DOI:  https://doi.org/10.1016/j.jbc.2021.100329
  2. Nat Biotechnol. 2021 Jan 28.
    Prensner JR, Enache OM, Luria V, Krug K, Clauser KR, Dempster JM, Karger A, Wang L, Stumbraite K, Wang VM, Botta G, Lyons NJ, Goodale A, Kalani Z, Fritchman B, Brown A, Alan D, Green T, Yang X, Jaffe JD, Roth JA, Piccioni F, Kirschner MW, Ji Z, Root DE, Golub TR.
      Although genomic analyses predict many noncanonical open reading frames (ORFs) in the human genome, it is unclear whether they encode biologically active proteins. Here we experimentally interrogated 553 candidates selected from noncanonical ORF datasets. Of these, 57 induced viability defects when knocked out in human cancer cell lines. Following ectopic expression, 257 showed evidence of protein expression and 401 induced gene expression changes. Clustered regularly interspaced short palindromic repeat (CRISPR) tiling and start codon mutagenesis indicated that their biological effects required translation as opposed to RNA-mediated effects. We found that one of these ORFs, G029442-renamed glycine-rich extracellular protein-1 (GREP1)-encodes a secreted protein highly expressed in breast cancer, and its knockout in 263 cancer cell lines showed preferential essentiality in breast cancer-derived lines. The secretome of GREP1-expressing cells has an increased abundance of the oncogenic cytokine GDF15, and GDF15 supplementation mitigated the growth-inhibitory effect of GREP1 knockout. Our experiments suggest that noncanonical ORFs can express biologically active proteins that are potential therapeutic targets.
    DOI:  https://doi.org/10.1038/s41587-020-00806-2
  3. NPJ Genom Med. 2021 Jan 25. 6(1): 4
    Erady C, Boxall A, Puntambekar S, Suhas Jagannathan N, Chauhan R, Chong D, Meena N, Kulkarni A, Kasabe B, Prathivadi Bhayankaram K, Umrania Y, Andreani A, Nel J, Wayland MT, Pina C, Lilley KS, Prabakaran S.
      Uncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.
    DOI:  https://doi.org/10.1038/s41525-020-00167-4