Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A human microprotein that interacts with the mRNA decapping complex

Abstract

Proteomic detection of non-annotated microproteins indicates the translation of hundreds of small open reading frames (smORFs) in human cells, but whether these microproteins are functional or not is unknown. Here, we report the discovery and characterization of a 7-kDa human microprotein we named non-annotated P-body dissociating polypeptide (NoBody). NoBody interacts with mRNA decapping proteins, which remove the 5′ cap from mRNAs to promote 5′-to-3′ decay. Decapping proteins participate in mRNA turnover and nonsense-mediated decay (NMD). NoBody localizes to mRNA-decay-associated RNA–protein granules called P-bodies. Modulation of NoBody levels reveals that its abundance is anticorrelated with cellular P-body numbers and alters the steady-state levels of a cellular NMD substrate. These results implicate NoBody as a novel component of the mRNA decapping complex and demonstrate potential functionality of a newly discovered microprotein.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The LOC550643/LINC01420 gene encodes the NoBody peptide in a short open reading frame (sORF).
Figure 2: NoBody enriches a complex of proteins involved in mRNA decapping and crosslinks to EDC4.
Figure 3: Sequence dependence of NoBody–EDC4 co-precipitation.
Figure 4: NoBody localizes to P-bodies and its expression level is inversely correlated with P-body numbers.
Figure 5: Perturbation of NoBody expression modulates levels of a nonsense-mediated decay substrate in cells.

Similar content being viewed by others

References

  1. Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. & Weissman, J.S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Ingolia, N.T., Lareau, L.F. & Weissman, J.S. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789–802 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Slavoff, S.A. et al. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat. Chem. Biol. 9, 59–64 (2013).

    CAS  PubMed  Google Scholar 

  4. Vanderperre, B. et al. Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One 8, e70698 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Saghatelian, A. & Couso, J.P. Discovery and characterization of smORF-encoded bioactive polypeptides. Nat. Chem. Biol. 11, 909–916 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Storz, G., Wolf, Y.I. & Ramamurthi, K.S. Small proteins can no longer be ignored. Annu. Rev. Biochem. 83, 753–777 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Magny, E.G. et al. Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames. Science 341, 1116–1120 (2013).

    CAS  PubMed  Google Scholar 

  8. Anderson, D.M. et al. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160, 595–606 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Lee, C. et al. The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance. Cell Metab. 21, 443–454 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Slavoff, S.A., Heo, J., Budnik, B.A., Hanakahi, L.A. & Saghatelian, A. A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining. J. Biol. Chem. 289, 10950–10957 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Carvunis, A.R. et al. Proto-genes and de novo gene birth. Nature 487, 370–374 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Fillman, C. & Lykke-Andersen, J. RNA decapping inside and outside of processing bodies. Curr. Opin. Cell Biol. 17, 326–331 (2005).

    CAS  PubMed  Google Scholar 

  13. Sheth, U. & Parker, R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300, 805–808 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. dos Santos, G. et al. FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res. 43, D690–D697 (2015).

    CAS  PubMed  Google Scholar 

  15. Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Kent, W.J. BLAT--the BLAST-like alignment tool. Genome res. 12, 656–664 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Thierry-Mieg, D. & Thierry-Mieg, J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome biol. 7 (Suppl. 1), S12.1–S12.14 (2006).

    Google Scholar 

  19. Peng, X. et al. Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). Nucleic Acids Res. 43, D737–D742 (2015).

    CAS  PubMed  Google Scholar 

  20. Mellacheruvu, D. et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat. Methods 10, 730–736 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Parker, R. & Sheth, U. P bodies and the control of mRNA translation and degradation. Mol. Cell 25, 635–646 (2007).

    CAS  PubMed  Google Scholar 

  22. Eulalio, A., Behm-Ansmant, I. & Izaurralde, E. P bodies: at the crossroads of post-transcriptional pathways. Nat. Rev. Mol. Cell Biol. 8, 9–22 (2007).

    CAS  PubMed  Google Scholar 

  23. Fenger-Grøn, M., Fillman, C., Norrild, B. & Lykke-Andersen, J. Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. Mol. Cell 20, 905–915 (2005).

    PubMed  Google Scholar 

  24. Eulalio, A., Behm-Ansmant, I., Schweizer, D. & Izaurralde, E. P-body formation is a consequence, not the cause, of RNA-mediated gene silencing. Mol. Cell. Biol. 27, 3970–3981 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Aizer, A. et al. The dynamics of mammalian P body transport, assembly, and disassembly in vivo. Mol. Biol. Cell 19, 4154–4166 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Conti, E. & Izaurralde, E. Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. Curr. Opin. Cell Biol. 17, 316–325 (2005).

    CAS  PubMed  Google Scholar 

  27. Popp, M.W. & Maquat, L.E. Organizing principles of mammalian nonsense-mediated mRNA decay. Annu. Rev. Genet. 47, 139–165 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Lejeune, F., Li, X. & Maquat, L.E. Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol. Cell 12, 675–687 (2003).

    CAS  PubMed  Google Scholar 

  29. Li, Y., Song, M. & Kiledjian, M. Differential utilization of decapping enzymes in mammalian mRNA decay pathways. RNA 17, 419–428 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Lykke-Andersen, J. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell. Biol. 22, 8114–8121 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Lehman, T.A. et al. p53 mutations, ras mutations, and p53-heat shock 70 protein complexes in human lung carcinoma cell lines. Cancer Res. 51, 4090–4096 (1991).

    CAS  PubMed  Google Scholar 

  32. Yamashita, A., Ohnishi, T., Kashima, I., Taya, Y. & Ohno, S. Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes Dev. 15, 2215–2228 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Martin, L. et al. Identification and characterization of small molecules that inhibit nonsense-mediated RNA decay and suppress nonsense p53 mutations. Cancer Res. 74, 3104–3113 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Nickless, A. et al. Intracellular calcium regulates nonsense-mediated mRNA decay. Nat. Med. 20, 961–966 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Brumbaugh, K.M. et al. The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells. Mol. Cell 14, 585–598 (2004).

    CAS  PubMed  Google Scholar 

  36. Keeling, K.M. et al. Attenuation of nonsense-mediated mRNA decay enhances in vivo nonsense suppression. PLoS One 8, e60478 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Franks, T.M. & Lykke-Andersen, J. The control of mRNA decapping and P-body formation. Mol. Cell 32, 605–615 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Braun, J.E. et al. A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5′ exonucleolytic degradation. Nat. Struct. Mol. Biol. 19, 1324–1331 (2012).

    CAS  PubMed  Google Scholar 

  39. Ma, J. et al. Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. J. Proteome Res. 13, 1757–1765 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Johnson, M. et al. NCBI BLAST: a better web interface. Nucleic Acids Res. 36, W5–W9 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Karolchik, D. et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42, D764–D770 (2014).

    CAS  PubMed  Google Scholar 

  42. Tiscornia, G., Singer, O. & Verma, I.M. Production and purification of lentiviral vectors. Nat. Protoc. 1, 241–245 (2006).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank A. Ting for the generous use of her Zeiss Axio Observer inverted confocal microscope. This study was supported by a George E. Hewitt Foundation for medical research Postdoctoral Fellowship (Q.C.), NIH (R01 GM102491, A.S.), the NCI Cancer Center Support Grant P30 (CA014195 MASS core, A.S.), The Leona M. and Harry B. Helmsley Charitable Trust grant (#2012-PG-MED002, A.S.), and Dr. Frederick Paulsen Chair/Ferring Pharmaceuticals (A.S.). S.A.S. was supported by Yale University West Campus start-up funds, an American Cancer Society Institutional Research Grant Individual Award for New Investigators from the Yale Cancer Center (IRG-58-012-57) and a NIH Ruth L. Kirchstein postdoctoral fellowship (1F32GM099408). N.G.D. was supported by an Anderson Endowed Postdoctoral Fellowship in the Biological Sciences.

Author information

Authors and Affiliations

Authors

Contributions

S.A.S. and A.S. conceived the project. N.G.D., J.M., L.W., Q.C., K.H.L., S.A.S. and A.S. designed the experiments. S.A.S. conducted the majority of the experiments and data analyses, including the identification of NoBody, the discovery of NoBody-binding partners, cellular imaging, and NMD studies. N.G.D. performed NoBody purification and in vitro EDC4 co-purification and crosslinking. J.M. generated NoBody expression constructs, and J.M. and Q.C. carried out the cellular EDC4-NoBody crosslinking experiments. L.W. assisted with identification of NoBody binding partners and co-immunoprecipitation experiments. K.H.L. carried out cellular imaging. E.O.C. and J.L.-A. provided advice and experimental help with NMD studies. B.A.B. provided proteomics assistance. N.G.D., A.S. and S.A.S. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Alan Saghatelian or Sarah A Slavoff.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Tables 1 and 2, Supplementary Figures 1–16 and Supplementary Note. (PDF 2619 kb)

Supplementary Dataset 1

Immunoprecipitation mass spectrometry data for NoBody pulldowns with anti-FLAG antibody. (XLSX 360 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

D'Lima, N., Ma, J., Winkler, L. et al. A human microprotein that interacts with the mRNA decapping complex. Nat Chem Biol 13, 174–180 (2017). https://doi.org/10.1038/nchembio.2249

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchembio.2249

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing