A human microprotein that interacts with the mRNA decapping complex

Proteomic detection of non-annotated microproteins indicates the translation of hundreds of small open reading frames in human cells, but whether these microproteins are functional is unknown. Here, we report the discovery and characterization of a 7-kilodalton 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’-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 anti-correlated 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.

[1]  Jiao Ma,et al.  Discovery of Human sORF-Encoded Polypeptides (SEPs) in Cell Lines and Tissue , 2014, Journal of proteome research.

[2]  David Haussler,et al.  The UCSC Genome Browser database: 2014 update , 2013, Nucleic Acids Res..

[3]  D. Schwartz,et al.  Analysis of recombinant yeast decapping enzyme. , 2003, RNA.

[4]  Xinfu Jiao,et al.  The hDcp2 protein is a mammalian mRNA decapping enzyme , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Nicholas T. Ingolia,et al.  Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.

[6]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[7]  John M. Shelton,et al.  A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance , 2015, Cell.

[8]  Frances M. G. Pearl,et al.  Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames , 2013, Science.

[9]  Jean Thierry-Mieg,et al.  Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR) , 2014, Nucleic Acids Res..

[10]  Mark Johnson,et al.  NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..

[11]  Jim Thurmond,et al.  FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations , 2014, Nucleic Acids Res..

[12]  I. Verma,et al.  Production and purification of lentiviral vectors , 2006, Nature Protocols.

[13]  Y. Wolf,et al.  Small proteins can no longer be ignored. , 2014, Annual review of biochemistry.

[14]  Y. Taya,et al.  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. , 2001, Genes & development.

[15]  L. Maquat,et al.  Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. , 2003, Molecular cell.

[16]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[17]  J. Rinn,et al.  Peptidomic discovery of short open reading frame-encoded peptides in human cells , 2012, Nature chemical biology.

[18]  J. Lykke-Andersen Identification of a Human Decapping Complex Associated with hUpf Proteins in Nonsense-Mediated Decay , 2002, Molecular and Cellular Biology.

[19]  Roy Parker,et al.  P bodies and the control of mRNA translation and degradation. , 2007, Molecular cell.

[20]  E. Conti,et al.  Nonsense-mediated mRNA decay: molecular insights and mechanistic variations across species. , 2005, Current opinion in cell biology.

[21]  Amber L. Couzens,et al.  The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data , 2013, Nature Methods.

[22]  S. Rivella,et al.  Identi fi cation and Characterization of Small Molecules That Inhibit Nonsense-Mediated RNA Decay and Suppress Nonsense p53 Mutations , 2022 .

[23]  p53 mutations, ras mutations, and p53-heat shock 70 protein complexes in human lung carcinoma cell lines. , 1991, Cancer research.

[24]  Juan Pablo Couso,et al.  Discovery and characterization of smORF-encoded bioactive polypeptides. , 2015, Nature chemical biology.

[25]  D. Bedwell,et al.  Attenuation of Nonsense-Mediated mRNA Decay Enhances In Vivo Nonsense Suppression , 2013, PloS one.

[26]  J. Lykke-Andersen,et al.  The control of mRNA decapping and P-body formation. , 2008, Molecular cell.

[27]  Changhan Lee,et al.  The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance. , 2015, Cell metabolism.

[28]  Isabelle Behm-Ansmant,et al.  P-Body Formation Is a Consequence, Not the Cause, of RNA-Mediated Gene Silencing , 2007, Molecular and Cellular Biology.

[29]  Anton J. Enright,et al.  The zebrafish reference genome sequence and its relationship to the human genome , 2013, Nature.

[30]  François-Michel Boisvert,et al.  Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome , 2013, PloS one.

[31]  J. Lykke-Andersen,et al.  RNA decapping inside and outside of processing bodies. , 2005, Current opinion in cell biology.

[32]  L. Maquat,et al.  Organizing principles of mammalian nonsense-mediated mRNA decay. , 2013, Annual review of genetics.

[33]  M. Kiledjian,et al.  Differential utilization of decapping enzymes in mammalian mRNA decay pathways. , 2011, RNA.

[34]  Roy Parker,et al.  Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies , 2003 .

[35]  J. Lykke-Andersen,et al.  Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping. , 2005, Molecular cell.

[36]  E. Izaurralde,et al.  P bodies: at the crossroads of post-transcriptional pathways , 2007, Nature Reviews Molecular Cell Biology.

[37]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[38]  Roy Parker,et al.  Eukaryotic mRNA decapping. , 2004, Annual review of biochemistry.

[39]  J. Thierry-Mieg,et al.  AceView: a comprehensive cDNA-supported gene and transcripts annotation , 2006, Genome Biology.

[40]  L. Maquat,et al.  The mRNA surveillance protein hSMG-1 functions in genotoxic stress response pathways in mammalian cells. , 2004, Molecular cell.

[41]  Alan Saghatelian,et al.  A Human Short Open Reading Frame (sORF)-encoded Polypeptide That Stimulates DNA End Joining* , 2014, The Journal of Biological Chemistry.

[42]  Robert H Singer,et al.  The dynamics of mammalian P body transport, assembly, and disassembly in vivo. , 2008, Molecular biology of the cell.

[43]  César A. Hidalgo,et al.  Proto-genes and de novo gene birth , 2012, Nature.

[44]  D. Piwnica-Worms,et al.  Intracellular Calcium Regulates Nonsense-Mediated mRNA Decay , 2014, Nature Medicine.

[45]  Joerg E Braun,et al.  A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5′ exonucleolytic degradation , 2012, Nature Structural &Molecular Biology.