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    The abundance of short proteins in the mammalian proteome

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    Author
    Frith, MC; Forrest, AR; Nourbakhsh, E; Pang, KC; Kai, C; Kawai, J; Carninci, P; Hayashizaki, Y; Bailey, TL; Grimmond, SM
    Date
    2006-04-01
    Source Title
    PLoS Genetics
    Publisher
    PUBLIC LIBRARY SCIENCE
    University of Melbourne Author/s
    Grimmond, Sean
    Affiliation
    Centre for Cancer Research
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Frith, M. C., Forrest, A. R., Nourbakhsh, E., Pang, K. C., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Bailey, T. L. & Grimmond, S. M. (2006). The abundance of short proteins in the mammalian proteome. PLOS GENETICS, 2 (4), pp.515-528. https://doi.org/10.1371/journal.pgen.0020052.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/258245
    DOI
    10.1371/journal.pgen.0020052
    Abstract
    Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and non-synonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a "dark matter" subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.

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