Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

Martin Lee Miller, Søren Brunak, JV Olsen, M Vermeulen, A Santamaria, C Kumar, LJ Jensen, F Gnad, J Cox, Thomas Skøt Jensen, EA Nigg, M Mann

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.
    Original languageEnglish
    JournalScience Signaling
    Volume3
    Issue number104
    Pages (from-to)ra3
    ISSN1945-0877
    DOIs
    Publication statusPublished - 2010

    Cite this

    Miller, Martin Lee ; Brunak, Søren ; Olsen, JV ; Vermeulen, M ; Santamaria, A ; Kumar, C ; Jensen, LJ ; Gnad, F ; Cox, J ; Jensen, Thomas Skøt ; Nigg, EA ; Mann, M. / Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. In: Science Signaling. 2010 ; Vol. 3, No. 104. pp. ra3.
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    title = "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis",
    abstract = "Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20{\%} of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.",
    author = "Miller, {Martin Lee} and S{\o}ren Brunak and JV Olsen and M Vermeulen and A Santamaria and C Kumar and LJ Jensen and F Gnad and J Cox and Jensen, {Thomas Sk{\o}t} and EA Nigg and M Mann",
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    Miller, ML, Brunak, S, Olsen, JV, Vermeulen, M, Santamaria, A, Kumar, C, Jensen, LJ, Gnad, F, Cox, J, Jensen, TS, Nigg, EA & Mann, M 2010, 'Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis', Science Signaling, vol. 3, no. 104, pp. ra3. https://doi.org/10.1126/scisignal.2000475

    Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. / Miller, Martin Lee; Brunak, Søren; Olsen, JV; Vermeulen, M; Santamaria, A; Kumar, C; Jensen, LJ; Gnad, F; Cox, J; Jensen, Thomas Skøt; Nigg, EA; Mann, M.

    In: Science Signaling, Vol. 3, No. 104, 2010, p. ra3.

    Research output: Contribution to journalJournal articleResearchpeer-review

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    T1 - Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis

    AU - Miller, Martin Lee

    AU - Brunak, Søren

    AU - Olsen, JV

    AU - Vermeulen, M

    AU - Santamaria, A

    AU - Kumar, C

    AU - Jensen, LJ

    AU - Gnad, F

    AU - Cox, J

    AU - Jensen, Thomas Skøt

    AU - Nigg, EA

    AU - Mann, M

    PY - 2010

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    N2 - Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.

    AB - Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.

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    DO - 10.1126/scisignal.2000475

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    SP - ra3

    JO - Science Signaling

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    SN - 1945-0877

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    ER -