Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells

Journal article


Rogers, Samuel, McLoy, Rachel A., Parker, Benjamin L., Chaudhuri, Rima, Gayevskiy, Velimir, Hoffman, Nolan John, Watkins, D. Neil, Daly, Roger J., James, David E. and Burgess, Andrew 2015. Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells. Data in Brief. 5, pp. 45 - 52. https://doi.org/10.1016/j.dib.2015.08.010
AuthorsRogers, Samuel, McLoy, Rachel A., Parker, Benjamin L., Chaudhuri, Rima, Gayevskiy, Velimir, Hoffman, Nolan John, Watkins, D. Neil, Daly, Roger J., James, David E. and Burgess, Andrew
Abstract

The presence or absence of a phosphorylation on a substrate at any particular point in time is a functional readout of the balance in activity between the regulatory kinase and the counteracting phosphatase. Understanding how stable or short-lived a phosphorylation site is required for fully appreciating the biological consequences of the phosphorylation. Our current understanding of kinases and their substrates is well established; however, the role phosphatases play is less understood. Therefore, we utilized a phosphatase dependent model of mitotic exit to identify potential substrates that are preferentially dephosphorylated. Using this method, we identified > 16,000 phosphosites on > 3300 unique proteins, and quantified the temporal phosphorylation changes that occur during early mitotic exit ( McCloy et al., 2015 ). Furthermore, we annotated the majority of these phosphorylation sites with a high confidence upstream kinase using published, motif and prediction based methods. The results from this study have been deposited into the ProteomeXchange repository with identifier PXD001559. Here we provide additional analysis of this dataset; for each of the major mitotic kinases we identified motifs that correlated strongly with phosphorylation status. These motifs could be used to predict the stability of phosphorylated residues in proteins of interest, and help infer potential functional roles for uncharacterized phosphorylations. In addition, we provide validation at the single cell level that serine residues phosphorylated by Cdk are stable during phosphatase dependent mitotic exit. In summary, this unique dataset contains information on the temporal mitotic stability of thousands of phosphorylation sites regulated by dozens of kinases, and information on the potential preference that phosphatases have at both the protein and individual phosphosite level. The compellation of this data provides an invaluable resource for the wider research community.

Year2015
JournalData in Brief
Journal citation5, pp. 45 - 52
PublisherElsevier Inc.
ISSN2352-3409
Digital Object Identifier (DOI)https://doi.org/10.1016/j.dib.2015.08.010
Scopus EID2-s2.0-84940769949
Open accessOpen access
Page range45 - 52
Research GroupMary MacKillop Institute for Health Research
Publisher's version
Additional information

© 2015 The Authors. Published by Elsevier Inc.This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Place of publicationNetherlands
Permalink -

https://acuresearchbank.acu.edu.au/item/86zz4/dataset-from-the-global-phosphoproteomic-mapping-of-early-mitotic-exit-in-human-cells

  • 0
    total views
  • 0
    total downloads
  • 0
    views this month
  • 0
    downloads this month

Export as

Related outputs

Phosphoproteomics reveals conserved exercise-stimulated signaling and AMPK regulation of store-operated calcium entry
Nelson, Marin E., Parker, Benjamin L., Burchfield, James G., Hoffman, Nolan J., Needham, Elise J., Cooke, Kristen C., Naim, Timur, Sylow, Lykke, Ling, Naomi X. Y., Francis, Deanne, Norris, Dougall M., Chaudhuri, Rima, Oakhill, Jonathan S., Richter, Erik A., Lynch, Gordon S., Stockli, Jacqueline and James, David E. 2019. Phosphoproteomics reveals conserved exercise-stimulated signaling and AMPK regulation of store-operated calcium entry. The EMBO Journal. 38 (24), pp. 1 - 20. https://doi.org/10.15252/embj.2019102578
High dietary fat and sucrose results in an extensive and time-dependent deterioration in health of multiple physiological systems in mice
Burchfield, James G., Kebede, Melkam A., Meoli, Christopher C., Stockli, Jacqueline, Whitworth, P. Tess, Wright, Amanda L., Hoffman, Nolan John, Minard, Annabel Y., Ma, Xiuquan, Krycer, James R., Nelson, Marin E., Tan, Shi-Xlong, Yau, Belinda, Thomas, Kristen C., Wee, Natalie K.Y., Khor, Ee-Cheng, Enriquez, Ronaldo F., Vissel, Bryce, Biden, Trevor J., ... Fazakerley, Daniel J. 2018. High dietary fat and sucrose results in an extensive and time-dependent deterioration in health of multiple physiological systems in mice. Journal of Biological Chemistry. 293 (15), pp. 5731 - 5745. https://doi.org/10.1074/jbc.RA117.000808
Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance
Fazakerley, Daniel J., Chaudhuri, Rima, Yang, Pengyi, Maghzal, Ghassan J., Thomas, Kristen C., Krycer, James R., Humphrey, Sean J., Parker, Benjamin, Fisher-Wellman, Kelsey H., Meoli, Christopher C., Hoffman, Nolan, Diskin, Ciana, Burchfield, James G., Cowley, Mark J., Kaplan, Warren, Modrusan, Zora, Kolumam, Ganesh, Yang, Jean Y. H., Chen, Daniel L., ... James, David E. 2018. Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. eLife. 7, pp. 1 - 38. https://doi.org/10.7554/eLife.32111
High dietary fat intake increases fat oxidation and reduces skeletal muscle mitochondrial respiration in trained humans
Leckey, Jill J., Hoffman, Nolan, Parr, Evelyn, Devlin, Brooke, Trewin, Adam J., Stepto, Nigel K., Morton, James P., Burke, Louise and Hawley, John 2018. High dietary fat intake increases fat oxidation and reduces skeletal muscle mitochondrial respiration in trained humans. The FASEB Journal. 32 (6), pp. 2979 - 2991. https://doi.org/10.1096/fj.201700993R
Interactive roles for AMPK and glycogen from cellular energy sensing to exercise metabolism
Janzen, Natalie, Whitfield, Jamie and Hoffman, Nolan 2018. Interactive roles for AMPK and glycogen from cellular energy sensing to exercise metabolism. International Journal of Molecular Sciences. 19 (11), pp. 1 - 18. https://doi.org/10.3390/ijms19113344
High dietary fat and sucrose result in an extensive and time-dependent deterioration in health of multiple physiological systems in mice
Burchfield, James G., Kebede, Melkam A., Meoli, Christopher C., Stockli, Jacqueline, Whitworth, P. T., Wright, Amanda L., Hoffman, Nolan, Minard, Annabel Y., Ma, Xiuquan, Krycer, James R., Nelson, Marin E., Tan, Shi-XIong, Yau, Belinda, Thomas, Kristen C., Wee, Natalie K. P., Khor, Ee-Cheng, Enriquez, Ronaldo F., Vissel, Bryce, Biden, Trevor J., ... Fazakerley, Daniel J. 2018. High dietary fat and sucrose result in an extensive and time-dependent deterioration in health of multiple physiological systems in mice. Journal of Biological Chemistry. 293 (15), pp. 5731 - 5745. https://doi.org/10.1074/jbc.RA117.000808
High dietary fat intake increases fat oxidation and reduces skeletal muscle mitochondrial respiration in trained humans
Leckey, Jill J., Hoffman, Nolan J., Parr, Evelyn B., Devlin, Brooke L., Trewin, Adam J., Stepto, Nigel K., Morton, James P., Burke, Louise M. and Hawley, John A. 2018. High dietary fat intake increases fat oxidation and reduces skeletal muscle mitochondrial respiration in trained humans. FASEB Journal. 32 (6), pp. 2979 - 2991. https://doi.org/10.1096/fj.201700993R
Metabolomic analysis of insulin resistance across different mouse strains and diets
Stockli, Jacqueline, Fisher-Wellman, Kelsey H., Chaudhuri, Rima, Zeng, Xiao-Yi, Fazakerley, Daniel J., Meoli, Christopher C., Thomas, Kristen C., Hoffman, Nolan, Mangiafico, Salvatore P., Xirouchaki, Chrysovalantou E., Yang, Chieh H., Ilkayeva, Olga, Wong, Kari, Cooney, Gregory J., Andrikopoulos, Sofianos, Muoio, Deborah M. and James, David E. 2017. Metabolomic analysis of insulin resistance across different mouse strains and diets. Journal of Biological Chemistry. 292 (47), pp. 19135 - 19145. https://doi.org/10.1074/jbc.M117.818351
The autophagy initiator ULK1 sensitizes AMPK to allosteric drugs
Dite, Toby A., Ling, Naomi, Scott, John W., Hoque, Ashfaqul, Galic, Sandra, Parker, Benjamin L., Ngoei, Kevin R.W., Langendorf, Christopher G., O'Brien, Matthew, Kundu, Mondira, Viollet, Benoit, Steinberg, Gregory R., Sakamoto, Kei, Kemp, Bruce and Oakhill, Jonathan S. 2017. The autophagy initiator ULK1 sensitizes AMPK to allosteric drugs. Nature Communications. 8 (571), pp. 1 - 14. https://doi.org/10.1038/s41467-017-00628-y
Omics and exercise: global approaches for mapping exercise biological networks
Hoffman, Nolan John 2017. Omics and exercise: global approaches for mapping exercise biological networks. Cold Spring Harbor Perspectives in Medicine. 7 (10), pp. 1 - 17. https://doi.org/10.1101/cshperspect.a029884
Omics and exercise: global approaches for mapping exercise biological networks
Hoffman, Nolan John 2017. Omics and exercise: global approaches for mapping exercise biological networks. Cold Spring Harbor Perspectives in Medicine. 7 (10), pp. 1 - 17. https://doi.org/10.1101/cshperspect.a029884
mTORC2 and AMPK differentially regulate muscle triglyceride content via Perilipin 3
Kleinert, Maximilian, Parker, Benjamin L., Chaudhuri, Rima, Fazakerley, Daniel J., Serup, Annette, Thomas, Kristen C., Krycer, James R., Sylow, Lykke, Fritzen, Andreas M., Hoffman, Nolan John, Jeppesen, Jacob, Schjerling, Peter, Ruegg, Markus A., Kiens, Bente, James, David E. and Richter, Erik A. 2016. mTORC2 and AMPK differentially regulate muscle triglyceride content via Perilipin 3. Molecular Metabolism. 5 (8), pp. 646 - 655. https://doi.org/10.1016/j.molmet.2016.06.007
Glucose-6-phosphate dehydrogenase contributes to the regulation of glucose uptake in skeletal muscle
Lee-Young, Robert S., Hoffman, Nolan John, Murphy, Kate T., Henstridge, Darren C., Samocha-Bonet, Dorit, Siebel, Andrew L., Iliades, Peter, Zivanovic, Borivoj, Hong, Yet H., Colgan, Timothy D., Kraakman, Michael J., Bruce, Clinton R., Gregorevic, Paul, McConell, Glenn K., Lynch, Gordon S., Drummond, Grant R., Kingwell, Bronwyn A., Greenfield, Jerry R. and Febbraio, Mark A. 2016. Glucose-6-phosphate dehydrogenase contributes to the regulation of glucose uptake in skeletal muscle. Molecular Metabolism. 5 (11), pp. 1083 - 1091. https://doi.org/10.1016/j.molmet.2016.09.002
Global phosphoproteomic analysis of human skeletal muscle reveals a network of exercise-regulated kinases and AMPK substrates
Hoffman, Nolan John, Parker, Benjamin L., Chaudhuri, Rima, Fisher-Wellman, Kelsey H., Kleinert, Maximilian, Humphrey, Sean J., Yang, Pengyi, Holliday, Mira, Trefely, Sophie, Fazakerley, Daniel J., Stöckli, Jacqueline, Burchfield, James G., Jensen, Thomas E., Jothi, Raja, Kiens, Bente, Wojtaszewski, Jørgen F. P., Richter, Erik A. and James, David E. 2015. Global phosphoproteomic analysis of human skeletal muscle reveals a network of exercise-regulated kinases and AMPK substrates. Cell Metabolism. 22 (5), pp. 922 - 935. https://doi.org/10.1016/j.cmet.2015.09.001
The RabGAP TBC1D1 plays a central role in exercise-regulated glucose metabolism in skeletal muscle
Stockli, Jacqueline, Meoli, Christopher C., Hoffman, Nolan John, Fazakerley, Daniel J., Pant, Himani, Cleasby, Mark E., Ma, Xiuquan, Kleinert, Maximilian, Brandon, Amanda E., Lopez, Jamie A., Cooney, Gregory J. and James, David E. 2015. The RabGAP TBC1D1 plays a central role in exercise-regulated glucose metabolism in skeletal muscle. Diabetes. 64 (6), pp. 1914 - 1922. https://doi.org/10.2337/db13-1489
Global phosphoproteomic mapping of early mitotic exit in human cells identifies novel substrate dephosphorylation motifs
McLoy, Rachael A., Parker, Benjamin L., Rogers, Samuel, Chaudhuri, Rima, Gayevskiy, Velimir, Hoffman, Nolan John, Ali, Naveid, Watkins, D. Neil, Daly, Roger J., James, David E., Lorca, Thierry, Castro, Anna and Burgess, Andrew 2015. Global phosphoproteomic mapping of early mitotic exit in human cells identifies novel substrate dephosphorylation motifs. Molecular and Cellular Proteomics. 14 (8), pp. 2194 - 2212. https://doi.org/10.1074/mcp.M114.046938
PhosphOrtholog: A web-based tool for cross-species mapping of orthologous protein post-translational modifications
Chaudhuri, Rima, Sadrieh, Arash, Hoffman, Nolan J., Parker, Benjamin L., Humphrey, Sean J., Stockli, Jacqueline, Hill, Adam P., James, David E. and Yang, Jean Yee Hwa 2015. PhosphOrtholog: A web-based tool for cross-species mapping of orthologous protein post-translational modifications. BMC Genomics. 16 (617), pp. 1 - 14. https://doi.org/10.1186/s12864-015-1820-x
Structural basis for phosphorylation and lysine acetylation cross-talk in a kinase motif associated with myocardial ischemia and cardioprotection
Parker, Benjamin L., Shepherd, Nicholas E., Trefely, Sophie, Hoffman, Nolan John, White, Melanie Y., Engholm-Keller, Kasper, Hambly, Brett D., Larsen, Martin R., James, David E. and Cordwell, Stuart J. 2014. Structural basis for phosphorylation and lysine acetylation cross-talk in a kinase motif associated with myocardial ischemia and cardioprotection. Journal of Biological Chemistry. 289 (37), pp. 25890 - 25906. https://doi.org/10.1074/jbc.M114.556035
Grb10 deletion enhances muscle cell proliferation, differentiation and GLUT4 plasma membrane translocation
Mokbel, Nancy, Hoffman, Nolan John, Girgis, Christian M., Small, Lewin, Turner, Nigel, Daly, Roger J., Cooney, Gregory J. and Holt, Lowenna J. 2014. Grb10 deletion enhances muscle cell proliferation, differentiation and GLUT4 plasma membrane translocation. Journal of Cellular Physiology. 229 (11), pp. 1753 - 1764. https://doi.org/10.1002/jcp.24628
Structural basis for phosphorylation and lysine acetylation crosstalk in a kinase motif associated with myocardial ischemia and cardioprotection
Parker, Benjamin L., Shepherd, Nicholas E., Trefely, Sophie, Hoffman, Nolan John, White, Melanie Y., Engholm-Keller, Kasper, Hambly, Brett D., Larsen, Martin R., James, David E. and Cordwell, Stuart J. 2014. Structural basis for phosphorylation and lysine acetylation crosstalk in a kinase motif associated with myocardial ischemia and cardioprotection. Journal of Biological Chemistry. 289 (37), pp. 25890 - 25906. https://doi.org/10.1074/jbc.M114.556035
Transient silencing of a type IV P-type ATpase results in decreased GLUT4 translocation and altered signaling of MAPK and PI3K pathways
Hurst, Sarah, Hoffman, Nolan, Elmendorf, Jeffrey and Dhar, Madhu 2014. Transient silencing of a type IV P-type ATpase results in decreased GLUT4 translocation and altered signaling of MAPK and PI3K pathways. in: Obesity Epidemic United States: CreateSpace Independent Publishing Platform. pp. 1 - 21
Chromium enhances insulin responsiveness via AMPK
Hoffman, Nolan John, Penque, Brent A., Habegger, Kirk M., Sealls, Whitney, Tackett, Lixuan and Elmendorf, Jeffrey S. 2014. Chromium enhances insulin responsiveness via AMPK. Journal of Nutritional Biochemistry. 25 (5), pp. 565 - 572. https://doi.org/10.1016/j.jnutbio.2014.01.007
Ceramide accumulation in L6 skeletal muscle cells due to increased activity of ceramide synthase isoforms has opposing effects on insulin action to those caused by palmitate treatment
Frangioudakis, Georgia, Diakanastasis, Barbara, Liao, Bing-Qing M., Saville, Jennifer T., Hoffman, Nolan John, Mitchell, Todd W. and Schmitz-Peiffer, Carsten 2013. Ceramide accumulation in L6 skeletal muscle cells due to increased activity of ceramide synthase isoforms has opposing effects on insulin action to those caused by palmitate treatment. Diabetologia. 56 (12), pp. 2697 - 2701. https://doi.org/10.1007/s00125-013-3035-5
AMPK enhances insulin-stimulated GLUT4 regulation via lowering membrane cholesterol
Hoffman, Nolan John, Habegger, Kirk M., Ridenour, Colin M., Broznick, Joseph T. and Elmendon, Jeffrey S. 2012. AMPK enhances insulin-stimulated GLUT4 regulation via lowering membrane cholesterol. Endocrinology. 153 (5), pp. 2130 - 2141. https://doi.org/10.1210/en.2011-2099
Signaling, cytoskeletal and membrane mechanisms regulating GLUT4 exocytosis
Hoffman, Nolan John and Elmendorf, Jeffrey S. 2011. Signaling, cytoskeletal and membrane mechanisms regulating GLUT4 exocytosis. Trends in Endocrinology and Metabolism. 22 (3), pp. 110 - 116. https://doi.org/10.1016/j.tem.2010.12.001