Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells

Sci. Signal., 28 June 2011
Vol. 4, Issue 179, p. rs5
DOI: 10.1126/scisignal.2001497

Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells

  1. Arminja N. Kettenbach1,2,
  2. Devin K. Schweppe1,
  3. Brendan K. Faherty1,
  4. Dov Pechenick1,
  5. Alexandre A. Pletnev2,3, and
  6. Scott A. Gerber1,2,*
  1. 1Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA.
  2. 2Norris Cotton Cancer Center, Lebanon, NH 03756, USA.
  3. 3Department of Chemistry, Dartmouth College, Hanover, NH 03755, USA.
  1. *To whom correspondence should be addressed. E-mail: scott.a.gerber{at}dartmouth.edu

Abstract

Mitosis is a process involving a complex series of events that require careful coordination. Protein phosphorylation by a small number of kinases, in particular Aurora A, Aurora B, the cyclin-dependent kinase–cyclin complex Cdk1/cyclinB, and Polo-like kinase 1 (Plk1), orchestrates almost every step of cell division, from entry into mitosis to cytokinesis. To discover more about the functions of Aurora A, Aurora B, and kinases of the Plk family, we mapped mitotic phosphorylation sites to these kinases through the combined use of quantitative phosphoproteomics and selective targeting of kinase activities by small-molecule inhibitors. Using this integrated approach, we connected 778 phosphorylation sites on 562 proteins with these enzymes in cells arrested in mitosis. By connecting the kinases to protein complexes, we associated these kinases with functional modules. In addition to predicting previously unknown functions, this work establishes additional substrate-recognition motifs for these kinases and provides an analytical template for further use in dissecting kinase signaling events in other areas of cellular signaling and systems biology.

Citation:

A. N. Kettenbach, D. K. Schweppe, B. K. Faherty, D. Pechenick, A. A. Pletnev, and S. A. Gerber, Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells. Sci. Signal. 4, rs5 (2011).

TRAMM/TrappC12 plays a role in chromosome congression, kinetochore stability, and CENP-E recruitment
M. P. Milev, B. Hasaj, D. Saint-Dic, S. Snounou, Q. Zhao, and M. Sacher
JCB 209, 221-234 (27 April 2015)

Communication between the N and C Termini Is Required for Copper-stimulated Ser/Thr Phosphorylation of Cu(I)-ATPase (ATP7B)
L. T. Braiterman, A. Gupta, R. Chaerkady, R. N. Cole, and A. L. Hubbard
J Biol Chem 290, 8803-8819 (3 April 2015)

Phosphorylation of Targeting Protein for Xenopus Kinesin-like Protein 2 (TPX2) at Threonine 72 in Spindle Assembly
S. Y. Shim, I. P. de Castro, G. Neumayer, J. Wang, S. K. Park, K. Sanada, and M. D. Nguyen
J Biol Chem 290, 9122-9134 (3 April 2015)

Glycogen Synthase Kinase-3 (GSK3) Inhibition Induces Prosurvival Autophagic Signals in Human Pancreatic Cancer Cells
B. Marchand, D. Arsenault, A. Raymond-Fleury, F.-M. Boisvert, and M.-J. Boucher
J Biol Chem 290, 5592-5605 (27 February 2015)

Opposing roles for JNK and Aurora A in regulating the association of WDR62 with spindle microtubules
N. R. Lim, Y. Y. C. Yeap, T. T. Zhao, Y. Y. Yip, S. C. Wong, D. Xu, C.-S. Ang, N. A. Williamson, Z. Xu, M. A. Bogoyevitch et al.
J. Cell Sci. 128, 527-540 (1 February 2015)

Quantitative comparison of a human cancer cell surface proteome between interphase and mitosis
N. Ozlu, M. H. Qureshi, Y. Toyoda, B. Y. Renard, G. Mollaoglu, N. E. Ozkan, S. Bulbul, I. Poser, W. Timm, A. A. Hyman et al.
EMBO J. 34, 251-265 (13 January 2015)

Protein folding creates structure-based, noncontiguous consensus phosphorylation motifs recognized by kinases
M. L. Duarte, D. A. Pena, F. A. Nunes Ferraz, D. A. Berti, T. J. Paschoal Sobreira, H. M. Costa-Junior, M. M. Abdel Baqui, M.-H. Disatnik, J. Xavier-Neto, P. S. Lopes de Oliveira et al.
Sci Signal 7, ra105-ra105 (4 November 2014)

Identification of Extracellular Signal-regulated Kinase 1 (ERK1) Direct Substrates using Stable Isotope Labeled Kinase Assay-Linked Phosphoproteomics
L. Xue, P. Wang, P. Cao, J.-k. Zhu, and W. A. Tao
MCP 13, 3199-3210 (1 November 2014)

STAG2 promotes error correction in mitosis by regulating kinetochore-microtubule attachments
M. Kleyman, L. Kabeche, and D. A. Compton
J. Cell Sci. 127, 4225-4233 (1 October 2014)

Ki67 Antigen Contributes to the Timely Accumulation of Protein Phosphatase 1{gamma} on Anaphase Chromosomes
M. Takagi, Y. Nishiyama, A. Taguchi, and N. Imamoto
J Biol Chem 289, 22877-22887 (15 August 2014)

Method for identifying phosphorylated substrates of specific cyclin/cyclin-dependent kinase complexes
Y. Li, F. R. Cross, and B. T. Chait
Proc. Natl. Acad. Sci. USA 111, 11323-11328 (5 August 2014)

Evidence toward a Dual Phosphatase Mechanism That Restricts Aurora A (Thr-295) Phosphorylation during the Early Embryonic Cell Cycle
Q. Kang, J. Srividhya, J. Ipe, and J. R. Pomerening
J Biol Chem 289, 17480-17496 (20 June 2014)

Polo-like kinase 1 (PLK1) and protein phosphatase 6 (PP6) regulate DNA-dependent protein kinase catalytic subunit (DNA-PKcs) phosphorylation in mitosis
P. Douglas, R. Ye, L. Trinkle-Mulcahy, J. A. Neal, V. De Wever, N. A. Morrice, K. Meek, and S. P. Lees-Miller
Biosci. Rep. 34, e00113-271 (1 June 2014)

Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation
S. A. Singh, D. Winter, M. Kirchner, R. Chauhan, S. Ahmed, N. Ozlu, A. Tzur, J. A. Steen, and H. Steen
EMBO J. 33, 385-399 (18 February 2014)

Status of Large-scale Analysis of Post-translational Modifications by Mass Spectrometry
J. V. Olsen, and M. Mann
MCP 12, 3444-3452 (1 December 2013)

Identification of Direct Tyrosine Kinase Substrates Based on Protein Kinase Assay-Linked Phosphoproteomics
L. Xue, R. L. Geahlen, and W. A. Tao
MCP 12, 2969-2980 (1 October 2013)

Aurora B suppresses microtubule dynamics and limits central spindle size by locally activating KIF4A
R. Nunes Bastos, S. R. Gandhi, R. D. Baron, U. Gruneberg, E. A. Nigg, and F. A. Barr
JCB 202, 605-621 (19 August 2013)

Melanoma-associated mutations in protein phosphatase 6 cause chromosome instability and DNA damage owing to dysregulated Aurora-A
D. Hammond, K. Zeng, A. Espert, R. N. Bastos, R. D. Baron, U. Gruneberg, and F. A. Barr
J. Cell Sci. 126, 3429-3440 (1 August 2013)

Spatiotemporal organization of Aurora-B by APC/CCdh1 after mitosis coordinates cell spreading through FHOD1
S. Floyd, N. Whiffin, M. P. Gavilan, S. Kutscheidt, M. De Luca, C. Marcozzi, M. Min, J. Watkins, K. Chung, O. T. Fackler et al.
J. Cell Sci. 126, 2845-2856 (1 July 2013)

Specific removal of TACC3-ch-TOG-clathrin at metaphase deregulates kinetochore fiber tension
L. P. Cheeseman, E. F. Harry, A. D. McAinsh, I. A. Prior, and S. J. Royle
J. Cell Sci. 126, 2102-2113 (1 May 2013)

Systematic analysis of the Plk-mediated phosphoregulation in eukaryotes
Z. Liu, J. Ren, J. Cao, J. He, X. Yao, C. Jin, and Y. Xue
Brief Bioinform 14, 344-360 (1 May 2013)

Comparative Phosphoproteomic Analysis of Checkpoint Recovery Identifies New Regulators of the DNA Damage Response
V. A. Halim, M. Alvarez-Fernandez, Y. J. Xu, M. Aprelia, H. W. P. van den Toorn, A. J. R. Heck, S. Mohammed, and R. H. Medema
Sci Signal 6, rs9-rs9 (23 April 2013)

Genetics and Phosphoproteomics Reveal a Protein Phosphorylation Network in the Abscisic Acid Signaling Pathway in Arabidopsis thaliana
T. Umezawa, N. Sugiyama, F. Takahashi, J. C. Anderson, Y. Ishihama, S. C. Peck, and K. Shinozaki
Sci Signal 6, rs8-rs8 (9 April 2013)

Dynactin helps target Polo-like kinase 1 to kinetochores via its left-handed beta-helical p27 subunit
T.-Y. Yeh, A. K. Kowalska, B. R. Scipioni, F. K. Y. Cheong, M. Zheng, U. Derewenda, Z. S. Derewenda, and T. A. Schroer
EMBO J. 32, 1023-1035 (3 April 2013)

Aurora A is involved in central spindle assembly through phosphorylation of Ser 19 in P150Glued
D. Reboutier, M.-B. Troadec, J.-Y. Cremet, L. Chauvin, V. Guen, P. Salaun, and C. Prigent
JCB 201, 65-79 (1 April 2013)

Aurora at the pole and equator: overlapping functions of Aurora kinases in the mitotic spindle
H. Hochegger, N. Hegarat, and J. B. Pereira-Leal
Open Biol 3, 120185-120185 (20 March 2013)

Cdk1 and Plk1 mediate a CLASP2 phospho-switch that stabilizes kinetochore-microtubule attachments
A. R. R. Maia, Z. Garcia, L. Kabeche, M. Barisic, S. Maffini, S. Macedo-Ribeiro, I. M. Cheeseman, D. A. Compton, I. Kaverina, H. Maiato et al.
JCB 199, 285-301 (15 October 2012)

The where, when and how of microtubule nucleation - one ring to rule them all
N. Teixido-Travesa, J. Roig, and J. Luders
J. Cell Sci. 125, 4445-4456 (1 October 2012)

Plk1 Phosphorylates Sgt1 at the Kinetochores To Promote Timely Kinetochore-Microtubule Attachment
X. S. Liu, B. Song, J. Tang, W. Liu, S. Kuang, and X. Liu
Mol. Cell. Biol. 32, 4053-4067 (1 October 2012)

Regulation of the Cell Division Cycle in Trypanosoma brucei
Z. Li, B. Song, J. Tang, W. Liu, S. Kuang, and X. Liu
Eukaryot Cell 11, 1180-1190 (1 October 2012)

Aurora B is regulated by acetylation/deacetylation during mitosis in prostate cancer cells
M. Fadri-Moskwik, K. N. Weiderhold, A. Deeraksa, C. Chuang, J. Pan, S.-H. Lin, and L.-Y. Yu-Lee
FASEB J. 26, 4057-4067 (1 October 2012)

Polo-like kinase-1 regulates kinetochore-microtubule dynamics and spindle checkpoint silencing
D. Liu, O. Davydenko, and M. A. Lampson
JCB 198, 491-499 (20 August 2012)

A Highly Efficient Multifunctional Tandem Affinity Purification Approach Applicable to Diverse Organisms
H. Ma, J. R. McLean, L. F.-I. Chao, S. Mana-Capelli, M. Paramasivam, K. A. Hagstrom, K. L. Gould, and D. McCollum
MCP 11, 501-511 (1 August 2012)

Plk1 negatively regulates PRC1 to prevent premature midzone formation before cytokinesis
C.-K. Hu, N. Ozlu, M. Coughlin, J. J. Steen, and T. J. Mitchison
Mol. Biol. Cell 23, 2702-2711 (15 July 2012)

The Tlo Proteins Are Stoichiometric Components of Candida albicans Mediator Anchored via the Med3 Subunit
A. Zhang, K. O. Petrov, E. R. Hyun, Z. Liu, S. A. Gerber, and L. C. Myers
Eukaryot Cell 11, 874-884 (1 July 2012)

MMFPh: a maximal motif finder for phosphoproteomics datasets
T. Wang, A. N. Kettenbach, S. A. Gerber, and C. Bailey-Kellogg
Bioinformatics 28, 1562-1570 (15 June 2012)

Plk1 regulates the kinesin-13 protein Kif2b to promote faithful chromosome segregation
E. A. Hood, A. N. Kettenbach, S. A. Gerber, and D. A. Compton
Mol. Biol. Cell 23, 2264-2274 (15 June 2012)

Development of a Chemical Genetic Approach for Human Aurora B Kinase Identifies Novel Substrates of the Chromosomal Passenger Complex
R. C. C. Hengeveld, N. T. Hertz, M. J. M. Vromans, C. Zhang, A. L. Burlingame, K. M. Shokat, and S. M. A. Lens
MCP 11, 47-59 (1 May 2012)

Global Detection of Protein Kinase D-dependent Phosphorylation Events in Nocodazole-treated Human Cells
M. Franz-Wachtel, S. A. Eisler, K. Krug, S. Wahl, A. Carpy, A. Nordheim, K. Pfizenmaier, A. Hausser, and B. Macek
MCP 11, 160-170 (1 May 2012)

The role of clathrin in mitotic spindle organisation
S. J. Royle, S. A. Eisler, K. Krug, S. Wahl, A. Carpy, A. Nordheim, K. Pfizenmaier, A. Hausser, and B. Macek
J. Cell Sci. 125, 19-28 (1 January 2012)

Substrates of Mitotic Kinases
L. N. Johnson, S. A. Eisler, K. Krug, S. Wahl, A. Carpy, A. Nordheim, K. Pfizenmaier, A. Hausser, and B. Macek
Sci Signal 4, pe31-pe31 (28 June 2011)

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882