1
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Sexton JA, Potchernikov T, Bibeau JP, Casanova-Sepúlveda G, Cao W, Lou HJ, Boggon TJ, De La Cruz EM, Turk BE. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. Nat Commun 2024; 15:1426. [PMID: 38365893 PMCID: PMC10873347 DOI: 10.1038/s41467-024-45878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short, unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but specific aspects driving this conservation are unclear. Here, we screen a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and biochemical analysis of individual variants reveal distinct sequence requirements for actin binding and regulation by LIM kinase. LIM kinase recognition only partly explains sequence constraints on phosphoregulation, which are instead driven to a large extent by the capacity for phosphorylation to inactivate cofilin. We find loose sequence requirements for actin binding and phosphoinhibition, but collectively they restrict the N-terminus to sequences found in natural cofilins. Our results illustrate how a phosphorylation site can balance potentially competing sequence requirements for function and regulation.
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Affiliation(s)
- Joel A Sexton
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Tony Potchernikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Jeffrey P Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | | | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, 06520, USA.
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2
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Ballmer D, Lou HJ, Ishii M, Turk BE, Akiyoshi B. An unconventional regulatory circuitry involving Aurora B controls anaphase onset and error-free chromosome segregation in trypanosomes. bioRxiv 2024:2024.01.20.576407. [PMID: 38293145 PMCID: PMC10827227 DOI: 10.1101/2024.01.20.576407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Accurate chromosome segregation during mitosis requires that all chromosomes establish stable bi-oriented attachments with the spindle apparatus. Kinetochores form the interface between chromosomes and spindle microtubules and as such are under tight control by complex regulatory circuitry. As part of the chromosomal passenger complex (CPC), the Aurora B kinase plays a central role within this circuitry by destabilizing improper kinetochore-microtubule attachments and relaying the attachment status to the spindle assembly checkpoint, a feedback control system that delays the onset of anaphase by inhibiting the anaphase-promoting complex/cyclosome. Intriguingly, Aurora B is conserved even in kinetoplastids, an evolutionarily divergent group of eukaryotes, whose kinetochores are composed of a unique set of structural and regulatory proteins. Kinetoplastids do not have a canonical spindle checkpoint and it remains unclear how their kinetochores are regulated to ensure the fidelity and timing of chromosome segregation. Here, we show in Trypanosoma brucei, the kinetoplastid parasite that causes African sleeping sickness, that inhibition of Aurora B using an analogue-sensitive approach arrests cells in metaphase, with a reduction in properly bi-oriented kinetochores. Aurora B phosphorylates several kinetochore proteins in vitro, including the N-terminal region of the divergent Bub1-like protein KKT14. Depletion of KKT14 partially overrides the cell cycle arrest caused by Aurora B inhibition, while overexpression of a non-phosphorylatable KKT14 protein results in a prominent delay in the metaphase-to-anaphase transition. Finally, we demonstrate using a nanobody-based system that re-targeting the catalytic module of the CPC to the outer kinetochore is sufficient to promote mitotic exit but causes massive chromosome mis-segregation in anaphase. Our results indicate that the CPC and KKT14 are involved in an unconventional pathway controlling mitotic exit and error-free chromosome segregation in trypanosomes.
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Affiliation(s)
- Daniel Ballmer
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Midori Ishii
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent Edinburgh, EH9 3BF, United Kingdom
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Bungo Akiyoshi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
- The Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent Edinburgh, EH9 3BF, United Kingdom
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3
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Casanova-Sepúlveda G, Sexton JA, Turk BE, Boggon TJ. Autoregulation of the LIM kinases by their PDZ domain. Nat Commun 2023; 14:8441. [PMID: 38114480 PMCID: PMC10730565 DOI: 10.1038/s41467-023-44148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
LIM domain kinases (LIMK) are important regulators of actin cytoskeletal remodeling. These protein kinases phosphorylate the actin depolymerizing factor cofilin to suppress filament severing, and are key nodes between Rho GTPase cascades and actin. The two mammalian LIMKs, LIMK1 and LIMK2, contain consecutive LIM domains and a PDZ domain upstream of the C-terminal kinase domain. The roles of the N-terminal regions are not fully understood, and the function of the PDZ domain remains elusive. Here, we determine the 2.0 Å crystal structure of the PDZ domain of LIMK2 and reveal features not previously observed in PDZ domains including a core-facing arginine residue located at the second position of the 'x-Φ-G-Φ' motif, and that the expected peptide binding cleft is shallow and poorly conserved. We find a distal extended surface to be highly conserved, and when LIMK1 was ectopically expressed in yeast we find targeted mutagenesis of this surface decreases growth, implying increased LIMK activity. PDZ domain LIMK1 mutants expressed in yeast are hyperphosphorylated and show elevated activity in vitro. This surface in both LIMK1 and LIMK2 is critical for autoregulation independent of activation loop phosphorylation. Overall, our study demonstrates the functional importance of the PDZ domain to autoregulation of LIMKs.
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Affiliation(s)
| | - Joel A Sexton
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA.
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4
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Torres Robles J, Lou HJ, Shi G, Pan PL, Turk BE. Linear motif specificity in signaling through p38α and ERK2 mitogen-activated protein kinases. Proc Natl Acad Sci U S A 2023; 120:e2316599120. [PMID: 37988460 PMCID: PMC10691213 DOI: 10.1073/pnas.2316599120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) cascades are essential for eukaryotic cells to integrate and respond to diverse stimuli. Maintaining specificity in signaling through MAPK networks is key to coupling distinct inputs to appropriate cellular responses. Docking sites-short linear motifs found in MAPK substrates, regulators, and scaffolds-can promote signaling specificity through selective interactions, but how they do so remains unresolved. Here, we screened a proteomic library for sequences interacting with the MAPKs extracellular signal-regulated kinase 2 (ERK2) and p38α, identifying selective and promiscuous docking motifs. Sequences specific for p38α had high net charge and lysine content, and selective binding depended on a pair of acidic residues unique to the p38α docking interface. Finally, we validated a set of full-length proteins harboring docking sites selected in our screens to be authentic MAPK interactors and substrates. This study identifies features that help define MAPK signaling networks and explains how specific docking motifs promote signaling integrity.
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Affiliation(s)
- Jaylissa Torres Robles
- Department of Chemistry, Yale University, New Haven, CT06520
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | - Guangda Shi
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
| | | | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT06520
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5
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Sexton JA, Potchernikov T, Bibeau JP, Casanova-Sepúlveda G, Cao W, Lou HJ, Boggon TJ, De La Cruz EM, Turk BE. Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail. bioRxiv 2023:2023.06.30.547189. [PMID: 37425676 PMCID: PMC10327202 DOI: 10.1101/2023.06.30.547189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but the aspects of cofilin functionality driving this conservation are not clear. Here, we screened a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and subsequent biochemical analysis of individual variants revealed distinct sequence requirements for actin binding and regulation by LIM kinase. While the presence of a serine, rather than threonine, phosphoacceptor residue was essential for phosphorylation by LIM kinase, the native cofilin N-terminus was otherwise a suboptimal LIM kinase substrate. This circumstance was not due to sequence requirements for actin binding and severing, but rather appeared primarily to maintain the capacity for phosphorylation to inactivate cofilin. Overall, the individual sequence requirements for cofilin function and regulation were remarkably loose when examined separately, but collectively restricted the N-terminus to sequences found in natural cofilins. Our results illustrate how a regulatory phosphorylation site can balance potentially competing sequence requirements for function and regulation.
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Affiliation(s)
- Joel A. Sexton
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
| | - Tony Potchernikov
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Jeffrey P. Bibeau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | | | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Enrique M. De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520
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6
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Zhou W, Li W, Wang S, Salovska B, Hu Z, Tao B, Di Y, Punyamurtula U, Turk BE, Sessa WC, Liu Y. An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells. Nat Commun 2023; 14:3803. [PMID: 37365174 PMCID: PMC10293293 DOI: 10.1038/s41467-023-39514-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
The serine/threonine kinase AKT is a central node in cell signaling. While aberrant AKT activation underlies the development of a variety of human diseases, how different patterns of AKT-dependent phosphorylation dictate downstream signaling and phenotypic outcomes remains largely enigmatic. Herein, we perform a systems-level analysis that integrates methodological advances in optogenetics, mass spectrometry-based phosphoproteomics, and bioinformatics to elucidate how different intensity, duration, and pattern of Akt1 stimulation lead to distinct temporal phosphorylation profiles in vascular endothelial cells. Through the analysis of ~35,000 phosphorylation sites across multiple conditions precisely controlled by light stimulation, we identify a series of signaling circuits activated downstream of Akt1 and interrogate how Akt1 signaling integrates with growth factor signaling in endothelial cells. Furthermore, our results categorize kinase substrates that are preferably activated by oscillating, transient, and sustained Akt1 signals. We validate a list of phosphorylation sites that covaried with Akt1 phosphorylation across experimental conditions as potential Akt1 substrates. Our resulting dataset provides a rich resource for future studies on AKT signaling and dynamics.
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Affiliation(s)
- Wenping Zhou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06511, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wenxue Li
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Shisheng Wang
- Department of Pulmonary and Critical Care Medicine, and Proteomics-Metabolomics Analysis Platform, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Barbora Salovska
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Zhenyi Hu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Bo Tao
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yi Di
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA
| | - Ujwal Punyamurtula
- Master of Biotechnology ScM Program, Brown University, Providence, RI, 02912, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - William C Sessa
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA.
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Yansheng Liu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA.
- Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, 06516, USA.
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7
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McGeary MK, Damsky W, Daniels A, Song E, Micevic G, Huet-Calderwood C, Lou HJ, Paradkar S, Kaech S, Calderwood DA, Turk BE, Iwasaki A, Bosenberg MW. Setdb1 -loss induces type-I interferons and immune clearance of melanoma. bioRxiv 2023:2023.05.23.541922. [PMID: 37292991 PMCID: PMC10245815 DOI: 10.1101/2023.05.23.541922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite recent advances in the treatment of melanoma, many patients with metastatic disease still succumb to their disease. To identify tumor-intrinsic modulators of immunity to melanoma, we performed a whole-genome CRISPR screen in melanoma and identified multiple components of the HUSH complex, including Setdb1 , as hits. We found that loss of Setdb1 leads to increased immunogenicity and complete tumor clearance in a CD8+ T-cell dependent manner. Mechanistically, loss of Setdb1 causes de-repression of endogenous retroviruses (ERVs) in melanoma cells and triggers tumor-cell intrinsic type-I interferon signaling, upregulation of MHC-I expression, and increased CD8+ T-cell infiltration. Furthermore, spontaneous immune clearance observed in Setdb1 -/- tumors results in subsequent protection from other ERV-expressing tumor lines, supporting the functional anti-tumor role of ERV-specific CD8+ T-cells found in the Setdb1 -/- microenvironment. Blocking the type-I interferon receptor in mice grafted with Setdb1 -/- tumors decreases immunogenicity by decreasing MHC-I expression, leading to decreased T-cell infiltration and increased melanoma growth comparable to Setdb1 wt tumors. Together, these results indicate a critical role for Setdb1 and type-I interferons in generating an inflamed tumor microenvironment, and potentiating tumor-cell intrinsic immunogenicity in melanoma. This study further emphasizes regulators of ERV expression and type-I interferon expression as potential therapeutic targets for augmenting anti-cancer immune responses.
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8
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Shi G, Song C, Torres Robles J, Salichos L, Lou HJ, Lam TT, Gerstein M, Turk BE. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Sci Signal 2023; 16:eabm5518. [PMID: 36626580 PMCID: PMC9995140 DOI: 10.1126/scisignal.abm5518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Essential functions of mitogen-activated protein kinases (MAPKs) depend on their capacity to selectively phosphorylate a limited repertoire of substrates. MAPKs harbor a conserved groove located outside of the catalytic cleft that binds to short linear sequence motifs found in substrates and regulators. However, the weak and transient nature of these "docking" interactions poses a challenge to defining MAPK interactomes and associated sequence motifs. Here, we describe a yeast-based genetic screening pipeline to evaluate large collections of MAPK docking sequences in parallel. Using this platform, we analyzed a combinatorial library based on the docking sequences from the MAPK kinases MKK6 and MKK7, defining features critical for binding to the stress-activated MAPKs JNK1 and p38α. Our screen of a library consisting of ~12,000 sequences from the human proteome revealed multiple MAPK-selective interactors, including many that did not conform to previously defined docking motifs. Analysis of p38α/JNK1 exchange mutants identified specific docking groove residues that mediate selective binding. Last, we verified that docking sequences identified in the screen functioned in substrate recruitment in vitro and in cultured cells. Together, these studies establish an approach to characterize MAPK docking sequences and provide a resource for future investigation of signaling downstream of p38 and JNK.
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Affiliation(s)
- Guangda Shi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Claire Song
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jaylissa Torres Robles
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Leonidas Salichos
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA.,Keck MS and Proteomics Resource, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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9
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Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC. An atlas of substrate specificities for the human serine/threonine kinome. Nature 2023; 613:759-766. [PMID: 36631611 PMCID: PMC9876800 DOI: 10.1038/s41586-022-05575-3] [Citation(s) in RCA: 107] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is one of the most widespread post-translational modifications in biology1,2. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of serine and threonine phosphorylation have so far been identified, and several thousand have been associated with human diseases and biological processes3,4. For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein serine/threonine (Ser/Thr) kinases encoded in the human genome are responsible3. Here we used synthetic peptide libraries to profile the substrate sequence specificity of 303 Ser/Thr kinases, comprising more than 84% of those predicted to be active in humans. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. We used our kinome-wide dataset to computationally annotate and identify the kinases capable of phosphorylating every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites for which the putative protein kinases involved have been previously reported, our predictions were in excellent agreement. When this approach was applied to examine the signalling response of tissues and cell lines to hormones, growth factors, targeted inhibitors and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the intrinsic substrate specificity of the human Ser/Thr kinome, illuminate cellular signalling responses and provide a resource to link phosphorylation events to biological pathways.
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Affiliation(s)
- Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology & Medicine, Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center and The Rockefeller University, New York, NY, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander Kerelsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Junho Song
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amit Regev
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Cell and Developmental Biology Program, New York, NY, USA
| | - Katarina Liberatore
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Daniel M Cizin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin M Cohen
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Yilun Ma
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jaylissa Torres Robles
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Bert van de Kooij
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anne E van Vlimmeren
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole Andrée-Busch
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Norbert F Käufer
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maxim V Dorovkov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Alexey G Ryazanov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edward R Kastenhuber
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marcus D Goncalves
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Division of Endocrinology, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin D Hopkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Akio Yamashita
- Department of Investigative Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Alexei Degterev
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Mohamed Uduman
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Jingyi Lu
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Sean D Landry
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Bin Zhang
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Ian Cossentino
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Rune Linding
- Rewire Tx, Humboldt-Universität zu Berlin, Berlin, Germany
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Peter V Hornbeck
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Michael B Yaffe
- Center for Precision Cancer Medicine, Koch Institute for Integrative Cancer Biology, Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Divisions of Acute Care Surgery, Trauma, and Surgical Critical Care, and Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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10
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Stork BA, Dean A, Ortiz AR, Saha P, Putluri N, Planas-Silva MD, Mahmud I, Rajapakshe K, Coarfa C, Knapp S, Lorenzi PL, Kemp BE, Turk BE, Scott JW, Means AR, York B. Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 Regulates Hepatic Fuel Metabolism. Mol Metab 2022; 62:101513. [PMID: 35562082 PMCID: PMC9157561 DOI: 10.1016/j.molmet.2022.101513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 02/06/2023] Open
Abstract
Objective The liver is the primary internal metabolic organ that coordinates whole body energy homeostasis in response to feeding and fasting. Genetic ablation or pharmacological inhibition of calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2) has been shown to significantly improve hepatic health and peripheral insulin sensitivity upon overnutrition with high fat diet. However, the precise molecular underpinnings that explain this metabolic protection have remained largely undefined. Methods To characterize the role of CaMKK2 in hepatic metabolism, we developed and challenged liver-specific CaMKK2 knockout (CaMKK2LKO) mice with high fat diet and performed glucose and insulin tolerance tests to evaluate peripheral insulin sensitivity. We used a combination of RNA-Sequencing, glucose and fatty acid istotopic tracer studies, a newly developed Seahorse assay for measuring the oxidative capacity of purified peroxisomes, and a degenerate peptide libarary to identify putative CaMKK2 substrates that mechanistically explain the protective effects of hepatic CaMKK2 ablation. Results Consistent with previous findings, we show that hepatic CaMKK2 ablation significantly improves indices of peripheral insulin sensitivity. Mechanistically, we found that CaMKK2 phosphorylates and regulates GAPDH to promote glucose metabolism and PEX3 to blunt peroxisomal fatty acid catabolism in the liver. Conclusion CaMKK2 is a central metabolic fuel sensor in the liver that significantly contributes to whole body systems metabolism. Hepatic CaMKK2 is sufficient to toggle peripheral insulin sensitivity. CaMKK2 is required for hepatic glucose metabolism. Hepatic CaMKK2 balances glycolytic and fatty acid metabolism. CaMKK2 promotes glycolysis through regulation of GAPDH. CaMKK2 suppresses fatty acid metabolism through Pex3.
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Affiliation(s)
- Brittany A Stork
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Adam Dean
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Andrea R Ortiz
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Pradip Saha
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Nagireddy Putluri
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
| | | | - Iqbal Mahmud
- Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kimal Rajapakshe
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Cristian Coarfa
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Bruce E Kemp
- St. Vincent's Institute of Medical Research and Department of Medicine, University of Melbourne, Fitzroy, Victoria 3065, Australia; Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria 3000, Australia
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - John W Scott
- St. Vincent's Institute of Medical Research and Department of Medicine, University of Melbourne, Fitzroy, Victoria 3065, Australia; The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
| | - Anthony R Means
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030
| | - Brian York
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030.
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11
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Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA. Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry. Nat Commun 2022; 13:749. [PMID: 35136069 PMCID: PMC8826447 DOI: 10.1038/s41467-022-28427-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 01/25/2022] [Indexed: 12/26/2022] Open
Abstract
Tousled-like kinases (TLKs) are nuclear serine-threonine kinases essential for genome maintenance and proper cell division in animals and plants. A major function of TLKs is to phosphorylate the histone chaperone proteins ASF1a and ASF1b to facilitate DNA replication-coupled nucleosome assembly, but how TLKs selectively target these critical substrates is unknown. Here, we show that TLK2 selectivity towards ASF1 substrates is achieved in two ways. First, the TLK2 catalytic domain recognizes consensus phosphorylation site motifs in the ASF1 C-terminal tail. Second, a short sequence at the TLK2 N-terminus docks onto the ASF1a globular N-terminal domain in a manner that mimics its histone H3 client. Disrupting either catalytic or non-catalytic interactions through mutagenesis hampers ASF1 phosphorylation by TLK2 and cell growth. Our results suggest that the stringent selectivity of TLKs for ASF1 is enforced by an unusual interaction mode involving mutual recognition of a short sequence motifs by both kinase and substrate. Tousled-like kinase 2 (TLK2) phosphorylates ASF1 histone chaperones to promote nucleosome assembly in S phase. Here, the authors show that TLK2 targets ASF1 by simulating its client protein histone H3, exploiting a primordial protein interaction surface for regulatory control.
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Affiliation(s)
- Bertrand Simon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | | | - Guangda Shi
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - David A Calderwood
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA. .,Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
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12
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Schiapparelli P, Pirman NL, Mohler K, Miranda-Herrera PA, Zarco N, Kilic O, Miller C, Shah SR, Rogulina S, Hungerford W, Abriola L, Hoyer D, Turk BE, Guerrero-Cázares H, Isaacs FJ, Quiñones-Hinojosa A, Levchenko A, Rinehart J. Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function. Cell Rep 2021; 36:109416. [PMID: 34289367 PMCID: PMC8379681 DOI: 10.1016/j.celrep.2021.109416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/23/2020] [Accepted: 06/28/2021] [Indexed: 12/15/2022] Open
Abstract
Advances in genetic code expansion have enabled the production of proteins containing site-specific, authentic post-translational modifications. Here, we use a recoded bacterial strain with an expanded genetic code to encode phosphoserine into a human kinase protein. We directly encode phosphoserine into WNK1 (with-no-lysine [K] 1) or WNK4 kinases at multiple, distinct sites, which produced activated, phosphorylated WNK that phosphorylated and activated SPAK/OSR kinases, thereby synthetically activating this human kinase network in recoded bacteria. We used this approach to identify biochemical properties of WNK kinases, a motif for SPAK substrates, and small-molecule kinase inhibitors for phosphorylated SPAK. We show that the kinase inhibitors modulate SPAK substrates in cells, alter cell volume, and reduce migration of glioblastoma cells. Our work establishes a protein-engineering platform technology that demonstrates that synthetically active WNK kinase networks can accurately model cellular systems and can be used more broadly to target networks of phosphorylated proteins for research and discovery.
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Affiliation(s)
| | - Natasha L Pirman
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kyle Mohler
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | | | - Natanael Zarco
- Department of Neurologic Surgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Onur Kilic
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chad Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sagar R Shah
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Svetlana Rogulina
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - William Hungerford
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | | | - Andre Levchenko
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
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13
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Ghosh C, Uppala JK, Sathe L, Hammond CI, Anshu A, Pokkuluri PR, Turk BE, Dey M. Phosphorylation of Pal2 by the protein kinases Kin1 and Kin2 modulates HAC1 mRNA splicing in the unfolded protein response in yeast. Sci Signal 2021; 14:14/684/eaaz4401. [PMID: 34035143 DOI: 10.1126/scisignal.aaz4401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During cellular stress in the budding yeast Saccharomyces cerevisiae, an endoplasmic reticulum (ER)-resident dual kinase and RNase Ire1 splices an intron from HAC1 mRNA in the cytosol, thereby releasing its translational block. Hac1 protein then activates an adaptive cellular stress response called the unfolded protein response (UPR) that maintains ER homeostasis. The polarity-inducing protein kinases Kin1 and Kin2 contribute to HAC1 mRNA processing. Here, we showed that an RNA-protein complex that included the endocytic proteins Pal1 and Pal2 mediated HAC1 mRNA splicing downstream of Kin1 and Kin2. We found that Pal1 and Pal2 bound to the 3' untranslated region (3'UTR) of HAC1 mRNA, and a yeast strain lacking both Pal1 and Pal2 was deficient in HAC1 mRNA processing. We also showed that Kin1 and Kin2 directly phosphorylated Pal2, and that a nonphosphorylatable Pal2 mutant could not rescue the UPR defect in a pal1Δ pal2Δ strain. Thus, our work uncovers a Kin1/2-Pal2 signaling pathway that coordinates HAC1 mRNA processing and ER homeostasis.
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Affiliation(s)
- Chandrima Ghosh
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Jagadeesh Kumar Uppala
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Leena Sathe
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Charlotte I Hammond
- Department of Biological Sciences, Quinnipiac University, Hamden, CT 06518, USA
| | - Ashish Anshu
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - P Raj Pokkuluri
- Bioscience Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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14
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Cho E, Lou HJ, Kuruvilla L, Calderwood DA, Turk BE. PPP6C negatively regulates oncogenic ERK signaling through dephosphorylation of MEK. Cell Rep 2021; 34:108928. [PMID: 33789117 PMCID: PMC8068315 DOI: 10.1016/j.celrep.2021.108928] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/26/2021] [Accepted: 03/10/2021] [Indexed: 12/21/2022] Open
Abstract
Flux through the RAF-MEK-ERK protein kinase cascade is shaped by phosphatases acting on the core components of the pathway. Despite being an established drug target and a hub for crosstalk regulation, little is known about dephosphorylation of MEK, the central kinase within the cascade. Here, we identify PPP6C, a phosphatase frequently mutated or downregulated in melanoma, as a major MEK phosphatase in cells exhibiting oncogenic ERK pathway activation. Recruitment of MEK to PPP6C occurs through an interaction with its associated regulatory subunits. Loss of PPP6C causes hyperphosphorylation of MEK at activating and crosstalk phosphorylation sites, promoting signaling through the ERK pathway and decreasing sensitivity to MEK inhibitors. Recurrent melanoma-associated PPP6C mutations cause MEK hyperphosphorylation, suggesting that they promote disease at least in part by activating the core oncogenic pathway driving melanoma. Collectively, our studies identify a key negative regulator of ERK signaling that may influence susceptibility to targeted cancer therapies. Through an shRNA screen, Cho et al. identify PPP6C as a phosphatase that inactivates the kinase MEK, sensitizing tumor cells to clinical MEK inhibitors. This study suggests that cancer-associated loss-of-function PPP6C mutations prevalent in melanoma serve to activate the core oncogenic RAF-MEK-ERK pathway that drives the disease.
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Affiliation(s)
- Eunice Cho
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Leena Kuruvilla
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - David A Calderwood
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA.
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15
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Torres-Ayuso P, An E, Nyswaner KM, Bensen RC, Ritt DA, Specht SI, Das S, Andresson T, Cachau RE, Liang RJ, Ries AL, Robinson CM, Difilippantonio S, Gouker B, Bassel L, Karim BO, Miller CJ, Turk BE, Morrison DK, Brognard J. TNIK Is a Therapeutic Target in Lung Squamous Cell Carcinoma and Regulates FAK Activation through Merlin. Cancer Discov 2021; 11:1411-1423. [PMID: 33495197 DOI: 10.1158/2159-8290.cd-20-0797] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/21/2020] [Accepted: 01/20/2021] [Indexed: 12/14/2022]
Abstract
Lung squamous cell carcinoma (LSCC) is the second most prevalent type of lung cancer. Despite extensive genomic characterization, no targeted therapies are approved for the treatment of LSCC. Distal amplification of the 3q chromosome is the most frequent genomic alteration in LSCC, and there is an urgent need to identify efficacious druggable targets within this amplicon. We identify the protein kinase TNIK as a therapeutic target in LSCC. TNIK is amplified in approximately 50% of LSCC cases. TNIK genetic depletion or pharmacologic inhibition reduces the growth of LSCC cells in vitro and in vivo. In addition, TNIK inhibition showed antitumor activity and increased apoptosis in established LSCC patient-derived xenografts. Mechanistically, we identified the tumor suppressor Merlin/NF2 as a novel TNIK substrate and showed that TNIK and Merlin are required for the activation of focal adhesion kinase. In conclusion, our data identify targeting TNIK as a potential therapeutic strategy in LSCC. SIGNIFICANCE: Targeted therapies have not yet been approved for the treatment of LSCC, due to lack of identification of actionable cancer drivers. We define TNIK catalytic activity as essential for maintaining LSCC viability and validate the antitumor efficacy of TNIK inhibition in preclinical models of LSCC.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Pedro Torres-Ayuso
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland.
| | - Elvira An
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Katherine M Nyswaner
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Ryan C Bensen
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Daniel A Ritt
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Suzanne I Specht
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Sudipto Das
- Protein Characterization Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thorkell Andresson
- Protein Characterization Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Raul E Cachau
- Advanced Biomedical Computational Science, Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Roger J Liang
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - Amy L Ries
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Christina M Robinson
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Simone Difilippantonio
- Laboratory Animal Sciences Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Brad Gouker
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Laura Bassel
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Baktiar O Karim
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland
| | - John Brognard
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, NCI, Frederick, Maryland.
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16
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Komolov KE, Sulon SM, Bhardwaj A, van Keulen SC, Duc NM, Laurinavichyute DK, Lou HJ, Turk BE, Chung KY, Dror RO, Benovic JL. Structure of a GRK5-Calmodulin Complex Reveals Molecular Mechanism of GRK Activation and Substrate Targeting. Mol Cell 2020; 81:323-339.e11. [PMID: 33321095 DOI: 10.1016/j.molcel.2020.11.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/15/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022]
Abstract
The phosphorylation of G protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) facilitates arrestin binding and receptor desensitization. Although this process can be regulated by Ca2+-binding proteins such as calmodulin (CaM) and recoverin, the molecular mechanisms are poorly understood. Here, we report structural, computational, and biochemical analysis of a CaM complex with GRK5, revealing how CaM shapes GRK5 response to calcium. The CaM N and C domains bind independently to two helical regions at the GRK5 N and C termini to inhibit GPCR phosphorylation, though only the C domain interaction disrupts GRK5 membrane association, thereby facilitating cytoplasmic translocation. The CaM N domain strongly activates GRK5 via ordering of the amphipathic αN-helix of GRK5 and allosteric disruption of kinase-RH domain interaction for phosphorylation of cytoplasmic GRK5 substrates. These results provide a framework for understanding how two functional effects, GRK5 activation and localization, can cooperate under control of CaM for selective substrate targeting by GRK5.
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Affiliation(s)
- Konstantin E Komolov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Sarah M Sulon
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Siri C van Keulen
- Department of Computer Science, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea; Division of Precision Medicine, Research Institute, National Cancer Center, Goyang, South Korea
| | - Daniela K Laurinavichyute
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Ron O Dror
- Department of Computer Science, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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17
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Chetty AK, Sexton JA, Ha BH, Turk BE, Boggon TJ. Recognition of physiological phosphorylation sites by p21-activated kinase 4. J Struct Biol 2020; 211:107553. [PMID: 32585314 PMCID: PMC7395882 DOI: 10.1016/j.jsb.2020.107553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023]
Abstract
Many serine/threonine protein kinases discriminate between serine and threonine substrates as a filter to control signaling output. Among these, the p21-activated kinase (PAK) group strongly favors phosphorylation of Ser over Thr residues. PAK4, a group II PAK, almost exclusively phosphorylates its substrates on serine residues. The only well documented exception is LIM domain kinase 1 (LIMK1), which is phosphorylated on an activation loop threonine (Thr508) to promote its catalytic activity. To understand the molecular and kinetic basis for PAK4 substrate selectivity we compared its mode of recognition of LIMK1 (Thr508) with that of a known serine substrate, β-catenin (Ser675). We determined X-ray crystal structures of PAK4 in complex with synthetic peptides corresponding to its phosphorylation sites in LIMK1 and β-catenin to 1.9 Å and 2.2 Å resolution, respectively. We found that the PAK4 DFG + 1 residue, a key determinant of phosphoacceptor preference, adopts a sub-optimal orientation when bound to LIMK1 compared to β-catenin. In peptide kinase activity assays, we find that phosphoacceptor identity impacts catalytic efficiency but does not affect the Km value for both phosphorylation sites. Although catalytic efficiency of wild-type LIMK1 and β-catenin are equivalent, T508S mutation of LIMK1 creates a highly efficient substrate. These results suggest suboptimal phosphorylation of LIMK1 as a mechanism for controlling the dynamics of substrate phosphorylation by PAK4.
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Affiliation(s)
- Ashwin K. Chetty
- Yale College, New Haven, CT 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Joel A. Sexton
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Byung Hak Ha
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA.,Yale Cancer Center, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Titus J. Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA.,Department of Pharmacology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA.,Yale Cancer Center, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA.,To whom correspondence should be addressed
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18
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Cho E, Lou HJ, Turk BE. Abstract 3754: PPP6C regulation of ERK signaling in melanoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Melanoma, the deadliest form of skin cancer, is characterized by aberrant hyperactivation of the ERK mitogen-activated protein kinase signaling pathway. Inhibitors of BRAF and MEK1/2, both members of this pathway, have shown clinical efficacy and are used in combination to treat BRAFV600E melanoma, the most common melanoma genomic subtype. However, not all BRAFV600E melanomas respond to these inhibitors, and those that do respond eventually acquire resistance. To better understand mechanisms of drug susceptibility in BRAFV600E melanoma, we performed a loss-of-function screen to identify kinases and phosphatases that modulate sensitivity to two clinical MEK1/2 inhibitors. In this screen, we identified PPP6C, the catalytic subunit of protein phosphatase 6 (PP6), as a factor promoting sensitivity to MEK1/2 inhibition. PPP6C is a potential tumor suppressor mutated in 7-12% of melanomas, and has roles in cell cycle regulation and DNA damage repair. shRNA-mediated knockdown and CRISPR/Cas9-mediated knockout of PPP6C in BRAF mutant melanoma cells both lead to hyperactivation of MEK1/2 and ERK1/2, resulting in decreased sensitivity to pathway inhibitors. This finding was confirmed in a panel of BRAFV600E melanoma cell lines. Through in vitro biochemical and cell-based studies, we have established that PP6 directly dephosphorylates MEK1/2. As with complete loss of PPP6C, cells expressing most recurrent cancer-associated PPP6C mutants similarly have hyperactive ERK signaling. Our studies support a novel negative regulatory role for PPP6C in ERK signaling that contributes to its activity as a tumor suppressor and promotes pathway inhibitor sensitivity in BRAFV600E melanoma.
Citation Format: Eunice Cho, Hua Jane Lou, Benjamin E. Turk. PPP6C regulation of ERK signaling in melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3754.
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Terekhov SS, Mokrushina YA, Nazarov AS, Zlobin A, Zalevsky A, Bourenkov G, Golovin A, Belogurov A, Osterman IA, Kulikova AA, Mitkevich VA, Lou HJ, Turk BE, Wilmanns M, Smirnov IV, Altman S, Gabibov AG. A kinase bioscavenger provides antibiotic resistance by extremely tight substrate binding. Sci Adv 2020; 6:eaaz9861. [PMID: 32637600 PMCID: PMC7314540 DOI: 10.1126/sciadv.aaz9861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities are self-controlled by repertoires of lethal agents, the antibiotics. In their turn, these antibiotics are regulated by bioscavengers that are selected in the course of evolution. Kinase-mediated phosphorylation represents one of the general strategies for the emergence of antibiotic resistance. A new subfamily of AmiN-like kinases, isolated from the Siberian bear microbiome, inactivates antibiotic amicoumacin by phosphorylation. The nanomolar substrate affinity defines AmiN as a phosphotransferase with a unique catalytic efficiency proximal to the diffusion limit. Crystallographic analysis and multiscale simulations revealed a catalytically perfect mechanism providing phosphorylation exclusively in the case of a closed active site that counteracts substrate promiscuity. AmiN kinase is a member of the previously unknown subfamily representing the first evidence of a specialized phosphotransferase bioscavenger.
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Affiliation(s)
- Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anton S. Nazarov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Alexander Zlobin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Arthur Zalevsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | | | - Andrey Golovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, Russia
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya A. Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexandra A. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir A. Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | | | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Arizona State University, Tempe, AZ, USA
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
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20
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Cho E, Lou HJ, Turk BE. PPP6C Regulation of ERK Signaling in Melanoma. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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21
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Sang D, Pinglay S, Wiewiora RP, Selvan ME, Lou HJ, Chodera JD, Turk BE, Gümüş ZH, Holt LJ. Ancestral reconstruction reveals mechanisms of ERK regulatory evolution. eLife 2019; 8:38805. [PMID: 31407663 PMCID: PMC6692128 DOI: 10.7554/elife.38805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/03/2019] [Indexed: 01/21/2023] Open
Abstract
Protein kinases are crucial to coordinate cellular decisions and therefore their activities are strictly regulated. Previously we used ancestral reconstruction to determine how CMGC group kinase specificity evolved (Howard et al., 2014). In the present study, we reconstructed ancestral kinases to study the evolution of regulation, from the inferred ancestor of CDKs and MAPKs, to modern ERKs. Kinases switched from high to low autophosphorylation activity at the transition to the inferred ancestor of ERKs 1 and 2. Two synergistic amino acid changes were sufficient to induce this change: shortening of the β3-αC loop and mutation of the gatekeeper residue. Restoring these two mutations to their inferred ancestral state led to a loss of dependence of modern ERKs 1 and 2 on the upstream activating kinase MEK in human cells. Our results shed light on the evolutionary mechanisms that led to the tight regulation of a kinase that is central in development and disease.
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Affiliation(s)
- Dajun Sang
- Institute for Systems Genetics, New York University Langone Medical Center, New York, United States
| | - Sudarshan Pinglay
- Institute for Systems Genetics, New York University Langone Medical Center, New York, United States
| | - Rafal P Wiewiora
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States.,Memorial Sloan Kettering Cancer Center, New York, United States
| | - Myvizhi E Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - John D Chodera
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, United States
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van de Kooij B, Creixell P, van Vlimmeren A, Joughin BA, Miller CJ, Haider N, Simpson CD, Linding R, Stambolic V, Turk BE, Yaffe MB. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. eLife 2019; 8:44635. [PMID: 31124786 PMCID: PMC6570481 DOI: 10.7554/elife.44635] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/13/2019] [Indexed: 12/25/2022] Open
Abstract
Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for the entire Nek kinase family, except for Nek11. While all Nek kinases strongly select for hydrophobic residues in the −3 position, the family separates into four distinct groups based on specificity for a serine versus threonine phospho-acceptor, and preference for basic or acidic residues in other positions. Unlike Nek1-Nek9, Nek10 is a dual-specificity kinase that efficiently phosphorylates itself and peptide substrates on serine and tyrosine, and its activity is enhanced by tyrosine auto-phosphorylation. Nek10 dual-specificity depends on residues in the HRD+2 and APE-4 positions that are uncommon in either serine/threonine or tyrosine kinases. Finally, we show that the phosphorylation-site motifs for the mitotic kinases Nek6, Nek7 and Nek9 are essentially identical to that of their upstream activator Plk1, suggesting that Nek6/7/9 function as phospho-motif amplifiers of Plk1 signaling.
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Affiliation(s)
- Bert van de Kooij
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Pau Creixell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Anne van Vlimmeren
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Brian A Joughin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Nasir Haider
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Craig D Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vuk Stambolic
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Michael B Yaffe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston, United States
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23
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Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. PLoS Biol 2019; 17:e2006540. [PMID: 30897078 PMCID: PMC6445471 DOI: 10.1371/journal.pbio.2006540] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/02/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022] Open
Abstract
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates. While the impact of localization and recruitment on kinase-substrate targeting can be readily assessed, evaluating the relative importance of direct phosphorylation site interactions remains challenging. In this study, we examine the STE20 family of protein serine-threonine kinases to investigate basic mechanisms of substrate targeting. We used peptide arrays to define the phosphorylation site specificity for the majority of STE20 kinases and categorized them into four distinct groups. Using structure-guided mutagenesis, we identified key specificity-determining residues within the kinase catalytic cleft, including an unappreciated role for the kinase β3-αC loop region in controlling specificity. Exchanging key residues between the STE20 kinases p21-activated kinase 4 (PAK4) and Mammalian sterile 20 kinase 4 (MST4) largely interconverted their phosphorylation site preferences. In cells, a reprogrammed PAK4 mutant, engineered to recognize MST substrates, failed to phosphorylate PAK4 substrates or to mediate remodeling of the actin cytoskeleton. In contrast, this mutant could rescue signaling through the Hippo pathway in cells lacking multiple MST kinases. These observations formally demonstrate the importance of catalytic site specificity for directing protein kinase signal transduction pathways. Our findings further suggest that phosphorylation site specificity is both necessary and sufficient to mediate distinct signaling outputs of STE20 kinases and imply broad applicability to other kinase signaling systems.
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Affiliation(s)
- Chad J. Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bert van de Kooij
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Byung Hak Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oriana S. Fisher
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Natasha L. Pirman
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Michael B. Yaffe
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
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24
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Waldt N, Seifert A, Demiray YE, Devroe E, Turk BE, Reichardt P, Mix C, Reinhold A, Freund C, Müller AJ, Schraven B, Stork O, Kliche S. Filamin A Phosphorylation at Serine 2152 by the Serine/Threonine Kinase Ndr2 Controls TCR-Induced LFA-1 Activation in T Cells. Front Immunol 2018; 9:2852. [PMID: 30568657 PMCID: PMC6290345 DOI: 10.3389/fimmu.2018.02852] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/19/2018] [Indexed: 01/10/2023] Open
Abstract
The integrin LFA-1 (CD11a/CD18) plays a critical role in the interaction of T cells with antigen presenting cells (APCs) to promote lymphocyte differentiation and proliferation. This integrin can be present either in a closed or in an open active conformation and its activation upon T-cell receptor (TCR) stimulation is a critical step to allow interaction with APCs. In this study we demonstrate that the serine/threonine kinase Ndr2 is critically involved in the initiation of TCR-mediated LFA-1 activation (open conformation) in T cells. Ndr2 itself becomes activated upon TCR stimulation and phosphorylates the intracellular integrin binding partner Filamin A (FLNa) at serine 2152. This phosphorylation promotes the dissociation of FLNa from LFA-1, allowing for a subsequent association of Talin and Kindlin-3 which both stabilize the open conformation of LFA-1. Our data suggest that Ndr2 activation is a crucial step to initiate TCR-mediated LFA-1 activation in T cells.
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Affiliation(s)
- Natalie Waldt
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
| | - Anke Seifert
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
| | - Yunus Emre Demiray
- Institute of Biology, Department of Genetics and Molecular Neurobiology, Otto-von-Guericke University, Magdeburg, Germany
| | - Eric Devroe
- MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, United States
| | - Peter Reichardt
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
| | - Charlie Mix
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
| | - Annegret Reinhold
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
| | - Christian Freund
- Protein Biochemistry Group, Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Andreas J Müller
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany.,Intravital Microscopy of Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Burkhart Schraven
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany.,Department of Immune Control Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Oliver Stork
- Institute of Biology, Department of Genetics and Molecular Neurobiology, Otto-von-Guericke University, Magdeburg, Germany.,Center for Behavioral Brain Sciences, Magdeburg, Germany
| | - Stefanie Kliche
- Institute of Molecular and Clinical Immunology, Health Campus Immunology, Infectiology and Inflammation (GC-I3), Otto-von-Guericke-University, Magdeburg, Germany
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25
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Jeschke GR, Lou HJ, Weise K, Hammond CI, Demonch M, Brennwald P, Turk BE. Substrate priming enhances phosphorylation by the budding yeast kinases Kin1 and Kin2. J Biol Chem 2018; 293:18353-18364. [PMID: 30305396 DOI: 10.1074/jbc.ra118.005651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/04/2018] [Indexed: 12/27/2022] Open
Abstract
Multisite phosphorylation of proteins is a common mechanism for signal integration and amplification in eukaryotic signaling networks. Proteins are commonly phosphorylated at multiple sites in an ordered manner, whereby phosphorylation by one kinase primes the substrate by generating a recognition motif for a second kinase. Here we show that substrate priming promotes phosphorylation by Saccharomyces cerevisiae Kin1 and Kin2, kinases that regulate cell polarity, exocytosis, and the endoplasmic reticulum (ER) stress response. Kin1/Kin2 phosphorylated substrates within the context of a sequence motif distinct from those of their most closely related kinases. In particular, the rate of phosphorylation of a peptide substrate by Kin1/Kin2 increased >30-fold with incorporation of a phosphoserine residue two residues downstream of the phosphorylation site. Recognition of phosphorylated substrates by Kin1/Kin2 was mediated by a patch of basic residues located in the region of the kinase αC helix. We identified a set of candidate Kin1/Kin2 substrates reported to be dually phosphorylated at sites conforming to the Kin1/Kin2 consensus sequence. One of these proteins, the t-SNARE protein Sec9, was confirmed to be a Kin1/Kin2 substrate both in vitro and in vivo Sec9 phosphorylation by Kin1 in vitro was enhanced by prior phosphorylation at the +2 position. Recognition of primed substrates was not required for the ability of Kin2 to suppress the growth defect of secretory pathway mutants but was necessary for optimal growth under conditions of ER stress. These results suggest that at least some endogenous protein substrates of Kin1/Kin2 are phosphorylated in a priming-dependent manner.
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Affiliation(s)
- Grace R Jeschke
- From the Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520
| | - Hua Jane Lou
- From the Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520
| | - Keith Weise
- From the Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520
| | - Charlotte I Hammond
- the Department of Biology, Quinnipiac University, Hamden, Connecticut 06518, and
| | - Mallory Demonch
- the Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Patrick Brennwald
- the Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Benjamin E Turk
- From the Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520,.
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26
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Barber KW, Miller CJ, Jun JW, Lou HJ, Turk BE, Rinehart J. Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Biochemistry 2018; 57:4717-4725. [PMID: 29920078 DOI: 10.1021/acs.biochem.8b00410] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human proteome encodes >500 protein kinases and hundreds of thousands of potential phosphorylation sites. However, the identification of kinase-substrate pairs remains an active area of research because the relationships between individual kinases and these phosphorylation sites remain largely unknown. Many techniques have been established to discover kinase substrates but are often technically challenging to perform. Moreover, these methods frequently rely on substrate reagent pools that do not reflect human protein sequences or are biased by human cell line protein expression profiles. Here, we describe a new approach called SERIOHL-KILR (serine-oriented human library-kinase library reactions) to profile kinase substrate specificity and to identify candidate substrates for serine kinases. Using a purified library of >100000 serine-oriented human peptides expressed heterologously in Escherichia coli, we perform in vitro kinase reactions to identify phosphorylated human peptide sequences by liquid chromatography and tandem mass spectrometry. We compare our results for protein kinase A to those of a well-established positional scanning peptide library method, certifying that SERIOHL-KILR can identify the same predominant motif elements as traditional techniques. We then interrogate a small panel of cancer-associated PKCβ mutants using our profiling protocol and observe a shift in substrate specificity likely attributable to the loss of key polar contacts between the kinase and its substrates. Overall, we demonstrate that SERIOHL-KILR can rapidly identify candidate kinase substrates that can be directly mapped to human sequences for pathway analysis. Because this technique can be adapted for various kinase studies, we believe that SERIOHL-KILR will have many new victims in the future.
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Affiliation(s)
- Karl W Barber
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Chad J Miller
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jay W Jun
- Division of Nutritional Sciences , Cornell University , Ithaca , New York 14850 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
| | - Hua Jane Lou
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Benjamin E Turk
- Department of Pharmacology , Yale University , New Haven , Connecticut 06520 , United States
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology , Yale University , New Haven , Connecticut 06520 , United States.,Systems Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,The Cancer Systems Biology Consortium Research Center , Yale University , West Haven , Connecticut 06516 , United States
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27
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Miller CJ, Turk BE. Homing in: Mechanisms of Substrate Targeting by Protein Kinases. Trends Biochem Sci 2018; 43:380-394. [PMID: 29544874 DOI: 10.1016/j.tibs.2018.02.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/08/2018] [Accepted: 02/15/2018] [Indexed: 01/21/2023]
Abstract
Protein phosphorylation is the most common reversible post-translational modification in eukaryotes. Humans have over 500 protein kinases, of which more than a dozen are established targets for anticancer drugs. All kinases share a structurally similar catalytic domain, yet each one is uniquely positioned within signaling networks controlling essentially all aspects of cell behavior. Kinases are distinguished from one another based on their modes of regulation and their substrate repertoires. Coupling specific inputs to the proper signaling outputs requires that kinases phosphorylate a limited number of sites to the exclusion of hundreds of thousands of off-target phosphorylation sites. Here, we review recent progress in understanding mechanisms of kinase substrate specificity and how they function to shape cellular signaling networks.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA.
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28
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Abstract
A majority of the 90 human protein tyrosine kinases (PTKs) are understudied "orphan" enzymes with few or no known substrates. Designing experiments aimed at assaying the catalytic activity of these PTKs has been a long-running problem. In the past, researchers have used polypeptides with a randomized 4:1 molar ratio of glutamic acid to tyrosine as general PTK substrates. However, these substrates are inefficient and perform poorly for many applications. In this work, we apply the KINATEST-ID pipeline for artificial kinase substrate discovery to design a set of candidate "universal" PTK peptide substrate sequences. We identified two unique peptide sequences from this set that had robust activity with a panel of 15 PTKs tested in an initial screen. Kinetic characterization with seven receptor and nonreceptor PTKs confirmed these peptides to be efficient and general PTK substrates. The broad scope of these artificial substrates demonstrates that they should be useful as tools for probing understudied PTK activity.
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Affiliation(s)
- Laura J Marholz
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , 420 Washington Avenue Southeast , Minneapolis , Minnesota 55455 , United States
| | - Nicholas A Zeringo
- Department of Pharmacology , Yale University School of Medicine , P.O. Box 208066, 333 Cedar Street , New Haven , Connecticut 06520 , United States
| | - Hua Jane Lou
- Department of Pharmacology , Yale University School of Medicine , P.O. Box 208066, 333 Cedar Street , New Haven , Connecticut 06520 , United States
| | - Benjamin E Turk
- Department of Pharmacology , Yale University School of Medicine , P.O. Box 208066, 333 Cedar Street , New Haven , Connecticut 06520 , United States
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , 420 Washington Avenue Southeast , Minneapolis , Minnesota 55455 , United States
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Hara M, Lourido S, Petrova B, Lou HJ, Von Stetina JR, Kashevsky H, Turk BE, Orr-Weaver TL. Identification of PNG kinase substrates uncovers interactions with the translational repressor TRAL in the oocyte-to-embryo transition. eLife 2018; 7:33150. [PMID: 29480805 PMCID: PMC5826265 DOI: 10.7554/elife.33150] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/12/2018] [Indexed: 12/19/2022] Open
Abstract
The Drosophila Pan Gu (PNG) kinase complex regulates hundreds of maternal mRNAs that become translationally repressed or activated as the oocyte transitions to an embryo. In a previous paper (Hara et al., 2017), we demonstrated PNG activity is under tight developmental control and restricted to this transition. Here, examination of PNG specificity showed it to be a Thr-kinase yet lacking a clear phosphorylation site consensus sequence. An unbiased biochemical screen for PNG substrates identified the conserved translational repressor Trailer Hitch (TRAL). Phosphomimetic mutation of the PNG phospho-sites in TRAL reduced its ability to inhibit translation in vitro. In vivo, mutation of tral dominantly suppressed png mutants and restored Cyclin B protein levels. The repressor Pumilio (PUM) has the same relationship with PNG, and we also show that PUM is a PNG substrate. Furthermore, PNG can phosphorylate BICC and ME31B, repressors that bind TRAL in cytoplasmic RNPs. Therefore, PNG likely promotes translation at the oocyte-to-embryo transition by phosphorylating and inactivating translational repressors.
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Affiliation(s)
| | | | | | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | | | | | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Terry L Orr-Weaver
- Whitehead Institute, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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30
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Affiliation(s)
- Benjamin E. Turk
- Department of Pharmacology Yale School of Medicine New Haven CT USA
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31
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Abstract
The zinc-dependent metalloprotease anthrax lethal factor (LF) is the enzymatic component of a toxin thought to have a major role in Bacillus anthracis infections. Like many bacterial toxins, LF is a secreted protein that functions within host cells. LF is a highly selective protease that cleaves a limited number of substrates in a site-specific manner, thereby impacting host signal transduction pathways. The major substrates of LF are mitogen-activated protein kinase kinases (MKKs), which lie in the middle of three-component phosphorylation cascades mediating numerous functions in a variety of cells and tissues. How LF targets its limited substrate repertoire has been an active area of investigation. LF recognizes a specific sequence motif surrounding the scissile bonds of substrate proteins. X-ray crystallography of the protease in complex with peptide substrates has revealed the structural basis of selectivity for the LF cleavage site motif. In addition to having interactions proximal to the cleavage site, LF binds directly to a more distal region in its substrates through a so-called exosite interaction. This exosite has been mapped to a surface within a non-catalytic domain of LF with previously unknown function. A putative LF-binding site has likewise been identified on the catalytic domains of MKKs. Here we review our current state of understanding of LF-substrate interactions and discuss the implications for the design and discovery of inhibitors that may have utility as anthrax therapeutics.
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Affiliation(s)
- Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
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32
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Advani G, Lim YC, Catimel B, Lio DSS, Ng NLY, Chüeh AC, Tran M, Anasir MI, Verkade H, Zhu HJ, Turk BE, Smithgall TE, Ang CS, Griffin M, Cheng HC. Csk-homologous kinase (Chk) is an efficient inhibitor of Src-family kinases but a poor catalyst of phosphorylation of their C-terminal regulatory tyrosine. Cell Commun Signal 2017; 15:29. [PMID: 28784162 PMCID: PMC5547543 DOI: 10.1186/s12964-017-0186-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background C-terminal Src kinase (Csk) and Csk-homologous kinase (Chk) are the major endogenous inhibitors of Src-family kinases (SFKs). They employ two mechanisms to inhibit SFKs. First, they phosphorylate the C-terminal tail tyrosine which stabilizes SFKs in a closed inactive conformation by engaging the SH2 domain in cis. Second, they employ a non-catalytic inhibitory mechanism involving direct binding of Csk and Chk to the active forms of SFKs that is independent of phosphorylation of their C-terminal tail. Csk and Chk are co-expressed in many cell types. Contributions of the two mechanisms towards the inhibitory activity of Csk and Chk are not fully clear. Furthermore, the determinants in Csk and Chk governing their inhibition of SFKs by the non-catalytic inhibitory mechanism are yet to be defined. Methods We determined the contributions of the two mechanisms towards the inhibitory activity of Csk and Chk both in vitro and in transduced colorectal cancer cells. Specifically, we assayed the catalytic activities of Csk and Chk in phosphorylating a specific peptide substrate and a recombinant SFK member Src. We employed surface plasmon resonance spectroscopy to measure the kinetic parameters of binding of Csk, Chk and their mutants to a constitutively active mutant of the SFK member Hck. Finally, we determined the effects of expression of recombinant Chk on anchorage-independent growth and SFK catalytic activity in Chk-deficient colorectal cancer cells. Results Our results revealed Csk as a robust enzyme catalysing phosphorylation of the C-terminal tail tyrosine of SFKs but a weak non-catalytic inhibitor of SFKs. In contrast, Chk is a poor catalyst of SFK tail phosphorylation but binds SFKs with high affinity, enabling it to efficiently inhibit SFKs with the non-catalytic inhibitory mechanism both in vitro and in transduced colorectal cancer cells. Further analyses mapped some of the determinants governing this non-catalytic inhibitory mechanism of Chk to its kinase domain. Conclusions SFKs are activated by different upstream signals to adopt multiple active conformations in cells. SFKs adopting these conformations can effectively be constrained by the two complementary inhibitory mechanisms of Csk and Chk. Furthermore, the lack of this non-catalytic inhibitory mechanism accounts for SFK overactivation in the Chk-deficient colorectal cancer cells. Electronic supplementary material The online version of this article (doi:10.1186/s12964-017-0186-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gahana Advani
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ya Chee Lim
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,PAP Rashidah Sa'adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Bruno Catimel
- Walter and Eliza Hall Institute for Medical Research and Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daisy Sio Seng Lio
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nadia L Y Ng
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia.,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anderly C Chüeh
- Walter and Eliza Hall Institute for Medical Research and Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mai Tran
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mohd Ishtiaq Anasir
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Heather Verkade
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hong-Jian Zhu
- Department of Surgery, University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ching-Seng Ang
- Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael Griffin
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Heung-Chin Cheng
- Department of Biochemistry & Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Biotechnology and Molecular Science Institute, University of Melbourne, Parkville, VIC, 3010, Australia. .,Cell Signalling Research Laboratories, School of Biomedical Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.
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Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) phosphorylate a variety of substrates important for survival and proliferation, and their activity is frequently deregulated in tumors. ERK pathway inhibitors have shown clinical efficacy as anti-cancer drugs, but most patients eventually relapse due to reactivation of the pathway. One factor limiting the efficacy of current therapeutics is the difficulty in reaching clinically effective inhibition of the ERK pathway in the absence of on-target toxicities. Here, we describe an assay suitable for high throughput screening to discover substrate selective ERK1/2 inhibitors, which may have a larger therapeutic window than conventional inhibitors. Specifically, we aim to target a substrate-binding pocket within the ERK1/2 catalytic domain outside of the catalytic cleft. The assay uses an AlphaScreen format to detect phosphorylation of a high-efficiency substrate harboring an essential docking site motif. Pilot screening established that the assay is suitably robust for high-throughput screening. Importantly, the assay can be conducted at high ATP concentrations, which we show reduces the discovery of conventional ATP-competitive inhibitors. These studies provide the basis for high-throughput screens to discover new classes of non-conventional ERK1/2 inhibitors.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Yagmur Muftuoglu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, United States.
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Abstract
![]()
Eukaryotic
protein kinases typically phosphorylate substrates in
the context of specific sequence motifs, contributing to specificity
essential for accurate signal transmission. Protein kinases recognize
their target sequences through complementary interactions within the
active site cleft. As a step toward the construction of orthogonal
kinase signaling systems, we have re-engineered the protein kinase
Pim1 to alter its phosphorylation consensus sequence. Residues in
the Pim1 catalytic domain interacting directly with a critical arginine
residue in the substrate were substituted to produce a kinase mutant
that instead accommodates a hydrophobic residue. We then introduced
a compensating mutation into a Pim1 substrate, the pro-apoptotic protein
BAD, to reconstitute phosphorylation both in vitro and in living cells. Coexpression of the redesigned kinase with
its substrate in cells protected them from apoptosis. Such orthogonal
kinase–substrate pairs provide tools to probe the functional
consequences of specific phosphorylation events in living cells and
to design synthetic signaling pathways.
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Affiliation(s)
- Catherine Chen
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Wutigri Nimlamool
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Chad J. Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
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35
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Cobbaut M, Derua R, Döppler H, Lou HJ, Vandoninck S, Storz P, Turk BE, Seufferlein T, Waelkens E, Janssens V, Van Lint J. Differential regulation of PKD isoforms in oxidative stress conditions through phosphorylation of a conserved Tyr in the P+1 loop. Sci Rep 2017; 7:887. [PMID: 28428613 PMCID: PMC5430542 DOI: 10.1038/s41598-017-00800-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/13/2017] [Indexed: 01/06/2023] Open
Abstract
Protein kinases are essential molecules in life and their crucial function requires tight regulation. Many kinases are regulated via phosphorylation within their activation loop. This loop is embedded in the activation segment, which additionally contains the Mg2+ binding loop and a P + 1 loop that is important in substrate binding. In this report, we identify Abl-mediated phosphorylation of a highly conserved Tyr residue in the P + 1 loop of protein kinase D2 (PKD2) during oxidative stress. Remarkably, we observed that the three human PKD isoforms display very different degrees of P + 1 loop Tyr phosphorylation and we identify one of the molecular determinants for this divergence. This is paralleled by a different activation mechanism of PKD1 and PKD2 during oxidative stress. Tyr phosphorylation in the P + 1 loop of PKD2 increases turnover for Syntide-2, while substrate specificity and the role of PKD2 in NF-κB signaling remain unaffected. Importantly, Tyr to Phe substitution renders the kinase inactive, jeopardizing its use as a non-phosphorylatable mutant. Since large-scale proteomics studies identified P + 1 loop Tyr phosphorylation in more than 70 Ser/Thr kinases in multiple conditions, our results do not only demonstrate differential regulation/function of PKD isoforms under oxidative stress, but also have implications for kinase regulation in general.
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Affiliation(s)
- Mathias Cobbaut
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium.,Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Rita Derua
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Heike Döppler
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Sandy Vandoninck
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Peter Storz
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Veerle Janssens
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium.,Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Johan Van Lint
- Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium. .,Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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36
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Goldberg AB, Cho E, Miller CJ, Lou HJ, Turk BE. Identification of a Substrate-selective Exosite within the Metalloproteinase Anthrax Lethal Factor. J Biol Chem 2016; 292:814-825. [PMID: 27909054 DOI: 10.1074/jbc.m116.761734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/23/2016] [Indexed: 01/02/2023] Open
Abstract
The metalloproteinase anthrax lethal factor (LF) is secreted by Bacillus anthracis to promote disease virulence through disruption of host signaling pathways. LF is a highly specific protease, exclusively cleaving mitogen-activated protein kinase kinases (MKKs) and rodent NLRP1B (NACHT leucine-rich repeat and pyrin domain-containing protein 1B). How LF achieves such restricted substrate specificity is not understood. Previous studies have suggested the existence of an exosite interaction between LF and MKKs that promotes cleavage efficiency and specificity. Through a combination of in silico prediction and site-directed mutagenesis, we have mapped an exosite to a non-catalytic region of LF. Mutations within this site selectively impair proteolysis of full-length MKKs yet have no impact on cleavage of short peptide substrates. Although this region appears important for cleaving all LF protein substrates, we found that mutation of specific residues within the exosite differentially affects MKK and NLRP1B cleavage in vitro and in cultured cells. One residue in particular, Trp-271, is essential for cleavage of MKK3, MKK4, and MKK6 but dispensable for targeting of MEK1, MEK2, and NLRP1B. Analysis of chimeric substrates suggests that this residue interacts with the MKK catalytic domain. We found that LF-W271A blocked ERK phosphorylation and growth in a melanoma cell line, suggesting that it may provide a highly selective inhibitor of MEK1/2 for use as a cancer therapeutic. These findings provide insight into how a bacterial toxin functions to specifically impair host signaling pathways and suggest a general strategy for mapping protease exosite interactions.
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Affiliation(s)
- Allison B Goldberg
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eunice Cho
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Chad J Miller
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Hua Jane Lou
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Benjamin E Turk
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
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37
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B. Goldberg A, E. Turk B. Inhibitors of the Metalloproteinase Anthrax Lethal Factor. Curr Top Med Chem 2016; 16:2350-8. [DOI: 10.2174/1568026616666160413135732] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 11/22/2022]
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Mathea S, Abdul Azeez KR, Salah E, Tallant C, Wolfreys F, Konietzny R, Fischer R, Lou HJ, Brennan PE, Schnapp G, Pautsch A, Kessler BM, Turk BE, Knapp S. Structure of the Human Protein Kinase ZAK in Complex with Vemurafenib. ACS Chem Biol 2016; 11:1595-602. [PMID: 26999302 DOI: 10.1021/acschembio.6b00043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The mixed lineage kinase ZAK is a key regulator of the MAPK pathway mediating cell survival and inflammatory response. ZAK is targeted by several clinically approved kinase inhibitors, and inhibition of ZAK has been reported to protect from doxorubicin-induced cardiomyopathy. On the other hand, unintended targeting of ZAK has been linked to severe adverse effects such as the development of cutaneous squamous cell carcinoma. Therefore, both specific inhibitors of ZAK, as well as anticancer drugs lacking off-target activity against ZAK, may provide therapeutic benefit. Here, we report the first crystal structure of ZAK in complex with the B-RAF inhibitor vemurafenib. The cocrystal structure displayed a number of ZAK-specific features including a highly distorted P loop conformation enabling rational inhibitor design. Positional scanning peptide library analysis revealed a unique substrate specificity of the ZAK kinase including unprecedented preferences for histidine residues at positions -1 and +2 relative to the phosphoacceptor site. In addition, we screened a library of clinical kinase inhibitors identifying several inhibitors that potently inhibit ZAK, demonstrating that this kinase is commonly mistargeted by currently used anticancer drugs.
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Affiliation(s)
- Sebastian Mathea
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Kamal R. Abdul Azeez
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
| | - Eidarus Salah
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Cynthia Tallant
- Structural
Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX37DQ, United Kingdom
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Finn Wolfreys
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Rebecca Konietzny
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Roman Fischer
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Hua Jane Lou
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Paul E. Brennan
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Gisela Schnapp
- Lead Discovery and Optimisation Support, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, 88400, Germany
| | - Alexander Pautsch
- Lead Discovery and Optimisation Support, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, 88400, Germany
| | - Benedikt M. Kessler
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
| | - Benjamin E. Turk
- Department
of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Stefan Knapp
- Target
Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford, OX37FZ, United Kingdom
- Institute
for Pharmaceutical Chemistry and Buchmann Institute for Molecular
Life Sciences (BMLS), Johann Wolfgang Goethe University, Frankfurt am Main, 60438, Germany
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39
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Hamill S, Lou HJ, Turk BE, Boggon TJ. Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases. Mol Cell 2016; 62:397-408. [PMID: 27153537 PMCID: PMC4860616 DOI: 10.1016/j.molcel.2016.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 01/07/2023]
Abstract
Cofilin/actin-depolymerizing factor (ADF) proteins are critical nodes that relay signals from protein kinase cascades to the actin cytoskeleton, in particular through site-specific phosphorylation at residue Ser3. This is important for regulation of the roles of cofilin in severing and stabilizing actin filaments. Consequently, cofilin/ADF Ser3 phosphorylation is tightly controlled as an almost exclusive substrate for LIM kinases. Here we determine the LIMK1:cofilin-1 co-crystal structure. We find an interface that is distinct from canonical kinase-substrate interactions. We validate this previously unobserved mechanism for high-fidelity kinase-substrate recognition by in vitro kinase assays, examination of cofilin phosphorylation in mammalian cells, and functional analysis in S. cerevisiae. The interface is conserved across all LIM kinases. Remarkably, we also observe both pre- and postphosphotransfer states in the same crystal lattice. This study therefore provides a molecular understanding of how kinase-substrate recognition acts as a gatekeeper to regulate actin cytoskeletal dynamics.
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Affiliation(s)
- Stephanie Hamill
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520,Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520
| | - Titus J. Boggon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520,Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520,Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520,To who correspondence should be addressed:
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40
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Abstract
Eukaryotic protein kinases phosphorylate substrates at serine, threonine, and tyrosine residues that fall within the context of short sequence motifs. Knowing the phosphorylation site motif for a protein kinase facilitates designing substrates for kinase assays and mapping phosphorylation sites in protein substrates. Here, we describe an arrayed peptide library protocol for rapidly determining kinase phosphorylation consensus sequences. This method uses a set of peptide mixtures in which each of the 20 amino acid residues is systematically substituted at nine positions surrounding a central site of phosphorylation. Peptide mixtures are arrayed in multiwell plates and analyzed by radiolabel assay with the kinase of interest. The preferred sequence is determined from the relative rate of phosphorylation of each peptide in the array. Consensus peptides based on these sequences typically serve as efficient and specific kinase substrates for high-throughput screening or incorporation into biosensors.
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Affiliation(s)
- Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, 208066, New Haven, CT, 06520, USA.
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Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R. Unmasking determinants of specificity in the human kinome. Cell 2015; 163:187-201. [PMID: 26388442 PMCID: PMC4644237 DOI: 10.1016/j.cell.2015.08.057] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Revised: 04/09/2015] [Accepted: 08/12/2015] [Indexed: 01/01/2023]
Abstract
Protein kinases control cellular responses to environmental cues by swift and accurate signal processing. Breakdowns in this high-fidelity capability are a driving force in cancer and other diseases. Thus, our limited understanding of which amino acids in the kinase domain encode substrate specificity, the so-called determinants of specificity (DoS), constitutes a major obstacle in cancer signaling. Here, we systematically discover several DoS and experimentally validate three of them, named the αC1, αC3, and APE-7 residues. We demonstrate that DoS form sparse networks of non-conserved residues spanning distant regions. Our results reveal a likely role for inter-residue allostery in specificity and an evolutionary decoupling of kinase activity and specificity, which appear loaded on independent groups of residues. Finally, we uncover similar properties driving SH2 domain specificity and demonstrate how the identification of DoS can be utilized to elucidate a greater understanding of the role of signaling networks in cancer (Creixell et al., 2015 [this issue of Cell]). Residues driving specificity in the kinase and SH2 domains are globally identified Three new such residues, termed αC1, αC3, and APE-7, are experimentally validated Specificity and catalytic activity appear to be encoded in distinct sets of residues The global identification of determinants allows the modeling of rewiring mutations
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Affiliation(s)
- Pau Creixell
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Antonio Palmeri
- Centre for Molecular Bioinformatics, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cristina C Santini
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Morten Nielsen
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rune Linding
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark.
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Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R. Kinome-wide decoding of network-attacking mutations rewiring cancer signaling. Cell 2015; 163:202-17. [PMID: 26388441 PMCID: PMC4644236 DOI: 10.1016/j.cell.2015.08.056] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 04/09/2015] [Accepted: 08/12/2015] [Indexed: 12/17/2022]
Abstract
Cancer cells acquire pathological phenotypes through accumulation of mutations that perturb signaling networks. However, global analysis of these events is currently limited. Here, we identify six types of network-attacking mutations (NAMs), including changes in kinase and SH2 modulation, network rewiring, and the genesis and extinction of phosphorylation sites. We developed a computational platform (ReKINect) to identify NAMs and systematically interpreted the exomes and quantitative (phospho-)proteomes of five ovarian cancer cell lines and the global cancer genome repository. We identified and experimentally validated several NAMs, including PKCγ M501I and PKD1 D665N, which encode specificity switches analogous to the appearance of kinases de novo within the kinome. We discover mutant molecular logic gates, a drift toward phospho-threonine signaling, weakening of phosphorylation motifs, and kinase-inactivating hotspots in cancer. Our method pinpoints functional NAMs, scales with the complexity of cancer genomes and cell signaling, and may enhance our capability to therapeutically target tumor-specific networks. Mutations perturbing signaling networks are systematically classified and interpreted Several such functional mutations are identified in cancer and experimentally validated The results suggest that a single point mutant can have profound signaling effects Systematic interpretation of genomic data may assist future precision-medicine efforts
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Affiliation(s)
- Pau Creixell
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Erwin M Schoof
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Craig D Simpson
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - James Longden
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lara Perryman
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Thomas R Cox
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Nevena Zivanovic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Antonio Palmeri
- Centre for Molecular Bioinformatics, University of Rome Tor Vergata, 00133 Rome, Italy
| | | | | | - Jesper Ferkinghoff-Borg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | | | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Janine T Erler
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rune Linding
- Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), 2200 Copenhagen, Denmark.
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43
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Ronkina N, Johansen C, Bohlmann L, Lafera J, Menon MB, Tiedje C, Laaß K, Turk BE, Iversen L, Kotlyarov A, Gaestel M. Comparative Analysis of Two Gene-Targeting Approaches Challenges the Tumor-Suppressive Role of the Protein Kinase MK5/PRAK. PLoS One 2015; 10:e0136138. [PMID: 26295581 PMCID: PMC4546416 DOI: 10.1371/journal.pone.0136138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 07/27/2015] [Indexed: 01/19/2023] Open
Abstract
MK5 (MAPK-activated protein kinase 5) or PRAK (p38-regulated and -activated kinase) are alternative names for a serine/threonine protein kinase downstream to ERK3/4 and p38 MAPK. A previous gene targeting approach for MK5/PRAK (termed here MK5/PRAK-Δex8) revealed a seemingly tumor-suppressive role of MK5/PRAK in DMBA-induced one step skin carcinogenesis and Ras-induced transformation. Here we demonstrate that an alternative targeting strategy of MK5/PRAK (termed MK5/PRAK-Δex6) increased neither tumor incidence in the one step skin carcinogenesis model, nor Ras-induced transformation in primary cells. Interestingly, due to the targeting strategies and exon skipping both knockouts do not completely abolish the generation of MK5/PRAK protein, but express MK5/PRAK deletion mutants with different biochemical properties depending on the exon targeted: Targeting of exon 6 leads to expression of an unstable cytoplasmic catalytically inactive MK5/PRAK-Δex6 mutant while targeting of exon 8 results in a more stable nuclear MK5/PRAK-Δex8 mutant with residual catalytic activity. The different properties of the MK5/PRAK deletion mutants could be responsible for the observed discrepancy between the knockout strains and challenge the role of MK5/PRAK in p53-dependent tumor suppression. Further MK5/PRAK knockout and knock-in mouse strains will be necessary to assign a physiological function to MK5/PRAK in this model organism.
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Affiliation(s)
- Natalia Ronkina
- Department of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Claus Johansen
- Department of Dermatology, Aarhus University Hospital, Aarhus C, Denmark
| | - Lisa Bohlmann
- Department of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Juri Lafera
- Department of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Manoj B. Menon
- Department of Biochemistry, Hannover Medical School, Hannover, Germany
| | | | - Kathrin Laaß
- Department of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States of America
| | - Lars Iversen
- Department of Dermatology, Aarhus University Hospital, Aarhus C, Denmark
| | - Alexey Kotlyarov
- Department of Biochemistry, Hannover Medical School, Hannover, Germany
| | - Matthias Gaestel
- Department of Biochemistry, Hannover Medical School, Hannover, Germany
- * E-mail:
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44
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Fisher OS, Deng H, Liu D, Zhang Y, Wei R, Deng Y, Zhang F, Louvi A, Turk BE, Boggon TJ, Su B. Structure and vascular function of MEKK3-cerebral cavernous malformations 2 complex. Nat Commun 2015; 6:7937. [PMID: 26235885 PMCID: PMC4526114 DOI: 10.1038/ncomms8937] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/25/2015] [Indexed: 01/04/2023] Open
Abstract
Cerebral cavernous malformations 2 (CCM2) loss is associated with the familial form of CCM disease. The protein kinase MEKK3 (MAP3K3) is essential for embryonic angiogenesis in mice and interacts physically with CCM2, but how this interaction is mediated and its relevance to cerebral vasculature are unknown. Here we report that Mekk3 plays an intrinsic role in embryonic vascular development. Inducible endothelial Mekk3 knockout in neonatal mice is lethal due to multiple intracranial haemorrhages and brain blood vessels leakage. We discover direct interaction between CCM2 harmonin homology domain (HHD) and the N terminus of MEKK3, and determine a 2.35 Å cocrystal structure. We find Mekk3 deficiency impairs neurovascular integrity, which is partially dependent on Rho-ROCK signalling, and that disruption of MEKK3:CCM2 interaction leads to similar neurovascular leakage. We conclude that CCM2:MEKK3-mediated regulation of Rho signalling is required for maintenance of neurovascular integrity, unravelling a mechanism by which CCM2 loss leads to disease.
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Affiliation(s)
- Oriana S. Fisher
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Hanqiang Deng
- Department of Microbiology and Immunology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Dou Liu
- Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Ya Zhang
- Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
- Departments of Hematology and Dermotology, XiangYa Hospital, Central South University, Changsha 410008, China
| | - Rong Wei
- Department of Microbiology and Immunology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
- Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
- Departments of Hematology and Dermotology, XiangYa Hospital, Central South University, Changsha 410008, China
| | - Yong Deng
- Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Fan Zhang
- Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
- Departments of Hematology and Dermotology, XiangYa Hospital, Central South University, Changsha 410008, China
| | - Angeliki Louvi
- Department of Neurosurgery, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Titus J. Boggon
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
| | - Bing Su
- Department of Microbiology and Immunology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
- Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
- Departments of Hematology and Dermotology, XiangYa Hospital, Central South University, Changsha 410008, China
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Abstract
The p21-activated kinases (PAKs) are a family of six serine/threonine kinases that act as key effectors of RHO family GTPases in mammalian cells. PAKs are subdivided into two groups: type I PAKs (PAK1, PAK2, and PAK3) and type II PAKs (PAK4, PAK5, and PAK6). Although these groups are involved in common signaling pathways, recent work indicates that the two groups have distinct modes of regulation and have both unique and common substrates. Here, we review recent insights into the molecular level details that govern regulation of type II PAK signaling. We also consider mechanisms by which signal transduction is regulated at the level of substrate specificity. Finally, we discuss the implications of these studies for clinical targeting of these kinases.
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Affiliation(s)
| | - Elizabeth M Morse
- Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520
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46
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Etheridge RD, Alaganan A, Tang K, Lou HJ, Turk BE, Sibley LD. The Toxoplasma pseudokinase ROP5 forms complexes with ROP18 and ROP17 kinases that synergize to control acute virulence in mice. Cell Host Microbe 2015; 15:537-50. [PMID: 24832449 DOI: 10.1016/j.chom.2014.04.002] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/24/2014] [Accepted: 03/20/2014] [Indexed: 11/28/2022]
Abstract
Polymorphic rhoptry-secreted kinases (ROPs) are essential virulence factors of Toxoplasma gondii. In particular, the pseudokinase ROP5 is the major determinant of acute virulence in mice, but the underlying mechanisms are unclear. We developed a tandem affinity protein tagging and purification approach in T. gondii and used it to show that ROP5 complexes with the active kinases ROP18 and ROP17. Biochemical analyses indicate that ROP18 and ROP17 have evolved to target adjacent and essential threonine residues in switch region I of immunity-related guanosine triphosphatases (GTPases) (IRGs), a family of host defense molecules that function to control intracellular pathogens. The combined activities of ROP17 and ROP18 contribute to avoidance of IRG recruitment to the intracellular T. gondii-containing vacuole, thus protecting the parasite from clearance in interferon-activated macrophages. These studies reveal an intricate, multilayered parasite survival strategy involving pseudokinases that regulate multiple active kinase complexes to synergistically thwart innate immunity.
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Affiliation(s)
- Ronald D Etheridge
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Aditi Alaganan
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Keliang Tang
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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47
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Howard CJ, Hanson-Smith V, Kennedy KJ, Miller CJ, Lou HJ, Johnson AD, Turk BE, Holt LJ. Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. eLife 2014; 3. [PMID: 25310241 PMCID: PMC4228266 DOI: 10.7554/elife.04126] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/09/2014] [Indexed: 01/02/2023] Open
Abstract
Protein kinases have evolved diverse specificities to enable cellular information processing. To gain insight into the mechanisms underlying kinase diversification, we studied the CMGC protein kinases using ancestral reconstruction. Within this group, the cyclin dependent kinases (CDKs) and mitogen activated protein kinases (MAPKs) require proline at the +1 position of their substrates, while Ime2 prefers arginine. The resurrected common ancestor of CDKs, MAPKs, and Ime2 could phosphorylate substrates with +1 proline or arginine, with preference for proline. This specificity changed to a strong preference for +1 arginine in the lineage leading to Ime2 via an intermediate with equal specificity for proline and arginine. Mutant analysis revealed that a variable residue within the kinase catalytic cleft, DFGx, modulates +1 specificity. Expansion of Ime2 kinase specificity by mutation of this residue did not cause dominant deleterious effects in vivo. Tolerance of cells to new specificities likely enabled the evolutionary divergence of kinases. DOI:http://dx.doi.org/10.7554/eLife.04126.001 All living things have enzymes called protein kinases that transfer chemical tags called phosphates onto other proteins. Adding a phosphate to a protein can change the protein's activity—for example, by switching it on or off—and many biological processes involve large networks of kinases that phosphorylate hundreds of proteins. Humans have approximately 500 different protein kinases, which can each phosphorylate many proteins, and so human cells are regulated by tens of thousands of different phosphorylation sites. This raises a number of questions: how have these different kinases evolved over evolutionary history? And how have they come to recognize, and phosphorylate, so many different sites? Howard, Hanson-Smith et al. studied members of a large family of protein kinases called the CMGC group. These enzymes are found in all organisms that have a cell nucleus, including animals, plants, and fungi. All proteins, including kinases, are built up of a chain of smaller molecules called amino acids, and the ability of a kinase to phosphorylate a protein depends on the kinase recognizing a short string of amino acids known as a motif. The phosphate is added in the middle of this motif at the so-called ‘0’ position. Howard, Hanson-Smith et al. found that all of the CMGC protein kinases tested ‘preferred’ an arginine or proline amino acid at the ‘+1’ position of this motif. However, some kinases preferred motifs with an arginine amino acid at this position, and others preferred a proline instead. Howard, Hanson-Smith et al. predicted how the ancestors of a number of CMGC protein kinases might have looked and then ‘resurrected’ them by producing them in yeast cells. When the preference of these ancestral enzymes was tested, the oldest ancestor was found to slightly prefer motifs that had a proline amino acid at the +1 position. Testing six more recent ancestors showed that, over a billion years of evolution, this amino acid preference became broader to include both proline and arginine—and that some modern protein kinases subsequently evolved and specialized to prefer arginine at the +1 position, thus creating a new specificity. Kinases are sometimes likened to microchips in complex electronic networks. In this analogy, expanding the specificity of a kinase could be like creating many ‘loose wires’ and cause short-circuits. From their evolutionary analysis, Howard, Hanson-Smith et al. were able to identify a structural change in the enzyme that causes an expansion of kinase specificity, which allowed them to directly test this idea in cells. Expanding the specificity of a protein kinase that controls sexual cell division in yeast cells did not stop the yeast from dividing to produce spores, suggesting that these changes are more readily tolerated than was expected. Howard, Hanson-Smith et al. suggest that this unexpected robustness of cellular circuits enabled the evolution of the wide variety of protein kinases seen today. DOI:http://dx.doi.org/10.7554/eLife.04126.002
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Affiliation(s)
- Conor J Howard
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Victor Hanson-Smith
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Kristopher J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Chad J Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, United States
| | - Liam J Holt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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48
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Deng Y, Alicea-Velázquez NL, Bannwarth L, Lehtonen SI, Boggon TJ, Cheng HC, Hytönen VP, Turk BE. Global analysis of human nonreceptor tyrosine kinase specificity using high-density peptide microarrays. J Proteome Res 2014; 13:4339-46. [PMID: 25164267 PMCID: PMC4184454 DOI: 10.1021/pr500503q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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Protein
kinases phosphorylate substrates in the context of specific
phosphorylation site sequence motifs. The knowledge of the specific
sequences that are recognized by kinases is useful for mapping sites
of phosphorylation in protein substrates and facilitates the generation
of model substrates to monitor kinase activity. Here, we have adapted
a positional scanning peptide library method to a microarray format
that is suitable for the rapid determination of phosphorylation site
motifs for tyrosine kinases. Peptide mixtures were immobilized on
glass slides through a layer of a tyrosine-free Y33F mutant avidin
to facilitate the analysis of phosphorylation by radiolabel assay.
A microarray analysis provided qualitatively similar results in comparison
with the solution phase peptide library “macroarray”
method. However, much smaller quantities of kinases were required
to phosphorylate peptides on the microarrays, which thus enabled a
proteome scale analysis of kinase specificity. We illustrated this
capability by microarray profiling more than 80% of the human nonreceptor
tyrosine kinases (NRTKs). Microarray results were used to generate
a universal NRTK substrate set of 11 consensus peptides for in vitro
kinase assays. Several substrates were highly specific for their cognate
kinases, which should facilitate their incorporation into kinase-selective
biosensors.
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Affiliation(s)
- Yang Deng
- Department of Pharmacology, Yale University School of Medicine , New Haven, Connecticut 06520, United States
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49
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Chen CD, Tung TY, Liang J, Zeldich E, Tucker Zhou TB, Turk BE, Abraham CR. Identification of cleavage sites leading to the shed form of the anti-aging protein klotho. Biochemistry 2014; 53:5579-87. [PMID: 25110992 PMCID: PMC4151695 DOI: 10.1021/bi500409n] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Membrane
protein shedding is a critical step in many normal and
pathological processes. The anti-aging protein klotho (KL), mainly
expressed in kidney and brain, is secreted into the serum and CSF,
respectively. KL is proteolytically released, or shed, from the cell
surface by ADAM10 and ADAM17, which are the α-secretases that
also cleave the amyloid precursor protein and other proteins. The
transmembrane KL is a coreceptor with the FGF receptor for FGF23,
whereas the shed form acts as a circulating hormone. However, the
precise cleavage sites in KL are unknown. KL contains two major cleavage
sites: one close to the juxtamembrane region and another between the
KL1 and KL2 domains. We identified the cleavage site involved in KL
release by mutating potential sheddase(s) recognition sequences and
examining the production of the KL extracellular fragments in transfected
COS-7 cells. Deletion of amino acids T958 and L959 results in a 50–60%
reduction in KL shedding, and an additional P954E mutation results
in further reduction of KL shedding by 70–80%. Deletion of
amino acids 954–962 resulted in a 94% reduction in KL shedding.
This mutant also had moderately decreased cell surface expression,
yet had overall similar subcellular localization as that of WT KL,
as demonstrated by immunofluorescence. Cleavage-resistant mutants
could function as a FGFR coreceptor for FGF23, but they lost activity
as a soluble form of KL in proliferation and transcriptional reporter
assays. Cleavage between the KL1 and KL2 domains is dependent on juxtamembrane
cleavage. Our results shed light onto mechanisms underlying KL release
from the cell membrane and provide a target for potential pharmacologic
interventions aimed at regulating KL secretion.
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Affiliation(s)
- Ci-Di Chen
- Departments of Biochemistry, ‡Biology, and §Pharmacology and Experimental Therapeutics, Boston University School of Medicine , Boston, Massachusetts 02118, United States
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50
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Goodwin JM, Svensson RU, Lou HJ, Winslow MM, Turk BE, Shaw RJ. An AMPK-independent signaling pathway downstream of the LKB1 tumor suppressor controls Snail1 and metastatic potential. Mol Cell 2014; 55:436-50. [PMID: 25042806 DOI: 10.1016/j.molcel.2014.06.021] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 04/08/2014] [Accepted: 06/12/2014] [Indexed: 12/21/2022]
Abstract
The serine/threonine kinase LKB1 is a tumor suppressor whose loss is associated with increased metastatic potential. In an effort to define biochemical signatures of metastasis associated with LKB1 loss, we discovered that the epithelial-to-mesenchymal transition transcription factor Snail1 was uniquely upregulated upon LKB1 deficiency across cell types. The ability of LKB1 to suppress Snail1 levels was independent of AMPK but required the related kinases MARK1 and MARK4. In a screen for substrates of these kinases involved in Snail regulation, we identified the scaffolding protein DIXDC1. Similar to loss of LKB1, DIXDC1 depletion results in upregulation of Snail1 in a FAK-dependent manner, leading to increased cell invasion. MARK1 phosphorylation of DIXDC1 is required for its localization to focal adhesions and ability to suppress metastasis in mice. DIXDC1 is frequently downregulated in human cancers, which correlates with poor survival. This study defines an AMPK-independent phosphorylation cascade essential for LKB1-dependent control of metastatic behavior.
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Affiliation(s)
- Jonathan M Goodwin
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Robert U Svensson
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Monte M Winslow
- Department of Genetics and Pathology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Reuben J Shaw
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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