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Zhang R, Li S, Feng W, Qian S, Chellappa AJ, Wang F. Rim4 is a Thermal Sensor and Driver of Meiosis-specific Stress Granules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574866. [PMID: 38260504 PMCID: PMC10802437 DOI: 10.1101/2024.01.09.574866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Rim4 is a meiosis-specific RNA-binding protein (RBP) that sequesters mRNAs to suppress their translation. Previous work has defined the Rim4 C-terminal low-complexity domain (LCD) as sequences that form self-propagating amyloid-like aggregates. Here, we uncovered a dynamic and reversible form of Rim4 self-assembly primarily triggered by heat during meiosis, proportionally from 30°C to 42°C. The formed thermal Rim4 condensates in cell promptly stimulates stress granule (SG) assembly, recruiting SG-resident proteins, such as Pab1 and Pbp1, and strikingly, decreases the required temperature for meiotic SG formation (∼33°C) by ∼9°C as compared to mitosis (∼42°C). This sensitization of meiotic SG formation to heat effectively prevents meiosis progression and sporulation under harmful thermal turbulence. Meanwhile, the Rim4-positive meiotic SGs protect Rim4 and Rim4-sequestered mRNAs from autophagy to allow a rapid recovery from stalled meiosis upon the stress relief. Mechanistically, we found that the yeast 14-3-3 proteins (Bmh1 and Bmh2) and nucleic acids brake initiation of heat-induced Rim4 self-assembly, and Hsp104 facilitates the restoration of intracellular Rim4 distribution during the recovery.
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2
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Padmarajan J, Edilyam AK, Subramanian VV. Rapamycin-Induced Translocation of Meiotic Nuclear Proteins in Saccharomyces cerevisiae. Methods Mol Biol 2024; 2818:213-226. [PMID: 39126477 DOI: 10.1007/978-1-0716-3906-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
Conditional depletion of proteins is a potential strategy to elucidate protein function, especially in complex cellular processes like meiosis. Several methods are available to effectively deplete a protein in a conditional manner. Conditional loss of a protein function can be achieved by depleting it from its region of action by degrading it. A conditional loss of protein function can also be achieved by sequestering it to a functionally unavailable compartment inside the cell. This chapter describes anchor away, a conditional depletion tool that can deplete a protein both temporally and spatially by translocation. It utilizes the affinity of FRB to bind FKBP12 in the presence of rapamycin for a quick and efficient translocation of the protein to a designated location. Anchor away is a reliable tool for the study of meiotic proteins, as only small quantities of rapamycin are required to efficiently and rapidly translocate the protein of interest without compromising meiotic progression.
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Affiliation(s)
- Jinsha Padmarajan
- Indian Institute of Science Education and Research (IISER), Tirupati, Andhra Pradesh, India
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3
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Differential Expression of RSK4 Transcript Isoforms in Cancer and Its Clinical Relevance. Int J Mol Sci 2022; 23:ijms232314569. [PMID: 36498899 PMCID: PMC9737342 DOI: 10.3390/ijms232314569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/11/2022] [Accepted: 11/12/2022] [Indexed: 11/24/2022] Open
Abstract
While we previously revealed RSK4 as a therapeutic target in lung and bladder cancers, the wider role of this kinase in other cancers remains controversial. Indeed, other reports instead proposed RSK4 as a tumour suppressor in colorectal and gastric cancers and are contradictory in breast malignancies. One explanation for these discrepancies may be the expression of different RSK4 isoforms across cancers. Four RNAs are produced from the RSK4 gene, with two being protein-coding. Here, we analysed the expression of the latter across 30 normal and 33 cancer tissue types from the combined GTEx/TCGA dataset and correlated it with clinical features. This revealed the expression of RSK4 isoforms 1 and 2 to be independent prognostic factors for patient survival, pathological stage, cancer metastasis, recurrence, and immune infiltration in brain, stomach, cervical, and kidney cancers. However, we found that upregulation of either isoform can equally be associated with good or bad prognosis depending on the cancer type, and changes in the expression ratio of isoforms fail to predict clinical outcome. Hence, differential isoform expression alone cannot explain the contradictory roles of RSK4 in cancers, and further research is needed to highlight the underlying mechanisms for the context-dependent function of this kinase.
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4
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Ng K, Bland T, Hirani N, Goehring NW. An analog sensitive allele permits rapid and reversible chemical inhibition of PKC-3 activity in C. elegans. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000610. [PMID: 35996692 PMCID: PMC9391946 DOI: 10.17912/micropub.biology.000610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022]
Abstract
Engineered analog sensitive kinases provide a highly effective method for acute, controllable, and highly selective inhibition of kinase activity. Here we describe the design and characterization of an analog sensitive allele of the polarity kinase, PKC-3. This allele supports normal function as measured by its ability to exclude PAR-2 from the anterior membrane of zygotes, and is rapidly and reversibly inhibited in a dose-dependent manner by the ATP analog 1NA-PP1. This allele provides a new tool to explore the role of PKC-3 in diverse contexts within C. elegans , particularly those in which acute and reversible control of PKC-3 kinase activity may be desired.
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Affiliation(s)
- KangBo Ng
- Francis Crick Institute, London, NW1 1AT, UK
,
Institute for the Physics of Living Systems, University College London, WC1E 6BT, UK
| | - Tom Bland
- Francis Crick Institute, London, NW1 1AT, UK
,
Institute for the Physics of Living Systems, University College London, WC1E 6BT, UK
| | | | - Nathan W. Goehring
- Francis Crick Institute, London, NW1 1AT, UK
,
Institute for the Physics of Living Systems, University College London, WC1E 6BT, UK
,
Correspondence to: Nathan W. Goehring (
)
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5
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Rezende Miranda R, Zhang C. Reactivity-based chemical-genetic study of protein kinases. RSC Med Chem 2022; 13:783-797. [PMID: 35923719 PMCID: PMC9298188 DOI: 10.1039/d1md00389e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The human protein kinase superfamily comprises over 500 members that operate in nearly every signal transduction pathway and regulate essential cellular processes. Deciphering the functional roles of protein kinases with small-molecule inhibitors is essential to enhance our understanding of cell signaling and to facilitate the development of new therapies. However, it is rather challenging to identify selective kinase inhibitors because of the conserved nature of the ATP binding site. A number of chemical-genetic approaches have been developed during the past two decades to enable selective chemical perturbation of the activity of individual kinases. Herein, we review the development and application of chemical-genetic strategies that feature the use of covalent inhibitors targeting cysteine residues to dissect the cellular functions of protein kinases.
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Affiliation(s)
- Renata Rezende Miranda
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester New York 14623 USA
| | - Chao Zhang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- USC Norris Comprehensive Cancer Center, University of Southern California Los Angeles California 90089 USA
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6
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Feng W, Argüello-Miranda O, Qian S, Wang F. Cdc14 spatiotemporally dephosphorylates Atg13 to activate autophagy during meiotic divisions. J Cell Biol 2022; 221:213046. [PMID: 35238874 PMCID: PMC8919667 DOI: 10.1083/jcb.202107151] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/07/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
Autophagy is a conserved eukaryotic lysosomal degradation pathway that responds to environmental and cellular cues. Autophagy is essential for the meiotic exit and sporulation in budding yeast, but the underlying molecular mechanisms remain unknown. Here, we show that autophagy is maintained during meiosis and stimulated in anaphase I and II. Cells with higher levels of autophagy complete meiosis faster, and genetically enhanced autophagy increases meiotic kinetics and sporulation efficiency. Strikingly, our data reveal that the conserved phosphatase Cdc14 regulates meiosis-specific autophagy. Cdc14 is activated in anaphase I and II, accompanying its subcellular relocation from the nucleolus to the cytoplasm, where it dephosphorylates Atg13 to stimulate Atg1 kinase activity and thus autophagy. Together, our findings reveal a meiosis-tailored mechanism that spatiotemporally controls meiotic autophagy activity to ensure meiosis progression, exit, and sporulation.
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Affiliation(s)
- Wenzhi Feng
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Suhong Qian
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Fei Wang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX,Correspondence to Fei Wang:
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7
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Heineike BM, El-Samad H. Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:642336. [PMID: 37744115 PMCID: PMC10512328 DOI: 10.3389/ffunb.2021.642336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/24/2021] [Indexed: 09/26/2023]
Abstract
Functional divergence of duplicate genes, or paralogs, is an important driver of novelty in evolution. In the model yeast Saccharomyces cerevisiae, there are 547 paralog gene pairs that survive from an interspecies Whole Genome Hybridization (WGH) that occurred ~100MYA. In this work, we report that ~1/6th (110) of these WGH paralogs pairs (or ohnologs) are differentially expressed with a striking pattern upon Protein Kinase A (PKA) inhibition. One member of each pair in this group has low basal expression that increases upon PKA inhibition, while the other has moderate and unchanging expression. For these genes, expression of orthologs upon PKA inhibition in the non-WGH species Kluyveromyces lactis and for PKA-related stresses in other budding yeasts shows unchanging expression, suggesting that lack of responsiveness to PKA was likely the typical ancestral phenotype prior to duplication. Promoter sequence analysis across related budding yeast species further revealed that the subsequent emergence of PKA-dependence took different evolutionary routes. In some examples, regulation by PKA and differential expression appears to have arisen following the WGH, while in others, regulation by PKA appears to have arisen in one of the two parental lineages prior to the WGH. More broadly, our results illustrate the unique opportunities presented by a WGH event for generating functional divergence by bringing together two parental lineages with separately evolved regulation into one species. We propose that functional divergence of two ohnologs can be facilitated through such regulatory divergence.
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Affiliation(s)
- Benjamin M. Heineike
- Bioinformatics Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Hana El-Samad
- Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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8
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The promise and current status of CDK12/13 inhibition for the treatment of cancer. Future Med Chem 2020; 13:117-141. [PMID: 33295810 DOI: 10.4155/fmc-2020-0240] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CDK12 and CDK13 are Ser/Thr protein kinases that regulate transcription and co-transcriptional processes. Genetic silencing of CDK12 is associated with genomic instability in a variety of cancers, including difficult-to-treat breast, ovarian, colorectal, brain and pancreatic cancers, and is synthetic lethal with PARP, MYC or EWS/FLI inhibition. CDK13 is amplified in hepatocellular carcinoma. Consequently, selective CDK12/13 inhibitors constitute powerful research tools as well as promising anti-cancer therapeutics, either alone or in combination therapy. Herein the authors discuss the role of CDK12 and CDK13 in normal and cancer cells, describe their utility as a biomarker and therapeutic target, review the medicinal chemistry optimization of existing CDK12/13 inhibitors and outline strategies for the rational design of CDK12/13 selective inhibitors.
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9
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Pyrimidine and fused pyrimidine derivatives as promising protein kinase inhibitors for cancer treatment. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02656-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome. Int J Mol Sci 2020; 21:ijms21207637. [PMID: 33076458 PMCID: PMC7588962 DOI: 10.3390/ijms21207637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.
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11
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Tellier M, Zaborowska J, Caizzi L, Mohammad E, Velychko T, Schwalb B, Ferrer-Vicens I, Blears D, Nojima T, Cramer P, Murphy S. CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation. Nucleic Acids Res 2020; 48:7712-7727. [PMID: 32805052 PMCID: PMC7641311 DOI: 10.1093/nar/gkaa514] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/12/2022] Open
Abstract
Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Justyna Zaborowska
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Livia Caizzi
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eusra Mohammad
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Björn Schwalb
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ivan Ferrer-Vicens
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Daniel Blears
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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12
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Wang F, Zhang R, Feng W, Tsuchiya D, Ballew O, Li J, Denic V, Lacefield S. Autophagy of an Amyloid-like Translational Repressor Regulates Meiotic Exit. Dev Cell 2020; 52:141-151.e5. [PMID: 31991104 DOI: 10.1016/j.devcel.2019.12.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/26/2019] [Accepted: 12/26/2019] [Indexed: 12/30/2022]
Abstract
We explored the potential for autophagy to regulate budding yeast meiosis. Following pre-meiotic DNA replication, we blocked autophagy by chemical inhibition of Atg1 kinase or engineered degradation of Atg14 and observed homologous chromosome segregation followed by sister chromatid separation; cells then underwent additional rounds of spindle formation and disassembly without DNA re-replication, leading to aberrant chromosome segregation. Analysis of cell-cycle regulators revealed that autophagy inhibition prevents meiosis II-specific expression of Clb3 and leads to the aberrant persistence of Clb1 and Cdc5, two substrates of a meiotic ubiquitin ligase activated by Ama1. Lastly, we found that during meiosis II, autophagy degrades Rim4, an amyloid-like translational repressor whose timed clearance regulates protein production from its mRNA targets, which include CLB3 and AMA1. Strikingly, engineered Clb3 or Ama1 production restored meiotic termination in the absence of autophagy. Thus, autophagy destroys a master regulator of meiotic gene expression to enable irreversible meiotic exit.
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Affiliation(s)
- Fei Wang
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Rudian Zhang
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wenzhi Feng
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Dai Tsuchiya
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Olivia Ballew
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jiajia Li
- Department of Internal Medicine, Center for Autophagy Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Soni Lacefield
- Department of Biology, Indiana University, Bloomington, IN, USA.
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13
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Greenleaf AL. Human CDK12 and CDK13, multi-tasking CTD kinases for the new millenium. Transcription 2019; 10:91-110. [PMID: 30319007 PMCID: PMC6602566 DOI: 10.1080/21541264.2018.1535211] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/25/2018] [Accepted: 09/28/2018] [Indexed: 01/27/2023] Open
Abstract
As the new millennium began, CDK12 and CDK13 were discovered as nucleotide sequences that encode protein kinases related to cell cycle CDKs. By the end of the first decade both proteins had been qualified as CTD kinases, and it was emerging that both are heterodimers containing a Cyclin K subunit. Since then, many studies on CDK12 have shown that, through phosphorylating the CTD of transcribing RNAPII, it plays critical roles in several stages of gene expression, notably RNA processing; it is also crucial for maintaining genome stability. Fewer studies on CKD13 have clearly shown that it is functionally distinct from CDK12. CDK13 is important for proper expression of a number of genes, but it also probably plays yet-to-be-discovered roles in other processes. This review summarizes much of the work on CDK12 and CDK13 and attempts to evaluate the results and place them in context. Our understanding of these two enzymes has begun to mature, but we still have much to learn about both. An indicator of one major area of medically-relevant future research comes from the discovery that CDK12 is a tumor suppressor, notably for certain ovarian and prostate cancers. A challenge for the future is to understand CDK12 and CDK13 well enough to explain how their loss promotes cancer development and how we can intercede to prevent or treat those cancers. Abbreviations: CDK: cyclin-dependent kinase; CTD: C-terminal repeat domain of POLR2A; CTDK-I: CTD kinase I (yeast); Ctk1: catalytic subunit of CTDK-I; Ctk2: cyclin-like subunit of CTDK-I; PCAP: phosphoCTD-associating protein; POLR2A: largest subunit of RNAPII; SRI domain: Set2-RNAPII Interacting domain.
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Affiliation(s)
- Arno L. Greenleaf
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
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14
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Hannaford M, Loyer N, Tonelli F, Zoltner M, Januschke J. A chemical-genetics approach to study the role of atypical Protein Kinase C in Drosophila. Development 2019; 146:dev170589. [PMID: 30635282 PMCID: PMC6361133 DOI: 10.1242/dev.170589] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 12/21/2018] [Indexed: 12/11/2022]
Abstract
Studying the function of proteins using genetics in cycling cells is complicated by the fact that there is often a delay between gene inactivation and the time point of phenotypic analysis. This is particularly true when studying kinases that have pleiotropic functions and multiple substrates. Drosophila neuroblasts (NBs) are rapidly dividing stem cells and an important model system for the study of cell polarity. Mutations in multiple kinases cause NB polarity defects, but their precise functions at particular time points in the cell cycle are unknown. Here, we use chemical genetics and report the generation of an analogue-sensitive allele of Drosophila atypical Protein Kinase C (aPKC). We demonstrate that the resulting mutant aPKC kinase can be specifically inhibited in vitro and in vivo Acute inhibition of aPKC during NB polarity establishment abolishes asymmetric localization of Miranda, whereas its inhibition during NB polarity maintenance does not in the time frame of normal mitosis. However, aPKC helps to sharpen the pattern of Miranda, by keeping it off the apical and lateral cortex after nuclear envelope breakdown.
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Affiliation(s)
- Matthew Hannaford
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD5 1EH, UK
| | - Nicolas Loyer
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD5 1EH, UK
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD5 1EH, UK
| | - Martin Zoltner
- Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD5 1EH, UK
| | - Jens Januschke
- Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD5 1EH, UK
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15
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Lin AW, Gill KK, Castañeda MS, Matucci I, Eder N, Claxton S, Flynn H, Snijders AP, George R, Ultanir SK. Chemical genetic identification of GAK substrates reveals its role in regulating Na +/K +-ATPase. Life Sci Alliance 2018; 1:e201800118. [PMID: 30623173 PMCID: PMC6312924 DOI: 10.26508/lsa.201800118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 12/15/2022] Open
Abstract
Novel GAK phosphorylation targets are identified using chemical genetic methods. One of the substrates is the α subunit of the Na+/K+-ATPase, phosphorylation of which is necessary for its surface trafficking from endosomes. Conserved functions of NAK family kinases are described. Cyclin G–associated kinase (GAK) is a ubiquitous serine/threonine kinase that facilitates clathrin uncoating during vesicle trafficking. GAK phosphorylates a coat adaptor component, AP2M1, to help achieve this function. GAK is also implicated in Parkinson's disease through genome-wide association studies. However, GAK's role in mammalian neurons remains unclear, and insight may come from identification of further substrates. Employing a chemical genetics method, we show here that the sodium potassium pump (Na+/K+-ATPase) α-subunit Atp1a3 is a GAK target and that GAK regulates Na+/K+-ATPase trafficking to the plasma membrane. Whole-cell patch clamp recordings from CA1 pyramidal neurons in GAK conditional knockout mice show a larger change in resting membrane potential when exposed to the Na+/K+-ATPase blocker ouabain, indicating compromised Na+/K+-ATPase function in GAK knockouts. Our results suggest a modulatory role for GAK via phosphoregulation of substrates such as Atp1a3 during cargo trafficking.
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Affiliation(s)
- Amy W Lin
- Kinase and Brain Development Lab, The Francis Crick Institute, London, United Kingdom
| | - Kalbinder K Gill
- Kinase and Brain Development Lab, The Francis Crick Institute, London, United Kingdom
| | | | - Irene Matucci
- Kinase and Brain Development Lab, The Francis Crick Institute, London, United Kingdom
| | - Noreen Eder
- Kinase and Brain Development Lab, The Francis Crick Institute, London, United Kingdom.,Mass Spectrometry Platform, The Francis Crick Institute, London, United Kingdom
| | - Suzanne Claxton
- Kinase and Brain Development Lab, The Francis Crick Institute, London, United Kingdom
| | - Helen Flynn
- Mass Spectrometry Platform, The Francis Crick Institute, London, United Kingdom
| | | | - Roger George
- Protein Purification Facility, The Francis Crick Institute, London, United Kingdom
| | - Sila K Ultanir
- Kinase and Brain Development Lab, The Francis Crick Institute, London, United Kingdom
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16
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Baltussen LL, Negraes PD, Silvestre M, Claxton S, Moeskops M, Christodoulou E, Flynn HR, Snijders AP, Muotri AR, Ultanir SK. Chemical genetic identification of CDKL5 substrates reveals its role in neuronal microtubule dynamics. EMBO J 2018; 37:embj.201899763. [PMID: 30266824 PMCID: PMC6293278 DOI: 10.15252/embj.201899763] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/07/2018] [Accepted: 08/31/2018] [Indexed: 01/23/2023] Open
Abstract
Loss‐of‐function mutations in CDKL5 kinase cause severe neurodevelopmental delay and early‐onset seizures. Identification of CDKL5 substrates is key to understanding its function. Using chemical genetics, we found that CDKL5 phosphorylates three microtubule‐associated proteins: MAP1S, EB2 and ARHGEF2, and determined the phosphorylation sites. Substrate phosphorylations are greatly reduced in CDKL5 knockout mice, verifying these as physiological substrates. In CDKL5 knockout mouse neurons, dendritic microtubules have longer EB3‐labelled plus‐end growth duration and these altered dynamics are rescued by reduction of MAP1S levels through shRNA expression, indicating that CDKL5 regulates microtubule dynamics via phosphorylation of MAP1S. We show that phosphorylation by CDKL5 is required for MAP1S dissociation from microtubules. Additionally, anterograde cargo trafficking is compromised in CDKL5 knockout mouse dendrites. Finally, EB2 phosphorylation is reduced in patient‐derived human neurons. Our results reveal a novel activity‐dependent molecular pathway in dendritic microtubule regulation and suggest a pathological mechanism which may contribute to CDKL5 deficiency disorder.
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Affiliation(s)
- Lucas L Baltussen
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Priscilla D Negraes
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Margaux Silvestre
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Suzanne Claxton
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | - Max Moeskops
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
| | | | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Alysson R Muotri
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA .,Department of Pediatrics/Cellular & Molecular Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, School of Medicine, Rady Children's Hospital San Diego, University of California San Diego, La Jolla, CA, USA
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London, UK
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17
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Galbraith MD, Andrysik Z, Pandey A, Hoh M, Bonner EA, Hill AA, Sullivan KD, Espinosa JM. CDK8 Kinase Activity Promotes Glycolysis. Cell Rep 2018; 21:1495-1506. [PMID: 29117556 DOI: 10.1016/j.celrep.2017.10.058] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/21/2017] [Accepted: 10/13/2017] [Indexed: 12/27/2022] Open
Abstract
Aerobic glycolysis, also known as the Warburg effect, is a hallmark of cancerous tissues. Despite its importance in cancer development, our understanding of mechanisms driving this form of metabolic reprogramming is incomplete. We report here an analysis of colorectal cancer cells engineered to carry a single point mutation in the active site of the Mediator-associated kinase CDK8, creating hypomorphic alleles sensitive to bulky ATP analogs. Transcriptome analysis revealed that CDK8 kinase activity is required for the expression of many components of the glycolytic cascade. CDK8 inhibition impairs glucose transporter expression, glucose uptake, glycolytic capacity and reserve, as well as cell proliferation and anchorage-independent growth, both in normoxia and hypoxia. Importantly, CDK8 impairment sensitizes cells to pharmacological glycolysis inhibition, a result reproduced with Senexin A, a dual inhibitor of CDK8/CDK19. Altogether, these results contribute to our understanding of CDK8 as an oncogene, and they justify investigations to target CDK8 in highly glycolytic tumors.
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Affiliation(s)
- Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Zdenek Andrysik
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ahwan Pandey
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Maria Hoh
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elizabeth A Bonner
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Amanda A Hill
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquín M Espinosa
- Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA.
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18
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Baltussen LL, Rosianu F, Ultanir SK. Kinases in synaptic development and neurological diseases. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:343-352. [PMID: 29241837 DOI: 10.1016/j.pnpbp.2017.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/08/2017] [Accepted: 12/09/2017] [Indexed: 10/18/2022]
Abstract
Neuronal morphogenesis and synapse development is essential for building a functioning nervous system, and defects in these processes are associated with neurological disorders. Our understanding of molecular components and signalling events that contribute to neuronal development and pathogenesis is limited. Genes associated with neurodevelopmental and neurodegenerative diseases provide entry points for elucidating molecular events that contribute to these conditions. Several protein kinases, enzymes that regulate protein function by phosphorylating their substrates, are genetically linked to neurological disorders. Identifying substrates of these kinases is key to discovering their function and providing insight for possible therapies. In this review, we describe how various methods for kinase-substrate identification helped elucidate kinase signalling pathways important for neuronal development and function. We describe recent advances on roles of kinases TAOK2, TNIK and CDKL5 in neuronal development and the converging pathways of LRRK2, PINK1 and GAK in Parkinson's Disease.
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Affiliation(s)
- Lucas L Baltussen
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Flavia Rosianu
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom.
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19
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Umaña AC, Iwahori S, Kalejta RF. Direct Substrate Identification with an Analog Sensitive (AS) Viral Cyclin-Dependent Kinase (v-Cdk). ACS Chem Biol 2018; 13:189-199. [PMID: 29215867 DOI: 10.1021/acschembio.7b00972] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Viral cyclin-dependent kinases (v-Cdks) functionally emulate their cellular Cdk counterparts. Such viral mimicry is an established phenomenon that we extend here through chemical genetics. Kinases contain gatekeeper residues that limit the size of molecules that can be accommodated within the enzyme active site. Mutating gatekeeper residues to smaller amino acids allows larger molecules access to the active site. Such mutants can utilize bio-orthoganol ATPs for phosphate transfer and are inhibited by compounds ineffective against the wild type protein, and thus are referred to as analog-sensitive (AS) kinases. We identified the gatekeeper residues of the v-Cdks encoded by Epstein-Barr virus (EBV) and human cytomegalovirus (HCMV) and mutated them to generate AS kinases. The AS-v-Cdks are functional and utilize different ATP derivatives with a specificity closely matching their cellular ortholog, AS-Cdk2. The AS derivative of the EBV v-Cdk was used to transfer a thiolated phosphate group to targeted proteins which were then purified through covalent capture and identified by mass spectrometry. Pathway analysis of these newly identified direct substrates of the EBV v-Cdk extends the potential influence of this kinase into all stages of gene expression (transcription, splicing, mRNA export, and translation). Our work demonstrates the biochemical similarity of the cellular and viral Cdks, as well as the utility of AS v-Cdks for substrate identification to increase our understanding of both viral infections and Cdk biology.
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Affiliation(s)
- Angie C. Umaña
- Institute for Molecular Virology
and McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Satoko Iwahori
- Institute for Molecular Virology
and McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Robert F. Kalejta
- Institute for Molecular Virology
and McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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20
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White FM, Wolf-Yadlin A. Methods for the Analysis of Protein Phosphorylation-Mediated Cellular Signaling Networks. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:295-315. [PMID: 27049636 DOI: 10.1146/annurev-anchem-071015-041542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein phosphorylation-mediated cellular signaling networks regulate almost all aspects of cell biology, including the responses to cellular stimulation and environmental alterations. These networks are highly complex and comprise hundreds of proteins and potentially thousands of phosphorylation sites. Multiple analytical methods have been developed over the past several decades to identify proteins and protein phosphorylation sites regulating cellular signaling, and to quantify the dynamic response of these sites to different cellular stimulation. Here we provide an overview of these methods, including the fundamental principles governing each method, their relative strengths and weaknesses, and some examples of how each method has been applied to the analysis of complex signaling networks. When applied correctly, each of these techniques can provide insight into the topology, dynamics, and regulation of protein phosphorylation signaling networks.
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Affiliation(s)
- Forest M White
- Department of Biological Engineering and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
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21
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Bartkowiak B, Yan C, Greenleaf AL. Engineering an analog-sensitive CDK12 cell line using CRISPR/Cas. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1179-87. [PMID: 26189575 DOI: 10.1016/j.bbagrm.2015.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/08/2015] [Accepted: 07/14/2015] [Indexed: 11/15/2022]
Abstract
The RNA Polymerase II C-terminal domain (CTD) kinase CDK12 has been implicated as a tumor suppressor and regulator of DNA damage response genes. Although much has been learned about CDK12 and its activity, due to the lack of a specific inhibitor and the complications posed by long term RNAi depletion, much is still unknown about the particulars of CDK12 function. Therefore gaining a better understanding of CDK12's roles at the molecular level will be challenging without the development of additional tools. In order to address these issues we have used the CRISPR/Cas gene engineering system to create a mammalian cell line in which the only functional copy of CDK12 is selectively inhibitable by a cell-permeable adenine analog (analog-sensitive CDK12). Inhibition of CDK12 results in a perturbation of the phosphorylation patterns on the CTD and an arrest in cellular proliferation. This cell line should serve as a powerful tool for future studies.
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Affiliation(s)
| | - Christopher Yan
- Department of Biochemistry, Duke University Medical Center, United States
| | - Arno L Greenleaf
- Department of Biochemistry, Duke University Medical Center, United States.
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22
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Robichaux MA, Chenaux G, Ho HYH, Soskis MJ, Greenberg ME, Henkemeyer M, Cowan CW. EphB1 and EphB2 intracellular domains regulate the formation of the corpus callosum and anterior commissure. Dev Neurobiol 2015; 76:405-20. [PMID: 26148571 DOI: 10.1002/dneu.22323] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/28/2015] [Accepted: 06/30/2015] [Indexed: 12/24/2022]
Abstract
The two cortical hemispheres of the mammalian forebrain are interconnected by major white matter tracts, including the corpus callosum (CC) and the posterior branch of the anterior commissure (ACp), that bridge the telencephalic midline. We show here that the intracellular signaling domains of the EphB1 and EphB2 receptors are critical for formation of both the ACp and CC. We observe partial and complete agenesis of the corpus callosum, as well as highly penetrant ACp misprojection phenotypes in truncated EphB1/2 mice that lack intracellular signaling domains. Consistent with the roles for these receptors in formation of the CC and ACp, we detect expression of these receptors in multiple brain regions associated with the formation of these forebrain structures. Taken together, our findings suggest that a combination of forward and reverse EphB1/2 receptor-mediated signaling contribute to ACp and CC axon guidance.
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Affiliation(s)
- Michael A Robichaux
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, Massachusetts, 02478.,Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - George Chenaux
- Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390.,Developmental Biology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Hsin-Yi Henry Ho
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, 02115
| | - Michael J Soskis
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, 02115
| | - Michael E Greenberg
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, 02115
| | - Mark Henkemeyer
- Developmental Biology, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Christopher W Cowan
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, Massachusetts, 02478.,Department of Psychiatry, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390
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23
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Kamber RA, Shoemaker CJ, Denic V. Receptor-Bound Targets of Selective Autophagy Use a Scaffold Protein to Activate the Atg1 Kinase. Mol Cell 2015; 59:372-81. [PMID: 26166702 DOI: 10.1016/j.molcel.2015.06.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/03/2015] [Accepted: 06/03/2015] [Indexed: 01/10/2023]
Abstract
Selective autophagy eliminates protein aggregates, damaged organelles, and other targets that otherwise accumulate and cause disease. Autophagy receptors mediate selectivity by connecting targets to the autophagosome membrane. It has remained unknown whether receptors perform additional functions. Here, we show that in yeast certain receptor-bound targets activate Atg1, the kinase that controls autophagosome formation. Specifically, we found that in nutrient-rich conditions, Atg1 is active only in a multisubunit complex comprising constitutive protein aggregates, their autophagy receptor, and a scaffold protein, Atg11. Development of a cell-free assay for Atg1-mediated phosphorylation enabled us to activate Atg1 with purified receptor-bound aggregates and Atg11. Another target, damaged peroxisomes, also activated Atg1 using Atg11 with a distinct receptor. Our work reveals that receptor-target complexes activate Atg1 to drive formation of selective autophagosomes. This regulatory logic is a key similarity between selective autophagy and bulk autophagy, which is initiated by a distinct Atg1 activation mechanism during starvation.
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Affiliation(s)
- Roarke A Kamber
- Northwest Labs, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher J Shoemaker
- Northwest Labs, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vladimir Denic
- Northwest Labs, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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24
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Kelley M, Yochem J, Krieg M, Calixto A, Heiman MG, Kuzmanov A, Meli V, Chalfie M, Goodman MB, Shaham S, Frand A, Fay DS. FBN-1, a fibrillin-related protein, is required for resistance of the epidermis to mechanical deformation during C. elegans embryogenesis. eLife 2015; 4. [PMID: 25798732 PMCID: PMC4395870 DOI: 10.7554/elife.06565] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/20/2015] [Indexed: 12/19/2022] Open
Abstract
During development, biomechanical forces contour the body and provide shape to internal organs. Using genetic and molecular approaches in combination with a FRET-based tension sensor, we characterized a pulling force exerted by the elongating pharynx (foregut) on the anterior epidermis during C. elegans embryogenesis. Resistance of the epidermis to this force and to actomyosin-based circumferential constricting forces is mediated by FBN-1, a ZP domain protein related to vertebrate fibrillins. fbn-1 was required specifically within the epidermis and FBN-1 was expressed in epidermal cells and secreted to the apical surface as a putative component of the embryonic sheath. Tiling array studies indicated that fbn-1 mRNA processing requires the conserved alternative splicing factor MEC-8/RBPMS. The conserved SYM-3/FAM102A and SYM-4/WDR44 proteins, which are linked to protein trafficking, function as additional components of this network. Our studies demonstrate the importance of the apical extracellular matrix in preventing mechanical deformation of the epidermis during development. DOI:http://dx.doi.org/10.7554/eLife.06565.001 For an animal embryo to develop, its cells must organize themselves into tissues and organs. For example, skin and the lining of internal organs—such as the lungs and gut—are made from cells called epithelial cells, which are tightly linked to form flat sheets. In a microscopic worm called Caenorhabditis elegans, the outermost layer of epithelial cells (called the epidermis) forms over the surface of the embryo early on in embryonic development. Shortly afterwards, the embryonic epidermis experiences powerful contractions along the surface of the embryo. The force generated by these contractions converts the embryo from an oval shape to a roughly cylindrical form. These contractions also squeeze the internal tissues and organs, which correspondingly elongate along with the epidermis. It has been known for decades that such ‘mechanical’ forces are important for the normal development of embryos. However, it remains poorly understood how these forces generate tissues and organs of the proper shape—partly because it is difficult to measure forces in living embryos. It is also not clear how the mechanical properties of specific tissues are controlled. Now, Kelley, Yochem, Krieg et al. have analyzed the development of C. elegans' embryos and discovered a novel mechanical interplay between the feeding organ (called the pharynx) and the worm's epidermis. The experiments involved studying several mutant worms that perturb epidermal contractions and disrupt the attachment of the pharynx to the epidermis. These studies suggested that the pharynx exerts a strong inward pulling force on the epidermis during development. Using recently developed methods, Kelley, Yochem, Krieg et al. then measured mechanical forces within intact worm embryos and demonstrated that greater forces were experienced in cells that were being pulled by the pharynx. Kelley, Yochem, Krieg et al. further analyzed how the epidermis normally resists this pulling force from the pharynx and implicated a protein called FBN-1. This worm protein is structurally related to a human protein that is affected in people with a disorder called Marfan Syndrome. Worm embryos without the FBN-1 protein become severely deformed because they are unable to withstand mechanical forces at the epidermis. FBN-1 is normally synthesized and then transported to the outside of the worm embryo by epidermal cells, where it is thought to assemble into a meshwork of long fibers. This provides a strong scaffold that attaches to the epidermis to prevent the epidermis from undergoing excessive deformation while it experiences mechanical forces. The work of Kelley, Yochem, Krieg et al. provides an opportunity to understand how FBN-1 and other fiber-forming proteins are produced and transported to the cell surface. Moreover, these findings may have implications for human diseases and birth defects that result from an inability of tissues to respond appropriately to mechanical forces. DOI:http://dx.doi.org/10.7554/eLife.06565.002
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Affiliation(s)
- Melissa Kelley
- Department of Molecular Biology, University of Wyoming, Laramie, United States
| | - John Yochem
- Department of Molecular Biology, University of Wyoming, Laramie, United States
| | - Michael Krieg
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Andrea Calixto
- Department of Biological Sciences, Columbia University, New York, United States
| | - Maxwell G Heiman
- Department of Genetics, Harvard Medical School, Boston Children's Hospital, Boston, United States
| | - Aleksandra Kuzmanov
- Department of Molecular Biology, University of Wyoming, Laramie, United States
| | - Vijaykumar Meli
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, United States
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, United States
| | - Miriam B Goodman
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, New York, United States
| | - Alison Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, United States
| | - David S Fay
- Department of Molecular Biology, University of Wyoming, Laramie, United States
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25
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Bartkowiak B, Greenleaf AL. Expression, purification, and identification of associated proteins of the full-length hCDK12/CyclinK complex. J Biol Chem 2014; 290:1786-95. [PMID: 25429106 PMCID: PMC4340420 DOI: 10.1074/jbc.m114.612226] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The coupling of transcription and associated processes has been shown to be dependent on the RNA polymerase II (RNAPII) C-terminal repeat domain (CTD) and the phosphorylation of the heptad repeats of which it is composed (consensus sequence Y1S2P3T4S5P6S7). Two primary S2 position CTD kinases have been identified in higher eukaryotes: P-TEFb and CDK12/CyclinK. The more recently discovered CDK12 appears to act at the 3'-end of the transcription unit and has been identified as a tumor suppressor for ovarian cancer; however much is still unknown about the in vivo roles of CDK12/CyclinK. In an effort to further characterize these roles we have purified to near homogeneity and characterized, full-length, active, human CDK12/CyclinK, and identified hCDK12-associated proteins via mass spectrometry. We find that employing a "2A" peptide-linked multicistronic construct containing CDK12 and CyclinK results in the efficient production of active, recombinant enzyme in the baculovirus/Sf9 expression system. Using GST-CTD fusion protein substrates we find that CDK12/CyclinK prefers a substrate with unmodified repeats or one that mimics prephosphorylation at the S7 position of the CTD; also the enzyme is sensitive to the inhibitor flavopiridol at higher concentrations. Identification of CDK12-associating proteins reveals a strong enrichment for RNA-processing factors suggesting that CDK12 affects RNA processing events in two distinct ways: Indirectly through generating factor-binding phospho-epitopes on the CTD of elongating RNAPII and directly through binding to specific factors.
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Affiliation(s)
- Bartlomiej Bartkowiak
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
| | - Arno L Greenleaf
- From the Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710
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26
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Ultanir SK, Yadav S, Hertz NT, Oses-Prieto JA, Claxton S, Burlingame AL, Shokat KM, Jan LY, Jan YN. MST3 kinase phosphorylates TAO1/2 to enable Myosin Va function in promoting spine synapse development. Neuron 2014; 84:968-82. [PMID: 25456499 PMCID: PMC4407996 DOI: 10.1016/j.neuron.2014.10.025] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2014] [Indexed: 11/16/2022]
Abstract
Mammalian Sterile 20 (Ste20)-like kinase 3 (MST3) is a ubiquitously expressed kinase capable of enhancing axon outgrowth. Whether and how MST3 kinase signaling might regulate development of dendritic filopodia and spine synapses is unknown. Through shRNA-mediated depletion of MST3 and kinase-dead MST3 expression in developing hippocampal cultures, we found that MST3 is necessary for proper filopodia, dendritic spine, and excitatory synapse development. Knockdown of MST3 in layer 2/3 pyramidal neurons via in utero electroporation also reduced spine density in vivo. Using chemical genetics, we discovered thirteen candidate MST3 substrates and identified the phosphorylation sites. Among the identified MST3 substrates, TAO kinases regulate dendritic filopodia and spine development, similar to MST3. Furthermore, using stable isotope labeling by amino acids in culture (SILAC), we show that phosphorylated TAO1/2 associates with Myosin Va and is necessary for its dendritic localization, thus revealing a mechanism for excitatory synapse development in the mammalian CNS.
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Affiliation(s)
- Sila K Ultanir
- Departments of Physiology, Biochemistry, and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
| | - Smita Yadav
- Departments of Physiology, Biochemistry, and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicholas T Hertz
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Suzanne Claxton
- Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lily Y Jan
- Departments of Physiology, Biochemistry, and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuh-Nung Jan
- Departments of Physiology, Biochemistry, and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
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27
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Wanless AG, Lin Y, Weiss EL. Cell morphogenesis proteins are translationally controlled through UTRs by the Ndr/LATS target Ssd1. PLoS One 2014; 9:e85212. [PMID: 24465507 PMCID: PMC3897418 DOI: 10.1371/journal.pone.0085212] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/24/2013] [Indexed: 11/19/2022] Open
Abstract
Eukaryotic cells control their growth and morphogenesis to maintain integrity and viability. Free-living cells are further challenged by their direct interaction with the environment and in many cases maintain a resilient cell wall to stay alive under widely varying conditions. For these organisms, stringent and highly localized control of the cell wall's remodeling and expansion is crucial for cell growth and reproduction. In the budding yeast Saccharomyces cerevisiae the RNA binding protein Ssd1 helps control cell wall remodeling by repressing translation of proteins involved in wall expansion. Ssd1 is itself negatively regulated by the highly conserved Ndr/LATS protein kinase Cbk1. We sought to identify mRNA regions that confer Ssd1-mediated translational control. After validating a GFP reporter system as a readout of Ssd1 activity we found that 3′ untranslated regions of the known Ssd1 targets CTS1, SIM1 and UTH1 are sufficient for Cbk1-regulated translational control. The 5′ untranslated region of UTH1 also facilitated Ssd1-mediated translational control in a heterologous context. The CTS1 and SIM1 3′ untranslated regions confer Ssd1 binding, and the SIM1 3′ untranslated region improves Ssd1 immunoprecipitation of the endogenous SIM1 transcript. However, SIM1's 3′ untranslated region is not essential for Ssd1-regulated control of the message's translation. We propose that Ssd1 regulates translation of its target message primarily through UTRs and the SIM1 message through multiple potential points of interaction, permitting fine translational control in various contexts.
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Affiliation(s)
- Antony G. Wanless
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Yuan Lin
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Eric L. Weiss
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
- * E-mail:
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28
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Abstract
As with other groups of protein kinases, approximately 10% of the RTKs (receptor tyrosine kinases) in the human proteome contain intracellular pseudokinases that lack one or more conserved catalytically important residues. These include ErbB3, a member of the EGFR (epidermal growth factor receptor) family, and a series of unconventional Wnt receptors. We showed previously that, despite its reputation as a pseudokinase, the ErbB3 TKD (tyrosine kinase domain) does retain significant, albeit weak, kinase activity. This led us to suggest that a subgroup of RTKs may be able to signal even with very inefficient kinases. Recent work suggests that this is not the case, however. Other pseudokinase RTKs have not revealed significant kinase activity, and mutations that impair ErbB3's weak kinase activity have not so far been found to exhibit signalling defects. These findings therefore point to models in which the TKDs of pseudokinase RTKs participate in receptor signalling by allosterically regulating associated kinases (such as ErbB3 regulation of ErbB2) and/or function as regulated 'scaffolds' for other intermolecular interactions central to signal propagation. Further structural and functional studies, particularly of the pseudokinase RTKs involved in Wnt signalling, are required to shed new light on these intriguing signalling mechanisms.
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Tay YD, Patel A, Kaemena DF, Hagan IM. Mutation of a conserved residue enhances the sensitivity of analogue-sensitised kinases to generate a novel approach to the study of mitosis in fission yeast. J Cell Sci 2013; 126:5052-61. [PMID: 23986474 DOI: 10.1242/jcs.135301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chemical genetic strategy in which mutational enlargement of the ATP-binding site sensitises of a protein kinase to bulky ATP analogues has proved to be an elegant tool for the generation of conditional analogue-sensitive kinase alleles in a variety of model organisms. Here, we describe a novel substitution mutation in the kinase domain that can enhance the sensitivity of analogue-sensitive kinases. Substitution of a methionine residue to phenylalanine in the +2 position after HRDLKxxN motif of the subdomain VIb within the kinase domain markedly increased the sensitivities of the analogue-sensitive kinases to ATP analogues in three out of five S. pombe kinases (i.e. Plo1, Orb5 and Wee1) that harbor this conserved methionine residue. Kinome alignment established that a methionine residue is found at this site in 5-9% of kinases in key model organisms, suggesting that a broader application of this structural modification may enhance ATP analogue sensitivity of analogue-sensitive kinases in future studies. We also show that the enhanced sensitivity of the wee1.as8 allele in a cdc25.22 background can be exploited to generate highly synchronised mitotic and S phase progression at 36°C. Proof-of-principle experiments show how this novel synchronisation technique will prove of great use in the interrogation of the mitotic or S-phase functions through temperature sensitivity mutation of molecules of interest in fission yeast.
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Affiliation(s)
- Ye-Dee Tay
- CRUK Cell Division Group, Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX, UK
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DeNicola GF, Martin ED, Chaikuad A, Bassi R, Clark J, Martino L, Verma S, Sicard P, Tata R, Atkinson RA, Knapp S, Conte MR, Marber MS. Mechanism and consequence of the autoactivation of p38α mitogen-activated protein kinase promoted by TAB1. Nat Struct Mol Biol 2013; 20:1182-90. [PMID: 24037507 PMCID: PMC3822283 DOI: 10.1038/nsmb.2668] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 08/02/2013] [Indexed: 11/09/2022]
Abstract
p38α mitogen-activated protein kinase (p38α) is activated by a variety of mechanisms, including autophosphorylation initiated by TGFβ-activated kinase 1 binding protein 1 (TAB1) during myocardial ischemia and other stresses. Chemical-genetic approaches and coexpression in mammalian, bacterial and cell-free systems revealed that mouse p38α autophosphorylation occurs in cis by direct interaction with TAB1(371-416). In isolated rat cardiac myocytes and perfused mouse hearts, TAT-TAB1(371-416) rapidly activates p38 and profoundly perturbs function. Crystal structures and characterization in solution revealed a bipartite docking site for TAB1 in the p38α C-terminal kinase lobe. TAB1 binding stabilizes active p38α and induces rearrangements within the activation segment by helical extension of the Thr-Gly-Tyr motif, allowing autophosphorylation in cis. Interference with p38α recognition by TAB1 abolishes its cardiac toxicity. Such intervention could potentially circumvent the drawbacks of clinical pharmacological inhibitors of p38 catalytic activity.
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Affiliation(s)
- Gian Felice DeNicola
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Eva Denise Martin
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Apirat Chaikuad
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford OX3 7LD, UK
| | - Rekha Bassi
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - James Clark
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Sharwari Verma
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Pierre Sicard
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
| | - Renée Tata
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - R Andrew Atkinson
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Stefan Knapp
- University of Oxford, Nuffield Department of Clinical Medicine, Structural Genomics Consortium, Oxford OX3 7LD, UK
- Department of Biochemistry and Molecular Biology, George Washington University, Washington, DC 20037, USA
- University of Oxford, Nuffield Department of Clinical Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Maria R Conte
- Randall Division of Cell and Molecular Biophysics, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Michael S Marber
- King's College London British Heart Foundation Centre of Excellence. The Rayne Institute, St Thomas' Hospital Campus, London, SE1 7EH, UK
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Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM. A neo-substrate that amplifies catalytic activity of parkinson's-disease-related kinase PINK1. Cell 2013; 154:737-47. [PMID: 23953109 PMCID: PMC3950538 DOI: 10.1016/j.cell.2013.07.030] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/30/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
Mitochondria have long been implicated in the pathogenesis of Parkinson's disease (PD). Mutations in the mitochondrial kinase PINK1 that reduce kinase activity are associated with mitochondrial defects and result in an autosomal-recessive form of early-onset PD. Therapeutic approaches for enhancing the activity of PINK1 have not been considered because no allosteric regulatory sites for PINK1 are known. Here, we show that an alternative strategy, a neo-substrate approach involving the ATP analog kinetin triphosphate (KTP), can be used to increase the activity of both PD-related mutant PINK1(G309D) and PINK1(WT). Moreover, we show that application of the KTP precursor kinetin to cells results in biologically significant increases in PINK1 activity, manifest as higher levels of Parkin recruitment to depolarized mitochondria, reduced mitochondrial motility in axons, and lower levels of apoptosis. Discovery of neo-substrates for kinases could provide a heretofore-unappreciated modality for regulating kinase activity.
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Affiliation(s)
- Nicholas T. Hertz
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Amandine Berthet
- Gladstone Institute of Neurological Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin L. Sos
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kurt S. Thorn
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Al L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Graduate Programs in Neuroscience and Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M. Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
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Hertz NT, Wang BT, Allen JJ, Zhang C, Dar AC, Burlingame AL, Shokat KM. Chemical genetic approach for kinase-substrate mapping by covalent capture of thiophosphopeptides and analysis by mass spectrometry. ACTA ACUST UNITED AC 2013; 2:15-36. [PMID: 23836541 DOI: 10.1002/9780470559277.ch090201] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mapping kinase-substrate interactions demands robust methods to rapidly and unequivocally identify substrates from complex protein mixtures. Toward this goal, we present a method in which a kinase, engineered to utilize synthetic ATPγS analogs, specifically thiophosphorylates its substrates in a complex lysate. The thiophosphate label provides a bio-orthogonal tag that can be used to affinity purify and identify labeled proteins. Following the labeling reaction, proteins are digested with trypsin; thiol-containing peptides are then covalently captured and non-thiol-containing peptides are washed from the resin. Oxidation-promoted hydrolysis, at sites of thiophosphorylation, releases phosphopeptides for analysis by tandem mass spectrometry. By incorporating two specificity gates-kinase engineering and peptide affinity purification-this method yields high-confidence substrate identifications. This method gives both the identity of the substrates and phosphorylation-site localization. With this information, investigators can analyze the biological significance of the phosphorylation mark immediately following confirmation of the kinase-substrate relationship. Here, we provide an optimized version of this technique to further enable widespread utilization of this technology. Curr. Protoc. Chem Biol. 2:15-36. © 2010 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nicholas T Hertz
- Chemistry and Chemical Biology Graduate Program, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California
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33
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Fleißner A. Turning the switch: using chemical genetics to elucidate protein kinase functions in filamentous fungi. FUNGAL BIOL REV 2013. [DOI: 10.1016/j.fbr.2013.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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34
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Xue L, Tao WA. Current technologies to identify protein kinase substrates in high throughput. ACTA ACUST UNITED AC 2013; 8:216-227. [PMID: 25110472 DOI: 10.1007/s11515-013-1257-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since the discovery of protein phosphorylation as an important modulator of many cellular processes, the involvement of protein kinases in diseases, such as cancer, diabetes, cardiovascular diseases, and central nervous system pathologies, has been extensively documented. Our understanding of many disease pathologies at the molecular level, therefore, requires the comprehensive identification of substrates targeted by protein kinases. In this review, we focus on recent techniques for kinase substrate identification in high throughput, in particular on genetic and proteomic approaches. Each method with its inherent advantages and limitations is discussed.
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Affiliation(s)
- Liang Xue
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA ; Department of Medicinal Chemistry & Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA ; Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA ; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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35
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A chemical genetic approach reveals distinct EphB signaling mechanisms during brain development. Nat Neurosci 2012; 15:1645-54. [PMID: 23143520 PMCID: PMC3509236 DOI: 10.1038/nn.3249] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 10/01/2012] [Indexed: 12/15/2022]
Abstract
EphB receptor tyrosine kinases control multiple steps in nervous system development. However, it remains unclear whether EphBs regulate these different developmental processes directly or indirectly. In addition, as EphBs signal through multiple mechanisms, it has been challenging to define which signaling functions of EphBs regulate particular developmental events. To address these issues, we engineered triple knockin mice in which the kinase activity of three neuronally expressed EphBs can be rapidly, reversibly, and specifically blocked. Using these mice we demonstrate that the tyrosine kinase activity of EphBs is required for axon guidance in vivo. By contrast, EphB-mediated synaptogenesis occurs normally when the kinase activity of EphBs is inhibited suggesting that EphBs mediate synapse development by an EphB tyrosine kinase-independent mechanism. Taken together, these experiments reveal that EphBs control axon guidance and synaptogenesis by distinct mechanisms, and provide a new mouse model for dissecting EphB function in development and disease.
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36
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Wong A, Zhang YW, Jeschke GR, Turk BE, Rudnick G. Cyclic GMP-dependent stimulation of serotonin transport does not involve direct transporter phosphorylation by cGMP-dependent protein kinase. J Biol Chem 2012; 287:36051-8. [PMID: 22942288 DOI: 10.1074/jbc.m112.394726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The serotonin transporter (SERT) is responsible for reuptake of serotonin (5-hydroxytryptamine) after its exocytotic release from neurons. It is the primary target for antidepressants and stimulants, including "ecstasy" (3,4-methylenedioxymethamphetamine). SERT is regulated by several processes, including a cyclic GMP signaling pathway involving nitric oxide synthase, guanylyl cyclase, and cGMP-dependent protein kinase (PKG). Here, we show that SERT was phosphorylated in a PKG Iα-dependent manner in vitro, but that SERT was not a direct substrate of PKG. We generated an analog-sensitive gatekeeper residue mutant of PKG Iα (M438G) that efficiently used the ATP analog N(6)-benzyl-ATP. This mutant, but not the wild type (WT) kinase, used the ATP analog to phosphorylate both a model peptide substrate as well as an established protein substrate of PKG (vasodilator-stimulated phosphoprotein). PKG Iα M438G effectively substituted for the WT kinase in stimulating SERT-mediated 5-hydroxytryptamine transport in cultured cells. Addition of either WT or mutant PKG Iα M438G to membranes containing SERT in vitro led to radiolabel incorporation from [γ-(33)P]ATP but not from similarly labeled N(6)-benzyl-ATP, indicating that SERT was phosphorylated by another kinase that could not utilize the ATP analog. These results are consistent with the proposed SERT phosphorylation site, Thr-276, being highly divergent from the consensus PKG phosphorylation site sequence, which we verified through peptide library screening. Another proposed SERT kinase, the p38 mitogen-activated protein kinase, could not substitute for PKG in this assay, and p38 inhibitors did not block PKG-dependent phosphorylation of SERT. The results suggest that PKG initiates a kinase cascade that leads to phosphorylation of SERT by an as yet unidentified protein kinase.
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Affiliation(s)
- Albert Wong
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520-8066, USA
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37
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The S. pombe cytokinesis NDR kinase Sid2 activates Fin1 NIMA kinase to control mitotic commitment through Pom1/Wee1. Nat Cell Biol 2012; 14:738-45. [PMID: 22684255 PMCID: PMC4284365 DOI: 10.1038/ncb2514] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 05/08/2012] [Indexed: 01/24/2023]
Abstract
Mitotic exit integrates the reversal of the phosphorylation events initiated by mitotic kinases with a controlled cytokinesis event that cleaves the cell in two. The Mitotic Exit Network (MEN) of budding yeast regulates both processes, while the fission yeast equivalent, the Septum Initiation Network (SIN), only controls the execution of cytokinesis. The components and architecture of the SIN and MEN are highly conserved1. It is currently assumed that the functions of the core SIN/MEN components are restricted to their characterised roles at the end of mitosis. We now show that the NDR kinase component of the fission yeast SIN, Sid2/Mob1, acts independently of the other known SIN components in G2 phase of the cell cycle to control the timing of mitotic commitment. Sid2/Mob1 promotes mitotic commitment by directly activating the NIMA related kinase Fin1. Fin1’s activation promotes its own destruction, thereby making Fin1 activation a transient feature of G2 phase. This spike of Fin1 activation modulates the activity of the Pom1/Cdr1/Cdr2 geometry network towards Wee1.
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38
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Hengeveld RCC, Hertz NT, Vromans MJM, Zhang C, Burlingame AL, Shokat KM, Lens SMA. Development of a chemical genetic approach for human aurora B kinase identifies novel substrates of the chromosomal passenger complex. Mol Cell Proteomics 2012; 11:47-59. [PMID: 22267324 DOI: 10.1074/mcp.m111.013912] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To understand how the chromosomal passenger complex ensures chromosomal stability, it is crucial to identify its substrates and to find ways to specifically inhibit the enzymatic core of the complex, Aurora B. We therefore developed a chemical genetic approach to selectively inhibit human Aurora B. By mutating the gatekeeper residue Leu-154 in the kinase active site, the ATP-binding pocket was enlarged, but kinase function was severely disrupted. A unique second site suppressor mutation was identified that rescued kinase activity in the Leu-154 mutant and allowed the accommodation of bulky N(6)-substituted adenine analogs. Using this analog-sensitive Aurora B kinase, we found that retention of the chromosomal passenger complex at the centromere depends on Aurora B kinase activity. Furthermore, analog-sensitive Aurora B was able to use bulky ATPγS analogs and could thiophosphorylate multiple proteins in cell extracts. Utilizing an unbiased approach for kinase substrate mapping, we identified several novel substrates of Aurora B, including the nucleosomal-binding protein HMGN2. We confirmed that HMGN2 is a bona fide Aurora B substrate in vivo and show that its dynamic association to chromatin is controlled by Aurora B.
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Affiliation(s)
- Rutger C C Hengeveld
- Department of Medical Oncology, University Medical Center, 3584 CG Utrecht, The Netherlands
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39
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Mass Spectrometric Tools for Systematic Analysis of Protein Phosphorylation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 106:3-32. [DOI: 10.1016/b978-0-12-396456-4.00014-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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40
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Sensitizing plant protein kinases to specific inhibition by ATP-competitive molecules. Methods Mol Biol 2011; 779:185-97. [PMID: 21837567 DOI: 10.1007/978-1-61779-264-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
The highly conserved nature of the protein kinase catalytic domain and the low permeability of plant cell membranes pose a challenge to the development of specific inhibitors that target individual protein kinases in vivo. Here, we describe a chemical-genetic approach to specifically sensitize individual plant kinases to cell-permeable small molecules that do not inhibit wild-type kinases. In this approach, a single amino-acid substitution is introduced in the ATP-binding site of the enzyme enabling specific binding of ATP-competitive molecules. Cell-permeable molecules can then be used to specifically target the sensitized allele in transgenic Arabidopsis thaliana plants that do not express the wild-type form of the kinase. This strategy provides a useful tool for the functional characterization of protein kinases in planta and for the dissection of the signaling pathways in which they are involved.
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41
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Toxoplasma and Plasmodium protein kinases: roles in invasion and host cell remodelling. Int J Parasitol 2011; 42:21-32. [PMID: 22154850 DOI: 10.1016/j.ijpara.2011.11.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 11/16/2011] [Accepted: 11/16/2011] [Indexed: 11/20/2022]
Abstract
Some apicomplexan parasites have evolved distinct protein kinase families to modulate host cell structure and function. Toxoplasma gondii rhoptry protein kinases and pseudokinases are involved in virulence and modulation of host cell signalling. The proteome of Plasmodium falciparum contains a family of putative kinases called FIKKs, some of which are exported to the host red blood cell and might play a role in erythrocyte remodelling. In this review we will discuss kinases known to be critical for host cell invasion, intracellular growth and egress, focusing on (i) calcium-dependent protein kinases and (ii) the secreted kinases that are unique to Toxoplasma (rhoptry protein kinases and pseudokinases) and Plasmodium (FIKKs).
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42
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Dittrich ACN, Devarenne TP. An ATP analog-sensitive version of the tomato cell death suppressor protein kinase Adi3 for use in substrate identification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:269-73. [PMID: 22027266 DOI: 10.1016/j.bbapap.2011.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/03/2011] [Accepted: 10/06/2011] [Indexed: 01/19/2023]
Abstract
Adi3 is a protein kinase from tomato that functions as a cell death suppressor and its substrates are not well defined. As a step toward identifying Adi3 substrates we developed an ATP analog-sensitive version of Adi3 in which the ATP-binding pocket is mutated to allow use of bulky ATP analogs. Met385 was identified as the "gatekeeper" residue and the M385G mutation allows for the use of two bulky ATP analogs. Adi3(M385G) can also specifically utilize N(6)-benzyl-ATP to phosphorylate a known substrate and provides a tool for identifying Adi3 substrates.
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Affiliation(s)
- Anna C Nelson Dittrich
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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43
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Moffat LD, Brown SBA, Grassie ME, Ulke-Lemée A, Williamson LM, Walsh MP, MacDonald JA. Chemical genetics of zipper-interacting protein kinase reveal myosin light chain as a bona fide substrate in permeabilized arterial smooth muscle. J Biol Chem 2011; 286:36978-91. [PMID: 21880706 DOI: 10.1074/jbc.m111.257949] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Zipper-interacting protein kinase (ZIPK) has been implicated in Ca(2+)-independent smooth muscle contraction, although its specific role is unknown. The addition of ZIPK to demembranated rat caudal arterial strips induced an increase in force, which correlated with increases in LC(20) and MYPT1 phosphorylation. However, because of the number of kinases capable of phosphorylating LC(20) and MYPT1, it has proven difficult to identify the mechanism underlying ZIPK action. Therefore, we set out to identify bona fide ZIPK substrates using a chemical genetics method that takes advantage of ATP analogs with bulky substituents at the N(6) position and an engineered ZIPK capable of utilizing such substrates. (32)P-Labeled 6-phenyl-ATP and ZIPK-L93G mutant protein were added to permeabilized rat caudal arterial strips, and substrate proteins were detected by autoradiography following SDS-PAGE. Mass spectrometry identified LC(20) as a direct target of ZIPK in situ for the first time. Tissues were also exposed to 6-phenyl-ATP and ZIPK-L93G in the absence of endogenous ATP, and putative ZIPK substrates were identified by Western blotting. LC(20) was thereby confirmed as a direct target of ZIPK; however, no phosphorylation of MYPT1 was detected. We conclude that ZIPK is involved in the regulation of smooth muscle contraction through direct phosphorylation of LC(20).
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Affiliation(s)
- Lori D Moffat
- Smooth Muscle Research Group and the Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
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Cohen D, Fernandez D, Lázaro-Diéguez F, Müsch A. The serine/threonine kinase Par1b regulates epithelial lumen polarity via IRSp53-mediated cell-ECM signaling. ACTA ACUST UNITED AC 2011; 192:525-40. [PMID: 21282462 PMCID: PMC3101094 DOI: 10.1083/jcb.201007002] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Par1b regulates cell–ECM signaling and dictates epithelial lumenal organization by targeting IRSp53, a Rho GTPase adaptor and scaffolding protein. The serine/threonine kinase Par1b promotes cell–cell adhesion and determines the polarity of the luminal domain in epithelial cells. In this study, we demonstrate that Par1b also regulates cell–extracellular matrix (ECM) signaling in kidney-derived Madin–Darby canine kidney (MDCK) cells and identified the rho–guanosine triphosphatase adaptor and scaffolding protein IRSp53 as a Par1b substrate involved in this pathway. Par1b overexpression inhibits basal lamina formation, cell spreading, focal adhesion, stress fiber formation, and compaction, whereas Par1b depletion has the opposite effect. IRSp53 depletion mimics Par1b overexpression on cell–ECM signaling and lumen polarity but had no effect on adherens junction formation. Par1b directly phosphorylates IRSp53 on S366 in cell lysates and stimulates phosphorylation on S453/3/5 via an indirect mechanism. A Par1b phosphorylation–deficient IRSp53 mutant but not the wild-type protein efficiently rescues both the cell spreading and the lumen polarity defects in Par1b MDCK cells. Our data suggest a model in which Par1b phosphorylation prevents recruitment of IRSp53 effector proteins to its Src homology domain 3 by promoting 14-3-3 binding in the vicinity of that domain.
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Affiliation(s)
- David Cohen
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
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45
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Chi Y, Clurman BE. Mass spectrometry-based identification of protein kinase substrates utilizing engineered kinases and thiophosphate labeling. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2010; 2:ch100151. [PMID: 21743840 PMCID: PMC3131159 DOI: 10.1002/9780470559277.ch100151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein kinases constitute a large enzyme family with key roles in cellular signal transduction. One way to elucidate the functions of protein kinases is to systematically identify their downstream targets. We present here a simple and effective method to identify direct protein kinase substrates in native cell lysates. First, we isolate the activity of the kinase of interest by engineering the normal kinase to utilize bulky ATP analogs that cannot be used by normal cellular kinases. This allows specific labeling of substrates with thiophosphate tags by performing kinase reactions in cell lysates that also include bulky ATP-γ-S analogs. After digesting the proteins in the reaction mixture, thiophosphopeptides are isolated using a single-step capture-and-release protocol and identified by mass spectrometry. This technique is easy to use and generally applicable.
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Affiliation(s)
- Yong Chi
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
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46
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Davis RE, Ngo VN, Lenz G, Tolar P, Young RM, Romesser PB, Kohlhammer H, Lamy L, Zhao H, Yang Y, Xu W, Shaffer AL, Wright G, Xiao W, Powell J, Jiang JK, Thomas CJ, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Johnson NA, Rimsza LM, Campo E, Jaffe ES, Wilson WH, Delabie J, Smeland EB, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pierce SK, Staudt LM. Chronic active B-cell-receptor signalling in diffuse large B-cell lymphoma. Nature 2010; 463:88-92. [PMID: 20054396 DOI: 10.1038/nature08638] [Citation(s) in RCA: 1228] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Accepted: 11/04/2009] [Indexed: 12/15/2022]
Abstract
A role for B-cell-receptor (BCR) signalling in lymphomagenesis has been inferred by studying immunoglobulin genes in human lymphomas and by engineering mouse models, but genetic and functional evidence for its oncogenic role in human lymphomas is needed. Here we describe a form of 'chronic active' BCR signalling that is required for cell survival in the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL). The signalling adaptor CARD11 is required for constitutive NF-kappaB pathway activity and survival in ABC DLBCL. Roughly 10% of ABC DLBCLs have mutant CARD11 isoforms that activate NF-kappaB, but the mechanism that engages wild-type CARD11 in other ABC DLBCLs was unknown. An RNA interference genetic screen revealed that a BCR signalling component, Bruton's tyrosine kinase, is essential for the survival of ABC DLBCLs with wild-type CARD11. In addition, knockdown of proximal BCR subunits (IgM, Ig-kappa, CD79A and CD79B) killed ABC DLBCLs with wild-type CARD11 but not other lymphomas. The BCRs in these ABC DLBCLs formed prominent clusters in the plasma membrane with low diffusion, similarly to BCRs in antigen-stimulated normal B cells. Somatic mutations affecting the immunoreceptor tyrosine-based activation motif (ITAM) signalling modules of CD79B and CD79A were detected frequently in ABC DLBCL biopsy samples but rarely in other DLBCLs and never in Burkitt's lymphoma or mucosa-associated lymphoid tissue lymphoma. In 18% of ABC DLBCLs, one functionally critical residue of CD79B, the first ITAM tyrosine, was mutated. These mutations increased surface BCR expression and attenuated Lyn kinase, a feedback inhibitor of BCR signalling. These findings establish chronic active BCR signalling as a new pathogenetic mechanism in ABC DLBCL, suggesting several therapeutic strategies.
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Affiliation(s)
- R Eric Davis
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Calcium-dependent signaling and kinases in apicomplexan parasites. Cell Host Microbe 2009; 5:612-22. [PMID: 19527888 DOI: 10.1016/j.chom.2009.05.017] [Citation(s) in RCA: 241] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 05/25/2009] [Accepted: 05/29/2009] [Indexed: 02/08/2023]
Abstract
Calcium controls many critical events in the complex life cycles of apicomplexan parasites including protein secretion, motility, and development. Calcium levels are normally tightly regulated and rapid release of calcium into the cytosol activates a family of calcium-dependent protein kinases (CDPKs), which are normally characteristic of plants. CDPKs present in apicomplexans have acquired a number of unique domain structures likely reflecting their diverse functions. Calcium regulation in parasites is closely linked to signaling by cyclic nucleotides and their associated kinases. This Review summarizes the pivotal roles that calcium- and cyclic nucleotide-dependent kinases play in unique aspects of parasite biology.
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Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol 2009; 29:4852-63. [PMID: 19581288 DOI: 10.1128/mcb.00609-09] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Saccharomyces cerevisiae kinase Bur1 is involved in coupling transcription elongation to chromatin modification, but not all important Bur1 targets in the elongation complex are known. Using a chemical genetics strategy wherein Bur1 kinase was engineered to be regulated by a specific inhibitor, we found that Bur1 phosphorylates the Spt5 C-terminal repeat domain (CTD) both in vivo and in isolated elongation complexes in vitro. Deletion of the Spt5 CTD or mutation of the Spt5 serines targeted by Bur1 reduces recruitment of the PAF complex, which functions to recruit factors involved in chromatin modification and mRNA maturation to elongating polymerase II (Pol II). Deletion of the Spt5 CTD showed the same defect in PAF recruitment as rapid inhibition of Bur1 kinase activity, and this Spt5 mutation led to a decrease in histone H3K4 trimethylation. Brief inhibition of Bur1 kinase activity in vivo also led to a significant decrease in phosphorylation of the Pol II CTD at Ser-2, showing that Bur1 also contributes to Pol II Ser-2 phosphorylation. Genetic results suggest that Bur1 is essential for growth because it targets multiple factors that play distinct roles in transcription.
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Dar AC, Lopez MS, Shokat KM. Small molecule recognition of c-Src via the Imatinib-binding conformation. ACTA ACUST UNITED AC 2008; 15:1015-22. [PMID: 18940662 PMCID: PMC2702663 DOI: 10.1016/j.chembiol.2008.09.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 09/20/2008] [Accepted: 09/24/2008] [Indexed: 01/07/2023]
Abstract
The cancer drug, Imatinib, is a selective Abl kinase inhibitor that does not inhibit the closely related kinase c-Src. This one drug and its ability to selectively inhibit Abl over c-Src has been a guiding principle in virtually all kinase drug discovery efforts in the last 15 years. A prominent hypothesis explaining the selectivity of Imatinib is that Abl has an intrinsic ability to adopt an inactive conformation (termed DFG-out), whereas c-Src appears to pay a high intrinsic energetic penalty for adopting this conformation, effectively excluding Imatinib from its ATP pocket. This explanation of the difference in binding affinity of Imatinib for Abl versus c-Src makes the striking prediction that it would not be possible to design an inhibitor that binds to the DFG-out conformation of c-Src with high affinity. We report the discovery of a series of such inhibitors. We use structure-activity relationships and X-ray crystallography to confirm our findings. These studies suggest that small molecules are capable of inducing the generally unfavorable DFG-out conformation in c-Src. Structural comparison between c-Src in complex with these inhibitors allows us to speculate on the differential selectivity of Imatinib for c-Src and Abl.
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Affiliation(s)
- Arvin C Dar
- Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, Genentech Hall, 600 16(th) Street, University of California, San Francisco, San Francisco, CA 94158, USA
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