201
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Sayegh J, Webb K, Cheng D, Bedford MT, Clarke SG. Regulation of protein arginine methyltransferase 8 (PRMT8) activity by its N-terminal domain. J Biol Chem 2007; 282:36444-53. [PMID: 17925405 DOI: 10.1074/jbc.m704650200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human protein arginine methyltransferase PRMT8 has been recently described as a type I enzyme in brain that is localized to the plasma membrane by N-terminal myristoylation. The amino acid sequence of human PRMT8 is almost 80% identical to human PRMT1, the major protein arginine methyltransferase activity in mammalian cells. However, the activity of a recombinant PRMT8 GST fusion protein toward methyl-accepting substrates is much lower than that of a GST fusion of PRMT1. We show here that both His-tagged and GST fusion species lacking the initial 60 amino acid residues of PRMT8 have enhanced enzymatic activity, suggesting that the N-terminal domain may regulate PRMT8 activity. This conclusion is supported by limited proteolysis experiments showing an increase in the activity of the digested full-length protein, consistent with the loss of the N-terminal domain. In contrast, the activity of the N-terminal truncated protein was slightly diminished by limited proteolysis. Significantly, we detect automethylation at two sites in the N-terminal domain, as well as binding sites for SH3 domain-containing proteins. We suggest that the N-terminal domain may function as an autoregulator that may be displaced by interaction with one or more physiological inducers.
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Affiliation(s)
- Joyce Sayegh
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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202
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Zhang L, Lee KC, Bhojani MS, Khan AP, Shilman A, Holland EC, Ross BD, Rehemtulla A. Molecular imaging of Akt kinase activity. Nat Med 2007; 13:1114-9. [PMID: 17694068 DOI: 10.1038/nm1608] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 05/17/2007] [Indexed: 11/09/2022]
Abstract
The serine/threonine kinase Akt mediates mitogenic and anti-apoptotic responses that result from activation of multiple signaling cascades. It is considered a key determinant of tumor aggressiveness and is a major target for anticancer drug development. Here, we describe a new reporter molecule whose bioluminescence activity within live cells and in mice can be used to measure Akt activity. Akt activity in cultured cells and tumor xenografts was monitored quantitatively and dynamically in response to activation or inhibition of receptor tyrosine kinase, inhibition of phosphoinositide 3-kinase, or direct inhibition of Akt. The results provide unique insights into the pharmacokinetics and pharmacodynamics of agents that modulate Akt activity, revealing the usefulness of this reporter for rapid dose and schedule optimization in the drug development process.
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Affiliation(s)
- Limin Zhang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
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203
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Hutti JE, Turk BE, Asara JM, Ma A, Cantley LC, Abbott DW. IkappaB kinase beta phosphorylates the K63 deubiquitinase A20 to cause feedback inhibition of the NF-kappaB pathway. Mol Cell Biol 2007; 27:7451-61. [PMID: 17709380 PMCID: PMC2169042 DOI: 10.1128/mcb.01101-07] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Misregulation of NF-kappaB signaling leads to infectious, inflammatory, or autoimmune disorders. IkappaB kinase beta (IKKbeta) is an essential activator of NF-kappaB and is known to phosphorylate the NF-kappaB inhibitor, IkappaBalpha, allowing it to undergo ubiquitin-mediated proteasomal degradation. However, beyond IkappaBalpha, few additional IKKbeta substrates have been identified. Here we utilize a peptide library and bioinformatic approach to predict likely substrates of IKKbeta. This approach predicted Ser381 of the K63 deubiquitinase A20 as a likely site of IKKbeta phosphorylation. While A20 is a known negative regulator of innate immune signaling pathways, the mechanisms regulating the activity of A20 are poorly understood. We show that IKKbeta phosphorylates A20 in vitro and in vivo at serine 381, and we further show that this phosphorylation event increases the ability of A20 to inhibit the NF-kappaB signaling pathway. Phosphorylation of A20 by IKKbeta thus represents part of a novel feedback loop that regulates the duration of NF-kappaB signaling following activation of innate immune signaling pathways.
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Affiliation(s)
- Jessica E Hutti
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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204
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Abstract
The serine/threonine kinase Akt, also known as protein kinase B (PKB), is a central node in cell signaling downstream of growth factors, cytokines, and other cellular stimuli. Aberrant loss or gain of Akt activation underlies the pathophysiological properties of a variety of complex diseases, including type-2 diabetes and cancer. Here, we review the molecular properties of Akt and the approaches used to characterize its true cellular targets. In addition, we discuss those Akt substrates that are most likely to contribute to the diverse cellular roles of Akt, which include cell survival, growth, proliferation, angiogenesis, metabolism, and migration.
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Affiliation(s)
- Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard School of Public Health, SPH2-117, Boston, MA 02115, USA.
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205
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Ubersax JA, Ferrell JE. Mechanisms of specificity in protein phosphorylation. Nat Rev Mol Cell Biol 2007; 8:530-41. [PMID: 17585314 DOI: 10.1038/nrm2203] [Citation(s) in RCA: 1005] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A typical protein kinase must recognize between one and a few hundred bona fide phosphorylation sites in a background of approximately 700,000 potentially phosphorylatable residues. Multiple mechanisms have evolved that contribute to this exquisite specificity, including the structure of the catalytic site, local and distal interactions between the kinase and substrate, the formation of complexes with scaffolding and adaptor proteins that spatially regulate the kinase, systems-level competition between substrates, and error-correction mechanisms. The responsibility for the recognition of substrates by protein kinases appears to be distributed among a large number of independent, imperfect specificity mechanisms.
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Affiliation(s)
- Jeffrey A Ubersax
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305-5174, USA.
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206
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Li T, Li F, Zhang X. Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach. Proteins 2007; 70:404-14. [PMID: 17680694 DOI: 10.1002/prot.21563] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein phosphorylation plays important roles in a variety of cellular processes. Detecting possible phosphorylation sites and their corresponding protein kinases is crucial for studying the function of many proteins. This article presents a new prediction system, called PhoScan, to predict phosphorylation sites in a kinase-family-specific way. Common phosphorylation features and kinase-specific features are extracted from substrate sequences of different protein kinases based on the analysis of published experiments, and a scoring system is developed for evaluating the possibility that a peptide can be phosphorylated by the protein kinase at the specific site in its sequence context. PhoScan can achieve a specificity of above 90% with sensitivity around 90% at kinase-family level on the data experimented. The system is applied on a set of human proteins collected from Swiss-Prot and sets of putative phosphorylation sites are predicted for protein kinase A, cyclin-dependent kinase, and casein kinase 2 families. PhoScan is available at http://bioinfo.au.tsinghua.edu.cn/phoscan/.
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Affiliation(s)
- Tingting Li
- Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China
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207
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Chang EJ, Begum R, Chait BT, Gaasterland T. Prediction of cyclin-dependent kinase phosphorylation substrates. PLoS One 2007; 2:e656. [PMID: 17668044 PMCID: PMC1924601 DOI: 10.1371/journal.pone.0000656] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 06/24/2007] [Indexed: 11/18/2022] Open
Abstract
Protein phosphorylation, mediated by a family of enzymes called cyclin-dependent kinases (Cdks), plays a central role in the cell-division cycle of eukaryotes. Phosphorylation by Cdks directs the cell cycle by modifying the function of regulators of key processes such as DNA replication and mitotic progression. Here, we present a novel computational procedure to predict substrates of the cyclin-dependent kinase Cdc28 (Cdk1) in the Saccharomyces cerevisiae. Currently, most computational phosphorylation site prediction procedures focus solely on local sequence characteristics. In the present procedure, we model Cdk substrates based on both local and global characteristics of the substrates. Thus, we define the local sequence motifs that represent the Cdc28 phosphorylation sites and subsequently model clustering of these motifs within the protein sequences. This restraint reflects the observation that many known Cdk substrates contain multiple clustered phosphorylation sites. The present strategy defines a subset of the proteome that is highly enriched for Cdk substrates, as validated by comparing it to a set of bona fide, published, experimentally characterized Cdk substrates which was to our knowledge, comprehensive at the time of writing. To corroborate our model, we compared its predictions with three experimentally independent Cdk proteomic datasets and found significant overlap. Finally, we directly detected in vivo phosphorylation at Cdk motifs for selected putative substrates using mass spectrometry.
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Affiliation(s)
- Emmanuel J Chang
- Department of Chemistry, York College of the City University of New York, Jamaica, New York, United States of America; Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, New York, New York, United States of America.
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208
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Moses AM, Hériché JK, Durbin R. Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biol 2007; 8:R23. [PMID: 17316440 PMCID: PMC1852407 DOI: 10.1186/gb-2007-8-2-r23] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 01/16/2007] [Accepted: 02/22/2007] [Indexed: 11/10/2022] Open
Abstract
Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy to predict the targets of CDKs and use it to identify new biologically interesting candidates. Our data suggest that regulatory modules may exist in protein sequence as clusters of short sequence motifs.
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Affiliation(s)
- Alan M Moses
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Jean-Karim Hériché
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
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209
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Fuller CM, Kovacs G, Anderson SJ, Benos DJ. The CLCAs: Proteins with Ion Channel, Cell Adhesion and Tumor Suppressor Functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007. [DOI: 10.1007/0-387-23250-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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210
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Huang SY, Tsai ML, Chen GY, Wu CJ, Chen SH. A Systematic MS-Based Approach for IdentifyinginvitroSubstrates of PKA and PKG in Rat Uteri. J Proteome Res 2007; 6:2674-84. [PMID: 17564427 DOI: 10.1021/pr070134c] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein phosphorylation is an important modulator of many cellular processes, and identification of kinase substrates provides critical insights for signal transduction. However, this identification process is often difficult and many kinase substrates remain unexplored. Herein, a systematic proteomics approach solely depending on MS detection is reported for identifying substrates of PKA and PKG, which are suspected to have similar specificity determinants, in pregnant rat uteri. Instead of radioisotopes that are commonly used to couple with MS for substrate identification, this study developed an efficient in vitro kinase assay on depleted tissue homogenates to reveal substrate candidates directly by MS. To facilitate MS detection, exogenous phosphatases were added to remove intrinsic phosphorylation followed by a heating step to inactivate all enzymes. No observable interference caused by endogenous kinases or background phosphorylation was detected in the control experiment in which no kinase was externally added. A total of 61 and 12 substrate candidates were identified in vitro for PKA and PKG, respectively, and most of these identified sites contain consensus motifs of each kinase with only a few sites overlapped, indicating a good specificity. Moreover, differential phosphoproteomics analysis using stable isotope dimethyl labeling and MS was performed to detect the change of protein phosphorylation upon kinase stimulation in vivo. Four identified in vitro PKA substrates including three reported sites on HSP27 or filamin A were significantly phosphorylated in vivo, giving them high confidence as physiological substrates in pregnant rat uteri. Moreover, telokin, a known PKG substrate on S1880, and actin-binding proteins such as Arp 3, titin, and desmuslin were also identified to be in vitro PKG substrates in pregnant rat uteri. These proteins are all expected to be involved in the regulation of actin-mediated cytoskeletal remodeling.
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Affiliation(s)
- Sheng-Yu Huang
- Department of Chemistry, National Cheng Kung University, No.1, Ta-Hsueh Road, Tainan, 701, Taiwan
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211
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Amanchy R, Periaswamy B, Mathivanan S, Reddy R, Tattikota SG, Pandey A. A curated compendium of phosphorylation motifs. Nat Biotechnol 2007; 25:285-6. [PMID: 17344875 DOI: 10.1038/nbt0307-285] [Citation(s) in RCA: 302] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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212
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Leparc GG, Mitra RD. Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic Acids Res 2007; 35:3192-202. [PMID: 17452356 PMCID: PMC1904267 DOI: 10.1093/nar/gkm187] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To better understand the complex role that alternative splicing plays in intracellular signaling, it is important to catalog the numerous splice variants involved in signal transduction. Therefore, we developed PASE (Prediction of Alternative Signaling Exons), a computational tool to identify novel alternative cassette exons that code for kinase phosphorylation or signaling protein-binding sites. We first applied PASE to the Caenorhabditis elegans genome. In this organism, our algorithm had an overall specificity of ≥76.4%, including 33 novel cassette exons that we experimentally verified. We then used PASE to analyze the human genome and made 804 predictions, of which 308 were found as alternative exons in the transcript database. We experimentally tested 384 of the remaining unobserved predictions and discovered 26 novel human exons for a total specificity of ≥41.5% in human. By using a test set of known alternatively spliced signaling exons, we determined that the sensitivity of PASE is ∼70%. GO term analysis revealed that our exon predictions were found in the introns of known signal transduction genes more often than expected by chance, indicating PASE enriches for splice variants that function in signaling pathways. Overall, PASE was able to uncover 59 novel alternative cassette exons in C. elegans and humans through a genome-wide ab initio prediction method that enriches for exons involved in signaling.
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Affiliation(s)
| | - Robi David Mitra
- *To whom correspondence should be addressed. Tel: +1-314-362-2751; Fax: +1-314-362-2156;
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213
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Savas S, Taylor IW, Wrana JL, Ozcelik H. Functional nonsynonymous single nucleotide polymorphisms from the TGF-β protein interaction network. Physiol Genomics 2007; 29:109-17. [PMID: 17190851 DOI: 10.1152/physiolgenomics.00226.2006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protein complexes mediated by protein-protein interactions are essential for many cellular functions. Transforming growth factor (TGF)-β signaling involves a cascade of protein-protein interactions and malfunctioning of this pathway has been implicated in human diseases. Using an in silico approach, we analyzed the naturally occurring human genetic variations from the proteins involved in the TGF-β signaling (10 TGF-β proteins and 242 other proteins interacting with them) to identify the ones that have potential biological consequences. All proteins were searched in the dbSNP database for the presence of nonsynonymous single nucleotide polymorphisms (nsSNPs). A total of 118 validated nsSNPs from 63 proteins were retrieved and analyzed in terms of 1) evolutionary conservation status, 2) being located in a functional protein domain or motif, and 3) altering putative protein motif or phosphorylation sites. Our results indicated the presence of 31 nsSNPs that occurred at evolutionarily conserved residues, 37 nsSNPs were located in protein domains, motifs, or repeats, and 46 nsSNPs were predicted to either create or abolish putative protein motifs or phosphorylation sites. We undertook this study to analyze the human genetic variations that can affect the protein function and the TGF-β signaling. The nsSNPs reported in here can be characterized by experimental approaches to elucidate their exact biological roles and whether they are related to human disease.
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Affiliation(s)
- Sevtap Savas
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
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214
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Rennefahrt UEE, Deacon SW, Parker SA, Devarajan K, Beeser A, Chernoff J, Knapp S, Turk BE, Peterson JR. Specificity profiling of Pak kinases allows identification of novel phosphorylation sites. J Biol Chem 2007; 282:15667-78. [PMID: 17392278 DOI: 10.1074/jbc.m700253200] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The p21-activated kinases (Paks) serve as effectors of the Rho family GTPases Rac and Cdc42. The six human Paks are divided into two groups based on sequence similarity. Group I Paks (Pak1 to -3) phosphorylate a number of substrates linking this group to regulation of the cytoskeleton and both proliferative and anti-apoptotic signaling. Group II Paks (Pak4 to -6) are thought to play distinct functional roles, yet their few known substrates are also targeted by Group I Paks. To determine if the two groups recognize distinct target sequences, we used a degenerate peptide library method to comprehensively characterize the consensus phosphorylation motifs of Group I and II Paks. We find that Pak1 and Pak2 exhibit virtually identical substrate specificity that is distinct from that of Pak4. Based on structural comparisons and mutagenesis, we identified two key amino acid residues that mediate the distinct specificities of Group I and II Paks and suggest a structural basis for these differences. These results implicate, for the first time, residues from the small lobe of a kinase in substrate selectivity. Finally, we utilized the Pak1 consensus motif to predict a novel Pak1 phosphorylation site in Pix (Pak-interactive exchange factor) and demonstrate that Pak1 phosphorylates this site both in vitro and in cultured cells. Collectively, these results elucidate the specificity of Pak kinases and illustrate a general method for the identification of novel sites phosphorylated by Paks.
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Affiliation(s)
- Ulrike E E Rennefahrt
- Division of Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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215
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Via A, Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M. False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinformatics 2007; 8:68. [PMID: 17331242 PMCID: PMC1821045 DOI: 10.1186/1471-2105-8-68] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 03/01/2007] [Indexed: 01/28/2023] Open
Abstract
Background False occurrences of functional motifs in protein sequences can be considered as random events due solely to the sequence composition of a proteome. Here we use a numerical approach to investigate the random appearance of functional motifs with the aim of addressing biological questions such as: How are organisms protected from undesirable occurrences of motifs otherwise selected for their functionality? Has the random appearance of functional motifs in protein sequences been affected during evolution? Results Here we analyse the occurrence of functional motifs in random sequences and compare it to that observed in biological proteomes; the behaviour of random motifs is also studied. Most motifs exhibit a number of false positives significantly similar to the number of times they appear in randomized proteomes (=expected number of false positives). Interestingly, about 3% of the analysed motifs show a different kind of behaviour and appear in biological proteomes less than they do in random sequences. In some of these cases, a mechanism of evolutionary negative selection is apparent; this helps to prevent unwanted functionalities which could interfere with cellular mechanisms. Conclusion Our thorough statistical and biological analysis showed that there are several mechanisms and evolutionary constraints both of which affect the appearance of functional motifs in protein sequences.
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Affiliation(s)
- Allegra Via
- Centro di Bioinformatica Molecolare, Department of Biology, University of Rome Tor Vergata, Roma
| | - Pier Federico Gherardini
- Centro di Bioinformatica Molecolare, Department of Biology, University of Rome Tor Vergata, Roma
| | - Enrico Ferraro
- Centro di Bioinformatica Molecolare, Department of Biology, University of Rome Tor Vergata, Roma
| | - Gabriele Ausiello
- Centro di Bioinformatica Molecolare, Department of Biology, University of Rome Tor Vergata, Roma
| | | | - Manuela Helmer-Citterich
- Centro di Bioinformatica Molecolare, Department of Biology, University of Rome Tor Vergata, Roma
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216
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Pei D, Wavreille AS. Reverse interactomics: decoding protein–protein interactions with combinatorial peptide libraries. ACTA ACUST UNITED AC 2007; 3:536-41. [PMID: 17639128 DOI: 10.1039/b706041f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Identification of binding partners is the crucial first step towards understanding the biological function of a protein. Many protein-protein interactions occur via modular domains that recognize short peptide motifs in their target proteins. Here we describe a chemical/bioinformatics approach for predicting the binding partners of modular domains. The optimal binding motif(s) of a protein domain is identified by screening a combinatorial peptide library. The resulting consensus sequence is used to search protein and genomic databases for potential binding proteins, which are subsequently confirmed (or disproved) by conventional protein binding assays (e.g. pull-down and co-immunoprecipitation).
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Affiliation(s)
- Dehua Pei
- Department of Chemistry, Ohio State University, Columbus, OH 43210, USA.
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217
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Bogoyevitch MA, Kobe B. Uses for JNK: the many and varied substrates of the c-Jun N-terminal kinases. Microbiol Mol Biol Rev 2006; 70:1061-95. [PMID: 17158707 PMCID: PMC1698509 DOI: 10.1128/mmbr.00025-06] [Citation(s) in RCA: 439] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The c-Jun N-terminal kinases (JNKs) are members of a larger group of serine/threonine (Ser/Thr) protein kinases from the mitogen-activated protein kinase family. JNKs were originally identified as stress-activated protein kinases in the livers of cycloheximide-challenged rats. Their subsequent purification, cloning, and naming as JNKs have emphasized their ability to phosphorylate and activate the transcription factor c-Jun. Studies of c-Jun and related transcription factor substrates have provided clues about both the preferred substrate phosphorylation sequences and additional docking domains recognized by JNK. There are now more than 50 proteins shown to be substrates for JNK. These include a range of nuclear substrates, including transcription factors and nuclear hormone receptors, heterogeneous nuclear ribonucleoprotein K, and the Pol I-specific transcription factor TIF-IA, which regulates ribosome synthesis. Many nonnuclear substrates have also been characterized, and these are involved in protein degradation (e.g., the E3 ligase Itch), signal transduction (e.g., adaptor and scaffold proteins and protein kinases), apoptotic cell death (e.g., mitochondrial Bcl2 family members), and cell movement (e.g., paxillin, DCX, microtubule-associated proteins, the stathmin family member SCG10, and the intermediate filament protein keratin 8). The range of JNK actions in the cell is therefore likely to be complex. Further characterization of the substrates of JNK should provide clearer explanations of the intracellular actions of the JNKs and may allow new avenues for targeting the JNK pathways with therapeutic agents downstream of JNK itself.
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Affiliation(s)
- Marie A Bogoyevitch
- Cell Signalling Laboratory, Biochemistry and Molecular Biology (M310), School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
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218
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Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks. Cell 2006; 127:635-48. [PMID: 17081983 DOI: 10.1016/j.cell.2006.09.026] [Citation(s) in RCA: 2753] [Impact Index Per Article: 152.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 08/01/2006] [Accepted: 09/19/2006] [Indexed: 11/26/2022]
Abstract
Cell signaling mechanisms often transmit information via posttranslational protein modifications, most importantly reversible protein phosphorylation. Here we develop and apply a general mass spectrometric technology for identification and quantitation of phosphorylation sites as a function of stimulus, time, and subcellular location. We have detected 6,600 phosphorylation sites on 2,244 proteins and have determined their temporal dynamics after stimulating HeLa cells with epidermal growth factor (EGF) and recorded them in the Phosida database. Fourteen percent of phosphorylation sites are modulated at least 2-fold by EGF, and these were classified by their temporal profiles. Surprisingly, a majority of proteins contain multiple phosphorylation sites showing different kinetics, suggesting that they serve as platforms for integrating signals. In addition to protein kinase cascades, the targets of reversible phosphorylation include ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different transcriptional regulators. The dynamic phosphoproteome provides a missing link in a global, integrative view of cellular regulation.
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Affiliation(s)
- Jesper V Olsen
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark
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219
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Morandell S, Stasyk T, Grosstessner-Hain K, Roitinger E, Mechtler K, Bonn GK, Huber LA. Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics 2006; 6:4047-56. [PMID: 16791829 DOI: 10.1002/pmic.200600058] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein phosphorylation is a key regulatory mechanism of cellular signalling processes. The analysis of phosphorylated proteins and the characterisation of phosphorylation sites under different biological conditions are some of the most challenging tasks in current proteomics research. Reduction of the sample complexity is one major step for the analysis of low-abundance kinase substrates, which can be achieved by various subcellular fractionation techniques. One strategy is the enrichment of phosphorylated proteins or peptides by immunoprecipitation or chromatography, e.g. immobilised metal affinity chromatography, prior to analysis. 2-DE gels are powerful tools for the analysis of phosphoproteins when combined with new multiplexing techniques like DIGE, phosphospecific stains, autoradiography or immunoblotting. In addition, several gel-free methods combining chromatography with highly sensitive MS have been successfully applied for the analysis of complex phosphoproteomes. Recently developed approaches like KESTREL or 'chemical genetics' and also protein microarrays offer new possibilities for the identification of specific kinase targets. This review summarises various strategies for the analyses of phosphoproteins with a special focus on the identification of novel kinase substrates.
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Affiliation(s)
- Sandra Morandell
- Division Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
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220
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To KKW, Sedelnikova OA, Samons M, Bonner WM, Huang LE. The phosphorylation status of PAS-B distinguishes HIF-1alpha from HIF-2alpha in NBS1 repression. EMBO J 2006; 25:4784-94. [PMID: 17024177 PMCID: PMC1618093 DOI: 10.1038/sj.emboj.7601369] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 08/29/2006] [Indexed: 12/21/2022] Open
Abstract
Hypoxia promotes genetic instability for tumor progression. Recent evidence indicates that the transcription factor HIF-1alpha impairs DNA mismatch repair, yet the role of HIF-1alpha isoform, HIF-2alpha, in tumor progression remains obscure. In pursuit of the involvement of HIF-alpha in chromosomal instability, we report here that HIF-1alpha, specifically its PAS-B, induces DNA double-strand breaks at least in part by repressing the expression of NBS1, a crucial DNA repair gene constituting the MRE11A-RAD50-NBS1 complex. Despite strong similarities between the two isoforms, HIF-2alpha fails to do so. We demonstrate that this functional distinction stems from phosphorylation of HIF-2alpha Thr-324 by protein kinase D1, which discriminates between subtle differences of the two PAS-B in amino-acid sequence, thereby precluding NBS1 repression. Hence, our findings delineate a molecular pathway that functionally distinguishes HIF-1alpha from HIF-2alpha, and arguing a unique role for HIF-1alpha in tumor progression by promoting genomic instability.
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Affiliation(s)
- Kenneth K -W To
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olga A Sedelnikova
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melissa Samons
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William M Bonner
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - L Eric Huang
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Neurosurgery, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Neurosurgery, University of Utah School of Medicine, 30 N 1900 E, Suite 3B409, Salt Lake City, UT 84112, USA. Tel.: +1 801 585 3221; Fax: +1 801 585 7845; E-mail:
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221
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Kalia LV, Pitcher GM, Pelkey KA, Salter MW. PSD-95 is a negative regulator of the tyrosine kinase Src in the NMDA receptor complex. EMBO J 2006; 25:4971-82. [PMID: 16990796 PMCID: PMC1618112 DOI: 10.1038/sj.emboj.7601342] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Accepted: 08/18/2006] [Indexed: 11/09/2022] Open
Abstract
The tyrosine kinase Src upregulates the activity of the N-methyl-D-aspartate subtype of glutamate receptor (NMDAR) and tyrosine phosphorylation of this receptor is critical for induction of NMDAR-dependent plasticity of synaptic transmission. A binding partner for Src within the NMDAR complex is the protein PSD-95. Here we demonstrate an interaction of PSD-95 with Src that does not require the well-characterized domains of PSD-95. Rather, we show binding to Src through a 12-amino-acid sequence in the N-terminal region of PSD-95, a region not previously known to participate in protein-protein interactions. This region interacts directly with the Src SH2 domain. Contrary to typical SH2 domain binding, the PSD-95-Src SH2 domain interaction is phosphotyrosine-independent. Binding of the Src-interacting region of PSD-95 inhibits Src kinase activity and reduces NMDAR phosphorylation. Intracellularly administering a peptide matching the Src SH2 domain-interacting region of PSD-95 depresses NMDAR currents in cultured neurons and inhibits induction of long-term potentiation in hippocampus. Thus, the PSD-95-Src SH2 domain interaction suppresses Src-mediated NMDAR upregulation, a finding that may be of broad importance for synaptic transmission and plasticity.
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Affiliation(s)
- Lorraine V Kalia
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Graham M Pitcher
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth A Pelkey
- Laboratory of Cellular and Synaptic Neurophysiology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Michael W Salter
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8. Tel.: +1 416 813 6272; Fax: +1 416 813 7921; E-mail:
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222
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Liu BA, Jablonowski K, Raina M, Arcé M, Pawson T, Nash PD. The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol Cell 2006; 22:851-868. [PMID: 16793553 DOI: 10.1016/j.molcel.2006.06.001] [Citation(s) in RCA: 222] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 05/19/2006] [Accepted: 06/02/2006] [Indexed: 01/07/2023]
Abstract
SH2 domains are interaction modules uniquely dedicated to the recognition of phosphotyrosine sites and are embedded in proteins that couple protein-tyrosine kinases to intracellular signaling pathways. Here, we report a comprehensive bioinformatics, structural, and functional view of the human and mouse complement of SH2 domain proteins. This information delimits the set of SH2-containing effectors available for PTK signaling and will facilitate the systems-level analysis of pTyr-dependent protein-protein interactions and PTK-mediated signal transduction. The domain-based architecture of SH2-containing proteins is of more general relevance for understanding the large family of protein interaction domains and the modular organization of the majority of human proteins.
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Affiliation(s)
- Bernard A Liu
- Ben May Institute for Cancer Research and the Committee on Cancer Biology, The University of Chicago, Chicago, Illinois 60637
| | - Karl Jablonowski
- Ben May Institute for Cancer Research and the Committee on Cancer Biology, The University of Chicago, Chicago, Illinois 60637
| | - Monica Raina
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada
| | - Michael Arcé
- Ben May Institute for Cancer Research and the Committee on Cancer Biology, The University of Chicago, Chicago, Illinois 60637
| | - Tony Pawson
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada.
| | - Piers D Nash
- Ben May Institute for Cancer Research and the Committee on Cancer Biology, The University of Chicago, Chicago, Illinois 60637.
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223
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Crean JK, Furlong F, Mitchell D, McArdle E, Godson C, Martin F. Connective tissue growth factor/CCN2 stimulates actin disassembly through Akt/protein kinase B-mediated phosphorylation and cytoplasmic translocation of p27(Kip-1). FASEB J 2006; 20:1712-4. [PMID: 16790529 DOI: 10.1096/fj.05-5010fje] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Connective tissue growth factor (CTGF/CCN2) is a 38-kDa secreted protein, a prototypic member of the CCN family, which is up-regulated in many diseases, including atherosclerosis, pulmonary fibrosis, and diabetic nephropathy. We previously showed that CTGF can cause actin disassembly with concurrent down-regulation of the small GTPase Rho A and proposed an integrated signaling network connecting focal adhesion dissolution and actin disassembly with cell polarization and migration. Here, we further delineate the role of CTGF in cell migration and actin disassembly in human mesangial cells, a primary target in the development of renal glomerulosclerosis. The functional response of mesangial cells to treatment with CTGF was associated with the phosphorylation of Akt/protein kinase B (PKB) and resultant phosphorylation of a number of Akt/PKB substrates. Two of these substrates were identified as FKHR and p27(Kip-1). CTGF stimulated the phosphorylation and cytoplasmic translocation of p27(Kip-1) on serine 10. Addition of the PI-3 kinase inhibitor LY294002 abrogated this response; moreover, addition of the Akt/PKB inhibitor interleukin (IL)-6-hydroxymethyl-chiro-inositol-2(R)-2-methyl-3-O-octadecylcarbonate prevented p27(Kip-1) phosphorylation in response to CTGF. Immunocytochemistry revealed that serine 10 phosphorylated p27(Kip-1) colocalized with the ends of actin filaments in cells treated with CTGF. Further investigation of other Akt/PKB sites on p27(Kip-1), revealed that phosphorylation on threonine 157 was necessary for CTGF mediated p27(Kip-1) cytoplasmic localization; mutation of the threonine 157 site prevented cytoplasmic localization, protected against actin disassembly and inhibited cell migration. CTGF also stimulated an increased association between Rho A and p27(Kip-1). Interestingly, this resulted in an increase in phosphorylation of LIM kinase and subsequent phosphorylation of cofilin, suggesting that CTGF mediated p27(Kip-1) activation results in uncoupling of the Rho A/LIM kinase/cofilin pathway. Confirming the central role of Akt/PKB, CTGF-stimulated actin depolymerization only in wild-type mouse embryonic fibroblasts (MEFs) compared to Akt-1/3 (PKB alpha/gamma) knockout MEFs. These data reveal important mechanistic insights into how CTGF may contribute to mesangial cell dysfunction in the diabetic milieu and sheds new light on the proposed role of p27(Kip-1) as a mediator of actin rearrangement.
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Affiliation(s)
- J K Crean
- University College Dublin, School of Biomolecular and Biomedical Science, Conway Institute of Biomolecular and Biomedical Research, Belfield, Dublin 4, Ireland.
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224
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Hu G, Barnes BJ. Interferon regulatory factor-5-regulated pathways as a target for colorectal cancer therapeutics. Expert Rev Anticancer Ther 2006; 6:775-84. [PMID: 16759167 DOI: 10.1586/14737140.6.5.775] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Colorectal cancer is the second most common cause of cancer-related death. A significant obstacle to successful management of patients with colorectal cancer is intrinsic drug resistance or, in patients who initially responded to chemotherapy, acquired drug resistance. Failure in normal apoptotic pathways often contributes to resistance to anticancer drugs or radiotherapy. As a result, the identification of genes that control cell death and apoptosis has come to the forefront of cancer research, leading to new targets and novel therapeutic strategies in the treatment of colorectal cancer. To this effect, the authors have recently identified a new apoptotic signaling pathway that occurs through the transcription factor interferon regulatory factor-5. Here, the different strategies for targeting the interferon regulatory factor-5 signaling pathway in colorectal cancer are discussed. These strategies can be applied to a new generation of cytotoxic agents, as well as to novel biological compounds that are directed at inducing and/or activating interferon regulatory factor-5 or key components of this pathway.
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Affiliation(s)
- Goudong Hu
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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225
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Schilling B, Gafni J, Torcassi C, Cong X, Row RH, LaFevre-Bernt MA, Cusack MP, Ratovitski T, Hirschhorn R, Ross CA, Gibson BW, Ellerby LM. Huntingtin phosphorylation sites mapped by mass spectrometry. Modulation of cleavage and toxicity. J Biol Chem 2006; 281:23686-97. [PMID: 16782707 DOI: 10.1074/jbc.m513507200] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Huntingtin (Htt) is a large protein of 3144 amino acids, whose function and regulation have not been well defined. Polyglutamine (polyQ) expansion in the N terminus of Htt causes the neurodegenerative disorder Huntington disease (HD). The cytotoxicity of mutant Htt is modulated by proteolytic cleavage with caspases and calpains generating N-terminal polyQ-containing fragments. We hypothesized that phosphorylation of Htt may modulate cleavage and cytotoxicity. In the present study, we have mapped the major phosphorylation sites of Htt using cell culture models (293T and PC12 cells) expressing full-length myc-tagged Htt constructs containing 23Q or 148Q repeats. Purified myc-tagged Htt was subjected to mass spectrometric analysis including matrix-assisted laser desorption/ionization mass spectrometry and nano-HPLC tandem mass spectrometry, used in conjunction with on-target alkaline phosphatase and protease digestions. We have identified more than six novel serine phosphorylation sites within Htt, one of which lies in the proteolytic susceptibility domain. Three of the sites have the consensus sequence for ERK1 phosphorylation, and addition of ERK1 inhibitor blocks phosphorylation at those sites. Other observed phosphorylation sites are possibly substrates for CDK5/CDC2 kinases. Mutation of amino acid Ser-536, which is located in the proteolytic susceptibility domain, to aspartic acid, inhibited calpain cleavage and reduced mutant Htt toxicity. The results presented here represent the first detailed mapping of the phosphorylation sites in full-length Htt. Dissection of phosphorylation modifications in Htt may provide clues to Huntington disease pathogenesis and targets for therapeutic development.
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Affiliation(s)
- Birgit Schilling
- The Buck Institute for Age Research, Novato, California 94945, USA
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226
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Katso RM, Pardo OE, Palamidessi A, Franz CM, Marinov M, De Laurentiis A, Downward J, Scita G, Ridley AJ, Waterfield MD, Arcaro A. Phosphoinositide 3-Kinase C2beta regulates cytoskeletal organization and cell migration via Rac-dependent mechanisms. Mol Biol Cell 2006; 17:3729-44. [PMID: 16775008 PMCID: PMC1593155 DOI: 10.1091/mbc.e05-11-1083] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Receptor-linked class I phosphoinositide 3-kinases (PI3Ks) induce assembly of signal transduction complexes through protein-protein and protein-lipid interactions that mediate cell proliferation, survival, and migration. Although class II PI3Ks have the potential to make the same phosphoinositides as class I PI3Ks, their precise cellular role is currently unclear. In this report, we demonstrate that class II phosphoinositide 3-kinase C2beta (PI3KC2beta) associates with the Eps8/Abi1/Sos1 complex and is recruited to the EGF receptor as part of a multiprotein signaling complex also involving Shc and Grb2. Increased expression of PI3KC2beta stimulated Rac activity in A-431 epidermoid carcinoma cells, resulting in enhanced membrane ruffling and migration speed of the cells. Conversely, expression of dominant negative PI3KC2beta reduced Rac activity, membrane ruffling, and cell migration. Moreover, PI3KC2beta-overexpressing cells were protected from anoikis and displayed enhanced proliferation, independently of Rac function. Taken together, these findings suggest that PI3KC2beta regulates the migration and survival of human tumor cells by distinct molecular mechanisms.
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Affiliation(s)
- Roy M. Katso
- *Ludwig Institute for Cancer Research, Royal Free and University College Hospital Medical School, London W1W 7BS, United Kingdom
| | | | - Andrea Palamidessi
- European Institute of Oncology, The FIRC Institute for Molecular Oncology, 20139 Milano, Italy
| | - Clemens M. Franz
- *Ludwig Institute for Cancer Research, Royal Free and University College Hospital Medical School, London W1W 7BS, United Kingdom
| | - Marin Marinov
- Division of Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, CH-8032 Zurich, Switzerland; and
| | - Angela De Laurentiis
- Division of Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, CH-8032 Zurich, Switzerland; and
| | - Julian Downward
- CRUK London Research Institute, London WC2A 3PX, United Kingdom
| | - Giorgio Scita
- European Institute of Oncology, The FIRC Institute for Molecular Oncology, 20139 Milano, Italy
| | - Anne J. Ridley
- *Ludwig Institute for Cancer Research, Royal Free and University College Hospital Medical School, London W1W 7BS, United Kingdom
- Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Michael D. Waterfield
- *Ludwig Institute for Cancer Research, Royal Free and University College Hospital Medical School, London W1W 7BS, United Kingdom
- Department of Biochemistry and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Alexandre Arcaro
- Division of Clinical Chemistry and Biochemistry, University Children’s Hospital Zurich, CH-8032 Zurich, Switzerland; and
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227
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Cai SL, Tee AR, Short JD, Bergeron JM, Kim J, Shen J, Guo R, Johnson CL, Kiguchi K, Walker CL. Activity of TSC2 is inhibited by AKT-mediated phosphorylation and membrane partitioning. ACTA ACUST UNITED AC 2006; 173:279-89. [PMID: 16636147 PMCID: PMC2063818 DOI: 10.1083/jcb.200507119] [Citation(s) in RCA: 281] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Loss of tuberin, the product of TSC2 gene, increases mammalian target of rapamycin (mTOR) signaling, promoting cell growth and tumor development. However, in cells expressing tuberin, it is not known how repression of mTOR signaling is relieved to activate this pathway in response to growth factors and how hamartin participates in this process. We show that hamartin colocalizes with hypophosphorylated tuberin at the membrane, where tuberin exerts its GTPase-activating protein (GAP) activity to repress Rheb signaling. In response to growth signals, tuberin is phosphorylated by AKT and translocates to the cytosol, relieving Rheb repression. Phosphorylation of tuberin at serines 939 and 981 does not alter its intrinsic GAP activity toward Rheb but partitions tuberin to the cytosol, where it is bound by 14-3-3 proteins. Thus, tuberin bound by 14-3-3 in response to AKT phosphorylation is sequestered away from its membrane-bound activation partner (hamartin) and its target GTPase (Rheb) to relieve the growth inhibitory effects of this tumor suppressor.
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Affiliation(s)
- Sheng-Li Cai
- Department of Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, 78957, USA
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228
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Turk BE, Lee DH, Yamakoshi Y, Klingenhoff A, Reichenberger E, Wright JT, Simmer JP, Komisarof JA, Cantley LC, Bartlett JD. MMP-20 is predominately a tooth-specific enzyme with a deep catalytic pocket that hydrolyzes type V collagen. Biochemistry 2006; 45:3863-74. [PMID: 16548514 PMCID: PMC2536712 DOI: 10.1021/bi052252o] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Matrix metalloproteinase-20 (MMP-20, enamelysin) has a highly restricted pattern of expression. In healthy tissues, MMP-20 is observed in the enamel organ and pulp organ of developing teeth and is present only as an activated enzyme. To identify other tissues that may express MMP-20, we performed a systematic mouse tissue expression screen. Among the non-tooth tissues assayed, MMP-20 transcripts were identified only in minute quantities within the large intestine. The murine Mmp20 promoter was cloned, sequenced, and assessed for potential tooth-specific regulatory elements. In silico analysis identified four promoter modules that were common to Mmp20 and at least two of three coregulated predominantly tooth-specific genes that encode ameloblastin, amelogenin, and enamelin. We asked if the highly restricted MMP-20 expression pattern was associated with a broad substrate specificity that might preclude its expression in other tissues. An iterative mixture-based random doedecamer peptide library screen with Edman sequencing of MMP-20 cleavage products revealed that, among MMPs previously screened, MMP-20 had unique substrate preferences. These preferences indicate that MMP-20 has a deep and wide catalytic pocket that can accommodate substrates with large aromatic residues in the P1' position. On the basis of matrices derived from the peptide library data, we identified and then confirmed that type V collagen is an MMP-20 substrate. Since type V collagen is not present in dental enamel but is an otherwise widely distributed collagen, and since only active MMP-20 has been observed in teeth, our data suggest that control of MMP-20 activity is primarily regulated by transcriptional means.
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Affiliation(s)
- Benjamin E. Turk
- Department of Pharmacology, Yale University, New Haven, CT 06520
| | - Daniel H. Lee
- Department of Cytokine Biology, Forsyth Institute, Boston, MA 02115
| | - Yasuo Yamakoshi
- University of Michigan Dental Research Laboratory, Ann Arbor, MI 48108
| | | | - Ernst Reichenberger
- Müchen, Germany Center for Restorative Medicine and Skeletal Development, Department for Oral Rehabilitation, Biomaterials and Skeletal Development, University of Connecticut School of Dental Medicine, Farmington, CT 06030
| | - J. Timothy Wright
- Department of Pediatric Dentistry, University of North Carolina, Chapel Hill, NC 27599
| | - James P. Simmer
- University of Michigan Dental Research Laboratory, Ann Arbor, MI 48108
| | | | - Lewis C. Cantley
- Department of Medicine, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02115
| | - John D. Bartlett
- Department of Cytokine Biology, Forsyth Institute, Boston, MA 02115
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115
- To whom correspondence should be addressed: Telephone: 617-262-5200 (ext 8388), Fax: 617-892-8303. E-mail:
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229
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Blanke S, Jäckle H. Novel guanine nucleotide exchange factor GEFmeso of Drosophila melanogaster interacts with Ral and Rho GTPase Cdc42. FASEB J 2006; 20:683-91. [PMID: 16581976 DOI: 10.1096/fj.05-5376com] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This article reports the identification and characterization of a DBL-like guanine nucleotide exchange factor (GEF) in Drosophila, called GEFmeso, as a novel binding target of the Ras-like GTPase Ral. Previous studies suggested that some aspects of Ral activity, which is involved in multiple cellular processes, are mediated through regulation of Rho GTPases. Here we show in vitro association of GEFmeso with the GTP-bound active form of Ral and the nucleotide-free form of the Rho GTPase Cdc42. GEFmeso fails to bind to other Rho GTPases, showing that Cdc42 is a specific interaction partner of this GEF. Unlike Ral and Cdc42, which are ubiquitously expressed, GEFmeso exerts distinct spatio-temporal expression patterns during embryonic development, suggesting a tissue-restricted function of the GEF in vivo. Based on previous observations that mutations in Cdc42 or overexpression of mutant alleles of Cdc42 lead to distinct effects on wing development, the effects of overexpression of dominant-negative and activated versions of Ral on wing development were analyzed. In addition, GEFmeso overexpression studies as well as RNAi experiments were performed. The results suggest that Ral, GEFmeso and Cdc42 act in the same developmental pathway and that GEFmeso mediates activation of Cdc42 in response to activated Ral in the context of Drosophila wing development.
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Affiliation(s)
- Stephen Blanke
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany
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230
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McLaughlin WA, Hou T, Wang W. Prediction of Binding Sites of Peptide Recognition Domains: An Application on Grb2 and SAP SH2 Domains. J Mol Biol 2006; 357:1322-34. [PMID: 16476443 DOI: 10.1016/j.jmb.2006.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Revised: 11/29/2005] [Accepted: 01/05/2006] [Indexed: 11/21/2022]
Abstract
Determination of the binding motif and identification of interaction partners of the modular domains such as SH2 domains can enhance our understanding of the regulatory mechanism of protein-protein interactions. We propose here a new computational method to achieve this goal by integrating the orthogonal information obtained from binding free energy estimation and peptide sequence analysis. We performed a proof-of-concept study on the SH2 domains of SAP and Grb2 proteins. The method involves the following steps: (1) estimating the binding free energy of a set of randomly selected peptides along with a sample of known binders; (2) clustering all these peptides using sequence and energy characteristics; (3) extracting a sequence motif, which is represented by a hidden Markov model (HMM), from the cluster of peptides containing the sample of known binders; and (4) scanning the human proteome to identify binding sites of the domain. The binding motifs of the SAP and Grb2 SH2 domains derived by the method agree well with those determined through experimental studies. Using the derived binding motifs, we have predicted new possible interaction partners for the Grb2 and SAP SH2 domains as well as possible interaction sites for interaction partners already known. We also suggested novel roles for the proteins by reviewing their top interaction candidates.
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Affiliation(s)
- William A McLaughlin
- Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0359, USA
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231
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Abstract
A surprisingly fewer than expected number of genes in the human genome suggests that sophistication of its biologic system is, in part, due to complex regulation of protein activities. The activities of most cellular proteins are regulated by post-translational modifications. One of the most important post-translational modifications is reversible protein phosphorylation, which decorates more than 30% of the proteome and regulates signal transduction pathways under normal conditions as well as in disorders such as diabetes, neurodegenerative diseases, autoimmune diseases and several forms of cancers. This review examines the recent developments in mass spectrometry-based methods for phosphoproteome analysis and its applications for the study of signal transduction pathways. The basic principles of non-mass spectrometry-based methods, such as chemical genetics and flow cytometry-based approaches, are also discussed as well as their specific advantages to signaling studies. Finally, signaling pathways are discussed in the light of large-scale protein interaction studies. The proteomic methods addressed in this review are emerging as some of the essential components in systems biology, which seeks to describe signaling networks through integration of diverse types of data and, in the future, to allow computational simulations of complex biologic pathways in health and disease.
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Affiliation(s)
- Mridul Mukherji
- The Skaggs Institute for Chemical Biology, Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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232
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Cao H, Deterding LJ, Venable JD, Kennington EA, Yates JR, Tomer KB, Blackshear PJ. Identification of the anti-inflammatory protein tristetraprolin as a hyperphosphorylated protein by mass spectrometry and site-directed mutagenesis. Biochem J 2006; 394:285-97. [PMID: 16262601 PMCID: PMC1386027 DOI: 10.1042/bj20051316] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Tristetraprolin (TTP) is a zinc-finger protein that binds to AREs (AU-rich elements) within certain mRNAs and causes destabilization of those mRNAs. Mice deficient in TTP develop a profound inflammatory syndrome with erosive arthritis, autoimmunity and myeloid hyperplasia. Previous studies showed that TTP is phosphorylated extensively in intact cells. However, limited information is available about the identities of these phosphorylation sites. We investigated the phosphorylation sites in human TTP from transfected HEK-293 cells by MS and site-directed mutagenesis. A number of phosphorylation sites including Ser66, Ser88, Thr92, Ser169, Ser186, Ser197, Ser218, Ser228, Ser276 and Ser296 were identified by MS analyses using MALDI (matrix-assisted laser-desorption-ionization)-MS, MALDI-tandem MS, LC (liquid chromatography)-tandem MS and multidimensional protein identification technology. Mutations of Ser197, Ser218 and Ser228 to alanine in the human protein significantly increased TTP's gel mobility (likely to be stoichiometric), whereas mutations at the other sites had little effect on its gel mobility. Dephosphorylation and in vivo labelling studies showed that mutant proteins containing multiple mutations were still phosphorylated, and all were able to bind to RNA probes containing AREs. Confocal microscopy showed a similar cytosolic localization of TTP among the various proteins. Ser197, Ser218 and Ser228 are predicted by motif scanning to be potential sites for protein kinase A, glycogen synthase kinase-3 and extracellular-signal-regulated kinase 1 (both Ser218 and Ser228) respectively. The present study has identified multiple phosphorylation sites in the anti-inflammatory protein TTP in mammalian cells and should provide the molecular basis for further studies on the function and regulation of TTP in controlling pro-inflammatory cytokines.
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Affiliation(s)
- Heping Cao
- Laboratories of Neurobiology and Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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233
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Xue Y, Li A, Wang L, Feng H, Yao X. PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics 2006; 7:163. [PMID: 16549034 PMCID: PMC1435943 DOI: 10.1186/1471-2105-7-163] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2005] [Accepted: 03/20/2006] [Indexed: 11/25/2022] Open
Abstract
Background As a reversible and dynamic post-translational modification (PTM) of proteins, phosphorylation plays essential regulatory roles in a broad spectrum of the biological processes. Although many studies have been contributed on the molecular mechanism of phosphorylation dynamics, the intrinsic feature of substrates specificity is still elusive and remains to be delineated. Results In this work, we present a novel, versatile and comprehensive program, PPSP (Prediction of PK-specific Phosphorylation site), deployed with approach of Bayesian decision theory (BDT). PPSP could predict the potential phosphorylation sites accurately for ~70 PK (Protein Kinase) groups. Compared with four existing tools Scansite, NetPhosK, KinasePhos and GPS, PPSP is more accurate and powerful than these tools. Moreover, PPSP also provides the prediction for many novel PKs, say, TRK, mTOR, SyK and MET/RON, etc. The accuracy of these novel PKs are also satisfying. Conclusion Taken together, we propose that PPSP could be a potentially powerful tool for the experimentalists who are focusing on phosphorylation substrates with their PK-specific sites identification. Moreover, the BDT strategy could also be a ubiquitous approach for PTMs, such as sumoylation and ubiquitination, etc.
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Affiliation(s)
- Yu Xue
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Ao Li
- Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Lirong Wang
- Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Huanqing Feng
- Department of Electronic Science and Technology, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xuebiao Yao
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Department of Physiology, Morehouse School of Medicine, Atlanta, GA 30310, USA
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234
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Xue Y, Li A, Wang L, Feng H, Yao X. PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory. BMC Bioinformatics 2006. [PMID: 16549034 DOI: 10.1186/1471‐2105‐7‐163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As a reversible and dynamic post-translational modification (PTM) of proteins, phosphorylation plays essential regulatory roles in a broad spectrum of the biological processes. Although many studies have been contributed on the molecular mechanism of phosphorylation dynamics, the intrinsic feature of substrates specificity is still elusive and remains to be delineated. RESULTS In this work, we present a novel, versatile and comprehensive program, PPSP (Prediction of PK-specific Phosphorylation site), deployed with approach of Bayesian decision theory (BDT). PPSP could predict the potential phosphorylation sites accurately for approximately 70 PK (Protein Kinase) groups. Compared with four existing tools Scansite, NetPhosK, KinasePhos and GPS, PPSP is more accurate and powerful than these tools. Moreover, PPSP also provides the prediction for many novel PKs, say, TRK, mTOR, SyK and MET/RON, etc. The accuracy of these novel PKs are also satisfying. CONCLUSION Taken together, we propose that PPSP could be a potentially powerful tool for the experimentalists who are focusing on phosphorylation substrates with their PK-specific sites identification. Moreover, the BDT strategy could also be a ubiquitous approach for PTMs, such as sumoylation and ubiquitination, etc.
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Affiliation(s)
- Yu Xue
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230027, China.
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235
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Yu M, Lowell CA, Neel BG, Gu H. Scaffolding adapter Grb2-associated binder 2 requires Syk to transmit signals from FcepsilonRI. THE JOURNAL OF IMMUNOLOGY 2006; 176:2421-9. [PMID: 16456001 DOI: 10.4049/jimmunol.176.4.2421] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Scaffolding adapter Grb2-associated binder 2 (Gab2) is a key component of FcepsilonRI signaling in mast cells, required for the activation of PI3K. To understand how Gab2 is activated in FcepsilonRI signaling, we asked which protein tyrosine kinase is required for Gab2 phosphorylation. We found that Gab2 tyrosyl phosphorylation requires Lyn and Syk. In agreement with published results, we found that Fyn also contributes to Gab2 tyrosyl phosphorylation. However, Syk activation is defective in Fyn(-/-) mast cells, suggesting that Syk is the proximal kinase responsible for Gab2 tyrosyl phosphorylation. Then, we asked which domains in Gab2 are required for Gab2 tyrosyl phosphorylation. We found that the Grb2-Src homology 3 (SH3) binding sites are required for, whereas the pleckstrin homology (PH) domain contributes to, Gab2 tyrosyl phosphorylation. Using a protein/lipid overlay assay, we determined that the Gab2 PH domain preferentially binds the PI3K lipid products, PI3, 4,5P3 and PI3, 4P2. Furthermore, the Grb2-SH3 binding sites and PH domain binding to PI3K lipid products are required for Gab2 function in FcepsilonRI-evoked degranulation and Akt activation. Our data strongly suggest a model for Gab2 action in FcepsilonRI signaling. The Grb2 SH3 binding sites play a critical role in bringing Gab2 to FcepsilonRI, whereupon Gab2 becomes tyrosyl-phosphorylated in a Syk-dependent fashion. Phosphorylated Gab2 results in recruitment and activation of PI3K, whose lipid products bind the PH domain of Gab2 and acts in positive feedback loop for sustained PI3K recruitment and phosphatidylinositol-3,4,5-trisphosphate production, required for FcepsilonRI-evoked degranulation of mast cells.
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Affiliation(s)
- Min Yu
- Cancer Biology Program, Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
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236
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Abbasi S, Lee JD, Su B, Chen X, Alcon JL, Yang J, Kellems RE, Xia Y. Protein Kinase-mediated Regulation of Calcineurin through the Phosphorylation of Modulatory Calcineurin-interacting Protein 1. J Biol Chem 2006; 281:7717-26. [PMID: 16415348 DOI: 10.1074/jbc.m510775200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calcineurin is a serine/threonine protein phosphatase that plays a critical role in many physiologic processes such as T-cell activation, skeletal myocyte differentiation, and cardiac hypertrophy. We previously showed that active MEKK3 is capable of stimulating calcineurin/nuclear factor of activated T-cells (NFAT) signaling in cardiac myocytes through phosphorylation of modulatory calcineurin-interacting protein 1 (MCIP1). However, the protein kinases that function downstream of MEKK3 to mediate MCIP1 phosphorylation and the mechanism of MCIP1-mediated calcineurin regulation have not been defined. Here, we show that MEK5 and big MAP kinase 1 (BMK1) function downstream of MEKK3 in a signaling cascade that induces calcineurin activity through phosphorylation of MCIP1. Genetic studies showed that BMK1-deficient mouse lung fibroblasts failed to mediate MCIP1 phosphorylation and activate calcineurin/NFAT in response to angiotensin II, a potent NFAT activator. Conversely, restoring BMK1 to the deficient cells restored angiotensin II-mediated calcineurin/NFAT activation. Thus, using BMK1-deficient mouse lung fibroblast cells, we provided the genetic evidence that BMK1 is required for angiotensin II-mediated calcineurin/NFAT activation through MICP1 phosphorylation. Finally, we discovered that phosphorylated MCIP1 dissociates from calcineurin and binds with 14-3-3, thereby relieving its inhibitory effect on calcineurin activity. In summary, our findings reveal a previously unrecognized essential regulatory role of mitogen-activated protein kinase signaling in calcineurin activation through the reversible phosphorylation of a calcineurin-interacting protein, MCIP1.
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Affiliation(s)
- Shahrzad Abbasi
- Department of Biochemistry and Molecular Biology, The University of Texas-Houston Medical School, Houston, Texas 77030, USA
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237
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Cho S, Savas S, Ozcelik H. Genetic Variation and the Mitogen-Activated Protein Kinase (MAPK) Signaling Pathway. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2006; 10:66-81. [PMID: 16584319 DOI: 10.1089/omi.2006.10.66] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Non-synonymous single nucleotide polymorphisms (nsSNPs) are known to alter protein function, contributing to disease susceptibility. This report explores the nature of nsSNPs in the gene products of the highly conserved mitogen-activated protein kinase (MAPK) signaling pathways already implicated in cancer development. MAPK signaling pathways regulate cellular processes such as proliferation, differentiation, apoptosis, and survival mediated through interconnected signaling cascades. Using the dbSNP database, we have identified 25 nsSNPs in 17 out of 98 MAPK genes studied. Computational algorithms were used to predict whether the amino acid substitutions were evolutionarily tolerated, or affected putative functional units such as phosphorylation sites, protein motifs and domains. This study predicts that 36% of nsSNPs are likely to have functional consequences, based on evolutionary conservation analysis, and 36% based on phosphorylation prediction analysis. All such nsSNPs represent potentially functional and disease-causing/modifying alleles. More interestingly, the epistatic relationships discussed in this report represent potential synergistic/ antagonistic/additive effects of nsSNP combinations found within the same protein, or within members of the same protein complex and cascades. This strategy can effectively determine which nsSNPs potentially alter protein function, and can be utilized to study the genetic architecture and disease association of other biological protein complexes and networks.
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Affiliation(s)
- Stewart Cho
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Canada
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238
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Kim BG, Kim HJ, Park HJ, Kim YJ, Yoon WJ, Lee SJ, Ryoo HM, Cho JY. Runx2 phosphorylation induced by fibroblast growth factor-2/protein kinase C pathways. Proteomics 2006; 6:1166-74. [PMID: 16421932 DOI: 10.1002/pmic.200500289] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Runx2 is a key transcription factor in osteoblast differentiation, and its activity is regulated by fibroblast growth factors (FGFs). Craniosynostosis, characterized by premature suture closure, results from mutations that generate constitutively active FGF receptors (FGFRs). We previously showed that FGF/FGFR-activated protein kinase C (PKC) is involved in the expression and activity of Runx2. Activated PKCdelta physically interacts with Runx2 in FGF2-stimulated MC3T3-E1 preosteoblastic cells. Immunopurified Runx2 protein reacted with PKCdelta kinase, and a phosphorylated 1460-Da peptide fragment (amino acids 241-252, 1380-Da) derived from Runx2 was also detected in MS analysis. Computer analysis predicted that Ser247 in this Runx2 can be a possible phosphorylation site by PKCdelta. We also showed that Runx2 activity after FGF stimulation correlates with the presence of the Runx2 Ser247 residue. The S247A (Ser --> Ala) mutation confers decreased transcriptional activity on a Runx2-responsive promoter after FGF treatment.
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Affiliation(s)
- Byung-Gyu Kim
- Department of Biochemistry, School of Dentistry, Kyungpook National University, Jung-Gu, Daegu, Korea
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239
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Brinkworth RI, Munn AL, Kobe B. Protein kinases associated with the yeast phosphoproteome. BMC Bioinformatics 2006; 7:47. [PMID: 16445868 PMCID: PMC1373605 DOI: 10.1186/1471-2105-7-47] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 01/31/2006] [Indexed: 02/08/2023] Open
Abstract
Background Protein phosphorylation is an extremely important mechanism of cellular regulation. A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphorylation sites in 216 peptide sequences. However, the protein kinases responsible for the phosphorylation of the identified proteins have not previously been assigned. Results We used Predikin in combination with other bioinformatic tools, to predict which of 116 unique protein kinases in yeast phosphorylates each experimentally determined site in the phosphoproteome. The prediction was based on the match between the phosphorylated 7-residue sequence and the predicted substrate specificity of each kinase, with the highest weight applied to the residues or positions that contribute most to the substrate specificity. We estimated the reliability of the predictions by performing a parallel prediction on phosphopeptides for which the kinase has been experimentally determined. Conclusion The results reveal that the functions of the protein kinases and their predicted phosphoprotein substrates are often correlated, for example in endocytosis, cytokinesis, transcription, replication, carbohydrate metabolism and stress response. The predictions link phosphoproteins of unknown function with protein kinases with known functions and vice versa, suggesting functions for the uncharacterized proteins. The study indicates that the phosphoproteins and the associated protein kinases represented in our dataset have housekeeping cellular roles; certain kinases are not represented because they may only be activated during specific cellular responses. Our results demonstrate the utility of our previously reported protein kinase substrate prediction approach (Predikin) as a tool for establishing links between kinases and phosphoproteins that can subsequently be tested experimentally.
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Affiliation(s)
- Ross I Brinkworth
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane 4072, Australia
| | - Alan L Munn
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane 4072, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane 4072, Australia
| | - Boštjan Kobe
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane 4072, Australia
- Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane 4072, Australia
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240
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Li J, Ballif BA, Powelka AM, Dai J, Gygi SP, Hsu VW. Phosphorylation of ACAP1 by Akt regulates the stimulation-dependent recycling of integrin beta1 to control cell migration. Dev Cell 2006; 9:663-73. [PMID: 16256741 DOI: 10.1016/j.devcel.2005.09.012] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Revised: 08/24/2005] [Accepted: 09/22/2005] [Indexed: 01/12/2023]
Abstract
Components of intracellular signaling that mediate the stimulation-dependent recycling of integrins are being identified, but key transport effectors that are the ultimate downstream targets remain unknown. ACAP1 has been shown recently to function as a transport effector in the cargo sorting of transferrin receptor (TfR) that undergoes constitutive recycling. We now show that ACAP1 also participates in the regulated recycling of integrin beta1 to control cell migration. However, in contrast to TfR recycling, the role of ACAP1 in beta1 recycling requires its phosphorylation by Akt, which is, in turn, regulated by a canonical signaling pathway. Disrupting the activities of either ACAP1 or Akt, or their assembly with endosomal beta1, inhibits beta1 recycling and cell migration. These findings advance an understanding of how integrin recycling is achieved during cell migration, and also address a basic issue of how intracellular signaling can interface with transport to achieve regulated recycling.
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Affiliation(s)
- Jian Li
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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241
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Martyn KD, Frederick LM, von Loehneysen K, Dinauer MC, Knaus UG. Functional analysis of Nox4 reveals unique characteristics compared to other NADPH oxidases. Cell Signal 2006; 18:69-82. [PMID: 15927447 DOI: 10.1016/j.cellsig.2005.03.023] [Citation(s) in RCA: 607] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 03/15/2005] [Accepted: 03/16/2005] [Indexed: 01/09/2023]
Abstract
Reactive oxygen species (ROS) are important signal transduction molecules in ligand-induced signaling, regulation of cell growth, differentiation, apoptosis and motility. Recently NADPH oxidases (Nox) homologous to Nox2 (gp91phox) of phagocyte cytochrome b558 have been identified, which are an enzymatic source for ROS generation in epithelial cells. This study was undertaken to delineate the requirements for ROS generation by Nox4. Nox4, in contrast to other Nox proteins, produces large amounts of hydrogen peroxide constitutively. Known cytosolic oxidase proteins or the GTPase Rac are not required for this activity. Nox4 associates with the protein p22phox on internal membranes, where ROS generation occurs. Knockdown and gene transfection studies confirmed that Nox4 requires p22phox for ROS generation. Mutational analysis revealed structural requirements affecting expression of the p22phox protein and Nox activity. Mechanistic insight into ROS regulation is significant for understanding fundamental cell biology and pathophysiological conditions.
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Affiliation(s)
- Kendra D Martyn
- Department of Immunology IMM28, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
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242
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Backert S, Selbach M. Tyrosine-phosphorylated bacterial effector proteins: the enemies within. Trends Microbiol 2005; 13:476-84. [PMID: 16099656 DOI: 10.1016/j.tim.2005.08.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2005] [Revised: 07/06/2005] [Accepted: 08/05/2005] [Indexed: 12/14/2022]
Abstract
The tyrosine phosphorylation of proteins has a central role during signal transduction in eukaryotes. Recent progress shows that tyrosine phosphorylation is also a common feature of several effector proteins translocated by bacterial type III and type IV secretion systems. The involvement of these secretion systems in disease development is exemplified by a variety of pathogenic processes: pedestal formation (Tir of EPEC and Citrobacter), cell scattering (CagA of Helicobacter), invasion (Tarp of Chlamydia) and possibly proinflammatory responses and cell proliferation (BepD-F of Bartonella). The discovery that different bacterial pathogens use this common strategy to subvert host-cell function suggests that more examples will soon emerge.
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Affiliation(s)
- Steffen Backert
- Otto-von-Guericke-Universität Magdeburg, Institut für Medizinische Mikrobiologie, Leipziger Str. 44, D-39120 Magdeburg, Germany.
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243
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Kobe B, Kampmann T, Forwood JK, Listwan P, Brinkworth RI. Substrate specificity of protein kinases and computational prediction of substrates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1754:200-9. [PMID: 16172032 DOI: 10.1016/j.bbapap.2005.07.036] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Revised: 07/13/2005] [Accepted: 07/14/2005] [Indexed: 10/25/2022]
Abstract
To ensure signalling fidelity, kinases must act only on a defined subset of cellular targets. Appreciating the basis for this substrate specificity is essential for understanding the role of an individual protein kinase in a particular cellular process. The specificity in the cell is determined by a combination of "peptide specificity" of the kinase (the molecular recognition of the sequence surrounding the phosphorylation site), substrate recruitment and phosphatase activity. Peptide specificity plays a crucial role and depends on the complementarity between the kinase and the substrate and therefore on their three-dimensional structures. Methods for experimental identification of kinase substrates and characterization of specificity are expensive and laborious, therefore, computational approaches are being developed to reduce the amount of experimental work required in substrate identification. We discuss the structural basis of substrate specificity of protein kinases and review the experimental and computational methods used to obtain specificity information.
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Affiliation(s)
- Bostjan Kobe
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia.
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244
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Wanke V, Pedruzzi I, Cameroni E, Dubouloz F, De Virgilio C. Regulation of G0 entry by the Pho80-Pho85 cyclin-CDK complex. EMBO J 2005; 24:4271-8. [PMID: 16308562 PMCID: PMC1356330 DOI: 10.1038/sj.emboj.7600889] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 11/04/2005] [Indexed: 11/08/2022] Open
Abstract
Eukaryotic cell proliferation is controlled by growth factors and essential nutrients. In their absence, cells may enter into a quiescent state (G0). In Saccharomyces cerevisiae, the conserved protein kinase A (PKA) and rapamycin-sensitive TOR (TORC1) pathways antagonize G0 entry in response to carbon and/or nitrogen availability primarily by inhibiting the PAS kinase Rim15 function. Here, we show that the phosphate-sensing Pho80-Pho85 cyclin-cyclin-dependent kinase (CDK) complex also participates in Rim15 inhibition through direct phosphorylation, thereby effectively sequestering Rim15 in the cytoplasm via its association with 14-3-3 proteins. Inactivation of either Pho80-Pho85 or TORC1 causes dephosphorylation of the 14-3-3-binding site in Rim15, thus enabling nuclear import of Rim15 and induction of the Rim15-controlled G0 program. Importantly, we also show that Pho80-Pho85 and TORC1 converge on a single amino acid in Rim15. Thus, Rim15 plays a key role in G0 entry through its ability to integrate signaling from the PKA, TORC1, and Pho80-Pho85 pathways.
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Affiliation(s)
- Valeria Wanke
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Ivo Pedruzzi
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Elisabetta Cameroni
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Frédérique Dubouloz
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
| | - Claudio De Virgilio
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
- Department of Microbiology & Molecular Medicine, CMU, University of Geneva, 1211 Geneva, Switzerland. Tel.: +41 22 379 54 95; Fax: +41 22 379 55 02; E-mail:
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245
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Giorgione JR, Lin JH, McCammon JA, Newton AC. Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem 2005; 281:1660-9. [PMID: 16293612 PMCID: PMC2913972 DOI: 10.1074/jbc.m510251200] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein kinase C (PKC) family members are allosterically activated following membrane recruitment by specific membrane-targeting modules. Conventional PKC isozymes are recruited to membranes by two such modules: a C1 domain, which binds diacylglycerol (DAG), and a C2 domain, which is a Ca2+-triggered phospholipid-binding module. In contrast, novel PKC isozymes respond only to DAG, despite the presence of a C2 domain. Here, we address the molecular mechanism of membrane recruitment of the novel isozyme PKCdelta. We show that PKCdelta and a conventional isozyme, PKCbetaII, bind membranes with comparable affinities. However, dissection of the contribution of individual domains to this binding revealed that, although the C2 domain is a major determinant in driving the interaction of PKCbetaII with membranes, the C2 domain of PKCdelta does not bind membranes. Instead, the C1B domain is the determinant that drives the interaction of PKCdelta with membranes. The C2 domain also does not play any detectable role in the activity or subcellular location of PKCdelta in cells; in vivo imaging studies revealed that deletion of the C2 domain does not affect the stimulus-dependent translocation or activity of PKCdelta. Thus, the increased affinity of the C1 domain of PKCdelta allows this isozyme to respond to DAG alone, whereas conventional PKC isozymes require the coordinated action of Ca2+ binding to the C2 domain and DAG binding to the C1 domain for activation.
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Affiliation(s)
| | | | | | - Alexandra C. Newton
- To whom correspondence should be addressed: Dept. of Pharmacology, University of California at San Diego, Leichtag 282, 9500 Gilman Dr., La Jolla, CA 92093-0721. Tel.: 858-534-4527; Fax: 858-822-5888;
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246
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Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, Gibson TJ, Lewis J, Serrano L, Russell RB. Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 2005; 3:e405. [PMID: 16279839 PMCID: PMC1283537 DOI: 10.1371/journal.pbio.0030405] [Citation(s) in RCA: 239] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 09/27/2005] [Indexed: 12/11/2022] Open
Abstract
Many aspects of cell signalling, trafficking, and targeting are governed by interactions between globular protein domains and short peptide segments. These domains often bind multiple peptides that share a common sequence pattern, or “linear motif” (e.g., SH3 binding to PxxP). Many domains are known, though comparatively few linear motifs have been discovered. Their short length (three to eight residues), and the fact that they often reside in disordered regions in proteins makes them difficult to detect through sequence comparison or experiment. Nevertheless, each new motif provides critical molecular details of how interaction networks are constructed, and can explain how one protein is able to bind to very different partners. Here we show that binding motifs can be detected using data from genome-scale interaction studies, and thus avoid the normally slow discovery process. Our approach based on motif over-representation in non-homologous sequences, rediscovers known motifs and predicts dozens of others. Direct binding experiments reveal that two predicted motifs are indeed protein-binding modules: a DxxDxxxD protein phosphatase 1 binding motif with a KD of 22 μM and a VxxxRxYS motif that binds Translin with a KD of 43 μM. We estimate that there are dozens or even hundreds of linear motifs yet to be discovered that will give molecular insight into protein networks and greatly illuminate cellular processes. Many protein interactions are mediated by short amino acid motifs. The authors describe a new approach to identify these interaction motifs and experimentally validate some of their binding predictions.
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Affiliation(s)
- Victor Neduva
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rune Linding
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | - Toby J Gibson
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joe Lewis
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Serrano
- 1European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robert B Russell
- 1European Molecular Biology Laboratory, Heidelberg, Germany
- 2European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, United Kingdom
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247
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Jones RB, Gordus A, Krall JA, MacBeath G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 2005; 439:168-74. [PMID: 16273093 DOI: 10.1038/nature04177] [Citation(s) in RCA: 544] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 08/30/2005] [Indexed: 11/09/2022]
Abstract
Although epidermal growth factor receptor (EGFR; also called ErbB1) and its relatives initiate one of the most well-studied signalling networks, there is not yet a genome-wide view of even the earliest step in this pathway: recruitment of proteins to the activated receptors. Here we use protein microarrays comprising virtually every Src homology 2 (SH2) and phosphotyrosine binding (PTB) domain encoded in the human genome to measure the equilibrium dissociation constant of each domain for 61 peptides representing physiological sites of tyrosine phosphorylation on the four ErbB receptors. This involved 77,592 independent biochemical measurements and provided a quantitative protein interaction network that reveals many new interactions, including ones that fall outside of our current view of domain selectivity. By slicing through the network at different affinity thresholds, we found surprising differences between the receptors. Most notably, EGFR and ErbB2 become markedly more promiscuous as the threshold is lowered, whereas ErbB3 does not. Because EGFR and ErbB2 are overexpressed in many human cancers, our results suggest that the extent to which promiscuity changes with protein concentration may contribute to the oncogenic potential of receptor tyrosine kinases, and perhaps other signalling proteins as well.
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Affiliation(s)
- Richard B Jones
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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248
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Yu GX, Park BH, Chandramohan P, Munavalli R, Geist A, Samatova NF. In silico discovery of enzyme-substrate specificity-determining residue clusters. J Mol Biol 2005; 352:1105-17. [PMID: 16140329 DOI: 10.1016/j.jmb.2005.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 08/10/2005] [Indexed: 11/24/2022]
Abstract
The binding between an enzyme and its substrate is highly specific, despite the fact that many different enzymes show significant sequence and structure similarity. There must be, then, substrate specificity-determining residues that enable different enzymes to recognize their unique substrates. We reason that a coordinated, not independent, action of both conserved and non-conserved residues determine enzymatic activity and specificity. Here, we present a surface patch ranking (SPR) method for in silico discovery of substrate specificity-determining residue clusters by exploring both sequence conservation and correlated mutations. As case studies we apply SPR to several highly homologous enzymatic protein pairs, such as guanylyl versus adenylyl cyclases, lactate versus malate dehydrogenases, and trypsin versus chymotrypsin. Without using experimental data, we predict several single and multi-residue clusters that are consistent with previous mutagenesis experimental results. Most single-residue clusters are directly involved in enzyme-substrate interactions, whereas multi-residue clusters are vital for domain-domain and regulator-enzyme interactions, indicating their complementary role in specificity determination. These results demonstrate that SPR may help the selection of target residues for mutagenesis experiments and, thus, focus rational drug design, protein engineering, and functional annotation to the relevant regions of a protein.
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Affiliation(s)
- Gong-Xin Yu
- Computational Biology Institute, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831, USA
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249
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Katsanakis KD, Pillay TS. Cross-talk between the Two Divergent Insulin Signaling Pathways Is Revealed by the Protein Kinase B (Akt)-mediated Phosphorylation of Adapter Protein APS on Serine 588. J Biol Chem 2005; 280:37827-32. [PMID: 16141217 DOI: 10.1074/jbc.m505959200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The APS adapter protein is recruited to the autophosphorylated kinase domain of the insulin receptor and initiates the phosphatidylinositol 3-kinase (PI3K)-independent pathway of insulin-stimulated glucose transport by recruiting CAP and c-Cbl. In this study, we have identified APS as a novel substrate for protein kinase B/Akt using an antibody that exhibits insulin-dependent immunoreactivity with a phosphospecific antibody raised against the protein kinase B substrate consensus sequence RXRXX(pS/pT) and a phosphospecific antibody that recognizes serine 21/9 of glycogen synthase kinase-3alpha/beta. This phosphorylation of APS is observed in both 3T3-L1 adipocytes and transfected cells. The insulin-stimulated serine phosphorylation of APS was inhibited by a PI3-kinase inhibitor, LY290004, a specific protein kinase B (PKB) inhibitor, deguelin, and knockdown of Akt. Serine 588 of APS is contained in a protein kinase B consensus sequence for phosphorylation conserved in APS across multiple species but not found in other members of this family, including SH2-B and Lnk. Mutation of serine 588 to alanine abolished the insulin-stimulated serine phosphorylation of APS and prevented the localization of APS to membrane ruffles. A glutathione S-transferase fusion protein containing amino acids 534-621 of APS was phosphorylated by purified PKB in vitro, and mutation of serine 588 abolished the PKB-mediated phosphorylation of APS in vitro. Taken together, this study identifies APS as a novel physiological substrate for PKB and the first serine phosphorylation site on APS. These data therefore reveal the molecular cross-talk between the insulin-activated PI3-kinase-dependent and -independent pathways previously thought to be distinct and divergent.
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Affiliation(s)
- Kostas D Katsanakis
- Institute of Cell Signaling and School of Biomedical Sciences, University of Nottingham Medical School, UK
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250
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Hu G, Mancl ME, Barnes BJ. Signaling through IFN regulatory factor-5 sensitizes p53-deficient tumors to DNA damage-induced apoptosis and cell death. Cancer Res 2005; 65:7403-12. [PMID: 16103093 DOI: 10.1158/0008-5472.can-05-0583] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human IFN regulatory factor-5 (IRF-5) is a candidate tumor suppressor gene that mediates cell arrest, apoptosis, and immune activation. Here we show that ectopic IRF-5 sensitizes p53-proficient and p53-deficient colon cancer cells to DNA damage-induced apoptosis. The combination IFN-beta and irinotecan (CPT-11) cooperatively inhibits cell growth and IRF-5 synergizes with it to further promote apoptosis. The synergism is due to IRF-5 signaling since a striking defect in apoptosis and cell death was observed in IRF-5-deficient cells, which correlated well with a reduction in DNA damage-induced cellular events. Components of this IRF-5 signaling pathway are investigated including a mechanism for DNA damage-induced IRF-5 activation. Thus, IRF-5-regulated pathways may serve as a target for cancer therapeutics.
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Affiliation(s)
- Guodong Hu
- Division of Viral Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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