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Bardwell AJ, Paul M, Yoneda KC, Andrade-Ludeña MD, Nguyen OT, Fruman DA, Bardwell L. The WW domain of IQGAP1 binds directly to the p110α catalytic subunit of PI 3-kinase. Biochem J 2023; 480:BCJ20220493. [PMID: 37145016 PMCID: PMC10625650 DOI: 10.1042/bcj20220493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/06/2023]
Abstract
IQGAP1 is a multi-domain cancer-associated protein that serves as a scaffold protein for multiple signaling pathways. Numerous binding partners have been found for the calponin homology, IQ and GAP-related domains in IQGAP1. Identification of a binding partner for its WW domain has proven elusive, however, even though a cell-penetrating peptide derived from this domain has marked anti-tumor activity. Here, using in vitro binding assays with human proteins and co-precipitation from human cells, we show that the WW domain of human IQGAP1 binds directly to the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K). In contrast, the WW domain does not bind to ERK1/2, MEK1/2, or the p85α regulatory subunit of PI3K when p85α is expressed alone. However, the WW domain is able to bind to the p110α/p85α heterodimer when both subunits are co-expressed, as well as to the mutationally activated p110α/p65α heterodimer. We present a model of the structure of the IQGAP1 WW domain, and experimentally identify key residues in the hydrophobic core and beta strands of the WW domain that are required for binding to p110α. These findings contribute to a more precise understanding of IQGAP1-mediated scaffolding, and of how IQGAP1-derived therapeutic peptides might inhibit tumorigenesis.
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Affiliation(s)
- A. Jane Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
| | - Madhuri Paul
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, U.S.A
| | - Kiku C. Yoneda
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
| | | | - Oanh T. Nguyen
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
| | - David A. Fruman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, U.S.A
| | - Lee Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, U.S.A
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Bardwell AJ, Wu B, Sarin KY, Waterman ML, Atwood SX, Bardwell L. ERK2 MAP kinase regulates SUFU binding by multisite phosphorylation of GLI1. Life Sci Alliance 2022; 5:e202101353. [PMID: 35831023 PMCID: PMC9279676 DOI: 10.26508/lsa.202101353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 01/03/2023] Open
Abstract
Crosstalk between the Hedgehog and MAPK signaling pathways occurs in several types of cancer and contributes to clinical resistance to Hedgehog pathway inhibitors. Here we show that MAP kinase-mediated phosphorylation weakens the binding of the GLI1 transcription factor to its negative regulator SUFU. ERK2 phosphorylates GLI1 on three evolutionarily conserved target sites (S102, S116, and S130) located near the high-affinity binding site for SUFU; these phosphorylations cooperate to weaken the affinity of GLI1-SUFU binding by over 25-fold. Phosphorylation of any one, or even any two, of the three sites does not result in the level of SUFU release seen when all three sites are phosphorylated. Tumor-derived mutations in R100 and S105, residues bordering S102, also diminish SUFU binding, collectively defining a novel evolutionarily conserved SUFU affinity-modulating region. In cultured mammalian cells, GLI1 variants containing phosphomimetic substitutions of S102, S116, and S130 displayed an increased ability to drive transcription. We conclude that multisite phosphorylation of GLI1 by ERK2 or other MAP kinases weakens GLI1-SUFU binding, thereby facilitating GLI1 activation and contributing to both physiological and pathological crosstalk.
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Affiliation(s)
- A Jane Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Beibei Wu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marian L Waterman
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, USA
| | - Scott X Atwood
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Lee Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
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3
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Syed A, Lukacsovich T, Pomeroy M, Bardwell AJ, Decker GT, Waymire KG, Purcell J, Huang W, Gui J, Padilla EM, Park C, Paul A, Pham TBT, Rodriguez Y, Wei S, Worthge S, Zebarjedi R, Zhang B, Bardwell L, Marsh JL, MacGregor GR. Miles to go (mtgo) encodes FNDC3 proteins that interact with the chaperonin subunit CCT3 and are required for NMJ branching and growth in Drosophila. Dev Biol 2018; 445:37-53. [PMID: 30539716 DOI: 10.1016/j.ydbio.2018.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/01/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022]
Abstract
Analysis of mutants that affect formation and function of the Drosophila larval neuromuscular junction (NMJ) has provided valuable insight into genes required for neuronal branching and synaptic growth. We report that NMJ development in Drosophila requires both the Drosophila ortholog of FNDC3 genes; CG42389 (herein referred to as miles to go; mtgo), and CCT3, which encodes a chaperonin complex subunit. Loss of mtgo function causes late pupal lethality with most animals unable to escape the pupal case, while rare escapers exhibit an ataxic gait and reduced lifespan. NMJs in mtgo mutant larvae have dramatically reduced branching and growth and fewer synaptic boutons compared with control animals. Mutant larvae show normal locomotion but display an abnormal self-righting response and chemosensory deficits that suggest additional functions of mtgo within the nervous system. The pharate lethality in mtgo mutants can be rescued by both low-level pan- and neuronal-, but not muscle-specific expression of a mtgo transgene, supporting a neuronal-intrinsic requirement for mtgo in NMJ development. Mtgo encodes three similar proteins whose domain structure is most closely related to the vertebrate intracellular cytosolic membrane-anchored fibronectin type-III domain-containing protein 3 (FNDC3) protein family. Mtgo physically and genetically interacts with Drosophila CCT3, which encodes a subunit of the TRiC/CCT chaperonin complex required for maturation of actin, tubulin and other substrates. Drosophila larvae heterozygous for a mutation in CCT3 that reduces binding between CCT3 and MTGO also show abnormal NMJ development similar to that observed in mtgo null mutants. Hence, the intracellular FNDC3-ortholog MTGO and CCT3 can form a macromolecular complex, and are both required for NMJ development in Drosophila.
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Affiliation(s)
- Adeela Syed
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Tamás Lukacsovich
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Miles Pomeroy
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - A Jane Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Gentry Thomas Decker
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Katrina G Waymire
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Judith Purcell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Weijian Huang
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - James Gui
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Emily M Padilla
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Cindy Park
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Antor Paul
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Thai Bin T Pham
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Yanete Rodriguez
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Stephen Wei
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Shane Worthge
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Ronak Zebarjedi
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - Bing Zhang
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211-7400, USA
| | - Lee Bardwell
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA
| | - J Lawrence Marsh
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA.
| | - Grant R MacGregor
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697-2300, USA.
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Bardwell AJ, Lagunes L, Zebarjedi R, Bardwell L. The WW domain of the scaffolding protein IQGAP1 is neither necessary nor sufficient for binding to the MAPKs ERK1 and ERK2. J Biol Chem 2017; 292:8750-8761. [PMID: 28396345 DOI: 10.1074/jbc.m116.767087] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/07/2017] [Indexed: 01/09/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) scaffold proteins, such as IQ motif containing GTPase activating protein 1 (IQGAP1), are promising targets for novel therapies against cancer and other diseases. Such approaches require accurate information about which domains on the scaffold protein bind to the kinases in the MAPK cascade. Results from previous studies have suggested that the WW domain of IQGAP1 binds to the cancer-associated MAPKs ERK1 and ERK2, and that this domain might thus offer a new tool to selectively inhibit MAPK activation in cancer cells. The goal of this work was therefore to critically evaluate which IQGAP1 domains bind to ERK1/2. Here, using quantitative in vitro binding assays, we show that the IQ domain of IQGAP1 is both necessary and sufficient for binding to ERK1 and ERK2, as well as to the MAPK kinases MEK1 and MEK2. Furthermore, we show that the WW domain is not required for ERK-IQGAP1 binding, and contributes little or no binding energy to this interaction, challenging previous models of how WW-based peptides might inhibit tumorigenesis. Finally, we show that the ERK2-IQGAP1 interaction does not require ERK2 phosphorylation or catalytic activity and does not involve known docking recruitment sites on ERK2, and we obtain an estimate of the dissociation constant (Kd ) for this interaction of 8 μm These results prompt a re-evaluation of published findings and a refined model of IQGAP scaffolding.
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Affiliation(s)
- A Jane Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
| | - Leonila Lagunes
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
| | - Ronak Zebarjedi
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
| | - Lee Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
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Bardwell AJ, Bardwell L. Two hydrophobic residues can determine the specificity of mitogen-activated protein kinase docking interactions. J Biol Chem 2015; 290:26661-74. [PMID: 26370088 DOI: 10.1074/jbc.m115.691436] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 11/06/2022] Open
Abstract
MAPKs bind to many of their upstream regulators and downstream substrates via a short docking motif (the D-site) on their binding partner. MAPKs that are in different families (e.g. ERK, JNK, and p38) can bind selectively to D-sites in their authentic substrates and regulators while discriminating against D-sites in other pathways. Here we demonstrate that the short hydrophobic region at the distal end of the D-site plays a critical role in determining the high selectivity of JNK MAPKs for docking sites in their cognate MAPK kinases. Changing just 1 or 2 key hydrophobic residues in this submotif is sufficient to turn a weak JNK-binding D-site into a strong one, or vice versa. These specificity-determining differences are also found in the D-sites of the ETS family transcription factors Elk-1 and Net. Moreover, swapping two hydrophobic residues between these D-sites switches the relative efficiency of Elk-1 and Net as substrates for ERK versus JNK, as predicted. These results provide new insights into docking specificity and suggest that this specificity can evolve rapidly by changes to just 1 or 2 amino acids.
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Affiliation(s)
- A Jane Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
| | - Lee Bardwell
- From the Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California 92697
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Abstract
Protein kinases often recognize their substrates and regulators through docking interactions that occur outside of the active site; these interactions can help us to understand kinase networks, and to target kinases with drugs. During mitogen-activated protein kinase (MAPK) signaling, the ability of MAPK kinases (MKKs, or MEKs) to recognize their cognate MAPKs is facilitated by a short docking motif (the D-site) in the MKK N terminus, which binds to a complementary region on the MAPK. MAPKs then recognize many of their targets using the same strategy, because many MAPK substrates also contain D-sites. The extent to which docking contributes to the specificity of MAPK transactions is incompletely understood. Here we characterize the selectivity of the interaction between MKK-derived D-sites and MAPKs by measuring the ability of D-site peptides to inhibit MAPK-mediated phosphorylation of D-site-containing substrates. We find that all MKK D-sites bind better to their cognate MAPKs than they do to non-cognate MAPKs. For instance, the MKK3 D-site peptide, which is a remarkably potent inhibitor of p38alpha (IC(50) < 10 nm), does not inhibit JNK1 or JNK2. Likewise, MAPKs generally bind as well or better to cognate D-sites than to non-cognate D-sites. For instance, JNK1 and JNK2 do not appreciably bind to any D-sites other than their cognate D-sites from MKK4 and MKK7. In general, cognate, within-pathway interactions are preferred about an order of magnitude over non-cognate interactions. However, the selectivity of MAPKs and their cognate MKK-derived D-sites for each other is limited in some cases; in particular, ERK2 is not very selective. We conclude that MAPK-docking sites in MAPK kinases bind selectively to their cognate MAPKs.
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Affiliation(s)
- A Jane Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697-2300, USA
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Ho DT, Bardwell AJ, Grewal S, Iverson C, Bardwell L. Interacting JNK-docking sites in MKK7 promote binding and activation of JNK mitogen-activated protein kinases. J Biol Chem 2006; 281:13169-13179. [PMID: 16533805 PMCID: PMC3017509 DOI: 10.1074/jbc.m601010200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
D-sites are a class of MAPK-docking sites that have been found in many MAPK regulators and substrates. A single functional, high affinity D-site has been identified near the N terminus of each of the MAPK kinases (MKKs or MEKs) MEK1, MEK2, MKK3, MKK4, and MKK6. Here we demonstrated that MKK7 recognizes its target JNK by a novel mechanism involving a partially cooperative interaction of three low affinity D-sites in the N-terminal domain of MKK7. Mutations of the conserved residues within any one of the three docking sites (D1, D2, and D3) disrupted the ability of the N-terminal domain of MKK7beta to bind JNK1 by about 50-70%. Moreover, mutation of any two of the three D-sites reduced binding by about 80-90%, and mutation of all three reduced binding by 95%. Full-length MKK7 containing combined D1/D2 mutations was compromised for binding to JNK1 and exhibited reduced JNK1 kinase activity when compared with wild-type MKK7. Peptide versions of the D-sites from MKK4 or the JIP-1 scaffold protein inhibited MKK7-JNK binding, suggesting that all three JNK regulators bind to the same region of JNK. Moreover, peptide versions of any of the three D-sites of MKK7 inhibited the ability of JNK1 and JNK2 to phosphorylate their transcription factor substrates c-Jun and ATF2, suggesting that D-site-containing substrates also compete with MKK7 for docking to JNK. Finally, MKK7-derived D-site peptides exhibited selective inhibition of JNK1 versus ERK2. We conclude that MKK7 contains three JNK-docking sites that interact to selectively bind JNK and contribute to JNK signal transmission and specificity.
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Affiliation(s)
- David T Ho
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
| | - A Jane Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
| | - Seema Grewal
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
| | - Corey Iverson
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
| | - Lee Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697.
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Bardwell AJ, Abdollahi M, Bardwell L. Anthrax lethal factor-cleavage products of MAPK (mitogen-activated protein kinase) kinases exhibit reduced binding to their cognate MAPKs. Biochem J 2004; 378:569-77. [PMID: 14616089 PMCID: PMC1223970 DOI: 10.1042/bj20031382] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Revised: 11/11/2003] [Accepted: 11/14/2003] [Indexed: 11/17/2022]
Abstract
Anthrax lethal toxin is the major cause of death in systemic anthrax. Lethal toxin consists of two proteins: protective antigen and LF (lethal factor). Protective antigen binds to a cell-surface receptor and transports LF into the cytosol. LF is a metalloprotease that targets MKKs [MAPK (mitogen-activated protein kinase) kinases]/MEKs [MAPK/ERK (extracellular-signal-regulated kinase) kinases], cleaving them to remove a small N-terminal stretch but leaving the bulk of the protein, including the protein kinase domain, intact. LF-mediated cleavage of MEK1 and MKK6 has been shown to inhibit signalling through their cognate MAPK pathways. However, the precise mechanism by which this proteolytic cleavage inhibits signal transmission has been unclear. Here we show that the C-terminal LF-cleavage products of MEK1, MEK2, MKK3, MKK4, MKK6 and MKK7 are impaired in their ability to bind to their MAPK substrates, suggesting a common mechanism for the LF-induced inhibition of signalling.
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Affiliation(s)
- A Jane Bardwell
- Department of Developmental and Cell Biology, 2208 Natural Sciences I, University of California, Irvine, CA 92697, U.S.A
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Ho DT, Bardwell AJ, Abdollahi M, Bardwell L. A docking site in MKK4 mediates high affinity binding to JNK MAPKs and competes with similar docking sites in JNK substrates. J Biol Chem 2003; 278:32662-72. [PMID: 12788955 PMCID: PMC3017503 DOI: 10.1074/jbc.m304229200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Specific docking interactions between MAPKs and their activating MAPK kinases (MKKs or MEKs) are crucial for efficient and accurate signal transmission. Here, we report the identification of a MAPK-docking site, or "D-site," in the N terminus of human MKK4/JNKK1. This docking site conforms to the consensus sequence for known D-sites in other MKKs and contains the first of the two cleavage sites for anthrax lethal factor protease that have been found in the N terminus of MKK4. This docking site was both necessary and sufficient for the high affinity binding of the MAPKs JNK1, JNK2, JNK3, p38 alpha, and p38 beta to MKK4. Mutations that altered conserved residues in this docking site reduced JNK/p38 binding. In addition, a peptide version of this docking site, as well as a peptide version of the JNK-binding site of the JIP-1 scaffold protein, inhibited both MKK4/JNK binding and MKK4-mediated phosphorylation of JNK1. These same peptides also inhibited JNK2-mediated phosphorylation of c-Jun and ATF2, suggesting that transcription factors, MKK4, and the JIP scaffold compete for docking to JNK. Finally, the selectivity of the MKK4, MEK1, and MEK2 D-sites for JNK versus ERK was quantified. The MEK1 and MEK2 D-sites displayed a strong selectivity for their cognate MAPK (ERK2) versus a non-cognate MAPK (JNK). In contrast, the MKK4 D-site exhibited only limited selectivity for JNK versus ERK.
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Affiliation(s)
- David T. Ho
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
| | - A. Jane Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
| | - Mahsa Abdollahi
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
| | - Lee Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697
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Bardwell AJ, Abdollahi M, Bardwell L. Docking sites on mitogen-activated protein kinase (MAPK) kinases, MAPK phosphatases and the Elk-1 transcription factor compete for MAPK binding and are crucial for enzymic activity. Biochem J 2003; 370:1077-85. [PMID: 12529172 PMCID: PMC1223246 DOI: 10.1042/bj20021806] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2002] [Revised: 01/13/2003] [Accepted: 01/15/2003] [Indexed: 11/17/2022]
Abstract
Mitogen-activated protein kinase (MAPK) cascades control gene expression patterns in response to extracellular stimuli. MAPK/ERK (extracellular-signal-regulated kinase) kinases (MEKs) activate MAPKs by phosphorylating them; activated MAPKs, in turn, phosphorylate target transcription factors, and are deactivated by phosphatases. One mechanism for maintaining signal specificity and efficiency is the interaction of MAPKs with their substrates and regulators through high-affinity docking sites. In the present study, we show that peptides corresponding to the MAPK-docking sites of MEK1, MEK2, Ste7, Elk-1 and MAPK phosphatase (MKP)-2 potently inhibit MEK2 phosphorylation of ERK2, ERK2 phosphorylation of Elk-1, and MKP-1 dephosphorylation of ERK2. Each peptide inhibited multiple reactions; for example, the MEK2 peptide inhibited not only MEK2, but also ERK2 and MKP-1. In addition, these docking-site peptides inhibited MEK2-ERK2 binding. The MAPK-docking site of MEK1 also potently stimulated ERK2-mediated phosphorylation of a target site on the same peptide. Control peptides with mutations of conserved basic and hydrophobic residues of the MAPK-docking site consensus lacked biological activity. We conclude that MEKs, MKPs and the Elk-1 transcription factor compete for binding to the same region of ERK2 via protein-protein interactions that are crucial for kinase/phosphatase activity.
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Affiliation(s)
- A Jane Bardwell
- Department of Developmental and Cell Biology, 5207 McGaugh Hall, University of California, Irvine, CA 92697-2300, USA
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Abstract
Signals transmitted by common components often elicit distinct (yet appropriate) outcomes. In yeast, two developmental options-mating and invasive growth-are both regulated by the same MAP kinase cascade. Specificity has been thought to result from specialized roles for the two MAP kinases, Kss1 and Fus3, and because Fus3 prevents Kss1 from gaining access to the mating pathway. Kss1 has been thought to participate in mating only when Fus3 is absent. Instead, we show that Kss1 is rapidly phosphorylated and potently activated by mating pheromone in wild-type cells, and that this is required for normal pheromone-induced gene expression. Signal identity is apparently maintained because active Fus3 limits the extent of Kss1 activation, thereby preventing inappropriate signal crossover.
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Affiliation(s)
- Walid Sabbagh
- Department of Developmental and Cell Biology University of California, Irvine Irvine, California 92697
| | - Laura J. Flatauer
- Department of Developmental and Cell Biology University of California, Irvine Irvine, California 92697
| | - A. Jane Bardwell
- Department of Developmental and Cell Biology University of California, Irvine Irvine, California 92697
| | - Lee Bardwell
- Department of Developmental and Cell Biology University of California, Irvine Irvine, California 92697
- Correspondence:
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Bardwell AJ, Flatauer LJ, Matsukuma K, Thorner J, Bardwell L. A conserved docking site in MEKs mediates high-affinity binding to MAP kinases and cooperates with a scaffold protein to enhance signal transmission. J Biol Chem 2001; 276:10374-86. [PMID: 11134045 PMCID: PMC3021106 DOI: 10.1074/jbc.m010271200] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The recognition of mitogen-activated protein kinases (MAPKs) by their upstream activators, MAPK/ERK kinases (MEKs), is crucial for the effective and accurate transmission of many signals. We demonstrated previously that the yeast MAPKs Kss1 and Fus3 bind with high affinity to the N terminus of the MEK Ste7, and proposed that a conserved motif in Ste7, the MAPK-docking site, mediates this interaction. Here we show that the corresponding sequences in human MEK1 and MEK2 are necessary and sufficient for the direct binding of the MAPKs ERK1 and ERK2. Mutations in MEK1, MEK2, or Ste7 that altered conserved residues in the docking site diminished binding of the cognate MAPKs. Furthermore, short peptides corresponding to the docking sites in these MEKs inhibited MEK1-mediated phosphorylation of ERK2 in vitro. In yeast cells, docking-defective alleles of Ste7 were modestly compromised in their ability to transmit the mating pheromone signal. This deficiency was dramatically enhanced when the ability of the Ste5 scaffold protein to associate with components of the MAPK cascade was also compromised. Thus, both the MEK-MAPK docking interaction and binding to the Ste5 scaffold make mutually reinforcing contributions to the efficiency of signaling by this MAPK cascade in vivo.
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Affiliation(s)
- A J Bardwell
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA.
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Laurance ME, Starr DB, Michelotti EF, Cheung E, Gonzalez C, Tam AW, Deikman J, Edwards CA, Bardwell AJ. Specific down-regulation of an engineered human cyclin D1 promoter by a novel DNA-binding ligand in intact cells. Nucleic Acids Res 2001; 29:652-61. [PMID: 11160886 PMCID: PMC30392 DOI: 10.1093/nar/29.3.652] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cyclin D1 is expressed at abnormally high levels in many cancers and has been specifically implicated in the development of breast cancer. In this report we have extensively analyzed the cyclin D1 promoter in a variety of cancer cell lines that overexpress the protein and identified two critical regulatory elements (CREs), a previously identified CRE at -52 and a novel site at -30. In vivo footprinting experiments demonstrated factors binding at both sites. We have used a novel DNA-binding ligand, GL020924, to target the site at -30 (-30-21) of the cyclin D1 promoter in MCF7 breast cancer cells. A binding site for this novel molecule was constructed by mutating 2 bp of the wild-type cyclin D1 promoter at the -30-21 site. Treatment with GL020924 specifically inhibited expression of the targeted cyclin D1 promoter construct in MCF7 cells in a concentration-dependent manner, thus validating the -30-21 site as a target for minor groove-binding ligands. In addition, this result validates our approach to regulating the expression of genes implicated in disease by targeting small DNA-binding ligands to key regulatory elements in the promoters of those genes.
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Affiliation(s)
- M E Laurance
- Genelabs Technologies Inc., 505 Penobscot Drive, Redwood City, CA 94063, USA.
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14
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Friedberg EC, Bardwell AJ, Bardwell L, Feaver WJ, Kornberg RD, Svejstrup JQ, Tomkinson AE, Wang Z. Nucleotide excision repair in the yeast Saccharomyces cerevisiae: its relationship to specialized mitotic recombination and RNA polymerase II basal transcription. Philos Trans R Soc Lond B Biol Sci 1995; 347:63-8. [PMID: 7746856 DOI: 10.1098/rstb.1995.0010] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nucleotide excision repair (NER) in eukaryotes is a biochemically complex process involving multiple gene products. The budding yeast Saccharomyces cerevisiae is an informative model for this process. Multiple genes and in some cases gene products that are indispensable for NER have been isolated from this organism. Homologues of many of these yeast genes are structurally and functionally conserved in higher organisms, including humans. The yeast Rad1/Rad10 heterodimeric protein complex is an endonuclease that is believed to participate in damage-specific incision of DNA during NER. This endonuclease is also required for specialized types of recombination. The products of the RAD3, SSL2(RAD25) SSL1 and TFB1 genes have dual roles in NER and in RNA polymerase II-dependent basal transcription.
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Affiliation(s)
- E C Friedberg
- Department of Pathology, University of Texas Southwestern Medical Cater, Dallas 75235, USA
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15
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Bardwell AJ, Bardwell L, Tomkinson AE, Friedberg EC. Specific cleavage of model recombination and repair intermediates by the yeast Rad1-Rad10 DNA endonuclease. Science 1994; 265:2082-5. [PMID: 8091230 DOI: 10.1126/science.8091230] [Citation(s) in RCA: 206] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The RAD1 and RAD10 genes of Saccharomyces cerevisiae are required for both nucleotide excision repair and certain mitotic recombination events. Here, model recombination and repair intermediates were used to show that Rad1-Rad10-mediated cleavage occurs at duplex-single-strand junctions. Moreover, cleavage occurs only on the strand containing the 3' single-stranded tail. Thus, both biochemical and genetic evidence indicate a role for the Rad1-Rad10 complex in the cleavage of specific recombination intermediates. Furthermore, these data suggest that Rad1-Rad10 endonuclease incises DNA 5' to damaged bases during nucleotide excision repair.
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Affiliation(s)
- A J Bardwell
- Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center at Dallas 75235
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16
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Bardwell AJ, Bardwell L, Wang Z, Siede W, Reagan MS, Tomkinson AE, Friedberg AS, Pittenger C, Feaver WJ, Svejstrup J. Recent insights on DNA repair. The mechanism of damaged nucleotide excision in eukaryotes and its relationship to other cellular processes. Ann N Y Acad Sci 1994; 726:281-91. [PMID: 8092684 DOI: 10.1111/j.1749-6632.1994.tb52829.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- A J Bardwell
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75235
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17
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Bardwell AJ, Bardwell L, Iyer N, Svejstrup JQ, Feaver WJ, Kornberg RD, Friedberg EC. Yeast nucleotide excision repair proteins Rad2 and Rad4 interact with RNA polymerase II basal transcription factor b (TFIIH). Mol Cell Biol 1994; 14:3569-76. [PMID: 8196602 PMCID: PMC358724 DOI: 10.1128/mcb.14.6.3569-3576.1994] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Rad2, Rad3, Rad4, and Ss12 proteins are required for nucleotide excision repair in yeast cells and are homologs of four human proteins which are involved in a group of hereditary repair-defective diseases. We have previously shown that Rad3 protein is one of the five subunits of purified RNA polymerase II basal transcription initiation factor b (TFIIH) and that Ss12 protein physically associates with factor b (W.J. Feaver, J.Q. Svejstrup, L. Bardwell, A.J. Bardwell, S. Buratowski, K.D. Gulyas, T.F. Donahue, E.C. Friedberg, and R.D. Kornberg, Cell 75:1379-1387, 1993). Here we show that the Rad2 and Rad4 proteins interact with purified factor b in vitro. Rad2 (a single-stranded DNA endonuclease) specifically interacts with the Tfb1 subunit of factor b, and we have mapped a limited region of the Rad2 polypeptide which is sufficient for this interaction. Rad2 also interacts directly with Ss12 protein (a putative DNA helicase). The binding of Rad2 and Rad4 proteins to factor b may define intermediates in the assembly of the nucleotide excision repair repairosome. Furthermore, the loading of factor b (or such intermediates) onto promoters during transcription initiation provides a mechanism for the preferential targeting of repair proteins to actively transcribing genes.
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Affiliation(s)
- A J Bardwell
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75235
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18
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Tomkinson AE, Bardwell AJ, Tappe N, Ramos W, Friedberg EC. Purification of Rad1 protein from Saccharomyces cerevisiae and further characterization of the Rad1/Rad10 endonuclease complex. Biochemistry 1994; 33:5305-11. [PMID: 8172904 DOI: 10.1021/bi00183a038] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The yeast recombination and repair proteins Rad1 and Rad10 associate with a 1:1 stoichiometry to form a stable complex with a relative molecular mass of 190 kDa. This complex, which has previously been shown to degrade single-stranded DNA endonucleolytically, also cleaves supercoiled duplex DNA molecules. In this reaction, supercoiled (form I) molecules are rapidly converted to nicked, relaxed (form II) molecules, presumably as a result of nicking at transient single-stranded regions in the supercoiled DNA. At high enzyme concentrations, there is a slow conversion of the form II molecules to linear (form III) molecules. The Rad1/Rad10 endonuclease does not preferentially cleave UV-irradiated DNA and has no detectable exonuclease activity. The nuclease activity of the Rad1/Rad10 complex is consistent with the predicted roles of the RAD1 and RAD10 genes of Saccharomyces cerevisiae in both the incision events of nucleotide excision repair and the removal of nonhomologous 3' single strands during intrachromosomal recombination between repeated sequences. In these pathways, the specificity and reactivity of the Rad1/Rad10 endonuclease will probably be modulated by further protein-protein interactions.
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Affiliation(s)
- A E Tomkinson
- Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas 75235
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19
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Friedberg EC, Bardwell AJ, Bardwell L, Wang Z, Dianov G. Transcription and nucleotide excision repair--reflections, considerations and recent biochemical insights. Mutat Res 1994; 307:5-14. [PMID: 7513823 DOI: 10.1016/0027-5107(94)90272-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recent years have witnessed considerable progress in the definition of the preferential repair of actively transcribed genes. Equally impressive progress has been achieved in our understanding of the genetic and biochemical complexity of the DNA-repair process called nucleotide excision repair (NER). Most recently studies in several laboratories have yielded observations which provide insights about how the processes of transcription and NER may be linked in prokaryotic and eukaryotic cells.
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Affiliation(s)
- E C Friedberg
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75235
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20
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Bardwell L, Bardwell AJ, Feaver WJ, Svejstrup JQ, Kornberg RD, Friedberg EC. Yeast RAD3 protein binds directly to both SSL2 and SSL1 proteins: implications for the structure and function of transcription/repair factor b. Proc Natl Acad Sci U S A 1994; 91:3926-30. [PMID: 8171014 PMCID: PMC43695 DOI: 10.1073/pnas.91.9.3926] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The RAD3 and SSL2 gene products are essential proteins that are also required for the nucleotide excision repair pathway. We have recently demonstrated that the RAD3 gene product along with the SSL1 and TFB1 gene products are subunits of RNA polymerase II basal transcription factor b. Additionally, the SSL2 gene product physically interacts with purified factor b. Here we combine an in vitro immunoprecipitation assay and an in vivo genetic assay to demonstrate a series of pairwise protein-protein interactions involving these components. RAD3 protein binds directly to both SSL2 protein and SSL1 protein in vitro. SSL1 protein interacts with itself and with RAD3 and TFB1 proteins in living yeast cells. An N-terminal, possibly noncatalytic, domain of SSL2 protein is sufficient for the factor b-SSL2 interaction, and a product of a DNA repair-defective allele of SSL2 is not defective in binding to factor b. We present genetic evidence suggesting that the DNA-repair function of SSL2 protein is not dependent on its essential function.
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Affiliation(s)
- L Bardwell
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75235
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21
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Feaver WJ, Svejstrup JQ, Bardwell L, Bardwell AJ, Buratowski S, Gulyas KD, Donahue TF, Friedberg EC, Kornberg RD. Dual roles of a multiprotein complex from S. cerevisiae in transcription and DNA repair. Cell 1993; 75:1379-87. [PMID: 8269516 DOI: 10.1016/0092-8674(93)90624-y] [Citation(s) in RCA: 267] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Yeast RNA polymerase II initiation factor b, homolog of human TFIIH, is a protein kinase capable of phosphorylating the C-terminal repeat domain of the polymerase; it possesses a DNA-dependent ATPase activity as well. The 85 kd and 50 kd subunits of factor b are now identified as RAD3 and SSL1 proteins, respectively; both are known to be involved in DNA repair. Factor b interacts specifically with another DNA repair protein, SSL2. The ATPase activity of factor b may be due entirely to that associated with a helicase function of RAD3. Factor b transcriptional activity was unaffected, however, by amino acid substitution at a conserved residue in the RAD3 nucleotide-binding domain, suggesting that the ATPase/helicase function is not required for transcription. These results identify factor b as a core repairosome, which may be responsible for the preferential repair of actively transcribed genes in eukaryotes.
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Affiliation(s)
- W J Feaver
- Department of Cell Biology, Stanford University School of Medicine, California 94305
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22
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Bardwell AJ, Bardwell L, Johnson DK, Friedberg EC. Yeast DNA recombination and repair proteins Rad1 and Rad10 constitute a complex in vivo mediated by localized hydrophobic domains. Mol Microbiol 1993; 8:1177-88. [PMID: 8361362 DOI: 10.1111/j.1365-2958.1993.tb01662.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The Saccharomyces cerevisiae Rad1 and Rad10 proteins are required for damage-specific incision during nucleotide excision repair and also for certain mitotic recombination events between repeated sequences. Previously we have demonstrated that Rad1 and Rad10 form a specific complex in vitro. Using the 'two-hybrid' genetic assay system we now report that Rad1 and Rad10 proteins are subunits of a specific complex in the cell nucleus. The Rad10-binding domain of Rad1 protein maps to a localized region between amino acids 809-997. The Rad1-binding domain of Rad10 protein maps between amino acids 90-210. These domains are evolutionarily conserved and are hydrophobic in character. Although significant homology exists between Rad10 and the human-DNA-repair protein Ercc1 in this region, we were unable to detect any interaction between Ercc1 and Rad1 proteins. We conclude that Rad1 and Rad10 operate in DNA repair and mitotic recombination as a constitutive complex.
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Affiliation(s)
- A J Bardwell
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas
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23
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Tomkinson AE, Bardwell AJ, Bardwell L, Tappe NJ, Friedberg EC. Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease. Nature 1993; 362:860-2. [PMID: 8479526 DOI: 10.1038/362860a0] [Citation(s) in RCA: 162] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Damage-specific recognition and incision of DNA during nucleotide excision repair in yeast and mammalian cells requires multiple gene products. Amino-acid sequence homology between several yeast and mammalian genes suggests that the mechanism of nucleotide excision repair is conserved in eukaryotes, but very little is known about its biochemistry. In the yeast Saccharomyces cerevisiae at least 6 genes are needed for this process, including RAD1 and RAD10 (ref. 1). Mutations in the two genes inactivate nucleotide excision repair and result in a reduced efficiency of mitotic recombinational events between repeated sequences. The Rad10 protein has a stable and specific interaction with Rad1 protein and also binds to single-stranded DNA and promotes annealing of homologous single-stranded DNA. The amino-acid sequence of the yeast Rad10 protein is homologous with that of the human excision repair gene ERCC1 (ref. 3). Here we demonstrate that a complex of purified Rad1 and Rad10 proteins specifically degrades single-stranded DNA by an endonucleolytic mechanism. This endonuclease activity is presumably required to remove non-homologous regions of single-stranded DNA during mitotic recombination between repeated sequences as previously suggested, and may also be responsible for the specific incision of damaged DNA during nucleotide excision repair.
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Affiliation(s)
- A E Tomkinson
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas 75235-9072
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