1
|
von Morgen P, Burdova K, Flower TG, O'Reilly NJ, Boulton SJ, Smerdon SJ, Macurek L, Hořejší Z. MRE11 stability is regulated by CK2-dependent interaction with R2TP complex. Oncogene 2017; 36:4943-4950. [PMID: 28436950 PMCID: PMC5531254 DOI: 10.1038/onc.2017.99] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/05/2017] [Accepted: 02/07/2017] [Indexed: 02/07/2023]
Abstract
The MRN (MRE11-RAD50-NBS1) complex is essential for repair of DNA double-strand breaks and stalled replication forks. Mutations of the MRN complex subunit MRE11 cause the hereditary cancer-susceptibility disease ataxia-telangiectasia-like disorder (ATLD). Here we show that MRE11 directly interacts with PIH1D1, a subunit of heat-shock protein 90 cochaperone R2TP complex, which is required for the assembly of large protein complexes, such as RNA polymerase II, small nucleolar ribonucleoproteins and mammalian target of rapamycin complex 1. The MRE11-PIH1D1 interaction is dependent on casein kinase 2 (CK2) phosphorylation of two acidic sequences within the MRE11 C terminus containing serines 558/561 and 688/689. Conversely, the PIH1D1 phospho-binding domain PIH-N is required for association with MRE11 phosphorylated by CK2. Consistent with these findings, depletion of PIH1D1 resulted in MRE11 destabilization and affected DNA-damage repair processes dependent on MRE11. Additionally, mutations of serines 688/689, which abolish PIH1D1 binding, also resulted in decreased MRE11 stability. As depletion of R2TP frequently leads to instability of its substrates and as truncation mutation of MRE11 lacking serines 688/689 leads to decreased levels of the MRN complex both in ATLD patients and an ATLD mouse model, our results suggest that the MRN complex is a novel R2TP complex substrate and that their interaction is regulated by CK2 phosphorylation.
Collapse
Affiliation(s)
- P von Morgen
- Department of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
| | - K Burdova
- Department of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - T G Flower
- Structural Biology of DNA-damage Signalling Laboratory, The Francis Crick Institute, London,UK
| | - N J O'Reilly
- Peptide Chemistry, The Francis Crick Institute, London, UK
| | - S J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - S J Smerdon
- Structural Biology of DNA-damage Signalling Laboratory, The Francis Crick Institute, London,UK
| | - L Macurek
- Department of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Z Hořejší
- Department of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Centre, Charterhouse Square, London, UK
| |
Collapse
|
2
|
Abstract
This study shows that the prenylated C‐terminus of RPGR can bind to PDE6δ with high affinity, suggesting two distinct binding sites of the RPGR/PDE6δ complex. The serine residue at the −3 position relative to the prenylated cysteine seems to play a key role in defining the selectivity of PDE6δ towards ciliary prenylated cargo.
Collapse
|
3
|
Hořejší Z, Stach L, Flower TG, Joshi D, Flynn H, Skehel JM, O'Reilly NJ, Ogrodowicz RW, Smerdon SJ, Boulton SJ. Phosphorylation-dependent PIH1D1 interactions define substrate specificity of the R2TP cochaperone complex. Cell Rep 2014; 7:19-26. [PMID: 24656813 PMCID: PMC3989777 DOI: 10.1016/j.celrep.2014.03.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/04/2014] [Accepted: 03/07/2014] [Indexed: 12/21/2022] Open
Abstract
The R2TP cochaperone complex plays a critical role in the assembly of multisubunit machines, including small nucleolar ribonucleoproteins (snoRNPs), RNA polymerase II, and the mTORC1 and SMG1 kinase complexes, but the molecular basis of substrate recognition remains unclear. Here, we describe a phosphopeptide binding domain (PIH-N) in the PIH1D1 subunit of the R2TP complex that preferentially binds to highly acidic phosphorylated proteins. A cocrystal structure of a PIH-N domain/TEL2 phosphopeptide complex reveals a highly specific phosphopeptide recognition mechanism in which Lys57 and 64 in PIH1D1, along with a conserved DpSDD phosphopeptide motif within TEL2, are essential and sufficient for binding. Proteomic analysis of PIH1D1 interactors identified R2TP complex substrates that are recruited by the PIH-N domain in a sequence-specific and phosphorylation-dependent manner suggestive of a common mechanism of substrate recognition. We propose that protein complexes assembled by the R2TP complex are defined by phosphorylation of a specific motif and recognition by the PIH1D1 subunit.
Collapse
Affiliation(s)
- Zuzana Hořejší
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - Lasse Stach
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Thomas G Flower
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Dhira Joshi
- Peptide Chemistry, London Research Institute, Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Helen Flynn
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - J Mark Skehel
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK; Biological Mass Spectrometry and Proteomics Group, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Nicola J O'Reilly
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK
| | - Roksana W Ogrodowicz
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stephen J Smerdon
- MRC National Institute for Medical Research, Division of Molecular Structure, The Ridgeway, Mill Hill, London NW7 1AA, UK.
| | - Simon J Boulton
- DNA Damage Response Laboratory, London Research Institute, Clare Hall, South Mimms EN6 3LD, UK.
| |
Collapse
|
4
|
Hancock DC, O'Reilly NJ. Synthetic peptides as antigens for antibody production. Methods Mol Biol 2005; 295:13-26. [PMID: 15596885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The use of synthetic peptide immunogens as a means to generate specific immunological reagents for a variety of purposes has increased markedly in recent years. In this chapter, we outline some of the salient factors to be considered when designing peptide immunogens and describe basic methodologies for the conjugation of short synthetic peptides to immunogenic carrier proteins.
Collapse
Affiliation(s)
- David C Hancock
- Signal Transduction Laboratory, Cancer Research UK, London Research Institute Laboratories, London, UK
| | | |
Collapse
|
5
|
Hancock DC, O'Reilly NJ. Production of polyclonal antibodies in rabbits. Methods Mol Biol 2005; 295:27-40. [PMID: 15596886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The generation of polyclonal antibodies to an antigen of interest is an important technique applicable to many areas of biological research. In this chapter, we describe a basic immunization procedure designed to generate polyclonal antisera in rabbits and two methods that are commonly employed in the subsequent preliminary characterization of antipeptide antibodies raised in this way.
Collapse
Affiliation(s)
- David C Hancock
- Signal Transduction Laboratory, Cancer Research UK, London Research Institute Laboratories, London, UK
| | | |
Collapse
|
6
|
|
7
|
Hart SL, Arancibia-Cárcamo CV, Wolfert MA, Mailhos C, O'Reilly NJ, Ali RR, Coutelle C, George AJ, Harbottle RP, Knight AM, Larkin DF, Levinsky RJ, Seymour LW, Thrasher AJ, Kinnon C. Lipid-mediated enhancement of transfection by a nonviral integrin-targeting vector. Hum Gene Ther 1998; 9:575-85. [PMID: 9525318 DOI: 10.1089/hum.1998.9.4-575] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.3] [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: 02/06/2023] Open
Abstract
Nonviral vectors consisting of integrin-targeting peptide/DNA (ID) complexes have the potential for widespread application in gene therapy. The transfection efficiency of this vector, however, has been limited by endosomal degradation. We now report that lipofectin (L) incorporated into the ID complexes enhances integrin-mediated transfection, increasing luciferase expression by more than 100-fold. The transfection efficiency of Lipofectin/Integrin-binding peptide/DNA (LID) complexes, assessed by beta-galactosidase reporter gene expression and X-gal staining, was improved from 1% to 10% to over 50% for three different cell lines, and from 0% to approximately 25% in corneal endothelium in vitro. Transfection complexes have been optimized with respect to their transfection efficiency and we have investigated their structure, function, and mode of transfection. Both ID and LID complexes formed particles, unlike the fibrous network formed by lipofectin/DNA complexes (LD). Integrin-mediated transfection by LID complexes was demonstrated by the substantially lower transfection efficiency of LKD complexes in which the integrin-biding peptide was substituted for K16 (K). Furthermore, the transfection efficiency of complexes was shown to be dependent on the amount of integrin-targeting ligand in the complex. Finally, a 34% reduction in integrin-mediated transfection efficiency by LID complexes was achieved with a competing monoclonal antibody. The role of lipofectin in LID complexes appears, therefore, to be that of a co-factor, enhancing the efficiency of integrin-mediated transfection. The mechanism of enhancement is likely to involve a reduction in the extent of endosomal degradation of DNA.
Collapse
Affiliation(s)
- S L Hart
- Molecular Immunology Unit, Institute of Child Health, University College London Medical School, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Lohmeyer M, Harrison PM, Kannan S, DeSantis M, O'Reilly NJ, Sternberg MJ, Salomon DS, Gullick WJ. Chemical synthesis, structural modeling, and biological activity of the epidermal growth factor-like domain of human cripto. Biochemistry 1997; 36:3837-45. [PMID: 9092813 DOI: 10.1021/bi961542p] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [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: 02/04/2023]
Abstract
Cripto, also known as human teratocarcinoma-derived growth factor 1 (TDGF-1), contains a 40 amino acid region with some similarity to the epidermal growth factor (EGF) domain. However, sequence homology is largely restricted to the classical cysteine/glycine motif with only limited similarities in other regions. Significant differences to human EGF include the absence of all seven residues between the two N-terminal half-cystines and a five-residue shorter loop between the third and fourth half-cystines. We examine the hypothesis that, in spite of these differences, cripto can adopt the characteristic EGF-like 1-3, 2-4, 5-6 disulfide bond pattern. A comparative structural model of the growth factor cripto was constructed on the basis of its similarity to EGF, transforming growth factor alpha (TGF-alpha), and the EGF-like domain of human clotting factor IX. The predicted disulfide bridges and disulfide-bridged loops were analyzed and appear viable in the modeled structure. Moreover, to ascertain the importance of disulfide arrangement for cripto bioactivity, two 47-residue peptides were synthesized and then refolded using either a simple oxidative or a controlled sequential refolding protocol. The cripto peptides were tested for their ability to stimulate MAP-kinase activity, for inhibition of beta-casein induction, and for Shc phosphorylation in MDA-MB 453 human mammary carcinoma cells and HC-11 mouse mammary epithelial cells. Data suggest that cripto does adopt the 1-3, 2-4, 5-6 disulfide pattern and thus forms the classical EGF-like fold in spite of the significant deletions within the folding domain. The predicted structure of cripto shows some of the characteristics of both the ErbB1- and ErbB3/ErbB4-binding growth factors.
Collapse
Affiliation(s)
- M Lohmeyer
- ICRF Molecular Oncology Laboratory, Hammersmith Hospital, Royal Postgraduate Medical School, London, U.K
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Borden KL, Lally JM, Martin SR, O'Reilly NJ, Solomon E, Freemont PS. In vivo and in vitro characterization of the B1 and B2 zinc-binding domains from the acute promyelocytic leukemia protooncoprotein PML. Proc Natl Acad Sci U S A 1996; 93:1601-6. [PMID: 8643677 PMCID: PMC39988 DOI: 10.1073/pnas.93.4.1601] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.3] [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: 02/01/2023] Open
Abstract
Acute promyelocytic leukemia (APL) has been ascribed to a chromosomal translocation event which results in a fusion protein comprising the PML protein and retinoic acid receptor alpha. PML is normally a component of a nuclear multiprotein complex which is disrupted in the APL disease state. Here, two newly defined cysteine/histidine-rich protein motifs called the B-box (B1 and B2) from PML have been characterized in terms of their effect on PML nuclear body formation, their dimerization, and their biophysical properties. We have shown that both peptides bind Zn2+, which induces changes in the peptides' structures. We demonstrate that mutants in both B1 and B2 do not form PML nuclear bodies in vivo and have a phenotype that is different from that observed in the APL disease state. Interestingly, these mutations do not affect the ability of wild-type PML to dimerize with mutant proteins in vitro, suggesting that the B1 and B2 domains are involved in an additional interaction central to PML nuclear body formation. This report in conjunction with our previous work demonstrates that the PML RING-Bl/B2 motif plays a fundamental role in formation of a large multiprotein complex, a function that may be common to those unrelated proteins which contain the motif.
Collapse
Affiliation(s)
- K L Borden
- Protein Structure Laboratory, Imperial Cancer Research Fund, London, United Kingdom
| | | | | | | | | | | |
Collapse
|
10
|
Borden KL, Lally JM, Martin SR, O'Reilly NJ, Etkin LD, Freemont PS. Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development. EMBO J 1995; 14:5947-56. [PMID: 8846787 PMCID: PMC394714 DOI: 10.1002/j.1460-2075.1995.tb00283.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [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: 11/08/2022] Open
Abstract
Xenopus nuclear factor XNF7, a maternally expressed protein, functions in patterning of the embryo. XNF7 contains a number of defined protein domains implicated in the regulation of some developmental processes. Among these is a tripartite motif comprising a zinc-binding RING finger and B-box domain next to a predicted alpha-helical coiled-coil domain. Interestingly, this motif is found in a variety of protein including several proto-oncoproteins. Here we describe the solution structure of the XNF7 B-box zinc-binding domain determined at physiological pH by 1H NMR methods. The B-box structure represents the first three-dimensional structure of this new motif and comprises a monomer have two beta-strands, two helical turns and three extended loop regions packed in a novel topology. The r.m.s. deviation for the best 18 structures is 1.15 A for backbone atoms and 1.94 A for all atoms. Structure calculations and biochemical data shows one zinc atom ligated in a Cys2-His2 tetrahedral arrangement. We have used mutant peptides to determine the metal ligation scheme which surprisingly shows that not all of the seven conserved cysteines/histidines in the B-box motif are involved in metal ligation. The B-box structure is not similar in tertiary fold to any other known zinc-binding motif.
Collapse
Affiliation(s)
- K L Borden
- Laboratory of Molecular Structure, National Institute for Medical Research, London, UK
| | | | | | | | | | | |
Collapse
|
11
|
Abstract
Synthetic peptides play an important role in many areas of biological research. Advances in synthetic chemistry and automation over the past few years have resulted in increasingly reliable and rapid syntheses. As a result, peptides are now frequently employed in immunological studies, structural studies, as enzyme substrates, in ligand/receptor studies, and as probes for a range of molecular interactions. This review describes solid-phase peptide synthesis and the applications of synthetic peptides in molecular biology and biochemistry.
Collapse
Affiliation(s)
- D C Hancock
- Biochemistry of the Cell Nucleus and Peptide Synthesis Laboratories, Imperial Cancer Research Fund, London, UK
| | | | | |
Collapse
|
12
|
Borden KL, Boddy MN, Lally J, O'Reilly NJ, Martin S, Howe K, Solomon E, Freemont PS. The solution structure of the RING finger domain from the acute promyelocytic leukaemia proto-oncoprotein PML. EMBO J 1995; 14:1532-41. [PMID: 7729428 PMCID: PMC398240 DOI: 10.1002/j.1460-2075.1995.tb07139.x] [Citation(s) in RCA: 239] [Impact Index Per Article: 8.2] [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: 11/10/2022] Open
Abstract
Acute promyelocytic leukaemia (APL) has been ascribed to a chromosomal translocation event which results in a fusion protein comprising the PML protein and the retinoic acid receptor alpha. PML is normally a component of a nuclear multiprotein complex (termed ND10, Kr bodies, nuclear bodies, PML oncogenic domains or PODs) which is disrupted in the APL disease state. PML contains a number of characterized motifs including a Zn2+ binding domain called the RING or C3HC4 finger. Here we describe the solution structure of the PML RING finger as solved by 1H NMR methods at physiological pH with r.m.s. deviations for backbone atoms of 0.88 and 1.39 A for all atoms. Additional biophysical studies including CD and optical spectroscopy, show that the PML RING finger requires Zn2+ for autonomous folding and that cysteines are used in metal ligation. A comparison of the structure with the previously solved equine herpes virus IE110 RING finger, shows significant differences suggesting that the RING motif is structurally diverse. The role of the RING domain in PML nuclear body formation was tested in vivo, by using site-directed mutagenesis and immunofluorescence on transiently transfected NIH 3T3 cells. Independently mutating two pairs of cysteines in each of the Zn2+ binding sites prevents PML nuclear body formation, suggesting that a fully folded RING domain is necessary for this process. These results suggest that the PML RING domain is probably involved in protein-protein interactions, a feature which may be common to other RING finger domains.
Collapse
Affiliation(s)
- K L Borden
- Laboratory of Molecular Structure, Biochemistry, National Institute for Medical Research, Mill Hill, London, UK
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Borden KL, Martin SR, O'Reilly NJ, Lally JM, Reddy BA, Etkin LD, Freemont PS. Characterisation of a novel cysteine/histidine-rich metal binding domain from Xenopus nuclear factor XNF7. FEBS Lett 1993; 335:255-60. [PMID: 8253208 DOI: 10.1016/0014-5793(93)80741-c] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [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: 01/29/2023]
Abstract
A 42 amino acid synthetic peptide corresponding to a newly defined cysteine/histidine-rich protein motif called B-box, from the Xenopus protein XNF7 has been characterised. The metal-binding stoichiometry and dissociation constant for zinc were determined by competition with the chromophoric chelator Br2BAPTA, demonstrating that one zinc atom binds per molecule of peptide despite the presence of seven putative metal ligands, and represents the first application of this method to measuring zinc stoichiometry of proteins and/or peptides. Cobalt binding studies indicate that the motif binds zinc more tightly than cobalt, that cysteines are used as ligands and that the cation is co-ordinated tetrahedrally. Circular dichroism and NMR studies both indicate that the B-box peptide is structured only in the presence of zinc, copper and to a lesser extent cobalt.
Collapse
Affiliation(s)
- K L Borden
- National Institute for Medical Research, The Ridgeway, London, UK
| | | | | | | | | | | | | |
Collapse
|
14
|
Lovering R, Hanson IM, Borden KL, Martin S, O'Reilly NJ, Evan GI, Rahman D, Pappin DJ, Trowsdale J, Freemont PS. Identification and preliminary characterization of a protein motif related to the zinc finger. Proc Natl Acad Sci U S A 1993; 90:2112-6. [PMID: 7681583 PMCID: PMC46035 DOI: 10.1073/pnas.90.6.2112] [Citation(s) in RCA: 244] [Impact Index Per Article: 7.9] [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
We have identified a protein motif, related to the zinc finger, which defines a newly discovered family of proteins. The motif was found in the sequence of the human RING1 gene, which is proximal to the major histocompatibility complex region on chromosome six. We propose naming this motif the "RING finger" and it is found in 27 proteins, all of which have putative DNA binding functions. We have synthesized a peptide corresponding to the RING1 motif and examined a number of properties, including metal and DNA binding. We provide evidence to support the suggestion that the RING finger motif is the DNA binding domain of this newly defined family of proteins.
Collapse
Affiliation(s)
- R Lovering
- Human Immunogenetics Laboratory, Imperial Cancer Research Fund, London, United Kingdom
| | | | | | | | | | | | | | | | | | | |
Collapse
|