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Comijn J, Berx G, Vermassen P, Verschueren K, van Grunsven L, Bruyneel E, Mareel M, Huylebroeck D, van Roy F. The two-handed E box binding zinc finger protein SIP1 downregulates E-cadherin and induces invasion. Mol Cell 2001; 7:1267-78. [PMID: 11430829 DOI: 10.1016/s1097-2765(01)00260-x] [Citation(s) in RCA: 1056] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transcriptional downregulation of E-cadherin appears to be an important event in the progression of various epithelial tumors. SIP1 (ZEB-2) is a Smad-interacting, multi-zinc finger protein that shows specific DNA binding activity. Here, we report that expression of wild-type but not of mutated SIP1 downregulates mammalian E-cadherin transcription via binding to both conserved E2 boxes of the minimal E-cadherin promoter. SIP1 and Snail bind to partly overlapping promoter sequences and showed similar silencing effects. SIP1 can be induced by TGF-beta treatment and shows high expression in several E-cadherin-negative human carcinoma cell lines. Conditional expression of SIP1 in E-cadherin-positive MDCK cells abrogates E-cadherin-mediated intercellular adhesion and simultaneously induces invasion. SIP1 therefore appears to be a promoter of invasion in malignant epithelial tumors.
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Verschueren K, Remacle JE, Collart C, Kraft H, Baker BS, Tylzanowski P, Nelles L, Wuytens G, Su MT, Bodmer R, Smith JC, Huylebroeck D. SIP1, a novel zinc finger/homeodomain repressor, interacts with Smad proteins and binds to 5'-CACCT sequences in candidate target genes. J Biol Chem 1999; 274:20489-98. [PMID: 10400677 DOI: 10.1074/jbc.274.29.20489] [Citation(s) in RCA: 387] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activation of transforming growth factor beta receptors causes the phosphorylation and nuclear translocation of Smad proteins, which then participate in the regulation of expression of target genes. We describe a novel Smad-interacting protein, SIP1, which was identified using the yeast two-hybrid system. Although SIP1 interacts with the MH2 domain of receptor-regulated Smads in yeast and in vitro, its interaction with full-length Smads in mammalian cells requires receptor-mediated Smad activation. SIP1 is a new member of the deltaEF1/Zfh-1 family of two-handed zinc finger/homeodomain proteins. Like deltaEF1, SIP1 binds to 5'-CACCT sequences in different promoters, including the Xenopus brachyury promoter. Overexpression of either full-length SIP1 or its C-terminal zinc finger cluster, which bind to the Xbra2 promoter in vitro, prevented expression of the endogenous Xbra gene in early Xenopus embryos. Therefore, SIP1, like deltaEF1, is likely to be a transcriptional repressor, which may be involved in the regulation of at least one immediate response gene for activin-dependent signal transduction pathways. The identification of this Smad-interacting protein opens new routes to investigate the mechanisms by which transforming growth factor beta members exert their effects on expression of target genes in responsive cells and in the vertebrate embryo.
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Chang H, Huylebroeck D, Verschueren K, Guo Q, Matzuk MM, Zwijsen A. Smad5 knockout mice die at mid-gestation due to multiple embryonic and extraembryonic defects. Development 1999; 126:1631-42. [PMID: 10079226 DOI: 10.1242/dev.126.8.1631] [Citation(s) in RCA: 284] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Smad5 has been implicated as a downstream signal mediator for several bone morphogenetic proteins (BMPs). To understand the in vivo function of Smad5, we generated mice deficient in Smad5 using embryonic stem (ES) cell technology. Homozygous mutant embryos die between E9.5 and E11.5, and display variable phenotypes. Morphological defects are first detected at E8.0 in the developing amnion, gut and heart (the latter defect being similar to BMP-2 knockout mice). At later stages, mutant embryos fail to undergo proper turning, have craniofacial and neural tube abnormalities, and are edematous. In addition, several extraembryonic lesions are observed. After E9.0, the yolk sacs of the mutants contain red blood cells but lack a well-organized vasculature, which is reminiscent of BMP-4, TGF-beta1 and TGF-beta type II receptor knockout mice. In addition, the allantois of many Smad5 mutants is fused to the chorion, but is not well-elongated. A unique feature of the Smad5 mutant embryos is that ectopic vasculogenesis and hematopoiesis is observed in the amnion, likely due to mislocation of allantois tissue. Despite the expression of Smad5 from gastrulation onwards, and in contrast to knockouts of Smad2 and Smad4, Smad5 only becomes essential later in extraembryonic and embryonic development.
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Cao L, Coventry B, Goreshnik I, Huang B, Sheffler W, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D. Design of protein-binding proteins from the target structure alone. Nature 2022; 605:551-560. [PMID: 35332283 PMCID: PMC9117152 DOI: 10.1038/s41586-022-04654-9] [Citation(s) in RCA: 247] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/15/2022] [Indexed: 12/03/2022]
Abstract
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1-5. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
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Research Support, N.I.H., Extramural |
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Fritze CE, Verschueren K, Strich R, Easton Esposito R. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J 1997; 16:6495-509. [PMID: 9351831 PMCID: PMC1170255 DOI: 10.1093/emboj/16.21.6495] [Citation(s) in RCA: 235] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The yeast SIR2 gene maintains inactive chromatin domains required for transcriptional repression at the silent mating-type loci and telomeres. We previously demonstrated that SIR2 also acts to repress mitotic and meiotic recombination between the tandem ribosomal RNA gene array (rDNA). Here we address whether rDNA chromatin structure is altered by loss of SIR2 function by in vitro and in vivo assays of sensitivity to micrococcal nuclease and dam methyltransferase, respectively, and present the first chromatin study that maps sites of SIR2 action within the rDNA locus. Control studies at the MAT alpha locus also revealed a previously undetected MNase-sensitive site at the a1-alpha 2 divergent promoter which is protected in sir2 mutant cells by the derepressed a1-alpha 2 regulator. In rDNA, SIR2 is required for a more closed chromatin structure in two regions: SRR1, the major SIR-Responsive Region in the non-transcribed spacer, and SRR2, in the 18S rRNA coding region. None of the changes in rDNA detected in sir2 mutants are due to the presence of the a1-alpha 2 repressor. Reduced recombination in the rDNA correlates with a small, reproducible transcriptional silencing position effect. Deletion and overexpression studies demonstrate that SIR2, but not SIR1, SIR3 or SIR4, is required for this rDNA position effect. Significantly, rDNA transcriptional silencing and rDNA chromatin accessibility respond to SIR2 dosage, indicating that SIR2 is a limiting component required for chromatin modeling in rDNA.
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MESH Headings
- Chromatin/ultrastructure
- Chromosomes, Fungal/ultrastructure
- DNA, Fungal/genetics
- DNA, Ribosomal/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Gene Expression Regulation, Fungal
- Histone Deacetylases
- Mating Factor
- Peptides/genetics
- RNA, Fungal/genetics
- RNA, Ribosomal, 18S/genetics
- Recombination, Genetic/physiology
- Regulatory Sequences, Nucleic Acid
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/ultrastructure
- Sequence Deletion
- Silent Information Regulator Proteins, Saccharomyces cerevisiae
- Sirtuin 2
- Sirtuins
- Trans-Activators/genetics
- Trans-Activators/physiology
- Transcription, Genetic/physiology
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Dewulf N, Verschueren K, Lonnoy O, Morén A, Grimsby S, Vande Spiegle K, Miyazono K, Huylebroeck D, Ten Dijke P. Distinct spatial and temporal expression patterns of two type I receptors for bone morphogenetic proteins during mouse embryogenesis. Endocrinology 1995; 136:2652-63. [PMID: 7750489 DOI: 10.1210/endo.136.6.7750489] [Citation(s) in RCA: 226] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Bone morphogenetic proteins (BMPs) are multifunctional proteins structurally related to transforming growth factor-beta (TGF beta) and activin that can induce cartilage and bone growth in vivo. Members of the TGF beta superfamily exert their biological effects via heteromeric serine/threonine kinase complexes of type I and type II receptors. We previously obtained six different type I receptors, termed activin receptor-like kinase-1 (ALK-1) to -6. ALK-5 is a TGF beta type I receptor, ALK-2 and ALK-4 are activin type I receptors, and ALK-3 and ALK-6 are type I receptors for osteogenic protein-1 (OP-1)/bone morphogenetic protein-7 (BMP-7) and BMP-4. Here we report the complementary DNA cloning of the mouse homolog of ALK-3, which is highly conserved between mouse and man. ALK-3 messenger RNA (mRNA) is ubiquitously expressed in various adult mouse tissues, whereas ALK-6 mRNA is only found in brain and lung. The distribution of ALK-3 and ALK-6 mRNA in the postimplantation mouse embryo [6.5-15.5 days postcoitum (pc)] was studied by in situ hybridization. ALK-3 was nearly ubiquitously expressed throughout these stages of development, but was notably absent in the liver. In contrast, ALK-6 showed a more restricted expression pattern. ALK-6 mRNA was absent in early postimplantation embryos, was detected first in 9.5 days pc embryos, and persisted until 15.5 days pc. In midgestation embryos, ALK-6 transcripts were detected in mesenchymal precartilage condensations, premuscle masses, blood vessels, central nervous system, parts of the developing ear and eye, and epithelium. The expression in sites of developing cartilage and bone supports the idea that ALK-3 and -6 are receptors for BMPs in vivo. In addition, the expression of these genes in many soft tissues suggests broader functions for BMPs in embryogenesis.
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Comparative Study |
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Remacle JE, Kraft H, Lerchner W, Wuytens G, Collart C, Verschueren K, Smith JC, Huylebroeck D. New mode of DNA binding of multi-zinc finger transcription factors: deltaEF1 family members bind with two hands to two target sites. EMBO J 1999; 18:5073-84. [PMID: 10487759 PMCID: PMC1171578 DOI: 10.1093/emboj/18.18.5073] [Citation(s) in RCA: 220] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
SIP1, a Smad-interacting protein, and deltaEF1, a transcriptional repressor involved in skeletal and T-cell development, belong to the same family of DNA binding proteins. SIP1 and deltaEF1 contain two separated clusters of zinc fingers, one N-terminal and one C-terminal. These clusters show high sequence homology and are highly conserved between SIP1 and deltaEF1. Each zinc finger cluster binds independently to a 5'-CACCT sequence. However, high-affinity binding sites for full-length SIP1 and deltaEF1 in the promoter regions of candidate target genes like Xenopus Xbra2, and human alpha4-integrin and E-cadherin, are bipartite elements composed of one CACCT and one CACCTG sequence, the orientation and spacing of which can vary. Using transgenic Xenopus embryos, we demonstrate that the integrity of these two sequences is necessary for correct spatial expression of a Xbra2 promoter-driven reporter gene. Both zinc finger clusters must be intact for the high-affinity binding of SIP1 to DNA and for its optimal repressor activity. Our results show that SIP1 binds as monomer and contacts one target sequence with the first zinc finger cluster, and the other with the second cluster. Our work redefines the optimal binding site and, consequently, candidate target genes for vertebrate members of the deltaEF1 family.
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research-article |
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Persson EK, Verstraete K, Heyndrickx I, Gevaert E, Aegerter H, Percier JM, Deswarte K, Verschueren KHG, Dansercoer A, Gras D, Chanez P, Bachert C, Gonçalves A, Van Gorp H, De Haard H, Blanchetot C, Saunders M, Hammad H, Savvides SN, Lambrecht BN. Protein crystallization promotes type 2 immunity and is reversible by antibody treatment. Science 2019; 364:364/6442/eaaw4295. [PMID: 31123109 DOI: 10.1126/science.aaw4295] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/05/2019] [Indexed: 01/05/2023]
Abstract
Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such as asthma. We found that CLCs derived from patients showed crystal packing and Gal10 structure identical to those of Gal10 crystals grown in vitro. When administered to the airways, crystalline Gal10 stimulated innate and adaptive immunity and acted as a type 2 adjuvant. By contrast, a soluble Gal10 mutein was inert. Antibodies directed against key epitopes of the CLC crystallization interface dissolved preexisting CLCs in patient-derived mucus within hours and reversed crystal-driven inflammation, goblet-cell metaplasia, immunoglobulin E (IgE) synthesis, and bronchial hyperreactivity (BHR) in a humanized mouse model of asthma. Thus, protein crystals may promote hallmark features of asthma and are targetable by crystal-dissolving antibodies.
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Research Support, Non-U.S. Gov't |
6 |
202 |
9
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De Genst EJ, Guilliams T, Wellens J, O'Day EM, Waudby CA, Meehan S, Dumoulin M, Hsu STD, Cremades N, Verschueren KHG, Pardon E, Wyns L, Steyaert J, Christodoulou J, Dobson CM. Structure and properties of a complex of α-synuclein and a single-domain camelid antibody. J Mol Biol 2010; 402:326-43. [PMID: 20620148 DOI: 10.1016/j.jmb.2010.07.001] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 07/01/2010] [Accepted: 07/02/2010] [Indexed: 10/19/2022]
Abstract
The aggregation of the intrinsically disordered protein α-synuclein to form fibrillar amyloid structures is intimately associated with a variety of neurological disorders, most notably Parkinson's disease. The molecular mechanism of α-synuclein aggregation and toxicity is not yet understood in any detail, not least because of the paucity of structural probes through which to study the behavior of such a disordered system. Here, we describe an investigation involving a single-domain camelid antibody, NbSyn2, selected by phage display techniques to bind to α-synuclein, including the exploration of its effects on the in vitro aggregation of the protein under a variety of conditions. We show using isothermal calorimetric methods that NbSyn2 binds specifically to monomeric α-synuclein with nanomolar affinity and by means of NMR spectroscopy that it interacts with the four C-terminal residues of the protein. This latter finding is confirmed by the determination of a crystal structure of NbSyn2 bound to a peptide encompassing the nine C-terminal residues of α-synuclein. The NbSyn2:α-synuclein interaction is mediated mainly by side-chain interactions while water molecules cross-link the main-chain atoms of α-synuclein to atoms of NbSyn2, a feature we believe could be important in intrinsically disordered protein interactions more generally. The aggregation behavior of α-synuclein at physiological pH, including the morphology of the resulting fibrillar structures, is remarkably unaffected by the presence of NbSyn2 and indeed we show that NbSyn2 binds strongly to the aggregated as well as to the soluble forms of α-synuclein. These results give strong support to the conjecture that the C-terminal region of the protein is not directly involved in the mechanism of aggregation and suggest that binding of NbSyn2 could be a useful probe for the identification of α-synuclein aggregation in vitro and possibly in vivo.
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Research Support, Non-U.S. Gov't |
15 |
144 |
10
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Tan J, Verschueren KHG, Anand K, Shen J, Yang M, Xu Y, Rao Z, Bigalke J, Heisen B, Mesters JR, Chen K, Shen X, Jiang H, Hilgenfeld R. pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses. J Mol Biol 2005; 354:25-40. [PMID: 16242152 PMCID: PMC7094468 DOI: 10.1016/j.jmb.2005.09.012] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 08/24/2005] [Accepted: 09/07/2005] [Indexed: 02/04/2023]
Abstract
The SARS coronavirus main proteinase (Mpro) is a key enzyme in the processing of the viral polyproteins and thus an attractive target for the discovery of drugs directed against SARS. The enzyme has been shown by X-ray crystallography to undergo significant pH-dependent conformational changes. Here, we assess the conformational flexibility of the Mpro by analysis of multiple crystal structures (including two new crystal forms) and by molecular dynamics (MD) calculations. The MD simulations take into account the different protonation states of two histidine residues in the substrate-binding site and explain the pH-activity profile of the enzyme. The low enzymatic activity of the Mpro monomer and the need for dimerization are also discussed.
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Research Support, Non-U.S. Gov't |
20 |
144 |
11
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de Winter JP, ten Dijke P, de Vries CJ, van Achterberg TA, Sugino H, de Waele P, Huylebroeck D, Verschueren K, van den Eijnden-van Raaij AJ. Follistatins neutralize activin bioactivity by inhibition of activin binding to its type II receptors. Mol Cell Endocrinol 1996; 116:105-14. [PMID: 8822271 DOI: 10.1016/0303-7207(95)03705-5] [Citation(s) in RCA: 142] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Follistatin is an activin-binding protein, which inhibits activin bioactivity in several biological systems. In the present study it is demonstrated that preincubation of iodinated activin A with follistatin, purified from porcine follicular fluid, completely abolished the binding of activin to activin type IIA, IIB2 and IIB4 receptors, and consequently to activin type IB receptor, transiently transfected in COS cells. Binding of activin A to membrane proteins on the activin-responsive P19 embryonal carcinoma cells was also prevented by this follistatin preparation. The same results were obtained with a carboxy-terminally truncated form of follistatin (FS-288), which is only present in minor amounts in the purified follistatin preparation. Since FS-288 has a high affinity for heparan sulfate proteoglycans on the cell surface, we tested whether membrane-bound FS-288 presents activin A to the different activin receptors, thereby facilitating activin binding. FS-288 did bind to the cell surface of transfected COS cells, but inhibited the binding of activin A to its receptors IIA, IIB2 and IIB4. Furthermore, after addition of FS-288 to K562 erythroleukemia cells, the total binding of activin via cell surface-bound FS-288 was increased, whereas the binding of activin A to activin type II and type I receptors present on these cells was inhibited. These findings reveal that different forms of follistatin can neutralize activin bioactivity by interference with binding of activin to all known activin type II receptors, rather than that they inhibit the binding of the type I receptor to the activin/activin type II receptor complex. In addition, our studies indicate that cell surface-associated follistatin cannot present ligand to signalling receptors.
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Verschueren K, Marcoen A. Representation of self and socioemotional competence in kindergartners: differential and combined effects of attachment to mother and to father. Child Dev 1999; 70:183-201. [PMID: 10191522 DOI: 10.1111/1467-8624.00014] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In the present study, we examined the differential predictive power and the joint or compensatory effects of representations of child-mother and child-father attachment for children's representation of self and their socioemotional competence. The representations of attachment were assessed by an attachment story completion task, completed once for mother and once for father (in counterbalanced order). Eighty participants (40 boys and 40 girls), aged between 55 and 77 months (M = 5 years 3 months), took place in the study. The socioemotional competence (peer social competence, disruptive behavior, anxious/withdrawn behavior, and school adjustment) and behavioral manifestations of self-esteem were evaluated by the kindergarten teacher. The inner representation of self (positiveness of self, perceived competence, and social acceptance) was assessed in a subgroup of 50 children. Results showed that the relative predictive power of child-mother and child-father attachments differed according to the domain of child functioning that was assessed. More specifically, it was found that the child's positiveness of self was better predicted by the quality of the child-mother attachment representation than by the quality of the child-father attachment representation. In contrast, the child's anxious/withdrawn behavioral problems were better predicted by the quality of the child-father attachment representation than by the quality of the child-mother attachment representation. With regard to the joint effects of child-mother and child-father attachment, it was found that a secure attachment to one parent can compensate for or buffer against an insecure attachment to the other parent. However, the buffering effect was not complete.
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Comparative Study |
26 |
138 |
13
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Verschueren K, Dewulf N, Goumans MJ, Lonnoy O, Feijen A, Grimsby S, Vandi Spiegle K, ten Dijke P, Morén A, Vanscheeuwijck P, Heldin CH, Miyazono K, Mummery C, Van Den Eijnden-Van Raaij J, Huylebroeck D. Expression of type I and type IB receptors for activin in midgestation mouse embryos suggests distinct functions in organogenesis. Mech Dev 1995; 52:109-23. [PMID: 7577669 DOI: 10.1016/0925-4773(95)00395-h] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Activins exert their effects by inducing heteromeric complexes of either of two different type I receptors, ActR-I or ActR-IB, and either of two type II receptors, ActR-II or ActR-IIB. We describe the cDNA cloning of the mouse homologue of human ActR-IB and analyze binding of radio-iodinated activin on type I/type II combinations of mouse receptors expressed from cDNA. We studied the distribution of ActR-I and ActR-IB mRNAs in postimplantation mouse embryos by in situ hybridization. In the 12.5-day postcoitum embryo, both mRNAs are found in the brain, spinal cord, some ganglia, vibrissae, lungs, body wall, stomach, gonads, ribs, limbs and shoulders. ActR-I mRNA, but not ActR-IB, is expressed in blood vessels, the heart, tongue, intervertebral discs and diaphragm. Conversely, only ActR-IB mRNA is detected in the olfactory region, eye, tooth primordium, esophagus, mesonephros, dorsal root ganglia and is strongly expressed in the spinal cord. Our results demonstrate similarities, but also differences and complementarities (mesenchymal versus epithelial expression) between the expression patterns of these type I receptors. Moreover, their expression patterns overlap with at least one of the type II activin receptors and/or one of activin subunits in some regions of the embryo, such as the brain, spinal cord, pituitary, whisker follicles, and the inner nuclear neuroblastic layer of the eye.
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94 |
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Verschueren KHG, Blanchet C, Felix J, Dansercoer A, De Vos D, Bloch Y, Van Beeumen J, Svergun D, Gutsche I, Savvides SN, Verstraete K. Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle. Nature 2019; 568:571-575. [DOI: 10.1038/s41586-019-1095-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/08/2019] [Indexed: 01/28/2023]
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68 |
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Verschueren KHG, Pumpor K, Anemüller S, Chen S, Mesters JR, Hilgenfeld R. A structural view of the inactivation of the SARS coronavirus main proteinase by benzotriazole esters. ACTA ACUST UNITED AC 2008; 15:597-606. [PMID: 18559270 PMCID: PMC7110992 DOI: 10.1016/j.chembiol.2008.04.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 04/16/2008] [Accepted: 04/17/2008] [Indexed: 01/04/2023]
Abstract
The main proteinase (Mpro) of the severe acute respiratory syndrome (SARS) coronavirus is a principal target for the design of anticoronaviral compounds. Benzotriazole esters have been reported as potent nonpeptidic inhibitors of the enzyme, but their exact mechanism of action remains unclear. Here we present crystal structures of SARS-CoV Mpro, the active-site cysteine of which has been acylated by benzotriazole esters that act as suicide inhibitors. In one of the structures, the thioester product has been hydrolyzed and benzoic acid is observed to bind to the hydrophobic S2 pocket. This structure also features the enzyme with a shortened N-terminal segment (“amputated N finger”). The results further the understanding of the important role of the N finger for catalysis as well as the design of benzotriazole inhibitors with improved specificity.
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Research Support, Non-U.S. Gov't |
17 |
65 |
16
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Tourwé D, Verschueren K, Frycia A, Davis P, Porreca F, Hruby VJ, Toth G, Jaspers H, Verheyden P, Van Binst G. Conformational restriction of Tyr and Phe side chains in opioid peptides: information about preferred and bioactive side-chain topology. Biopolymers 1996; 38:1-12. [PMID: 8679939 DOI: 10.1002/(sici)1097-0282(199601)38:1<1::aid-bip1>3.0.co;2-#] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The side chain of Tyr and Phe was fixed into the gauche(-) or gauche(+) conformation by using the Tic Htc structures, and into the trans conformation by using an aminobenzazepine-type (Aba) structure. When incorporated into dermorphin or deltorphin II, the Tic and Htc analogues all showed a large decrease in both mu and delta affinities and activities. Fixation of Phe(3) in the trans rotamer resulted in a large increase in delta affinity in the dermorphin analogue, whereas in the [Aba(3)-Gly(4)] deltorphin II analogue, good delta affinity is maintained despite the removal of the Glu side chain. Whereas several authors propose a gauche(-) preferred conformation for the Phe(3) side chain, these results suggest a trans conformation at the delta receptor. The use of these conformationally constrained residues for evaluating the preferred solution conformation in the flexible N-terminal tripeptide Tyr-D-Ala-Phe is illustrated. The (1)H-nmr parameters--chemical shift, temperature dependence, and nuclear Overhauser effects to the D-Ala(2) methyl protons in the different analogues--provide direct evidence to confirm the proposed sandwich conformation in the native peptides.
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Meersseman G, Verschueren K, Nelles L, Blumenstock C, Kraft H, Wuytens G, Remacle J, Kozak CA, Tylzanowski P, Niehrs C, Huylebroeck D. The C-terminal domain of Mad-like signal transducers is sufficient for biological activity in the Xenopus embryo and transcriptional activation. Mech Dev 1997; 61:127-40. [PMID: 9076683 DOI: 10.1016/s0925-4773(96)00629-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report the characterization of two vertebrate homologs of Drosophila mothers against dpp (Mad) isolated from the mouse and the Xenopus embryo, named MusMLP (mad-like protein) and XenMLP, respectively, together with a summary of their expression patterns in the embryo. Overexpression of XenMLP causes ventralization of Xenopus embryos and we demonstrate that the C-terminal domain is necessary and sufficient to confer this biological effect. This domain also has the potential for transcriptional activation, as shown in one-hybrid assays in mammalian cells. We further demonstrate that MLPs are multidomain proteins by showing a cis-negative effect of the N-terminal domain on the transactivation by the C-terminal domain and that the proline-rich, middle domain maximizes the activity of the C-terminal domain. We also mapped the MusMLP gene to a region on mouse chromosome 13 that corresponds to a region on human chromosome 5q that contains cancer-related genes.
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Vincent F, Charnock SJ, Verschueren KHG, Turkenburg JP, Scott DJ, Offen WA, Roberts S, Pell G, Gilbert HJ, Davies GJ, Brannigan JA. Multifunctional xylooligosaccharide/cephalosporin C deacetylase revealed by the hexameric structure of the Bacillus subtilis enzyme at 1.9A resolution. J Mol Biol 2003; 330:593-606. [PMID: 12842474 DOI: 10.1016/s0022-2836(03)00632-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Esterases and deacetylases active on carbohydrate ligands have been classified into 14 families based upon amino acid sequence similarities. Enzymes from carbohydrate esterase family seven (CE-7) are unusual in that they display activity towards both acetylated xylooligosaccharides and the antibiotic, cephalosporin C. The 1.9A structure of the multifunctional CE-7 esterase (hereinafter CAH) from Bacillus subtilis 168 reveals a classical alpha/beta hydrolase fold encased within a 32 hexamer. This is the first example of a hexameric alpha/beta hydrolase and is further evidence of the versatility of this particular fold, which is used in a wide variety of biological contexts. A narrow entrance tunnel leads to the centre of the molecule, where the six active-centre catalytic triads point towards the tunnel interior and thus are sequestered away from cytoplasmic contents. By analogy to self-compartmentalising proteases, the tunnel entrance may function to hinder access of large substrates to the poly-specific active centre. This would explain the observation that the enzyme is active on a variety of small, acetylated molecules. The structure of an active site mutant in complex with the reaction product, acetate, reveals details of the putative oxyanion binding site, and suggests that substrates bind predominantly through non-specific contacts with protein hydrophobic residues. Protein residues involved in catalysis are tethered by interactions with protein excursions from the canonical alpha/beta hydrolase fold. These excursions also mediate quaternary structure maintenance, so it would appear that catalytic competence is only achieved on protein multimerisation. We suggest that the acetyl xylan esterase (EC 3.1.1.72) and cephalosporin C deacetylase (EC 3.1.1.41) enzymes of the CE-7 family represent a single class of proteins with a multifunctional deacetylase activity against a range of small substrates.
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Van Ranst N, Verschueren K, Marcoen A. The meaning of grandparents as viewed by adolescent grandchildren: an empirical study in Belgium. Int J Aging Hum Dev 1995; 41:311-24. [PMID: 8821242 DOI: 10.2190/pplv-dwg7-hv9r-6lvb] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Why do adolescents value their grandparents? This was the leading question of an investigation among 563 adolescents and young adults in Flanders (Belgium). The Grandparent Meaning Scale which probes eleven a priori dimensions of meaning, was completed by 147 early adolescents (M = 12.5 years), 175 middle adolescents (M = 15.7 years), and 241 late adolescents (M = 18.9 years). Results show that adolescents generally find their grandparents important and feel close to them. Grandparents are valued primarily because they provide affection, reassurance of worth, and reliable alliance. Relational-affective and caregiving meanings were assigned more often to grandmothers whereas advising, teaching, and narrative roles were ascribed more frequently to grandfathers. Maternal grandparents were generally perceived as more important and closer than paternal grandparents. Early adolescents assigned more importance and meaning to their grandparents than middle and late adolescents. There were no differences between grandsons and granddaughters.
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Ju W, Hoffmann A, Verschueren K, Tylzanowski P, Kaps C, Gross G, Huylebroeck D. The bone morphogenetic protein 2 signaling mediator Smad1 participates predominantly in osteogenic and not in chondrogenic differentiation in mesenchymal progenitors C3H10T1/2. J Bone Miner Res 2000; 15:1889-99. [PMID: 11028440 DOI: 10.1359/jbmr.2000.15.10.1889] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The role of the bone morphogenetic protein (BMP)-signaling mediator Smad1 in osteogenic or chondrogenic differentiation was investigated in murine parental mesenchymal progenitors C3H10T1/2 and its derivatives constitutively expressing BMP-2 (C3H10T1/2-BMP-2) and, therefore, undergo BMP-mediated osteogenic/ chondrogenic development. The functions of the three Smad1 domains, that is, the N-terminal (MH1) domain, the C-terminal (MH2) domain, and the midregional proline-rich linker domain, were documented and compared with full-length Smadl. We showed that expression of the MH2 domain in parental C3H10T1/2 cells was sufficient to initiate osteogenic differentiation. Interestingly, MH1 was sufficient to initiate transcription of osteogenic marker genes like the osteocalcin or parathyroid hormone/parathyroid hormone-related protein (PTH/PTHrP) receptor. However, MH1 interfered with the histologically distinct formation of osteoblast-like cells. A dominant-negative effect on MH2-mediated osteogenic development in C3H10T1/2 cells was observed by the dose-dependent trans-expression of the midregional linker domain. Importantly, in contrast to osteogenic differentiation, Smad1 and its domains do not mimic or interfere with BMP-2-dependent chondrogenic development as monitored by the inability of MH2 to give rise to histologically distinct chondrocytes in parental C3H10T1/2 cells and by the inefficiency of the MH1 or linker domain to interfere with BMP-2-mediated chondrogenic differentiation.
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Wuytens G, Verschueren K, de Winter JP, Gajendran N, Beek L, Devos K, Bosman F, de Waele P, Andries M, van den Eijnden-van Raaij AJ, Smith JC, Huylebroeck D. Identification of two amino acids in activin A that are important for biological activity and binding to the activin type II receptors. J Biol Chem 1999; 274:9821-7. [PMID: 10092672 DOI: 10.1074/jbc.274.14.9821] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activins are members of the transforming growth factor-beta family of growth and differentiation factors. In this paper, we report the results of a structure-function analysis of activin A. The primary targets for directed mutagenesis were charged, individual amino acids located in accessible domains of the protein, concentrating on those that differ from transforming growth factor-beta2, the x-ray crystal structure of which is known. Based on the activities of the recombinant activin mutants in two bioassays, 4 out of 39 mutant proteins (D27K, K102A, K102E, and K102R) produced in a vaccinia virus system were selected for further investigation. After production in insect cells and purification of these four mutants to homogeneity, they were studied in bioassays and in cross-linking experiments involving transfected receptor combinations. Mutant D27K has a 2-fold higher specific bio-activity and binding affinity to an ActRIIA/ALK-4 activin receptor complex than wild type activin, whereas mutant K102E had no detectable biological activity and did not bind to any of the activin receptors. Mutant K102R and wild type activin bound to all the activin receptor combinations tested and were equipotent in bioassays. Our results with the Lys-102 mutants indicate that the positive charge of amino acid 102 is important for biological activity and type II receptor binding of activins.
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Lintermans A, Van Calster B, Van Hoydonck M, Pans S, Verhaeghe J, Westhovens R, Henry NL, Wildiers H, Paridaens R, Dieudonné AS, Leunen K, Morales L, Verschueren K, Timmerman D, De Smet L, Vergote I, Christiaens MR, Neven P. Aromatase inhibitor-induced loss of grip strength is body mass index dependent: hypothesis-generating findings for its pathogenesis. Ann Oncol 2011; 22:1763-9. [PMID: 21273342 DOI: 10.1093/annonc/mdq699] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Our preliminary results showed that tenosynovial changes and decrease in grip strength are associated with the aromatase inhibitor-induced musculoskeletal syndrome (AIMSS). Here, we report the final results and assess the relationship between grip strength and body mass index (BMI). PATIENTS AND METHODS We conducted a prospective study including postmenopausal early breast cancer patients receiving either an aromatase inhibitor (AI) or tamoxifen. Primary end point was change from baseline in tenosynovial abnormalities. Secondary end points were changes from baseline in morning stiffness, intra-articular fluid and grip strength and its association with BMI. RESULTS After 6 months of therapy, 74% [95% confidence interval (CI) 51% to 89%] of AI-treated patients had worsened tenosynovial abnormalities, 56% (95% CI 34% to 75%) had increased intra-articular fluid, and 22% (95% CI 9% to 45%) had increased morning stiffness. Grip strength decreased 8% for the left hand (95% CI 2% to 21%) and 11% for the right (95% CI 4% to 17%). Regression analysis suggested that grip strength decreased more for subjects with high or with low BMI. CONCLUSIONS AIMSS is characterized by tenosynovial changes, intra-articular fluid and morning stiffness. We hypothesize that the quadratic association between BMI and loss of grip strength reflects AI-induced changes on the endocrine control of the growth hormone insulin-like growth factor-I pathway.
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Research Support, Non-U.S. Gov't |
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Decleer W, Osmanagaoglu K, Verschueren K, Comhaire F, Devroey P. RCT to evaluate the influence of adjuvant medical treatment of peritoneal endometriosis on the outcome of IVF. Hum Reprod 2016; 31:2017-23. [PMID: 27370359 DOI: 10.1093/humrep/dew148] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 05/27/2016] [Indexed: 01/20/2023] Open
Abstract
STUDY QUESTION Does a 3-month adjuvant hormonal treatment of mild peritoneal endometriosis after laparoscopic surgery influence the outcome of IVF stimulation in terms of number of mature oocytes obtained per cycle? SUMMARY ANSWER Complementary medical treatment of mild peritoneal endometriosis does not influence the number of oocytes per treatment cycle. WHAT IS KNOWN ALREADY Endometriosis is a disease known to be related to infertility. However, the influence of superficial endometriosis-and its treatment-is still a matter of debate. STUDY DESIGN, SIZE, DURATION A prospective controlled, randomized, open label trial was performed between February 2012 and March 2014 and embryological and clinical outcomes were measured. Patients with laparoscopically diagnosed peritoneal endometriosis (n= 120) were treated by laser surgery after which they were sequentially randomized by computer-generated allocation to one of the two groups. The primary outcome of the trial was the number of Metaphase II (MII) oocytes. Sample size was chosen to detect a difference of two MII oocytes with a power of 80%. The control group (Group B) received the classical long protocol IVF stimulation, whereas the research group (Group A) had an additional pituitary suppression, of 3 months using a long-acting GnRH agonist, prior to IVF. PARTICIPANTS/ MATERIALS, SETTING, METHODS A total of 120 patients were included in the study, 61 of them in the study group and 59 patients in the control group. One patient of the control group was lost to follow up leading to 58 evaluable patients. MAIN RESULTS AND THE ROLE OF CHANCE There was no difference in terms of the number of MII oocytes obtained per cycle: 8.2 in both groups (difference in MII between A and B: 0.07 [-1.89; 2.04] 95% confidence interval (CI)). Pregnancy rate did not differ, being 39.3% for Group A (24 out of 61 patients) versus 39.7% for Group B (23 out of 58 patients) (95% CI around difference in pregnancy rate between A and B: -0.31% [-17.96%; 17.86%]). However, a significantly (P = 0.025) lower dose of FSH (2561 IU for Group A and 2303 IU for Group B, 95% CI around difference in FSH between B and A: -258.6 IU [-483.4 IU; -33.8 IU]) and a significantly (P = 0.004) shorter stimulation period (Group A 12.3 days and Group B 11.3 days, 95% CI around difference in stimulation period between B and A: -1.03 days [-1.73 days; -0.33 days]) were needed to reach adequate follicle maturation in the control group. LIMITATIONS, REASON FOR CAUTION The validity of this study is limited to mild peritoneal endometriosis, and does not apply to ovarian endometriosis, which is also commonly seen in infertility patients. WIDER IMPLICATIONS OF THE FINDINGS There is no indication for complementary medical treatment of peritoneal endometriosis in terms of IVF outcome. On the contrary, stimulation takes longer and requires a higher amount of medication. STUDY FUNDING/COMPETING INTERESTS There was no external funding for this clinical trial in the IVF Center, AZ Jan Palfijn, Ghent. There are no competing interests to declare. TRIAL REGISTRATION NUMBER EudraCT nr: 2012-000784-25. TRIAL REGISTRATION DATE First registration on 29 February 2012 and re-entered on 23 August 2012, NCT01682642 (due to a change of staff). DATE OF FIRST PATIENT'S ENROLLMENT 8 March 2012.
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Lintermans A, Laenen A, Van Calster B, Van Hoydonck M, Pans S, Verhaeghe J, Westhovens R, Henry NL, Wildiers H, Paridaens R, Dieudonné AS, Leunen K, Morales L, Verschueren K, Timmerman D, De Smet L, Vergote I, Christiaens MR, Neven P. Prospective study to assess fluid accumulation and tenosynovial changes in the aromatase inhibitor-induced musculoskeletal syndrome: 2-year follow-up data. Ann Oncol 2013; 24:350-355. [PMID: 23038762 DOI: 10.1093/annonc/mds290] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Aromatase inhibitors (AIs) frequently lead to the AI-induced musculoskeletal syndrome (AIMSS). Looking into its pathophysiology, 6 months of AI therapy thickens the tendon sheath with intra-articular fluid (IAF) retention and loss of grip strength. We here report 24-month follow-up data. PATIENTS AND METHODS A prospective cohort study of 33 postmenopausal breast cancer patients received adjuvant endocrine therapy; 27 received an AI and 6 received tamoxifen. At baseline, 6 and 24 months patients had a rheumatologic examination, including a grip strength test, and magnetic resonance imaging of both hands and wrists. The primary end point was tenosynovial changes; secondary end points were changes in morning stiffness, grip strength and IAF. RESULTS Twenty-three AI and 5 tamoxifen patients completed all investigations. Between month 6 and 24, IAF further increased in AI users (P = 0.04) but not in tamoxifen users, and grip strength further decreased in both groups. The worsened tenosynovial changes were strongly correlated with a decrease in grip strength. At 24 months, morning stiffness continued to be present in over a third of AI users. CONCLUSION AIMSS represents a substantial problem in breast cancer patients. It is associated with tenosynovial changes, IAF retention, joint stiffness and loss of grip strength that do not improve with prolonged use.
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Crabeel M, Huygen R, Verschueren K, Messenguy F, Tinel K, Cunin R, Glansdorff N. General amino acid control and specific arginine repression in Saccharomyces cerevisiae: physical study of the bifunctional regulatory region of the ARG3 gene. Mol Cell Biol 1985; 5:3139-48. [PMID: 3915770 PMCID: PMC369129 DOI: 10.1128/mcb.5.11.3139-3148.1985] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To characterize further the regulatory mechanism modulating the expression of the Saccharomyces cerevisiae ARG3 gene, i.e., the specific repression by arginine and the general amino acid control, we analyzed by deletion the region upstream of that gene, determined the nucleotide sequence of operator-constitutive-like mutations affecting the specific regulation, and examined the behavior of an ARG3-galK fusion engineered at the initiating codon of ARG3. Similarly to what was observed in previous studies on the HIS3 and HIS4 genes, our data show that the general regulation acts as a positive control and that a sequence containing the nucleotide TGACTC, between positions -364 and -282 upstream of the transcription start, functions as a regulatory target site. This sequence contains the most proximal of the two TGACTC boxes identified in front of ARG3. While the general control appears to modulate transcription efficiency, the specific repression by arginine displays a posttranscriptional component (F. Messenguy and E. Dubois, Mol. Gen. Genet. 189:148-156, 1983). Our deletion and gene fusion analyses confirm that the specific and general controls operate independently of each other and assign the site responsible for arginine-specific repression to between positions -170 and +22. In keeping with this assignment, the two operator-constitutive-like mutations were localized at positions -80 and -46, respectively, and thus in a region which is not transcribed. We discuss a hypothesis accounting for the involvement of untranscribed DNA in a posttranscriptional control.
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