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Delourme D, Brémaud L, Plazanet I, Pélissier P, Label P, Boizot N, Breton C, Durand S, Costa G. Transcriptomic monitoring of Douglas-fir heartwood formation. BMC Genom Data 2023; 24:69. [PMID: 37986039 PMCID: PMC10662504 DOI: 10.1186/s12863-023-01172-z] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
OBJECTIVES Molecular cues linked to heartwood formation open new (complementary) perspectives to genetic breeding programs of Douglas-fir, a tree species largely cultivated in Europe for the natural durability and civil engineering properties of its wood. DATA DESCRIPTION RNAs from a single genotype of Douglas-fir, extracted from three distinct wood zones (outer sapwood, inner sapwood and transition zone) at four vegetative seasons to generate an extensive RNA-seq dataset used to apprehend the in-wood dynamic and seasonality of heartwood formation in this hardwood model species. Previously published data collected on somatic embryos of the same genotype could be merged with the present dataset to upgrade grade the Douglas-fir reference transcriptome.
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Affiliation(s)
- Didier Delourme
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Laure Brémaud
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Idelette Plazanet
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | - Patrick Pélissier
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France
| | | | | | | | - Stéphanie Durand
- Université de Limoges, CAPTuR, UMR INSERM/CHU 1308, 2 Rue du Docteur Marcland, Limoges, F-87025, France
| | - Guy Costa
- Université de Limoges, LABCIS, UR 22722, 123 avenue Albert Thomas, Limoges, F-87060, France.
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Parenté A, Di Meo F, Lapeyronie E, Al Mansi M, Delourme D, Pélissier P, Brémaud L, Trouillas P, Blanquet V. GASP-1 and GASP-2, two closely structurally related proteins with a functional duality in antitrypsin inhibition specificity: a mechanistic point of view. FEBS J 2019; 287:909-924. [PMID: 31556966 DOI: 10.1111/febs.15072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 12/07/2018] [Revised: 06/05/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022]
Abstract
While GASP-1 and GASP-2 proteins are known to regulate myogenesis by inhibiting myostatin, their structural organization suggests a putative role as multivalent protease inhibitors controlling different protease activities. In this study, we show the noncompetitive and competitive antitrypsin activities of the full-length GASP-1 and GASP-2 proteins, respectively, by using a bacterial system production and in vitro enzymatic experiments. The role of the second Kunitz domain in this functional duality is described by assessing the antitrypsin activity of GASP-1/2 chimeric proteins. Molecular dynamics simulations support the experimental data to rationalize differences in binding modes between trypsin and the GASP-1 and GASP-2 second Kunitz domains. A new inhibition mechanism was evidenced for the second Kunitz domain of GASP-2, in which the conventional cationic residue of trypsin inhibitors was substituted by the strongly interacting glutamine residue.
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Affiliation(s)
- Alexis Parenté
- University of Limoges, INRA, PEIRENE EA7500, USC1061 GAMAA, France
| | | | - Eric Lapeyronie
- University of Limoges, INRA, PEIRENE EA7500, USC1061 GAMAA, France
| | | | - Didier Delourme
- University of Limoges, INRA, PEIRENE EA7500, USC1061 GAMAA, France
| | | | - Laure Brémaud
- University of Limoges, INRA, PEIRENE EA7500, USC1061 GAMAA, France
| | - Patrick Trouillas
- University of Limoges, INSERM, UMR 1248 IPPRITT, France.,RCPTM, Palacký University, Olomouc, Czech Republic
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Péré-Brissaud A, Blanchet X, Delourme D, Pélissier P, Forestier L, Delavaud A, Duprat N, Picard B, Maftah A, Brémaud L. Expression of SERPINA3s in cattle: focus on bovSERPINA3-7 reveals specific involvement in skeletal muscle. Open Biol 2016; 5:150071. [PMID: 26562931 PMCID: PMC4593666 DOI: 10.1098/rsob.150071] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
α₁-Antichymotrypsin is encoded by the unique SERPINA3 gene in humans, while it is encoded by a cluster of eight closely related genes in cattle. BovSERPINA3 proteins present a high degree of similarity and significant divergences in the reactive centre loop (RCL) domains which are responsible for the antiprotease activity. In this study, we analysed their expression patterns in a range of cattle tissues. Even if their expression is ubiquitous, we showed that the expression levels of each serpin vary in different tissues of 15-month-old Charolais bulls. Our results led us to focus on bovSERPINA3-7, one of the two most divergent members of the bovSERPINA3 family. Expression analyses showed that bovSERPINA3-7 protein presents different tissue-specific patterns with diverse degrees of N-glycosylation. Using a specific antibody raised against bovSERPINA3-7, Western blot analysis revealed a specific 96 kDa band in skeletal muscle. BovSERPINA3-7 immunoprecipitation and mass spectrometry revealed that this 96 kDa band corresponds to a complex of bovSERPINA3-7 and creatine kinase M-type. Finally, we reported that the bovSERPINA3-7 protein is present in slow-twitch skeletal myofibres. Precisely, bovSERPINA3-7 specifically colocalized with myomesin at the M-band region of sarcomeres where it could interact with other components such as creatine kinase M-type. This study opens new prospects on the bovSERPINA3-7 function in skeletal muscle and promotes opportunities for further understanding of the physiological role(s) of serpins.
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Affiliation(s)
| | - Xavier Blanchet
- INRA, Université de Limoges, UMR1061 Génétique Moléculaire Animale, Limoges, France
| | - Didier Delourme
- INRA, Université de Limoges, UMR1061 Génétique Moléculaire Animale, Limoges, France
| | - Patrick Pélissier
- INRA, Université de Limoges, UMR1061 Génétique Moléculaire Animale, Limoges, France
| | - Lionel Forestier
- INRA, Université de Limoges, UMR1061 Génétique Moléculaire Animale, Limoges, France
| | - Arnaud Delavaud
- UMR1213 Herbivores, UMRH-AMUVI, INRA de Clermont Ferrand Theix, St Genès Champanelle, France
| | - Nathalie Duprat
- INRA, Université de Limoges, UMR1061 Génétique Moléculaire Animale, Limoges, France
| | - Brigitte Picard
- UMR1213 Herbivores, UMRH-AMUVI, INRA de Clermont Ferrand Theix, St Genès Champanelle, France
| | - Abderrahman Maftah
- INRA, Université de Limoges, UMR1061 Génétique Moléculaire Animale, Limoges, France
| | - Laure Brémaud
- INRA, Université de Limoges, UMR1061 Génétique Moléculaire Animale, Limoges, France
- e-mail:
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Blanchet X, Péré-Brissaud A, Duprat N, Pinault E, Delourme D, Ouali A, Combet C, Maftah A, Pélissier P, Brémaud L. Mutagenesis of the bovSERPINA3-3 demonstrates the requirement of aspartate-371 for intermolecular interaction and formation of dimers. Protein Sci 2012; 21:977-86. [PMID: 22505318 DOI: 10.1002/pro.2078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 11/10/2022]
Abstract
The family of serpins is known to fold into a metastable state that is required for the proteinase inhibition mechanism. One of the consequences of this conformational flexibility is the tendency of some mutated serpins to form polymers, which occur through the insertion of the reactive center loop of one serpin molecule into the A-sheet of another. This "A-sheet polymerization" has remained an attractive explanation for the molecular mechanism of serpinopathies. Polymerization of serpins can also take place in vitro under certain conditions (e.g., pH or temperature). Surprisingly, on sodium dodecyl sulfate/polyacrylamide gel electrophoresis, bovSERPINA3-3 extracted from skeletal muscle or expressed in Escherichia coli was mainly observed as a homodimer. Here, in this report, by site-directed mutagenesis of recombinant bovSERPINA3-3, with substitution D371A, we demonstrate the importance of D371 for the intermolecular linkage observed in denaturing and reducing conditions. This residue influences the electrophoretic and conformational properties of bovSERPINA3-3. By structural modeling of mature bovSERPINA3-3, we propose a new "non-A-sheet swap" model of serpin homodimer in which D371 is involved at the molecular interface.
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Affiliation(s)
- X Blanchet
- Faculté des Sciences et Techniques, INRA, UMR1061 Unité de génétique Moléculaire Animale, Université de Limoges, FR 3503 GEIST, 87060 Limoges, France
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Herrera-Mendez CH, Brémaud L, Coulis G, Pélissier P, Sentandreu MA, Aubry L, Delourme D, Chambon C, Maftah A, Leveziel H, Ouali A. Purification of the skeletal muscle protein Endopin 1B and characterization of the genes encoding Endopin 1A and 1B isoforms. FEBS Lett 2006; 580:3477-84. [PMID: 16716310 DOI: 10.1016/j.febslet.2006.04.099] [Citation(s) in RCA: 11] [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] [Received: 01/26/2006] [Revised: 04/20/2006] [Accepted: 04/27/2006] [Indexed: 11/23/2022]
Abstract
In the present work, a new endopin-like serpin designed mEndopin 1B was purified from bovine muscle. Biochemical characterizations (amino acid sequencing and Maldi-Tof mass spectrometry peptide mapping) demonstrated that the purified protein is different from the previously described Endopin 1, renamed mEndopin 1A. The genes and cDNA of both endopins were characterized. The cDNA sequence of mEndopin 1B encodes a predicted protein of 411 amino-acids with a molecular mass of 43808Da. The mEndopin 1B gene comprised four coding exons and an additional 5' untranslated exon. The reactive site sequence of mEndopin 1B is somewhat different from that of mEndopin 1A. Nevertheless, both serpins have a similar peptidase inhibitory pattern against examined proteases (elastase, trypsin, plasmin and chymotrypsin). The high expression of both mEndopin 1A and 1B in bovine serum and tissues and their high efficiency to inhibit elastase (k(ass) approximately 10(6)-10(7) M(-1) s(-1)) suggested that these serpins might play a major role in inflammatory processes.
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Tassy C, Herrera-Mendez C, Sentandreu M, Aubry L, Brémaud L, Pélissier P, Delourme D, Brillard M, Gauthier F, Levéziel H, Ouali A. Muscle endopin 1, a muscle intracellular serpin which strongly inhibits elastase: purification, characterization, cellular localization and tissue distribution. Biochem J 2005; 388:273-80. [PMID: 15647007 PMCID: PMC1186716 DOI: 10.1042/bj20041921] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Revised: 01/04/2005] [Accepted: 01/13/2005] [Indexed: 11/17/2022]
Abstract
In the present work, an endopin-like elastase inhibitor was purified for the first time from bovine muscle. A three-step chromatography procedure was developed including successively SP-Sepharose, Q-Sepharose and EMD-DEAE 650. This procedure provides about 300 microg of highly pure inhibitor from 500 g of bovine diaphragm muscle. The N-terminal sequence of the muscle elastase inhibitor, together with the sequence of a trypsin-generated peptide, showed 100% similarity with the cDNA deduced sequence of chromaffin cell endopin 1. Hence, the muscle inhibitor was designated muscle endopin 1 (mEndopin 1). mEndopin 1 had a molecular mass of 70 kDa, as assessed by both gel filtration and SDS/PAGE. According to the association rates determined, mEndopin 1 is a potent inhibitor of elastase (kass=2.41x10(7) M(-1).s(-1)) and trypsin (kass=3.92x10(6) M(-1).s(-1)), whereas plasmin (kass=1.78x10(3) M(-1).s(-1)) and chymotrypsin (kass=1.0x10(2) M(-1).s(-1)) were only moderately inhibited. By contrast, no inhibition was detected against several other selected serine proteinases, as well as against cysteine proteinases of the papain family. The cellular location of mEndopin in muscle tissue and its tissue distribution were investigated using a highly specific rabbit antiserum. The results obtained demonstrate an intracellular location and a wide distribution in bovine tissues.
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Affiliation(s)
- Caroline Tassy
- *Station de Recherches sur la Viande, Laboratoire de Biochimie des Protéines, INRA de Theix, 63122 Saint Genès Champanelle, France
| | - Carlos H. Herrera-Mendez
- *Station de Recherches sur la Viande, Laboratoire de Biochimie des Protéines, INRA de Theix, 63122 Saint Genès Champanelle, France
| | - Miguel A. Sentandreu
- *Station de Recherches sur la Viande, Laboratoire de Biochimie des Protéines, INRA de Theix, 63122 Saint Genès Champanelle, France
| | - Laurent Aubry
- *Station de Recherches sur la Viande, Laboratoire de Biochimie des Protéines, INRA de Theix, 63122 Saint Genès Champanelle, France
| | - Laure Brémaud
- †Unité de Génétique Moleculaire Animale, UMR 1061, INRA-Université de Limoges, Faculté des Sciences et Techniques, 123 Avenue Albert Thomas, 87060 Limoges Cedex, France
| | - Patrick Pélissier
- †Unité de Génétique Moleculaire Animale, UMR 1061, INRA-Université de Limoges, Faculté des Sciences et Techniques, 123 Avenue Albert Thomas, 87060 Limoges Cedex, France
| | - Didier Delourme
- †Unité de Génétique Moleculaire Animale, UMR 1061, INRA-Université de Limoges, Faculté des Sciences et Techniques, 123 Avenue Albert Thomas, 87060 Limoges Cedex, France
| | - Michèle Brillard
- ‡Université François Rabelais, Laboratoire d'Enzymologie et Chimie des Protéines, 37032 Tours, France
| | - Francis Gauthier
- ‡Université François Rabelais, Laboratoire d'Enzymologie et Chimie des Protéines, 37032 Tours, France
| | - Hubert Levéziel
- †Unité de Génétique Moleculaire Animale, UMR 1061, INRA-Université de Limoges, Faculté des Sciences et Techniques, 123 Avenue Albert Thomas, 87060 Limoges Cedex, France
| | - Ahmed Ouali
- *Station de Recherches sur la Viande, Laboratoire de Biochimie des Protéines, INRA de Theix, 63122 Saint Genès Champanelle, France
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Grandjean F, Brémaud L, Robert J, Ratinaud MH. Alterations in the expression of cytochrome c oxidase subunits in doxorubicin-resistant leukemia K562 cells. Biochem Pharmacol 2002; 63:823-31. [PMID: 11911833 DOI: 10.1016/s0006-2952(01)00865-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [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: 11/21/2022]
Abstract
Doxorubicin (DOX), a widely used antitumoral drug, induces numerous modifications in sensitive cells, interacting with nuclear and mitochondrial DNA. In previous studies achieved in two K562 DOX-resistant sublines (K562/0.2R and K562/0.5R), we have shown stable mitochondrial damage comparatively with sensitive parental cells, such as decrease of cytochrome c oxidase activity (COX; EC 1.9.3.1) and cytochrome aa3 content. In order to explain these data, we have studied several COX genes and their expression, in relationship with altered COX activity and multidrug resistance (MDR) phenotype. We have observed a lower expression of the catalytic subunits COX I and II in MDR sublines, which was neither related to mutations in the corresponding mitochondrial genes, nor to a reduced transcription rate. In contrast, we have noticed an increase in both MDR K562 variants, in the mRNA expression of the catalytic subunit COX III, related to an increase in the half-life of these transcripts. Moreover, the doxorubicin resistance phenotype in K562 cells was accompanied by modifications of the expression and steady-state mRNA levels of several nuclear-encoded regulatory COX subunits. Thus, doxorubicin-resistant K562 cells represent an interesting model to study stable modifications concomitant to MDR phenotype. Our results seem to indicate compensatory mechanisms which highlight the complexity of regulatory systems of COX enzyme, involving coordinate regulation of both nuclear and mitochondrial subunit expression.
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Affiliation(s)
- Fabienne Grandjean
- Groupe Physiologie Moléculaire Mitochondriale et Immunitaire, Faculté de Médecine, UMR 6101, CNRS, 2 rue du Dr. Marcland, 87025 Cedex, Limoges, France
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Grandjean F, Brémaud L, Verdier M, Robert J, Ratinaud MH. Sequential gene expression of P-glycoprotein (P-gp), multidrug resistance-associated protein (MRP) and lung resistance protein: functional activity of P-gp and MRP present in the doxorubicin-resistant human K562 cell lines. Anticancer Drugs 2001; 12:247-58. [PMID: 11290872 DOI: 10.1097/00001813-200103000-00010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [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: 11/25/2022]
Abstract
Previous studies have reported that P-glycoprotein (P-gp), a transmembrane efflux pump involved in multidrug resistance (MDR), was overexpressed in the doxorubicin (Dox)-resistant human erythroleukemia cell line K562. Nevertheless, several results suggested that P-gp was not the only mechanism involved in these resistant cells. Sequential co-expression of other MDR-associated proteins was sometimes reported, as MDR-associated protein (MRP) and lung resistance protein (LRP), in different MDR cell lines. Thus, mRNA expression and stability of P-gp, MRP and LRP were analyzed, while their corresponding protein levels were quantified in correlation with functional assay, in the K562 cell line and two Dox-resistant variants (K562/R). Their P-gp content was in accordance with their degree of resistance, but not as much in the level of mRNA expression, suggesting a post-transcriptional regulation. On the other hand, MRP could play a minor role in MDR because of an unchanged expression in K562/R sublines. A surprising progressive disappearance of LRP in both resistant cells suggested that the original mechanism of drug redistribution may be operative, involving a negative role for LRP.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- ATP-Binding Cassette Transporters/genetics
- ATP-Binding Cassette Transporters/metabolism
- Antineoplastic Agents/toxicity
- Blotting, Northern
- Blotting, Southern
- Blotting, Western
- DNA Primers/chemistry
- Doxorubicin/pharmacology
- Drug Resistance, Multiple/genetics
- Drug Resistance, Neoplasm
- Enzyme Stability/physiology
- Flow Cytometry
- Gene Expression
- Genes, MDR/physiology
- Humans
- K562 Cells/drug effects
- K562 Cells/metabolism
- Multidrug Resistance-Associated Proteins
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Transcription, Genetic
- Tumor Cells, Cultured/drug effects
- Tumor Cells, Cultured/metabolism
- Vault Ribonucleoprotein Particles/genetics
- Vault Ribonucleoprotein Particles/metabolism
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Affiliation(s)
- F Grandjean
- Groupe Physiologie Moléculaire Mitochondriale et Immunitaire, UMR 6101, CNRS, Faculté de Médecine, 87025 Limoges Cedex, France
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