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Yilmaz O, Com E, Pineau C, Bobe J. Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio). Sci Rep 2023; 13:18795. [PMID: 37914813 PMCID: PMC10620220 DOI: 10.1038/s41598-023-46148-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023] Open
Abstract
The specific functions and essentiality of type II vitellogenin (Vtg2) in early zebrafish development were investigated in this study. A vtg2-mutant zebrafish line was produced and effects of genomic disturbance were observed in F2 females and F3 offspring. No change in vtg2 transcript has been detected, however, Vtg2 abundance in F2 female liver was 5×, and in 1 hpf F3 vtg2-mutant embryos was 3.8× less than Wt (p < 0.05). Fecundity was unaffected while fertilization rate was more than halved in F2 vtg2-mutant females (p < 0.05). Hatching rate was significantly higher in F3 vtg2-mutant embryos in comparison to Wt embryos. Survival rate declined drastically to 29% and 18% at 24 hpf and 20 dpf, respectively, in F3 vtg2-mutant embryos. The introduced mutation caused vitelline membrane deficiencies, significant mortalities at early embryonic stages, and morphological abnormalities in the surviving F3 vtg2-mutant larvae. Overrepresentation of histones, zona pellucida proteins, lectins, and protein degradation related proteins in F3 vtg2-mutant embryos provide evidence to impaired mechanisms involved in vitellin membrane formation. Overall findings imply a potential function of Vtg2 in acquisition of vitellin membrane integrity, among other reproductive functions, and therefore, its essentiality in early zebrafish embryo development.
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Affiliation(s)
- Ozlem Yilmaz
- Norwegian Institute of Marine Research, IMR, 5392, Storebø, Norway.
| | - Emmanuelle Com
- Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Univ Rennes, 35000, Rennes, France
- CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, Univ Rennes, 35000, Rennes, France
| | - Charles Pineau
- Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Univ Rennes, 35000, Rennes, France
- CNRS, Inserm, Biosit UAR 3480 US_S 018, Protim Core Facility, Univ Rennes, 35000, Rennes, France
| | - Julien Bobe
- UR1037, Laboratory of Fish Physiology and Genomics, INRAE, Campus de Beaulieu, 35042, Rennes Cedex, France
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2
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Charpentier M, Dupré E, Fortun A, Briand F, Maillasson M, Com E, Pineau C, Labarrière N, Rabu C, Lang F. hnRNP-A1 binds to the IRES of MELOE-1 antigen to promote MELOE-1 translation in stressed melanoma cells. Mol Oncol 2022; 16:594-606. [PMID: 34418284 PMCID: PMC8807352 DOI: 10.1002/1878-0261.13088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/05/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022] Open
Abstract
The major challenge in antigen-specific immunotherapy of cancer is to select the most relevant tumor antigens to target. To this aim, understanding their mode of expression by tumor cells is critical. We previously identified a melanoma-specific antigen, melanoma-overexpressed antigen 1 (MELOE-1)-coded for by a long noncoding RNA-whose internal ribosomal entry sequence (IRES)-dependent translation is restricted to tumor cells. This restricted expression is associated with the presence of a broad-specific T-cell repertoire that is involved in tumor immunosurveillance in melanoma patients. In the present work, we explored the translation control of MELOE-1 and provide evidence that heterogeneous nuclear ribonucleoprotein A1 (hnRNP-A1) binds to the MELOE-1 IRES and acts as an IRES trans-activating factor (ITAF) to promote the translation of MELOE-1 in melanoma cells. In addition, we showed that endoplasmic reticulum (ER) stress induced by thapsigargin, which promotes hnRNP-A1 cytoplasmic translocation, enhances MELOE-1 translation and recognition of melanoma cells by a MELOE-1-specific T-cell clone. These findings suggest that pharmacological stimulation of stress pathways may enhance the efficacy of immunotherapies targeting stress-induced tumor antigens such as MELOE-1.
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Affiliation(s)
| | - Emilie Dupré
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
| | - Agnès Fortun
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
| | | | - Mike Maillasson
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
- InsermCNRSSFR SantéInserm UMS 016CNRS UMS 3556Université de NantesNantesFrance
| | - Emmanuelle Com
- InsermEHESPIrset (Institut de recherche en santé, environnement et travail) – UMR‐S 1085Univ RennesRennesFrance
- ProtimBiosit – UMS 3480US‐S 018Univ RennesRennesFrance
| | - Charles Pineau
- InsermEHESPIrset (Institut de recherche en santé, environnement et travail) – UMR‐S 1085Univ RennesRennesFrance
- ProtimBiosit – UMS 3480US‐S 018Univ RennesRennesFrance
| | | | | | - François Lang
- InsermLabEx IGOCRCINAUniversité de NantesNantesFrance
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3
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Yilmaz O, Patinote A, Com E, Pineau C, Bobe J. Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs. BMC Genomics 2021; 22:308. [PMID: 33910518 PMCID: PMC8082894 DOI: 10.1186/s12864-021-07606-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND We previously reported the results of CRISPR/Cas9 knock-out (KO) of type-I and type-III vitellogenins (Vtgs) in zebrafish, which provided the first experimental evidence on essentiality and disparate functioning of Vtgs at different stages during early development. However, the specific contributions of different types of Vtg to major cellular processes remained to be investigated. The present study employed liquid chromatography and tandem mass spectrometry (LC-MS/MS) to meet this deficit. Proteomic profiles of zebrafish eggs lacking three type-I Vtgs simultaneously (vtg1-KO), or lacking only type III Vtg (vtg3-KO) were compared to those of wild type (Wt) eggs. Obtained spectra were searched against a zebrafish proteome database and identified proteins were quantified based on normalized spectral counts. RESULTS The vtg-KO caused severe changes in the proteome of 1-cell stage zebrafish eggs. These changes were disclosed by molecular signatures that highly resembled the proteomic phenotype of poor quality zebrafish eggs reported in our prior studies. Proteomic profiles of vtg-KO eggs and perturbations in abundances of hundreds of proteins revealed unique, noncompensable contributions of multiple Vtgs to protein and in energy homeostasis. The lack of this contribution appears to have a significant impact on endoplasmic reticulum and mitochondrial functions, and thus embryonic development, even after zygotic genome activation. Increased endoplasmic reticulum stress, Redox/Detox activities, glycolysis/gluconeogenesis, enrichment in cellular proliferation and in human neurodegenerative disease related activities in both vtg1- and vtg3-KO eggs were found to be indicators of the aforementioned conditions. Distinctive increase in apoptosis and Parkinson disease pathways, as well as the decrease in lipid metabolism related activities in vtg3-KO eggs implies compelling roles of Vtg3, the least abundant form of Vtgs in vertebrate eggs, in mitochondrial activities. Several differentially abundant proteins representing the altered molecular mechanisms have been identified as strong candidate markers for studying the details of these mechanisms during early embryonic development in zebrafish and possibly other vertebrates. CONCLUSIONS These findings indicate that the global egg proteome is subject to extensive modification depending on the presence or absence of specific Vtgs and that these modifications can have a major impact on developmental competence.
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Affiliation(s)
- Ozlem Yilmaz
- INRAE, LPGP, 35000, Rennes, France.
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway.
| | | | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset-UMR_S 1085, F-35042, Rennes cedex, France
- Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset-UMR_S 1085, F-35042, Rennes cedex, France
- Protim, Univ Rennes, F-35042, Rennes cedex, France
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4
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Dos Santos Morais R, El-Kirat-Chatel S, Burgain J, Simard B, Barrau S, Paris C, Borges F, Gaiani C. A Fast, Efficient and Easy to Implement Method to Purify Bacterial Pili From Lacticaseibacillus rhamnosus GG Based on Multimodal Chromatography. Front Microbiol 2020; 11:609880. [PMID: 33391233 PMCID: PMC7775309 DOI: 10.3389/fmicb.2020.609880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/24/2020] [Indexed: 01/02/2023] Open
Abstract
Pili are polymeric proteins located at the cell surface of bacteria. These filamentous proteins play a pivotal role in bacterial adhesion with the surrounding environment. They are found both in Gram-negative and Gram-positive bacteria but differ in their structural organization. Purifying these high molecular weight proteins is challenging and has certainly slowed down their characterization. Here, we propose a chromatography-based protocol, mainly relying on multimodal chromatography (core bead technology using Capto Core 700 resin), to purify sortase-dependent SpaCBA pili from the probiotic strain Lacticaseibacillus rhamnosus GG (LGG). Contrary to previously published methods, this purification protocol does not require specific antibodies nor complex laboratory equipment, including for the multimodal chromatography step, and provides high degree of protein purity. No other proteins were detectable by SDS-PAGE and the 260/280 nm ratio (∼0.6) of the UV spectrum confirmed the absence of any other co-purified macromolecules. One can obtain ∼50 μg of purified pili, starting from 1 L culture at OD600nm ≈ 1, in 2–3 working days. This simple protocol could be useful to numerous laboratories to purify pili from LGG easily. Therefore, the present work should boost specific studies dedicated to LGG SpaCBA pili and the characterization of the interactions occurring with their protein partners at the molecular level. Moreover, this straightforward purification process might be extended to the purification of sortase-dependant pili from other Gram-positive bacteria.
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Affiliation(s)
| | - Sofiane El-Kirat-Chatel
- Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), UMR 7564, CNRS-Université de Lorraine, Nancy, France
| | - Jennifer Burgain
- Laboratoire d'Ingénierie des Biomolécules, Université de Lorraine, Nancy, France
| | - Blandine Simard
- Laboratoire d'Ingénierie des Biomolécules, Université de Lorraine, Nancy, France
| | - Sarah Barrau
- Laboratoire d'Ingénierie des Biomolécules, Université de Lorraine, Nancy, France
| | - Cédric Paris
- Laboratoire d'Ingénierie des Biomolécules, Université de Lorraine, Nancy, France
| | - Frédéric Borges
- Laboratoire d'Ingénierie des Biomolécules, Université de Lorraine, Nancy, France
| | - Claire Gaiani
- Laboratoire d'Ingénierie des Biomolécules, Université de Lorraine, Nancy, France.,Institut Universitaire de France, Parris, France
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5
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Yilmaz O, Patinote A, Nguyen T, Com E, Pineau C, Bobe J. Genome editing reveals reproductive and developmental dependencies on specific types of vitellogenin in zebrafish (Danio rerio). Mol Reprod Dev 2019; 86:1168-1188. [DOI: 10.1002/mrd.23231] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 06/17/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Ozlem Yilmaz
- INRA, UR1037, Laboratory of Fish Physiology and GenomicsCampus de Beaulieu, French National Institute for Agricultural Research Rennes Cedex France
| | - Amélie Patinote
- INRA, UR1037, Laboratory of Fish Physiology and GenomicsCampus de Beaulieu, French National Institute for Agricultural Research Rennes Cedex France
| | - Thaovi Nguyen
- INRA, UR1037, Laboratory of Fish Physiology and GenomicsCampus de Beaulieu, French National Institute for Agricultural Research Rennes Cedex France
| | - Emmanuelle Com
- Protim, Inserm U1085, IrsetCampus de Beaulieu, Université de Rennes 1, Proteomics Core Facility Rennes Cedex France
| | - Charles Pineau
- Protim, Inserm U1085, IrsetCampus de Beaulieu, Université de Rennes 1, Proteomics Core Facility Rennes Cedex France
| | - Julien Bobe
- INRA, UR1037, Laboratory of Fish Physiology and GenomicsCampus de Beaulieu, French National Institute for Agricultural Research Rennes Cedex France
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6
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Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C. Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics 2019; 20:56. [PMID: 30654742 PMCID: PMC6337836 DOI: 10.1186/s12864-019-5431-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 01/03/2019] [Indexed: 01/02/2023] Open
Abstract
Background Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes. Results Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus sp. strains and sub-cellular fractions using a shotgun approach. First, we directly generated peptide sequence tags (PSTs) from the proteomics data. Second, we mapped PSTs onto the translated genomic sequence. Closely located hits (i.e., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism. Third, we evaluated each cluster and compared it to gene predictions from existing conventional genome annotation approaches. Finally, we integrated cluster locations into GFF files to use a genome viewer. We identified two potential novel genes, a ribosomal protein L22 and an aryl sulfotransferase and corrected the gene structure of a dihydrolipoamide acetyltransferase. We experimentally validated the results by RT-PCR and using transcriptomics data. Conclusions Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu. Data are available via ProteomeXchange under identifier PXD010618. Electronic supplementary material The online version of this article (10.1186/s12864-019-5431-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laetitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Ludovic Delage
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Alain Viari
- INRIA Grenoble-Rhône-Alpes, F-38330, Montbonnot-Saint-Martin, France
| | - Yves Vandenbrouck
- University Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000, Grenoble, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Andrés Ritter
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France.,Present address: Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France.,Protim, Univ Rennes, F-35042, Rennes cedex, France
| | - Dominique Marie
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | | | - Philippe Potin
- Sorbonne Université, UPMC, CNRS, UMR 8227, Integrative Biology of Marine Models, Biological Station, CS 90074, F-29688, Roscoff, France
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35042, Rennes cedex, France. .,Protim, Univ Rennes, F-35042, Rennes cedex, France.
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7
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Arsenieff L, Simon N, Rigaut-Jalabert F, Le Gall F, Chaffron S, Corre E, Com E, Bigeard E, Baudoux AC. First Viruses Infecting the Marine Diatom Guinardia delicatula. Front Microbiol 2019; 9:3235. [PMID: 30687251 PMCID: PMC6334475 DOI: 10.3389/fmicb.2018.03235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/12/2018] [Indexed: 11/17/2022] Open
Abstract
The marine diatom Guinardia delicatula is a cosmopolitan species that dominates seasonal blooms in the English Channel and the North Sea. Several eukaryotic parasites are known to induce the mortality of this species. Here, we report the isolation and characterization of the first viruses that infect G. delicatula. Viruses were isolated from the Western English Channel (SOMLIT-Astan station) during the late summer bloom decline of G. delicatula. A combination of laboratory approaches revealed that these lytic viruses (GdelRNAV) are small tailless particles of 35–38 nm in diameter that replicate in the host cytoplasm where both unordered particles and crystalline arrays are formed. GdelRNAV display a linear single-stranded RNA genome of ~9 kb, including two open reading frames encoding for replication and structural polyproteins. Phylogenetic relationships based on the RNA-dependent-RNA-polymerase gene marker showed that GdelRNAV are new members of the Bacillarnavirus, a monophyletic genus belonging to the order Picornavirales. GdelRNAV are specific to several strains of G. delicatula. They were rapidly and largely produced (<12 h, 9.34 × 104 virions per host cell). Our analysis points out the host's variable viral susceptibilities during the early exponential growth phase. Interestingly, we consistently failed to isolate viruses during spring and early summer while G. delicatula developed important blooms. While our study suggests that viruses do contribute to the decline of G. delicatula's late summer bloom, they may not be the primary mortality agents during the remaining blooms at SOMLIT-Astan. Future studies should focus on the relative contribution of the viral and eukaryotic pathogens to the control of Guinardia's blooms to understand the fate of these prominent organisms in marine systems.
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Affiliation(s)
- Laure Arsenieff
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Nathalie Simon
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Florence Le Gall
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, Nantes, France
| | - Erwan Corre
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.,Protim, Univ Rennes, Rennes, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Anne-Claire Baudoux
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
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8
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Yilmaz O, Patinote A, Nguyen T, Bobe J. Multiple vitellogenins in zebrafish (Danio rerio): quantitative inventory of genes, transcripts and proteins, and relation to egg quality. FISH PHYSIOLOGY AND BIOCHEMISTRY 2018; 44:1509-1525. [PMID: 29882000 DOI: 10.1007/s10695-018-0524-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Scrutiny of the zebrafish (Danio rerio) genomic database confirmed eight functional vitellogenin (vtg) genes, each with one or two transcript variants, and the encoded Vtg polypeptides were structurally and functionally characterized in detail by in silico and experimental analyses. There were five type I (vtgs1, 4, 5, 6, and 7), two type II (vtg2 and vtg8), and one type III (vtg3) vtg gene(s) encoding three major types of Vtg protein based on subdomain structure (Vtg-I, Vtg-II, and Vtg-III, respectively). Among various tissues of mature zebrafish, transcripts of the eight vtg genes were detected by RNA-Seq only in liver and intestine, with liver being the main site of vtg expression. All vtg transcripts except vtg8 were also detected in mature female liver by RT-qPCR. The relative abundances of Vtg proteins and their variants were quantified by LC-MS/MS in the liver of mature females and in eggs. The Vtgs were generally several fold more abundant in eggs, but profiles of abundance of the 19 different forms of Vtg evaluated were otherwise similar in liver and eggs, suggesting that yolk protein composition is determined largely by hepatic Vtg synthesis and secretion. Based on transcript and protein levels, Vtg-I is, by far, the dominant type of Vtg in zebrafish, followed by Vtg-II and then Vtg-III. When relative abundances of the different forms of Vtg were evaluated by LC-MS/MS in egg batches of good versus poor quality, no differences in the proportional abundance of individual forms of Vtg, or of different Vtg types, attributable to egg quality were observed.
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Affiliation(s)
- Ozlem Yilmaz
- Fish Physiology and Genomics Institute, INRA UR1037, Rennes Cedex, France.
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
| | - Amélie Patinote
- Fish Physiology and Genomics Institute, INRA UR1037, Rennes Cedex, France
| | - Thaovi Nguyen
- Fish Physiology and Genomics Institute, INRA UR1037, Rennes Cedex, France
| | - Julien Bobe
- Fish Physiology and Genomics Institute, INRA UR1037, Rennes Cedex, France
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9
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Dos Santos Morais R, Delalande O, Pérez J, Mias-Lucquin D, Lagarrigue M, Martel A, Molza AE, Chéron A, Raguénès-Nicol C, Chenuel T, Bondon A, Appavou MS, Le Rumeur E, Combet S, Hubert JF. Human Dystrophin Structural Changes upon Binding to Anionic Membrane Lipids. Biophys J 2018; 115:1231-1239. [PMID: 30197181 DOI: 10.1016/j.bpj.2018.07.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/16/2018] [Accepted: 07/31/2018] [Indexed: 11/19/2022] Open
Abstract
Scaffolding proteins play important roles in supporting the plasma membrane (sarcolemma) of muscle cells. Among them, dystrophin strengthens the sarcolemma through protein-lipid interactions, and its absence due to gene mutations leads to the severe Duchenne muscular dystrophy. Most of the dystrophin protein consists of a central domain made of 24 spectrin-like coiled-coil repeats (R). Using small angle neutron scattering (SANS) and the contrast variation technique, we specifically probed the structure of the three first consecutive repeats 1-3 (R1-3), a part of dystrophin known to physiologically interact with membrane lipids. R1-3 free in solution was compared to its structure adopted in the presence of phospholipid-based bicelles. SANS data for the protein/lipid complexes were obtained with contrast-matched bicelles under various phospholipid compositions to probe the role of electrostatic interactions. When bound to anionic bicelles, large modifications of the protein three-dimensional structure were detected, as revealed by a significant increase of the protein gyration radius from 42 ± 1 to 60 ± 4 Å. R1-3/anionic bicelle complexes were further analyzed by coarse-grained molecular dynamics simulations. From these studies, we report an all-atom model of R1-3 that highlights the opening of the R1 coiled-coil repeat when bound to the membrane lipids. This model is totally in agreement with SANS and click chemistry/mass spectrometry data. We conclude that the sarcolemma membrane anchoring that occurs during the contraction/elongation process of muscles could be ensured by this coiled-coil opening. Therefore, understanding these structural changes may help in the design of rationalized shortened dystrophins for gene therapy. Finally, our strategy opens up new possibilities for structure determination of peripheral and integral membrane proteins not compatible with different high-resolution structural methods.
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Affiliation(s)
- Raphael Dos Santos Morais
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France; Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, France; SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France
| | - Olivier Delalande
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Javier Pérez
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France
| | - Dominique Mias-Lucquin
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Mélanie Lagarrigue
- Université de Rennes, Rennes, France; Inserm U1085, Protim-Plate-forme Protéomique, Rennes, France
| | | | - Anne-Elisabeth Molza
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Angélique Chéron
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Céline Raguénès-Nicol
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Thomas Chenuel
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Arnaud Bondon
- CNRS 6226, Institut des Sciences Chimiques de Rennes, PRISM, Rennes, France
| | - Marie-Sousai Appavou
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, Garching, Germany
| | - Elisabeth Le Rumeur
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France
| | - Sophie Combet
- Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, Gif-sur-Yvette, France.
| | - Jean-François Hubert
- Université de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS UMR 6290, Rennes, France.
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10
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Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J. Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio). PLoS One 2017; 12:e0188084. [PMID: 29145436 PMCID: PMC5690628 DOI: 10.1371/journal.pone.0188084] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 10/31/2017] [Indexed: 01/08/2023] Open
Abstract
Egg quality is a complex biological trait and a major determinant of reproductive fitness in all animals. This study delivered the first proteomic portraits of egg quality in zebrafish, a leading biomedical model for early development. Egg batches of good and poor quality, evidenced by embryo survival for 24 h, were sampled immediately after spawning and used to create pooled or replicated sample sets whose protein extracts were subjected to different levels of fractionation before liquid chromatography and tandem mass spectrometry. Obtained spectra were searched against a zebrafish proteome database and detected proteins were annotated, categorized and quantified based on normalized spectral counts. Manually curated and automated enrichment analyses revealed poor quality eggs to be deficient of proteins involved in protein synthesis and energy and lipid metabolism, and of some vitellogenin products and lectins, and to have a surfeit of proteins involved in endo-lysosomal activities, autophagy, and apoptosis, and of some oncogene products, lectins and egg envelope proteins. Results of pathway and network analyses suggest that this aberrant proteomic profile results from failure of oocytes giving rise to poor quality eggs to properly transit through final maturation, and implicated Wnt signaling in the etiology of this defect. Quantitative comparisons of abundant proteins in good versus poor quality eggs revealed 17 candidate egg quality markers. Thus, the zebrafish egg proteome is clearly linked to embryo developmental potential, a phenomenon that begs further investigation to elucidate the root causes of poor egg quality, presently a serious and intractable problem in livestock and human reproductive medicine.
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Affiliation(s)
- Ozlem Yilmaz
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
| | - Amélie Patinote
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
| | - Thao Vi Nguyen
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
| | | | | | | | | | - Julien Bobe
- Laboratory of Fish Physiology and Genomics, INRA UR1037, Rennes Cedex, France
- * E-mail:
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11
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Becker E, Com E, Lavigne R, Guilleux MH, Evrard B, Pineau C, Primig M. The protein expression landscape of mitosis and meiosis in diploid budding yeast. J Proteomics 2017; 156:5-19. [DOI: 10.1016/j.jprot.2016.12.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/14/2016] [Accepted: 12/26/2016] [Indexed: 12/12/2022]
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12
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Jumeau F, Com E, Lane L, Duek P, Lagarrigue M, Lavigne R, Guillot L, Rondel K, Gateau A, Melaine N, Guével B, Sergeant N, Mitchell V, Pineau C. Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:3606-20. [PMID: 26168773 DOI: 10.1021/acs.jproteome.5b00170] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Chromosome-Centric Human Proteome Project (C-HPP) aims at cataloguing the proteins as gene products encoded by the human genome in a chromosome-centric manner. The existence of products of about 82% of the genes has been confirmed at the protein level. However, the number of so-called "missing proteins" remains significant. It was recently suggested that the expression of proteins that have been systematically missed might be restricted to particular organs or cell types, for example, the testis. Testicular function, and spermatogenesis in particular, is conditioned by the successive activation or repression of thousands of genes and proteins including numerous germ cell- and testis-specific products. Both the testis and postmeiotic germ cells are thus promising sites at which to search for missing proteins, and ejaculated spermatozoa are a potential source of proteins whose expression is restricted to the germ cell lineage. A trans-chromosome-based data analysis was performed to catalog missing proteins in total protein extracts from isolated human spermatozoa. We have identified and manually validated peptide matches to 89 missing proteins in human spermatozoa. In addition, we carefully validated three proteins that were scored as uncertain in the latest neXtProt release (09.19.2014). A focus was then given to the 12 missing proteins encoded on chromosomes 2 and 14, some of which may putatively play roles in ciliation and flagellum mechanistics. The expression pattern of C2orf57 and TEX37 was confirmed in the adult testis by immunohistochemistry. On the basis of transcript expression during human spermatogenesis, we further consider the potential for discovering additional missing proteins in the testicular postmeiotic germ cell lineage and in ejaculated spermatozoa. This project was conducted as part of the C-HPP initiatives on chromosomes 14 (France) and 2 (Switzerland). The mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium under the data set identifier PXD002367.
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Affiliation(s)
- Fanny Jumeau
- EA 4308-Department of Reproductive Biology-Spermiology-CECOS, CHRU-Lille , 59037, Lille cedex, France.,Inserm UMRS 1172, Centre Jean Pierre Aubert, IMPRT, University Lille Nord de France , 59045 Lille Cedex, France
| | - Emmanuelle Com
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
| | - Lydie Lane
- Department of Human Protein Sciences, Faculty of Medicine, University of Geneva , 1, rue Michel-Servet, 1211 Geneva 4, Switzerland.,SIB Swiss Institute of Bioinformatics, 1, rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - Paula Duek
- SIB Swiss Institute of Bioinformatics, 1, rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - Mélanie Lagarrigue
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
| | - Régis Lavigne
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
| | - Laëtitia Guillot
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
| | - Karine Rondel
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
| | - Alain Gateau
- SIB Swiss Institute of Bioinformatics, 1, rue Michel-Servet, 1211 Geneva 4, Switzerland
| | - Nathalie Melaine
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
| | - Blandine Guével
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
| | - Nicolas Sergeant
- Inserm UMRS 1172, Centre Jean Pierre Aubert, IMPRT, University Lille Nord de France , 59045 Lille Cedex, France
| | - Valérie Mitchell
- EA 4308-Department of Reproductive Biology-Spermiology-CECOS, CHRU-Lille , 59037, Lille cedex, France
| | - Charles Pineau
- Inserm U1085, Irset , Campus de Beaulieu, Rennes, 35042, France.,Protim, Campus de Beaulieu, Rennes, 35042, France
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13
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Darde TA, Sallou O, Becker E, Evrard B, Monjeaud C, Le Bras Y, Jégou B, Collin O, Rolland AD, Chalmel F. The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Res 2015; 43:W109-16. [PMID: 25883147 PMCID: PMC4489245 DOI: 10.1093/nar/gkv345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/06/2015] [Indexed: 12/23/2022] Open
Abstract
We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.
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Affiliation(s)
- Thomas A Darde
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Bertrand Evrard
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
| | - Cyril Monjeaud
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Yvan Le Bras
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Bernard Jégou
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Ecole des Hautes Études en Santé Publique, Avenue du Professeur Léon-Bernard, F-35043 Rennes, France
| | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Frédéric Chalmel
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
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14
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Becker E, Liu Y, Lardenois A, Walther T, Horecka J, Stuparevic I, Law MJ, Lavigne R, Evrard B, Demougin P, Riffle M, Strich R, Davis RW, Pineau C, Primig M. Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. J Proteomics 2015; 119:30-44. [PMID: 25662576 DOI: 10.1016/j.jprot.2015.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/16/2015] [Accepted: 01/25/2015] [Indexed: 12/29/2022]
Abstract
UNLABELLED Diploid budding yeast undergoes rapid mitosis when it ferments glucose, and in the presence of a non-fermentable carbon source and the absence of a nitrogen source it triggers sporulation. Rich medium with acetate is a commonly used pre-sporulation medium, but our understanding of the molecular events underlying the acetate-driven transition from mitosis to meiosis is still incomplete. We identified 263 proteins for which mRNA and protein synthesis are linked or uncoupled in fermenting and respiring cells. Using motif predictions, interaction data and RNA profiling we find among them 28 likely targets for Ume6, a subunit of the conserved Rpd3/Sin3 histone deacetylase-complex regulating genes involved in metabolism, stress response and meiosis. Finally, we identify 14 genes for which both RNA and proteins are detected exclusively in respiring cells but not in fermenting cells in our sample set, including CSM4, SPR1, SPS4 and RIM4, which were thought to be meiosis-specific. Our work reveals intertwined transcriptional and post-transcriptional control mechanisms acting when a MATa/α strain responds to nutritional signals, and provides molecular clues how the carbon source primes yeast cells for entering meiosis. BIOLOGICAL SIGNIFICANCE Our integrated genomics study provides insight into the interplay between the transcriptome and the proteome in diploid yeast cells undergoing vegetative growth in the presence of glucose (fermentation) or acetate (respiration). Furthermore, it reveals novel target genes involved in these processes for Ume6, the DNA binding subunit of the conserved histone deacetylase Rpd3 and the co-repressor Sin3. We have combined data from an RNA profiling experiment using tiling arrays that cover the entire yeast genome, and a large-scale protein detection analysis based on mass spectrometry in diploid MATa/α cells. This distinguishes our study from most others in the field-which investigate haploid yeast strains-because only diploid cells can undergo meiotic development in the simultaneous absence of a non-fermentable carbon source and nitrogen. Indeed, we report molecular clues how respiration of acetate might prime diploid cells for efficient spore formation, a phenomenon that is well known but poorly understood.
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Affiliation(s)
| | - Yuchen Liu
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | | | - Thomas Walther
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | - Joe Horecka
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | - Igor Stuparevic
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | - Michael J Law
- Rowan University, School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Régis Lavigne
- Inserm U1085 IRSET, Proteomics Core Facility Biogenouest, Université de Rennes 1, 35042 Rennes, France
| | - Bertrand Evrard
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | | | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Randy Strich
- Rowan University, School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Charles Pineau
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France; Inserm U1085 IRSET, Proteomics Core Facility Biogenouest, Université de Rennes 1, 35042 Rennes, France
| | - Michael Primig
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France.
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15
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Lardenois A, Stuparevic I, Liu Y, Law MJ, Becker E, Smagulova F, Waern K, Guilleux MH, Horecka J, Chu A, Kervarrec C, Strich R, Snyder M, Davis RW, Steinmetz LM, Primig M. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Res 2014; 43:115-28. [PMID: 25477386 PMCID: PMC4288150 DOI: 10.1093/nar/gku1185] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of distinct transcript isoforms during mitotic growth and meiotic development is unknown. In this study, we order developmentally regulated transcript isoforms according to their expression at specific stages during meiosis and gametogenesis, as compared to vegetative growth and starvation. We employ regulatory motif prediction, in vivo protein-DNA binding assays, genetic analyses and monitoring of epigenetic amino acid modification patterns to identify a novel role for Rpd3 and Ume6, two components of a histone deacetylase complex already known to repress early meiosis-specific genes in dividing cells, in mitotic repression of meiosis-specific transcript isoforms. Our findings classify developmental stage-specific early, middle and late meiotic transcript isoforms, and they point to a novel HDAC-dependent control mechanism for flexible transcript architecture during cell growth and differentiation. Since Rpd3 is highly conserved and ubiquitously expressed in many tissues, our results are likely relevant for development and disease in higher eukaryotes.
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Affiliation(s)
| | - Igor Stuparevic
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
| | - Yuchen Liu
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
| | - Michael J Law
- School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA
| | | | - Fatima Smagulova
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
| | - Karl Waern
- Department of Genetics, Stanford University, Stanford, CA 94395, USA
| | | | - Joe Horecka
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | - Angela Chu
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | | | - Randy Strich
- School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA
| | - Mike Snyder
- Department of Genetics, Stanford University, Stanford, CA 94395, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Michael Primig
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
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16
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Chalmel F, Com E, Lavigne R, Hernio N, Teixeira-Gomes AP, Dacheux JL, Pineau C. An integrative omics strategy to assess the germ cell secretome and to decipher sertoli-germ cell crosstalk in the Mammalian testis. PLoS One 2014; 9:e104418. [PMID: 25111155 PMCID: PMC4128672 DOI: 10.1371/journal.pone.0104418] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/08/2014] [Indexed: 12/11/2022] Open
Abstract
Mammalian spermatogenesis, which takes place in complex testicular structures called seminiferous tubules, is a highly specialized process controlled by the integration of juxtacrine, paracrine and endocrine information. Within the seminiferous tubules, the germ cells and Sertoli cells are surrounded by testicular fluid (TF), which probably contains most of the secreted proteins involved in crosstalk between these cells. It has already been established that germ cells can modulate somatic Sertoli cell function through the secretion of diffusible factors. We studied the germ cell secretome, which was previously considered inaccessible, by analyzing the TF collected by microsurgery in an “integrative omics” strategy combining proteomics, transcriptomics, genomics and interactomics data. This approach identified a set of proteins preferentially secreted by Sertoli cells or germ cells. An interaction network analysis revealed complex, interlaced cell-cell dialog between the secretome and membranome of seminiferous cells, mediated via the TF. We then focused on germ cell-secreted candidate proteins, and we identified several potential interacting partners located on the surface of Sertoli cells. Two interactions, APOH/CDC42 and APP/NGFR, were validated in situ, in a proximity ligation assay (PLA). Our results provide new insight into the crosstalk between germ cells and Sertoli cells occurring during spermatogenesis. Our findings also demonstrate that this “integrative omics” strategy is powerful enough for data mining and highlighting meaningful cell-cell communication events between different types of cells in a complex tissue, via a biological fluid. This integrative strategy could be applied more widely, to gain access to secretomes that have proved difficult to study whilst avoiding the limitations of in vitro culture.
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Affiliation(s)
- Frédéric Chalmel
- IRSET, Inserm U1085, Campus de Beaulieu, Rennes, France
- * E-mail: (CP); (FC)
| | - Emmanuelle Com
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
| | - Régis Lavigne
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
| | - Nolwen Hernio
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
| | - Ana-Paula Teixeira-Gomes
- INRA UMR 1282, Infectiologie et Santé Publique, Nouzilly, France
- INRA Plate-forme d'Analyse Intégrative des Biomolécules (PAIB), Nouzilly, France
| | | | - Charles Pineau
- Proteomics Core Facility Biogenouest, Inserm U1085 IRSET, Campus de Beaulieu, Rennes, France
- * E-mail: (CP); (FC)
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17
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Com E, Melaine N, Chalmel F, Pineau C. Proteomics and integrative genomics for unraveling the mysteries of spermatogenesis: the strategies of a team. J Proteomics 2014; 107:128-43. [PMID: 24751586 DOI: 10.1016/j.jprot.2014.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 04/09/2014] [Indexed: 11/25/2022]
Abstract
UNLABELLED The strikingly complex structural organization of the mammalian testis in vivo creates particular difficulties for studies of its organization, function and regulation. These difficulties are particularly pronounced for investigations of the molecular communication networks within the seminiferous tubules that govern spermatogenesis. The use of classical molecular and cell biology approaches to unravel this complexity has proved problematic, due to difficulties in maintaining differentiated germ cells in vitro, in particular. The lack of a suitable testing ground has led to a greater reliance on high-quality proteomic and genomic analyses as a prelude to the in vitro antx1d in vivo testing of hypotheses. In this study, we highlight the options currently available for research, as used in our laboratory, in which proteomic and integrative genomic strategies are applied to the study of spermatogenesis in mammals. We will comment on results providing insight into the molecular mechanisms underlying normal and pathological spermatogenesis and new perspectives for the treatment of male infertility in humans. Finally, we will discuss the relevance of our strategies and the unexpected potential and perspectives they offer to teams involved in the study of male reproduction, within the framework of the Human Proteome Project. SIGNIFICANCE Integrative genomics is becoming a powerful strategy for discovering the biological significance hidden in proteomic datasets. This work introduces some of the integrative genomic concepts and works used by our team to gain new insight into mammalian spermatogenesis, a remarkably sophisticated process. We demonstrate the relevance of these integrative approaches to understand the cellular cross talks established between the somatic Sertoli cells and the germ cell lineage, within the seminiferous epithelium. Our work also contributes to new knowledge on the pathophysiology of testicular function, with promising clinical applications. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Affiliation(s)
- Emmanuelle Com
- IRSET, Inserm U1085, Campus de Beaulieu, Rennes F-35042, France; Proteomics Core Facility Biogenouest, Campus de Beaulieu, Rennes F-35042, France
| | - Nathalie Melaine
- IRSET, Inserm U1085, Campus de Beaulieu, Rennes F-35042, France; Proteomics Core Facility Biogenouest, Campus de Beaulieu, Rennes F-35042, France
| | | | - Charles Pineau
- IRSET, Inserm U1085, Campus de Beaulieu, Rennes F-35042, France; Proteomics Core Facility Biogenouest, Campus de Beaulieu, Rennes F-35042, France.
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