DOCSLIB.ORG

Ovarian Dysgenesis and Premature Ovarian Failure (POF)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Ovarian Dysgenesis and Premature Ovarian Failure (POF) The Genes Involved in Hearing and Endocrine Disorders A Thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Medical and Human Sciences. 2012 Emma Mary Jenkinson School of Medicine CONTENTS Content Page List of Tables 7 List of Figures 10 Abstract 16 Declaration 17 Copyright statement 17 Acknowledgment 19 Abbreviations 20 Chapter 1: Introduction 24 1. Introduction 25 1.1. Sensorineural Hearing Loss 25 1.1.1 Genes which Regulate Ion Homeostasis in the Cochlear 28 1.1.2 Genes Responsible for Formation and Maintenance of the 29 Hair bundles 1.1.3 Genes Responsible for Maintenance of the Extracellular 32 Matrix 1.1.4 Transcription Factor Genes 34 1.1.5 Genes of Poorly Established Function 35 1.1.6 The Need for Further Research in Deafness Genetics 37 1.2 Hypothalamic Pituitary Gonadal axis 37 1.2.1 Hypogonadotropic Hypogonadism 39 1.2.2 Hypergonadotropic Hypogonadism: Premature Ovarian 52 Failure (POF) and Ovarian Dysgenesis 1.2.3 Premature Ovarian Failure and Sensorineural Hearing 71 Loss: Perrault Syndrome 1.3 The Evolution of Techniques in Genetic Medicine 80 1.3.1 Linkage Mapping 80 1.3.2 From Locus to Gene Mutation 83 1.3.3 Next Generation Sequencing 84 1.4 Aim 89 Chapter 2: Materials and Methods 91 2.Materials and Methods 92 2 2.1 Suppliers 92 2.2 Nucleic Acid procedures 92 2.2.1 DNA Extraction 92 2.2.2 RNA Extraction 92 2.2.3 Quantification of Nucleic Acids 93 2.2.4 Standard PCR Reaction 93 2.2.5 Agarose Gel Electrophoresis 94 2.2.6 Purification of PCR Products 95 2.2.7 Sequencing Reactions 95 2.2.8 Purification of Sequencing Products 96 2.2.9 Whole Genome Amplification 96 2.2.10 Reverse Transcription 96 2.2.11 Affymetrix Genome-wide Human SNP Array V6.0/250K 96 2.2.12 Sybr Green 97 2.2.13 Copy Number assay 97 2.2.14 Whole exome sequencing 97 2.2.15 Expression array 98 2.3 Data Analysis 98 2.4 Protein Procedures 98 2.4.1 Extraction of Protein from Zebrafish Embryos 98 2.4.2 Extraction of Protein from Mammalian tissue 99 2.4.3 SDS Polyacrylamide Gel Electrophoresis (SDS-Page) 100 2.4.4 Western Blot Analysis 100 2.4.5 Developing Western Blot 101 2.4.6 Stripping Western Blots 103 2.5 Zebrafish Model Organism Techniques 103 2.5.1 Zebrafish Care and Breeding 103 2.5.2 De-chorination of Embryos 103 2.5.3 Procedure for de-yolking embryos 104 2.6 Immunohistochemistry Techniques 104 2.6.1 Sectioning and Mounting of Embryonic Tissue 104 3 2.6.2 Immunohistochemistry of Tissue Sections 105 Chapter 3. Clinical Details of Patients Involved in the Study 108 3. Clinical Details of Patients Involved in the Study 109 3.1 Aim 109 3.2 Clinical Descriptions 110 3.2.1 Perrault Syndrome Cohort 110 3.2.2 Family with Hypogonadotropic Hypogonadism syndrome 120 Chapter 4. Mutational Screening in HSD17B4 and HARS2 123 4. Mutational Screening in HSD17B4 and HARS2 124 4.1 Introduction 124 4.2 Aim 124 4.3 Results 125 4.4 Discussion 129 Chapter 5. Autozygosity Mapping 130 5. Autozygosity Mapping 131 5.1 Introduction 131 5.2 Aim 133 5.3 Results 133 5.3.1 Perrault Syndrome 134 5.3.1.1 Family P1 134 5.3.1.2 Family P2 142 5.3.1.3 Family P4 143 5.3.1.4 Family P5 144 5.3.1.5 Family P8 146 5.3.2 Hypogonadotropic Hypogonadism Syndrome: Family HH1 150 5.4 Discussion 155 5.4.1 Identification of a Perrault syndrome locus on 155 Chromosome 19 5.4.2 Identification of a Homozygous Deletion within the Perrault 157 syndrome locus 5.4.3 NOBOX Haploinsufficiency in Family P5 158 5.4.4 Identification of a locus for Hypogonadotropic 160 Hypogonadism syndrome on Chr3 4 5.5 Conclusions 160 Chapter 6. Copy Number Deletion Investigations 161 6. Copy Number Deletion Investigations 162 6.1 Introduction 162 6.2 Aim 164 6.3 Results 164 6.3.1 Investigation of the Chr19 Homozygous Deletion detected 164 in Family P1 6.3.2 Investigation of the Chr7 Heterozygous Deletion detected 186 in Family P5 6.4 Discussion 190 6.4.1 Sequencing of CDKN2D, KRI1, AP1M2 and SLC44A2 in 190 Perrault Syndrome cohort. 6.4.2 Expression analysis in Family P1 191 6.4.3 Confirmation of the heterozygous deletion on chromosome 194 7 in Family P5 6.5 Conclusions 196 Chapter 7. Perrault Syndrome Investigations 197 7. Perrault Syndrome Investigations 198 7.1 Introduction 198 7.2 Aim 198 7.3 Results 198 7.3.1 Sanger Sequencing of Candidate Genes in 19p13.3-13.11 198 locus 7.3.2 Next Generation Sequencing of Family P1 199 7.3.3 Expression Experiments for variants detected in Family P1 206 7.3.4 Next Generation Sequencing of additional Perrault 212 syndrome patients 7.4 Discussion 213 7.4.1 Next Generation Sequencing of Family P1 213 7.4.2 Expression Experiments in Family P1 217 7.4.3 Whole Exome Sequencing of Patients P6:II:1 and P2:II:2 219 7.5 Conclusion 220 5 Chapter 8. Hypogonadotropic Hypogonadism Investigations 221 8. Hypogonadotropic Hypogonadism Investigations 222 8.1 Introduction 222 8.2 Aim 223 8.3 Results 223 8.3.1 Sanger sequencing of candidate genes within the 3p22.1- 223 p21.2 locus. 8.3.2 Zebrafish BSN knockdown model 231 8.4 Discussion 244 8.4.1 Identification of BSN mutations in Family HH1 244 8.4.2 BSN knockdown zebrafish model 245 8.5 Conclusion 247 Chapter 9. Discussion 248 9.Discussion 249 9.1 Perrault Syndrome; Summary and final conclusions. 249 9.2 Perrault syndrome; Future work. 250 9.3 Hypogonadotropic Hypogonadism syndrome; Summary and 252 final conclusions. 9.4 Hypogonadotropic Hypogonadism syndrome; Future work. 254 9.5 Final conclusions 255 9.6 New Findings and Published Data since Submission of 256 Thesis Chapter 10. Appendix 257 10.Appendix 258 10.1 References 292 10.2 Publications 311 Final Word Count = 71,970 6 List of Tables Table Page 1.1. Table of known deafness genes. 36 1.2. Table of known hypogonadotropic hypogonadism genes 52 1.3. Table of known hypergonadotropic hypogonadism genes 71 1.4. Phenotypic features of reported Perrault syndrome patients. 73 2.1. Standard PCR reaction mixture. 93 2.2. Standard sequencing reaction mixture. 95 2.3. Primer sequences for SYBR green experiments. 97 2.4. Antibodies and conditions used in western blotting experiments. 102 2.5. Antibodies and conditions used for immunohistochemistry 106 experiments. 3.1. Clinical features for affected individuals from Perrault syndrome 117 cohort. 3.2. Features of affected individuals from Family HH1. 122 4.1. Common polymorphisms detected during mutational screening 126 of HARS2 and HSD17B4. 4.2. List of samples that were sequenced for HARS2 and HSD17B4 129 from Perrault syndrome cohort. 5.1. Data for 19p13.2 homozygous deletion as displayed in ChAS 139 software. 5.2. Data for 7q35 heterozygous deletion detected in affected 145 individual P5:II:1, as displayed in ChAS analysis software. 5.3. All homozygous regions over 2Mb detected in affected 148 individuals from Perrault syndrome families. 6.1. List of patients from Perrault syndrome cohort that were 165 sequenced for AP1M2, CDKN2D, KRI1 and SLC44A2 mutations. 6.2. Details of multi species alignment for the chromosome 19 166 homozygous region deleted in Family P1. 6.3. Efficiency of individual primer assays as calculated from 175 validation experiments. 6.4. Average assay efficiency based on validation experiments. 175 7 6.5 Triplicate Ct values for individuals from Family P1. 176 6.6. Results of the Comparative Ct method analysis of SYBR green 177 based qPCR data. 6.7. Results of the Pfaffl method analysis of SYBR green based 177 qPCR data. 6.8. Expression array data for 10 genes surrounding the19p13.2 182 intergenic deletion. 7.1 Candidate genes from locus 19p13.3-13.11 sequenced in 199 Family P1. 7.2 Variations detected in 19p13.3-13.11 locus after filtering using 201 predefined criteria. 7.3 Polyphen2 and SIFT in-silico predictions for variants detected 205 using whole exome sequencing. 7.4 Sequencing of ethnically matched control samples for novel 206 variants. 7.5 Next generation sequencing coverage data for Perrault 212 syndrome patients. 8.1. In silico predictions for the p.R3361W BSN mutation. 226 8.2. Coverage data for whole exome sequencing of sample 227 HH1:III:4. 8.3. Next Generation exome data for 3p22.1-p21.2 locus in affected 228 individual HH1:III:4. 8.4. Non-synonymous BSN variants detected in a cohort of IHH 230 patients. 10.1. Primer sequences for coding exons of HSD17B4. 259 10.2. Primer sequences for coding exons of HARS2. 260 10.3. Primer sequences for the confirmation and breakpoint 261 determination of Family P1 homozygous deletion. 10.4. Primer sequences for coding exons of AP1M2, SLC44A2, 262 CDKN2D and KRI1. 10.5. cDNA concentrations used in validation experiment 1. 263 10.6. Results of GAPDH assay efficiency validation experiment 1. 264 10.7. Results of CDKN2D assay efficiency validation experiment 1. 264 8 10.8. Results of KRI1 assay efficiency validation experiment 1. 265 10.9. Results of SLC44A2 assay efficiency validation experiment 1. 265 10.10. Results of AP1M2 assay efficiency validation experiment 1. 266 10.11. cDNA concentrations used in validation experiment 2.
Load more

Recommended publications
  • In Silico Signature Prediction Modeling in Cytolethal Distending Toxin-Producing Escherichia Coli Strains
    eISSN 2234-0742 Genomics Inform 2017;15(2):69-80 G&I Genomics & Informatics https://doi.org/10.5808/GI.2017.15.2.69 ORIGINAL ARTICLE In Silico Signature Prediction Modeling in Cytolethal Distending Toxin-Producing Escherichia coli Strains Maryam Javadi, Mana Oloomi*, Saeid Bouzari Department of Molecular Biology, Pasteur Institute of Iran, Tehran 13164, Iran In this study, cytolethal distending toxin (CDT) producer isolates genome were compared with genome of pathogenic and commensal Escherichia coli strains. Conserved genomic signatures among different types of CDT producer E. coli strains were assessed. It was shown that they could be used as biomarkers for research purposes and clinical diagnosis by polymerase chain reaction, or in vaccine development. cdt genes and several other genetic biomarkers were identified as signature sequences in CDT producer strains. The identified signatures include several individual phage proteins (holins, nucleases, and terminases, and transferases) and multiple members of different protein families (the lambda family, phage-integrase family, phage-tail tape protein family, putative membrane proteins, regulatory proteins, restriction-modification system proteins, tail fiber-assembly proteins, base plate-assembly proteins, and other prophage tail-related proteins). In this study, a sporadic phylogenic pattern was demonstrated in the CDT-producing strains. In conclusion, conserved signature proteins in a wide range of pathogenic bacterial strains can potentially be used in modern vaccine-design strategies. Keywords: biomarkers, cytolethal distending toxin, genomic signature, multiple alignments, pathogenic Escherichia coli In this study, comparative genome analysis of CDT-pro- Introduction ducer E. coli isolates with other pathogenic and commensal strains was performed. Alignments between multiple The co-evolution of pathogenic bacteria and their hosts genomes led to the identification of a set of distinct leads to the generation of functional pathogen-host inter- (“signature”) sequence motifs.
    [Show full text]
  • 203-212 203 Overview and Perspectives on the Transcriptome of Paracoccidioides Brasiliensis
    Review Rev Iberoam Micol 2005; 22: 203-212 203 Overview and perspectives on the transcriptome of Paracoccidioides brasiliensis Rosângela V. Andrade1, Silvana P. da Silva2, Fernando A. G. Torres1, Marcio José Poças-Fonseca1, Ildinete Silva-Pereira1, Andrea Q. Maranhão1, Élida G. Campos1, Lídia Maria P. Moraes1, Rosália S. A. Jesuíno3, Maristela Pereira3, Célia M. A. Soares3, Maria Emília M. T. Walter1, Maria José A. Carvalho1, Nalvo F. Almeida4, Marcelo M. Brígido1 and Maria Sueli S. Felipe1 1Departamento de Biologia Celular, Universidade de Brasília, Brasília; 2Departamento de Bioquímica, Universidade Estadual de Londrina, Londrina; 3Departamento de Bioquímica, Universidade Federal de Goiás, Goiânia; 4Departamento de Computação e Estatística, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil Summary Paracoccidioides brasiliensis is a dimorphic and thermo-regulated fungus which is the causative agent of paracoccidioidomycosis, an endemic disease widespre- ad in Latin America that affects 10 million individuals. Pathogenicity is assumed to be a consequence of the dimorphic transition from mycelium to yeast cells during human infection. This review shows the results of the P. brasiliensis trans- criptome project which generated 6,022 assembled groups from mycelium and yeast phases. Computer analysis using the tools of bioinformatics revealed seve- ral aspects from the transcriptome of this pathogen such as: general and diffe- rential metabolism in mycelium and yeast cells; cell cycle, DNA replication, repair and recombination; RNA biogenesis apparatus; translation and protein fate machineries; cell wall; hydrolytic enzymes; proteases; GPI-anchored proteins; molecular chaperones; insights into drug resistance and transporters; oxidative stress response and virulence. The present analysis has provided a more com- prehensive view of some specific features considered relevant for the understan- ding of basic and applied knowledge of P.
    [Show full text]
  • (10) Patent No.: US 7608700 B2
    USOO7608700B2 (12) United States Patent (10) Patent No.: US 7,608,700 B2 Klaenhammer et al. (45) Date of Patent: Oct. 27, 2009 (54) LACTOBACILLUS ACIDOPHILUS NUCLEIC WO WO 2004/069 178 A2 8, 2004 ACID SEQUENCES ENCODING WO WO 2004/096992 A2 11/2004 STRESS-RELATED PROTEINS AND USES WO WO 2005/001057 A2 1, 2005 THEREFOR WO WO 2005/O12491 A2 2, 2005 (75) Inventors: Todd R. Klaenhammer, Raleigh, NC (US); Eric Altermann, Apex. NC (US); OTHER PUBLICATIONS M. Andrea Azcarate-Peril, Raleigh, NC (US); Olivia McAuliffe, Cork (IE): W. Bowie et al (Science, 1990, 257: 1306-1310).* Michael Russell, Newburgh, IN (US) Journal of Molecular Microbiology and Biotechnology (2002), 4(6), 525-532), abstract only.* (73) Assignee: North Carolina State University, Boehringer Mannheim Biochemicals (1991 Catalog p. 557); Raleigh, NC (US) Stratagene (1991 Product Catalog, p. 66); Gibco BRL (Catalogue & Reference Guide 1992, p. 292).* (*) Notice: Subject to any disclaimer, the term of this Promega (1993/1994 Catalog, pp. 90-91); New England BioLabs patent is extended or adjusted under 35 (Catalog 1986/1987, pp. 60-62).* U.S.C. 154(b) by 262 days. Abee et al. (1994) “Kinetic studies of the action of lactacin F, a bacteriocin produced by Lactobacillus johnsonii that formsporation (21) Appl. No.: 11/074,176 complexes in the cytoplasmic membrane' Appl. Environ. Microbiol. 60:1006-1013. (22) Filed: Mar. 7, 2005 Allison and Klaenhammer (1996) “Functional analysis of the gene encoding immunity to lactacin F. lafl. and its use as a Lactobacillus (65) Prior Publication Data specific, food-grade genetic marker Appl.
    [Show full text]
  • Protein Maturation and Proteolysis in Plant Plastids, Mitochondria, and Peroxisomes
    PP66CH04-VanWijk ARI 30 March 2015 20:57 Protein Maturation and Proteolysis in Plant Plastids, Mitochondria, and Peroxisomes Klaas J. van Wijk Department of Plant Biology, Cornell University, Ithaca, New York 14853; email: [email protected] Annu. Rev. Plant Biol. 2015. 66:75–111 Keywords First published online as a Review in Advance on proteome remodeling, endosymbiotic organelle, degron, proteostasis, January 12, 2015 degradomics, autophagy The Annual Review of Plant Biology is online at plant.annualreviews.org Abstract This article’s doi: Plastids, mitochondria, and peroxisomes are key organelles with dynamic 10.1146/annurev-arplant-043014-115547 proteomes in photosynthetic eukaryotes. Their biogenesis and activity must Copyright c 2015 by Annual Reviews. be coordinated and require intraorganellar protein maturation, degradation, All rights reserved and recycling. The three organelles together are predicted to contain ∼200 Annu. Rev. Plant Biol. 2015.66:75-111. Downloaded from www.annualreviews.org presequence peptidases, proteases, aminopeptidases, and specific protease chaperones/adaptors, but the substrates and substrate selection mechanisms are poorly understood. Similarly, lifetime determinants of organellar pro- teins, such as N-end degrons and tagging systems, have not been identi- fied, but the substrate recognition mechanisms likely share similarities be- tween organelles. Novel degradomics tools for systematic analysis of protein lifetime and proteolysis could define such protease-substrate relationships, Access provided by Chinese Academy of Agricultural Sciences (Agricultural Information Institute) on 05/10/16. For personal use only. degrons, and protein lifetime. Intraorganellar proteolysis is complemented by autophagy of whole organelles or selected organellar content, as well as by cytosolic protein ubiquitination and degradation by the proteasome.
    [Show full text]
  • BMC Genomics Biomed Central
    BMC Genomics BioMed Central Research article Open Access Cross genome comparisons of serine proteases in Arabidopsis and rice Lokesh P Tripathi and R Sowdhamini* Address: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India Email: Lokesh P Tripathi - [email protected]; R Sowdhamini* - [email protected] * Corresponding author Published: 09 August 2006 Received: 11 April 2006 Accepted: 09 August 2006 BMC Genomics 2006, 7:200 doi:10.1186/1471-2164-7-200 This article is available from: http://www.biomedcentral.com/1471-2164/7/200 © 2006 Tripathi and Sowdhamini; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. The availability of Arabidopsis thaliana and rice (Oryza sativa) genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species. Results: Despite the differences in genome sizes between Arabidopsis and rice, we identified a very similar number of serine protease-like proteins in the two plant species (206 and 222, respectively). Nearly 40% of the above sequences were identified as potential orthologues. Atypical members could be identified in the plant genomes for Deg, Clp, Lon, rhomboid proteases and species-specific members were observed for the highly populated subtilisin and serine carboxypeptidase families suggesting multiple lateral gene transfers.
    [Show full text]
  • Pfclpc Is an Essential Clp Chaperone Required for Plastid Integrity And
    bioRxiv preprint doi: https://doi.org/10.1101/080408; this version posted June 19, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. PfClpC Is An Essential Clp Chaperone Required For Plastid Integrity And Clp Protease Stability In Plasdmodium Falciparum Anat Florentin1,2, David W Cobb1, Jillian D Fishburn1, Michael J Cipriano2, Paul S Kim2, Manuel A Fierro1, Boris Striepen1,2, Vasant Muralidharan1,2* 1 Department of Cellular Biology 2 Center for Tropical and Emerging Global Diseases University of Georgia, Athens, Georgia, 30602, United States of America * Corresponding author and Lead Contact: E-mail: [email protected] (VM) 1 bioRxiv preprint doi: https://doi.org/10.1101/080408; this version posted June 19, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Summary The deadly malaria parasite, Plasmodium falciparum, contains a non-photosynthetic plastid known as the apicoplast, that functions to produce essential metabolites. Little is known about its biology or regulation, but drugs that target the apicoplast are clinically effective. Using phylogenetic analysis, we identified a putative complex of clp (caseinolytic protease) genes. We genetically targeted members of this apicoplast- regulatory complex and generated conditional mutants of the PfClpC chaperone and PfClpP protease and found that they co-localize in the apicoplast.
    [Show full text]
  • A Comprehensive Proteomic Analysis of Elaioplasts from Citrus Fruits
    Zhu et al. Horticulture Research (2018) 5:6 DOI 10.1038/s41438-017-0014-x Horticulture Research ARTICLE Open Access A comprehensive proteomic analysis of elaioplasts from citrus fruits reveals insights into elaioplast biogenesis and function Man Zhu1,2, Jiajia Lin1,2,JunliYe1,2,RuiWang3,ChaoYang3, Jinli Gong1,2,YunLiu1,2, Chongling Deng4, Ping Liu4, Chuanwu Chen4, Yunjiang Cheng1,2,XiuxinDeng 1,2 and Yunliu Zeng1,2 Abstract Elaioplasts of citrus peel are colorless plastids which accumulate significant amounts of terpenes. However, other functions of elaioplasts have not been fully characterized to date. Here, a LC–MS/MS shotgun technology was applied to identify the proteins from elaioplasts that were highly purified from young fruit peel of kumquat. A total of 655 putative plastid proteins were identified from elaioplasts according to sequence homology in silico and manual curation. Based on functional classification via Mapman, ~50% of the identified proteins fall into six categories, including protein metabolism, transport, and lipid metabolism. Of note, elaioplasts contained ATP synthase and ADP, ATP carrier proteins at high abundance, indicating important roles for ATP generation and transport in elaioplast biogenesis. Additionally, a comparison of proteins between citrus chromoplast and elaioplast proteomes suggest a high level of functional conservation. However, some distinctive protein profiles were also observed in both types of plastids notably for isoprene biosynthesis in elaioplasts, and carotenoid metabolism in chromoplasts. In conclusion, this comprehensive proteomic study provides new insights into the major metabolic pathways and unique 1234567890():,; 1234567890():,; characteristics of elaioplasts and chromoplasts in citrus fruit. Introduction from the surrounding cytoplasm rather than being syn- Plants contain several kinds of plastids, such as chlor- thesized in situ2,3.
    [Show full text]
  • Evolution of Dosage Compensation in Humans and Other Questions on Sex Chromosome Evolution in Eukaryotes Eugénie Pessia
    The Y rescued by the X ? : evolution of dosage compensation in humans and other questions on sex chromosome evolution in eukaryotes Eugénie Pessia To cite this version: Eugénie Pessia. The Y rescued by the X ? : evolution of dosage compensation in humans and other questions on sex chromosome evolution in eukaryotes. Biochemistry, Molecular Biology. Université Claude Bernard - Lyon I, 2013. English. NNT : 2013LYO10261. tel-01067259 HAL Id: tel-01067259 https://tel.archives-ouvertes.fr/tel-01067259 Submitted on 23 Sep 2014 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. No 261-2013 Année 2013 These` de l’universitedelyon´ Présentée devant L’UNIVERSITÉ CLAUDE BERNARD LYON 1 pour l’obtention du Diplomeˆ de doctorat (arrêté du 7 août 2006) soutenue publiquement le 12 décembre 2013 par Eugénie Pessia Comment le X vient-il à la rescousse du Y ? Évolution de la compensation de dosage des XY humains et autres questions sur l’évolution des chromosomes sexuels eucaryotes Directeur de thèse : Gabriel Marais Jury : Tatiana Giraud Rapporteur Judith Mank Rapporteur Gabriel Marais Directeur de thèse Marie S´emon Examinateur Frédéric Veyrunes Examinateur Cristina Vieira Examinateur 2 UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M.
    [Show full text]
  • Functional Characterization of the Clp Protease System in Arabidopsis Chloroplasts Through Reverse Genetics and Proteomics
    FUNCTIONAL CHARACTERIZATION OF THE CLP PROTEASE SYSTEM IN ARABIDOPSIS CHLOROPLASTS THROUGH REVERSE GENETICS AND PROTEOMICS A Dissertation Presented to the Faculty of the Graduate School of Cornell University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Andrea Rudella January 2007 FUNCTIONAL CHARACTERIZATION OF THE CLP PROTEASE SYSTEM IN ARABIDOPSIS CHLOROPLASTS THROUGH REVERSE GENETICS AND PROTEOMICS Andrea Rudella, Ph.D. Cornell University 2007 Proteases play an important role in regulating protein maturation, activity and life-time. The Clp protease system in Arabidopsis thaliana plastids accumulates at relatively high levels and consists of a proteolytic core and associated chaperones. The core is an assembly of five different catalytic ClpP subunits, four non-catalytic ClpR subunits, and two ClpS proteins with unknown function. ClpR,S are unique to photosynthetic organisms. Three ATP-dependent chaperones, ClpC1,C2,D, are expected to deliver substrates to the ClpPRS core. Control of Clp activity is not understood and Clp substrates are unknown. Arabidopsis T-DNA insertion Clp mutants were isolated and genotyped. Null mutants for ClpP4,P5 are embryo-lethal under both auto- and heterotrophic conditions. Mutants of ClpP3,R4 did not form seedlings under autotrophic conditions but developed albino seedlings under heterotrophic conditions, displaying limited greening under low light. Null mutants for the chaperones ClpC1 and ClpD have pale-green and wild-type phenotypes, respectively. ClpP,R core subunits are likely essential, while there are redundancies in the ClpC,D subfamily. Two mutants with partial loss of gene expression for ClpR1 and ClpR2 (clpr2-1) exhibited pale-green phenotypes, with clpr2-1 having a stronger phenotype.
    [Show full text]
  • Genome-Wide Survey of Prokaryotic Serine Proteases: Analysis Of
    BMC Genomics BioMed Central Research article Open Access Genome-wide survey of prokaryotic serine proteases: Analysis of distribution and domain architectures of five serine protease families in prokaryotes Lokesh P Tripathi1,2 and R Sowdhamini*1 Address: 1National Centre for Biological Sciences, TIFR, GKVK Campus, Bellary Road, Bangalore-560065, India and 2Current address: National Institute of Biomedical Innovation, 7-6-8 Asagi Saito Ibaraki-City, Osaka, 567-0085, Japan Email: Lokesh P Tripathi - [email protected]; R Sowdhamini* - [email protected] * Corresponding author Published: 19 November 2008 Received: 23 February 2008 Accepted: 19 November 2008 BMC Genomics 2008, 9:549 doi:10.1186/1471-2164-9-549 This article is available from: http://www.biomedcentral.com/1471-2164/9/549 © 2008 Tripathi and Sowdhamini; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Serine proteases are one of the most abundant groups of proteolytic enzymes found in all the kingdoms of life. While studies have established significant roles for many prokaryotic serine proteases in several physiological processes, such as those associated with metabolism, cell signalling, defense response and development, functional associations for a large number of prokaryotic serine proteases are relatively unknown. Current analysis is aimed at understanding the distribution and probable biological functions of the select serine proteases encoded in representative prokaryotic organisms. Results: A total of 966 putative serine proteases, belonging to five families, were identified in the 91 prokaryotic genomes using various sensitive sequence search techniques.
    [Show full text]
  • Functional Analysis of Peptidases from the Cyanobacterium Synechocystis
    Functional analysis of peptidases from the cyanobacterium Synechocystis sp. PCC 6803 Dissertation zur Erlangung des Doktorgrades der Fakultät für Biologie der Ludwig-Maximilians-Universität München vorgelegt von Elena Pojidaeva aus Moskau, Russland München 30.Juni 2004 1. Gutachter: Prof. Dr. R. G. Herrmann 2. Gutachter: Prof. Dr. H. Scheer Tag der mündlichen Prüfung: 16.09.2004 To my family CONTENT I CONTENT Abbreviations ……………………………………………………………………………………… V 1. INTRODUCTION ……………………………………………………………………………. 1 1.1 Proteolytic enzymes and their role in cell homeostasis ………………….………... 1 1.2 Characterization of the protease complement of cyanobacterial cells ……….. 7 1.2.1 The Clp peptidase family ………………………………………………………………. 8 1.2.2 The Deg peptidase family …………………………………………………………….… 9 1.2.3 The FtsH peptidase family ……………………………………………………………… 10 1.2.4 The Ctp family of carboxypeptidases …………………………………………………... 11 1.2.5 The SppA peptidase family ……………………………………………………………… 12 1.3 Cyanobacteria as models for the analysis of the photosynthetic machinery … 13 1.3.1 Structure of cyanobacterial photosynthetic complexes …………………………………. 13 1.3.2 Adaptation of cyanobacteria to environmental changes ………………………………… 17 1.3.2.1 Light acclimation …………………………………………………………….. 17 1.3.2.2 Heat stress ……………………………………………………………………. 19 1.3.2.3 Nutrient stress ……………………………………….……………………….. 20 2. MATERIALS AND METHODS ………………………………………..…………………. 22 2.1 Materials …………………………………………………………………………..……………. 22 2.1.1 Chemicals and enzymes …………………………………………………………………. 22 2.1.2 Molecular weight markers
    [Show full text]
  • Potential Implications of Mitochondrial Unfolded Protein Response in the Pathogenesis and Therapy of Dopaminergic Neuron Degeneration in Parkinson’S Disease
    Central JSM Biotechnology & Biomedical Engineering Bringing Excellence in Open Access Short Communication *Corresponding author Zhi Dong Zhou, Signature Research Program in Neuroscience and Behavioral Disorders, Duke-NUS Potential Implications of Graduate Medical School Singapore, Email: Submitted: 29 November 2017 Mitochondrial Unfolded Protein Accepted: 27 March 2017 Published: 28 March 2017 Response in the Pathogenesis and ISSN: 2333-7117 Copyright Therapy of Dopaminergic Neuron © 2017 Zhou et al. OPEN ACCESS Degeneration in Parkinson’s Keywords • Degeneration • Dopamine Disease • Mitochondria • Pathogenesis 1,3 1,3 1-3 Zhi Dong Zhou *, Yin Xia Chao , and Eng King Tan • Parkinson’s disease 1National Neuroscience Institute of Singapore, Singapore • Therapy 2Department of Neurology, Singapore General Hospital, Singapore • Unfold protein response 3Signature Research Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School Singapore Abstract Parkinson’s disease (PD) is the second most common neurodegenerative disease worldwide. The mitochondria dysfunction has long been appreciated in PD pathogenesis and can be the common pathological pathway contributing to dopaminergic (DA) neuron degeneration in PD. However mitochondria have its own quality control (QC) defensive systems to protect against stresses induced mitochondria impairment and cell degeneration. The mitochondrial QC system includes cellular QC and molecular QC systems. The mitochondrial cellular QC system includes mitophagy, mitofusion and mitofission processes. The mitochondria molecular QC system mainly refers to mitochondria unfolded protein response (mtUPR), including stress induced activation of expression of nucleus encoded mitochondria chaperones and proteases, which can be sent back to mitochondria to counteract against stress induced mitochondria impairment. So far little is known about mtUPR signaling pathway and its relevance to human diseases.
    [Show full text]