1
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Castellanos MDP, Wickramasinghe CD, Betrán E. The roles of gene duplications in the dynamics of evolutionary conflicts. Proc Biol Sci 2024; 291:20240555. [PMID: 38865605 DOI: 10.1098/rspb.2024.0555] [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: 08/08/2023] [Accepted: 04/02/2024] [Indexed: 06/14/2024] Open
Abstract
Evolutionary conflicts occur when there is antagonistic selection between different individuals of the same or different species, life stages or between levels of biological organization. Remarkably, conflicts can occur within species or within genomes. In the dynamics of evolutionary conflicts, gene duplications can play a major role because they can bring very specific changes to the genome: changes in protein dose, the generation of novel paralogues with different functions or expression patterns or the evolution of small antisense RNAs. As we describe here, by having those effects, gene duplication might spark evolutionary conflict or fuel arms race dynamics that takes place during conflicts. Interestingly, gene duplication can also contribute to the resolution of a within-locus evolutionary conflict by partitioning the functions of the gene that is under an evolutionary trade-off. In this review, we focus on intraspecific conflicts, including sexual conflict and illustrate the various roles of gene duplications with a compilation of examples. These examples reveal the level of complexity and the differences in the patterns of gene duplications within genomes under different conflicts. These examples also reveal the gene ontologies involved in conflict and the genomic location of the elements of the conflict. The examples provide a blueprint for the direct study of these conflicts or the exploration of the presence of similar conflicts in other lineages.
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Affiliation(s)
| | | | - Esther Betrán
- Department of Biology, University of Texas at Arlington , Arlington, TX 76019, USA
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2
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François CM, Pihl T, Dunoyer de Segonzac M, Hérault C, Hudry B. Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction. Nat Commun 2023; 14:6737. [PMID: 37872135 PMCID: PMC10593830 DOI: 10.1038/s41467-023-42496-9] [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: 04/21/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The molecular mechanisms connecting cellular metabolism with differentiation remain poorly understood. Here, we find that metabolic signals contribute to stem cell differentiation and germline homeostasis during Drosophila melanogaster spermatogenesis. We discovered that external citrate, originating outside the gonad, fuels the production of Acetyl-coenzyme A by germline ATP-citrate lyase (dACLY). We show that this pathway is essential during the final spermatogenic stages, where a high Acetyl-coenzyme A level promotes NatB-dependent N-terminal protein acetylation. Using genetic and biochemical experiments, we establish that N-terminal acetylation shields key target proteins, essential for spermatid differentiation, from proteasomal degradation by the ubiquitin ligase dUBR1. Our work uncovers crosstalk between metabolism and proteome stability that is mediated via protein post-translational modification. We propose that this system coordinates the metabolic state of the organism with gamete production. More broadly, modulation of proteome turnover by circulating metabolites may be a conserved regulatory mechanism to control cell functions.
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Affiliation(s)
- Charlotte M François
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Thomas Pihl
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | | | - Chloé Hérault
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Bruno Hudry
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France.
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3
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Li T, Ye Y, Wu P, Luo R, Zhang H, Zheng W. Proteasome β3 subunit (PSMB3) controls female reproduction by promoting ecdysteroidogenesis during sexual maturation in Bactrocera dorsalis. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 157:103959. [PMID: 37172766 DOI: 10.1016/j.ibmb.2023.103959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023]
Abstract
Steroid hormone 20-hydroxyecdysone (20E) plays critical roles in reproductive development in dipterans and several other insect species. Ecdysteroidogenesis in the glands of larval or nymphal insects and other arthropods has been extensively studied, but that in the adult gonads remains largely unknown. Here we identified a proteasome β3 subunit (PSMB3) from a highly invasive pest Bactrocera dorsalis, and found that this gene was crucial for ecdysone production during female reproduction. PSMB3 was enriched in the ovary, and it was upregulated during sexual maturation. RNAi-mediated depletion of PSMB3 resulted in retarded ovarian development and decreased fecundity. Additionally, knockdown of PSMB3 reduced 20E titer in hemolymph of B. dorsalis. Molecularly, RNA sequencing and qPCR validation revealed that PSMB3 depletion suppressed the expression of 20E biosynthetic genes in the ovary and 20E responsive genes in the ovary and fat body. Furthermore, exogenous 20E rescued the inhibition of the ovarian development caused by PSMB3 depletion. Taken together, this study provides new insights into the adult reproductive development-related biological processes controlled by PSMB3, and proposed a potential eco-friendly control strategy against this notorious agricultural pest.
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Affiliation(s)
- Tianran Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yinhao Ye
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Peng Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Rengang Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weiwei Zheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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4
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Hwangbo DS, Kwon YJ, Iwanaszko M, Jiang P, Abbasi L, Wright N, Alli S, Hutchison AL, Dinner AR, Braun RI, Allada R. Dietary Restriction Impacts Peripheral Circadian Clock Output Important for Longevity in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522718. [PMID: 36711760 PMCID: PMC9881908 DOI: 10.1101/2023.01.04.522718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circadian clocks may mediate lifespan extension by caloric or dietary restriction (DR). We find that the core clock transcription factor Clock is crucial for a robust longevity and fecundity response to DR in Drosophila. To identify clock-controlled mediators, we performed RNA-sequencing from abdominal fat bodies across the 24 h day after just 5 days under control or DR diets. In contrast to more chronic DR regimens, we did not detect significant changes in the rhythmic expression of core clock genes. Yet we discovered that DR induced de novo rhythmicity or increased expression of rhythmic clock output genes. Network analysis revealed that DR increased network connectivity in one module comprised of genes encoding proteasome subunits. Adult, fat body specific RNAi knockdown demonstrated that proteasome subunits contribute to DR-mediated lifespan extension. Thus, clock control of output links DR-mediated changes in rhythmic transcription to lifespan extension.
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Affiliation(s)
- Dae-Sung Hwangbo
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- Center for Sleep & Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Yong-Jae Kwon
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Marta Iwanaszko
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Peng Jiang
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- Center for Sleep & Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Ladan Abbasi
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Nicholas Wright
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Sarayu Alli
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Alan L. Hutchison
- James Franck Institute, Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Aaron R. Dinner
- James Franck Institute, Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Rosemary I Braun
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- Center for Sleep & Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
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5
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Fernando LM, Quesada-Candela C, Murray M, Ugoaru C, Yanowitz JL, Allen AK. Proteasomal subunit depletions differentially affect germline integrity in C. elegans. Front Cell Dev Biol 2022; 10:901320. [PMID: 36060813 PMCID: PMC9428126 DOI: 10.3389/fcell.2022.901320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
The 26S proteasome is a multi-subunit protein complex that is canonically known for its ability to degrade proteins in cells and maintain protein homeostasis. Non-canonical or non-proteolytic roles of proteasomal subunits exist but remain less well studied. We provide characterization of germline-specific functions of different 19S proteasome regulatory particle (RP) subunits in C. elegans using RNAi specifically from the L4 stage and through generation of endogenously tagged 19S RP lid subunit strains. We show functions for the 19S RP in regulation of proliferation and maintenance of integrity of mitotic zone nuclei, in polymerization of the synaptonemal complex (SC) onto meiotic chromosomes and in the timing of SC subunit redistribution to the short arm of the bivalent, and in turnover of XND-1 proteins at late pachytene. Furthermore, we report that certain 19S RP subunits are required for proper germ line localization of WEE-1.3, a major meiotic kinase. Additionally, endogenous fluorescent labeling revealed that the two isoforms of the essential 19S RP proteasome subunit RPN-6.1 are expressed in a tissue-specific manner in the hermaphrodite. Also, we demonstrate that the 19S RP subunits RPN-6.1 and RPN-7 are crucial for the nuclear localization of the lid subunits RPN-8 and RPN-9 in oocytes, further supporting the ability to utilize the C. elegans germ line as a model to study proteasome assembly real-time. Collectively, our data support the premise that certain 19S RP proteasome subunits are playing tissue-specific roles, especially in the germ line. We propose C. elegans as a versatile multicellular model to study the diverse proteolytic and non-proteolytic roles that proteasome subunits play in vivo.
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Affiliation(s)
| | - Cristina Quesada-Candela
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Makaelah Murray
- Department of Biology, Howard University, Washington, DC, United States
| | - Caroline Ugoaru
- Department of Biology, Howard University, Washington, DC, United States
| | - Judith L. Yanowitz
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Departments of Developmental Biology, Microbiology, and Molecular Genetics, The Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
| | - Anna K. Allen
- Department of Biology, Howard University, Washington, DC, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
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6
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Sharma H, Batra R, Kumar S, Kumar M, Kumar S, Balyan HS, Gupta PK. Identification and characterization of 20S proteasome genes and their relevance to heat/drought tolerance in bread wheat. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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7
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Leister H, Krause FF, Mahdavi R, Steinhoff U, Visekruna A. The Role of Immunoproteasomes in Tumor-Immune Cell Interactions in Melanoma and Colon Cancer. Arch Immunol Ther Exp (Warsz) 2022; 70:5. [PMID: 35064840 PMCID: PMC8783903 DOI: 10.1007/s00005-022-00644-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/14/2021] [Indexed: 11/27/2022]
Abstract
The participation of proteasomes in vital cellular and metabolic processes that are involved in tumor growth has made this protease complex an attractive target for cancer treatment. In contrast to ubiquitously available constitutive proteasome, the increased enzymatic activity of immunoproteasome is associated with tumor-infiltrating immune cells, such as antigen-presenting cells and T lymphocytes. In various tumors, an effective anti-tumor immunity is provided through generation of tumor-associated antigens by proteasomes, contributing crucially to cancer eradication by T lymphocytes. The knowledge regarding the role of immunoproteasomes in the communication between tumor cells and infiltrating immune cells is limited. Novel data suggest that the involvement of immunoproteasomes in tumorigenesis is more complex than previously thought. In the intestine, in which diverse signals from commensal bacteria and food can contribute to the onset of chronic inflammation and inflammation-driven cancer, immunoproteasomes exert tumorigenic properties by modulating the expression of pro-inflammatory factors. In contrast, in melanoma and non-small cell lung cancer, the immunoproteasome acts against cancer development by promoting an effective anti-tumor immunity. In this review, we highlight the potential of immunoproteasomes to either contribute to inflammatory signaling and tumor development, or to support anti-cancer immunity. Further, we discuss novel therapeutic options for cancer treatments that are associated with modulating the activity of immunoproteasomes in the tumor microenvironment.
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Affiliation(s)
- Hanna Leister
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Felix F Krause
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Rouzbeh Mahdavi
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Ulrich Steinhoff
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany
| | - Alexander Visekruna
- Institute for Medical Microbiology and Hygiene, Philipps-University Marburg, Marburg, Germany.
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8
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Cridland JM, Majane AC, Zhao L, Begun DJ. Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster. Genetics 2022; 220:iyab207. [PMID: 34791207 PMCID: PMC8733444 DOI: 10.1093/genetics/iyab207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Early work on de novo gene discovery in Drosophila was consistent with the idea that many such genes have male-biased patterns of expression, including a large number expressed in the testis. However, there has been little formal analysis of variation in the abundance and properties of de novo genes expressed in different tissues. Here, we investigate the population biology of recently evolved de novo genes expressed in the Drosophila melanogaster accessory gland, a somatic male tissue that plays an important role in male and female fertility and the post mating response of females, using the same collection of inbred lines used previously to identify testis-expressed de novo genes, thus allowing for direct cross tissue comparisons of these genes in two tissues of male reproduction. Using RNA-seq data, we identify candidate de novo genes located in annotated intergenic and intronic sequence and determine the properties of these genes including chromosomal location, expression, abundance, and coding capacity. Generally, we find major differences between the tissues in terms of gene abundance and expression, though other properties such as transcript length and chromosomal distribution are more similar. We also explore differences between regulatory mechanisms of de novo genes in the two tissues and how such differences may interact with selection to produce differences in D. melanogaster de novo genes expressed in the two tissues.
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Affiliation(s)
- Julie M Cridland
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Alex C Majane
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
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9
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Xia S, Ventura IM, Blaha A, Sgromo A, Han S, Izaurralde E, Long M. Rapid Gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation. Mol Biol Evol 2021; 39:6385248. [PMID: 34626117 PMCID: PMC8763131 DOI: 10.1093/molbev/msab296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It is conventionally assumed that conserved pathways evolve slowly with little participation of gene evolution. Nevertheless, it has been recently observed that young genes can take over fundamental functions in essential biological processes, for example, development and reproduction. It is unclear how newly duplicated genes are integrated into ancestral networks and reshape the conserved pathways of important functions. Here, we investigated origination and function of two autosomal genes that evolved recently in Drosophila: Poseidon and Zeus, which were created by RNA-based duplications from the X-linked CAF40, a subunit of the conserved CCR4–NOT deadenylase complex involved in posttranscriptional and translational regulation. Knockdown and knockout assays show that the two genes quickly evolved critically important functions in viability and male fertility. Moreover, our transcriptome analysis demonstrates that the three genes have a broad and distinct effect in the expression of hundreds of genes, with almost half of the differentially expressed genes being perturbed exclusively by one paralog, but not the others. Co-immunoprecipitation and tethering assays show that the CAF40 paralog Poseidon maintains the ability to interact with the CCR4–NOT deadenylase complex and might act in posttranscriptional mRNA regulation. The rapid gene evolution in the ancient posttranscriptional and translational regulatory system may be driven by evolution of sex chromosomes to compensate for the meiotic X chromosomal inactivation (MXCI) in Drosophila.
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Affiliation(s)
- Shengqian Xia
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Iuri M Ventura
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA.,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, 70040-020, Brazil
| | - Andreas Blaha
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Annamaria Sgromo
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuaibo Han
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Manyuan Long
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
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10
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Alzyoud E, Vedelek V, Réthi-Nagy Z, Lipinszki Z, Sinka R. Microtubule Organizing Centers Contain Testis-Specific γ-TuRC Proteins in Spermatids of Drosophila. Front Cell Dev Biol 2021; 9:727264. [PMID: 34660584 PMCID: PMC8511327 DOI: 10.3389/fcell.2021.727264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/10/2021] [Indexed: 11/17/2022] Open
Abstract
Microtubule nucleation in eukaryotes is primarily promoted by γ-tubulin and the evolutionary conserved protein complex, γ-Tubulin Ring Complex (γ-TuRC). γ-TuRC is part of the centrosome and basal body, which are the best-known microtubule-organizing centers. Centrosomes undergo intensive and dynamic changes during spermatogenesis, as they turn into basal bodies, a prerequisite for axoneme formation during spermatogenesis. Here we describe the existence of a novel, tissue-specific γ-TuRC in Drosophila. We characterize three genes encoding testis-specific components of γ-TuRC (t-γ-TuRC) and find that presence of t-γ-TuRC is essential to male fertility. We show the diverse subcellular distribution of the t-γ-TuRC proteins during post-meiotic development, at first at the centriole adjunct and then also on the anterior tip of the nucleus, and finally, they appear in the tail region, close to the mitochondria. We also prove the physical interactions between the t-γ-TuRC members, γ-tubulin and Mozart1. Our results further indicate heterogeneity in γ-TuRC composition during spermatogenesis and suggest that the different post-meiotic microtubule organizing centers are orchestrated by testis-specific gene products, including t-γ-TuRC.
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Affiliation(s)
- Elham Alzyoud
- Department of Genetics, University of Szeged, Szeged, Hungary
- Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Viktor Vedelek
- Department of Genetics, University of Szeged, Szeged, Hungary
| | - Zsuzsánna Réthi-Nagy
- Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged, Hungary
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zoltán Lipinszki
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Rita Sinka
- Department of Genetics, University of Szeged, Szeged, Hungary
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11
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Cafe SL, Nixon B, Ecroyd H, Martin JH, Skerrett-Byrne DA, Bromfield EG. Proteostasis in the Male and Female Germline: A New Outlook on the Maintenance of Reproductive Health. Front Cell Dev Biol 2021; 9:660626. [PMID: 33937261 PMCID: PMC8085359 DOI: 10.3389/fcell.2021.660626] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/22/2021] [Indexed: 01/07/2023] Open
Abstract
For fully differentiated, long lived cells the maintenance of protein homeostasis (proteostasis) becomes a crucial determinant of cellular function and viability. Neurons are the most well-known example of this phenomenon where the majority of these cells must survive the entire course of life. However, male and female germ cells are also uniquely dependent on the maintenance of proteostasis to achieve successful fertilization. Oocytes, also long-lived cells, are subjected to prolonged periods of arrest and are largely reliant on the translation of stored mRNAs, accumulated during the growth period, to support meiotic maturation and subsequent embryogenesis. Conversely, sperm cells, while relatively ephemeral, are completely reliant on proteostasis due to the absence of both transcription and translation. Despite these remarkable, cell-specific features there has been little focus on understanding protein homeostasis in reproductive cells and how/whether proteostasis is "reset" during embryogenesis. Here, we seek to capture the momentum of this growing field by highlighting novel findings regarding germline proteostasis and how this knowledge can be used to promote reproductive health. In this review we capture proteostasis in the context of both somatic cell and germline aging and discuss the influence of oxidative stress on protein function. In particular, we highlight the contributions of proteostasis changes to oocyte aging and encourage a focus in this area that may complement the extensive analyses of DNA damage and aneuploidy that have long occupied the oocyte aging field. Moreover, we discuss the influence of common non-enzymatic protein modifications on the stability of proteins in the male germline, how these changes affect sperm function, and how they may be prevented to preserve fertility. Through this review we aim to bring to light a new trajectory for our field and highlight the potential to harness the germ cell's natural proteostasis mechanisms to improve reproductive health. This manuscript will be of interest to those in the fields of proteostasis, aging, male and female gamete reproductive biology, embryogenesis, and life course health.
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Affiliation(s)
- Shenae L. Cafe
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Heath Ecroyd
- Molecular Horizons, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Jacinta H. Martin
- Department of Human Genetics, McGill University Health Centre Research Institute, Montreal, QC, Canada
| | - David A. Skerrett-Byrne
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Elizabeth G. Bromfield
- Priority Research Centre for Reproductive Science, Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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12
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Berruti G. Destruction or Reconstruction: A Subtle Liaison between the Proteolytic and Signaling Role of Protein Ubiquitination in Spermatogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1288:215-240. [PMID: 34453739 DOI: 10.1007/978-3-030-77779-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Ubiquitination is one of the most diverse forms of protein post-translational modification that changes the function of the landscape of substrate proteins in response to stimuli, without the need for "de novo" protein synthesis. Ubiquitination is involved in almost all aspects of eukaryotic cell biology, from the best-studied role in promoting the removal of faulty or unnecessary proteins by the way of the ubiquitin proteasome system and autophagy-lysosome pathway to the recruitment of proteins in specific non-proteolytic signaling pathways, as emerged by the more recent discoveries about the protein signature with peculiar types of ubiquitin chains. Spermatogenesis, on its own, is a complex cellular developmental process in which mitosis, meiosis, and cell differentiation coexist so to result in the continuous formation of haploid spermatozoa. Successful spermatogenesis is thus at the same time a mixed result of the precise expression and correct intracellular destination of structural proteins and enzymes, from one hand, and the fine removal by targeted degradation of unfolded or damaged proteins as well as of obsolete, outlived proteins, from the other hand. In this minireview, I will focus on the importance of the ubiquitin system all over the spermatogenic process, discussing both proteolytic and non-proteolytic functions of protein ubiquitination. Alterations in the ubiquitin system have been in fact implicated in pathologies leading to male infertility. Notwithstanding several aspects of the multifaceted world of the ubiquitin system have been clarified, the physiological meaning of the so-called ubiquitin code remains still partially elusive. The studies reviewed in this chapter provide information that could aid the investigators to pursue new promising discoveries in the understanding of human and animal reproductive potential.
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Abstract
It has long been acknowledged that changes in the regulation of gene expression may account for major organismal differences. However, we still do not fully understand how changes in gene expression evolve and how do such changes influence organisms' differences. We are even less aware of the impact such changes might have in restricting gene flow between species. Here, we focus on studies of gene expression and speciation in the Drosophila model. We review studies that have identified gene interactions in post-mating reproductive isolation and speciation, particularly those that modulate male gene expression. We also address studies that have experimentally manipulated changes in gene expression to test their effect in post-mating reproductive isolation. We highlight the need for a more in-depth analysis of the role of selection causing disrupted gene expression of such candidate genes in sterile/inviable hybrids. Moreover, we discuss the relevance to incorporate more routinely assays that simultaneously evaluate the potential effects of environmental factors and genetic background in modulating plastic responses in male genes and their potential role in speciation.
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Affiliation(s)
- Bahar Patlar
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada.,Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
| | - Alberto Civetta
- Department of Biology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada
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14
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Montooth KL, Dhawanjewar AS, Meiklejohn CD. Temperature-Sensitive Reproduction and the Physiological and Evolutionary Potential for Mother's Curse. Integr Comp Biol 2020; 59:890-899. [PMID: 31173136 PMCID: PMC6797906 DOI: 10.1093/icb/icz091] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Strict maternal transmission of mitochondrial DNA (mtDNA) is hypothesized to permit the accumulation of mitochondrial variants that are deleterious to males but not females, a phenomenon called mother’s curse. However, direct evidence that mtDNA mutations exhibit such sexually antagonistic fitness effects is sparse. Male-specific mutational effects can occur when the physiological requirements of the mitochondria differ between the sexes. Such male-specific effects could potentially occur if sex-specific cell types or tissues have energy requirements that are differentially impacted by mutations affecting energy metabolism. Here we summarize findings from a model mitochondrial–nuclear incompatibility in the fruit fly Drosophila that demonstrates sex-biased effects, but with deleterious effects that are generally larger in females. We present new results showing that the mitochondrial–nuclear incompatibility does negatively affect male fertility, but only when males are developed at high temperatures. The temperature-dependent male sterility can be partially rescued by diet, suggesting an energetic basis. Finally, we discuss fruitful paths forward in understanding the physiological scope for sex-specific effects of mitochondrial mutations in the context of the recent discovery that many aspects of metabolism are sexually dimorphic and downstream of sex-determination pathways in Drosophila. A key parameter of these models that remains to be quantified is the fraction of mitochondrial mutations with truly male-limited fitness effects across extrinsic and intrinsic environments. Given the energy demands of reproduction in females, only a small fraction of the mitochondrial mutational spectrum may have the potential to contribute to mother’s curse in natural populations.
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Affiliation(s)
- Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, 1104 T Street, Lincoln, NE 68502, USA
| | - Abhilesh S Dhawanjewar
- School of Biological Sciences, University of Nebraska-Lincoln, 1104 T Street, Lincoln, NE 68502, USA
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-Lincoln, 1104 T Street, Lincoln, NE 68502, USA
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15
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Kovács L, Nagy Á, Pál M, Deák P. Usp14 is required for spermatogenesis and ubiquitin stress responses in Drosophila melanogaster. J Cell Sci 2020; 133:133/2/jcs237511. [DOI: 10.1242/jcs.237511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Deubiquitylating (DUB) enzymes free covalently linked ubiquitin moieties from ubiquitin–ubiquitin and ubiquitin–protein conjugates, and thereby maintain the equilibrium between free and conjugated ubiquitin moieties and regulate ubiquitin-mediated cellular processes. Here, we performed genetic analyses of mutant phenotypes in Drosophila melanogaster and demonstrate that loss of Usp14 function results in male sterility, with defects in spermatid individualization and reduced testicular free monoubiquitin levels. These phenotypes were rescued by germline-specific overexpression of wild-type Usp14. Synergistic genetic interactions with Ubi-p63E and cycloheximide sensitivity suggest that ubiquitin shortage is a primary cause of male sterility. In addition, Usp14 is predominantly expressed in testes in Drosophila, indicating a higher demand for this DUB in testes that is also reflected by testis-specific loss-of-function Usp14 phenotypes. Collectively, these results suggest a major role of Usp14 in maintaining normal steady state free monoubiquitin levels during the later stages of Drosophila spermatogenesis.
This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Levente Kovács
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - Ágota Nagy
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - Margit Pál
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - Peter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
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Proteasome subunit α1 overexpression preferentially drives canonical proteasome biogenesis and enhances stress tolerance in yeast. Sci Rep 2019; 9:12418. [PMID: 31455793 PMCID: PMC6712033 DOI: 10.1038/s41598-019-48889-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/13/2019] [Indexed: 02/04/2023] Open
Abstract
The 26S proteasome conducts the majority of regulated protein catabolism in eukaryotes. At the heart of the proteasome is the barrel-shaped 20S core particle (CP), which contains two β-rings sandwiched between two α-rings. Whereas canonical CPs contain α-rings with seven subunits arranged α1-α7, a non-canonical CP in which a second copy of the α4 subunit replaces the α3 subunit occurs in both yeast and humans. The mechanisms that control canonical versus non-canonical CP biogenesis remain poorly understood. Here, we have repurposed a split-protein reporter to identify genes that can enhance canonical proteasome assembly in mutant yeast producing non-canonical α4-α4 CPs. We identified the proteasome subunit α1 as an enhancer of α3 incorporation, and find that elevating α1 protein levels preferentially drives canonical CP assembly under conditions that normally favor α4-α4 CP formation. Further, we demonstrate that α1 is stoichiometrically limiting for α-ring assembly, and that enhancing α1 levels is sufficient to increase proteasome abundance and enhance stress tolerance in yeast. Together, our data indicate that the abundance of α1 exerts multiple impacts on proteasome assembly and composition, and we propose that the limited α1 levels observed in yeast may prime cells for alternative proteasome assembly following environmental stimuli.
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Abstract
Background The formation of matured and individual sperm involves a series of molecular and spectacular morphological changes of the developing cysts in Drosophila melanogaster testis. Recent advances in RNA Sequencing (RNA-Seq) technology help us to understand the complexity of eukaryotic transcriptomes by dissecting different tissues and developmental stages of organisms. To gain a better understanding of cellular differentiation of spermatogenesis, we applied RNA-Seq to analyse the testis-specific transcriptome, including coding and non-coding genes. Results We isolated three different parts of the wild-type testis by dissecting and cutting the different regions: 1.) the apical region, which contains stem cells and developing spermatocytes 2.) the middle region, with enrichment of meiotic cysts 3.) the basal region, which contains elongated post-meiotic cysts with spermatids. Total RNA was isolated from each region and analysed by next-generation sequencing. We collected data from the annotated 17412 Drosophila genes and identified 5381 genes with significant transcript accumulation differences between the regions, representing the main stages of spermatogenesis. We demonstrated for the first time the presence and region specific distribution of 2061 lncRNAs in testis, with 203 significant differences. Using the available modENCODE RNA-Seq data, we determined the tissue specificity indices of Drosophila genes. Combining the indices with our results, we identified genes with region-specific enrichment in testis. Conclusion By multiple analyses of our results and integrating existing knowledge about Drosophila melanogaster spermatogenesis to our dataset, we were able to describe transcript composition of different regions of Drosophila testis, including several stage-specific transcripts. We present searchable visualizations that can facilitate the identification of new components that play role in the organisation and composition of different stages of spermatogenesis, including the less known, but complex regulation of post-meiotic stages. Electronic supplementary material The online version of this article (10.1186/s12864-018-5085-z) contains supplementary material, which is available to authorized users.
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Kondo S, Vedanayagam J, Mohammed J, Eizadshenass S, Kan L, Pang N, Aradhya R, Siepel A, Steinhauer J, Lai EC. New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes Dev 2017; 31:1841-1846. [PMID: 29051389 PMCID: PMC5695085 DOI: 10.1101/gad.303131.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/12/2017] [Indexed: 12/30/2022]
Abstract
In this study, Kondo et al. performed large-scale CRISPR/Cas9 mutagenesis of “conserved, essential” and “young, RNAi-lethal” genes and confirmed the lethality of conserved genes but not young genes. Additionally, two young gene mutants resulted in spermatogenesis and/or male sterility, indicating that young genes have a preferential impact on male reproductive system function. Relatively little is known about the in vivo functions of newly emerging genes, especially in metazoans. Although prior RNAi studies reported prevalent lethality among young gene knockdowns, our phylogenomic analyses reveal that young Drosophila genes are frequently restricted to the nonessential male reproductive system. We performed large-scale CRISPR/Cas9 mutagenesis of “conserved, essential” and “young, RNAi-lethal” genes and broadly confirmed the lethality of the former but the viability of the latter. Nevertheless, certain young gene mutants exhibit defective spermatogenesis and/or male sterility. Moreover, we detected widespread signatures of positive selection on young male-biased genes. Thus, young genes have a preferential impact on male reproductive system function.
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Affiliation(s)
- Shu Kondo
- Invertebrate Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Jaaved Mohammed
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA.,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York 10021, USA
| | - Sogol Eizadshenass
- Department of Biology, Yeshiva University, New York, New York 10033, USA
| | - Lijuan Kan
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Nan Pang
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Rajaguru Aradhya
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Josefa Steinhauer
- Department of Biology, Yeshiva University, New York, New York 10033, USA
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
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Baker RH, Narechania A, DeSalle R, Johns PM, Reinhardt JA, Wilkinson GS. Spermatogenesis Drives Rapid Gene Creation and Masculinization of the X Chromosome in Stalk-Eyed Flies (Diopsidae). Genome Biol Evol 2016; 8:896-914. [PMID: 26951781 PMCID: PMC4824122 DOI: 10.1093/gbe/evw043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such as dosage compensation. Numerous studies in model organisms have found complex and, at times contradictory, relationships among these genomic attributes highlighting the need to examine these patterns in other systems characterized by abundant sexual selection. Therefore, we examined the association among novel gene creation, tissue-specific gene expression, and chromosomal gene content within stalk-eyed flies. Flies in this family are characterized by strong sexual selection and the presence of a newly evolved X chromosome. We generated RNA-seq transcriptome data from the testes for three species within the family and from seven additional tissues in the highly dimorphic species, Teleopsis dalmanni. Analysis of dipteran gene orthology reveals dramatic testes-specific gene creation in stalk-eyed flies, involving numerous gene families that are highly conserved in other insect groups. Identification of X-linked genes for the three species indicates that the X chromosome arose prior to the diversification of the family. The most striking feature of this X chromosome is that it is highly masculinized, containing nearly twice as many testes-specific genes as expected based on its size. All the major processes that may drive differential sex chromosome gene content—creation of genes with male-specific expression, development of male-specific expression from pre-existing genes, and movement of genes with male-specific expression—are elevated on the X chromosome of T. dalmanni. This masculinization occurs despite evidence that testes expressed genes do not achieve the same levels of gene expression on the X chromosome as they do on the autosomes.
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Affiliation(s)
- Richard H Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY
| | - Philip M Johns
- Life Sciences Department, Yale-NUS College, Singapore, Singapore
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Actin Cytoskeletal Organization in Drosophila Germline Ring Canals Depends on Kelch Function in a Cullin-RING E3 Ligase. Genetics 2015; 201:1117-31. [PMID: 26384358 DOI: 10.1534/genetics.115.181289] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/13/2015] [Indexed: 12/21/2022] Open
Abstract
The Drosophila Kelch protein is required to organize the ovarian ring canal cytoskeleton. Kelch binds and cross-links F-actin in vitro, and it also functions with Cullin 3 (Cul3) as a component of a ubiquitin E3 ligase. How these two activities contribute to cytoskeletal remodeling in vivo is not known. We used targeted mutagenesis to investigate the mechanism of Kelch function. We tested a model in which Cul3-dependent degradation of Kelch is required for its function, but we found no evidence to support this hypothesis. However, we found that mutant Kelch deficient in its ability to interact with Cul3 failed to rescue the kelch cytoskeletal defects, suggesting that ubiquitin ligase activity is the principal activity required in vivo. We also determined that the proteasome is required with Kelch to promote the ordered growth of the ring canal cytoskeleton. These results indicate that Kelch organizes the cytoskeleton in vivo by targeting a protein substrate for degradation by the proteasome.
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21
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Whittington E, Zhao Q, Borziak K, Walters JR, Dorus S. Characterisation of the Manduca sexta sperm proteome: Genetic novelty underlying sperm composition in Lepidoptera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 62:183-193. [PMID: 25731083 DOI: 10.1016/j.ibmb.2015.02.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 06/04/2023]
Abstract
The application of mass spectrometry based proteomics to sperm biology has greatly accelerated progress in understanding the molecular composition and function of spermatozoa. To date, these approaches have been largely restricted to model organisms, all of which produce a single sperm morph capable of oocyte fertilisation. Here we apply high-throughput mass spectrometry proteomic analysis to characterise sperm composition in Manduca sexta, the tobacco hornworm moth, which produce heteromorphic sperm, including one fertilisation competent (eupyrene) and one incompetent (apyrene) sperm type. This resulted in the high confidence identification of 896 proteins from a co-mixed sample of both sperm types, of which 167 are encoded by genes with strict one-to-one orthology in Drosophila melanogaster. Importantly, over half (55.1%) of these orthologous proteins have previously been identified in the D. melanogaster sperm proteome and exhibit significant conservation in quantitative protein abundance in sperm between the two species. Despite the complex nature of gene expression across spermatogenic stages, a significant correlation was also observed between sperm protein abundance and testis gene expression. Lepidopteran-specific sperm proteins (e.g., proteins with no homology to proteins in non-Lepidopteran taxa) were present in significantly greater abundance on average than those with homology outside the Lepidoptera. Given the disproportionate production of apyrene sperm (96% of all mature sperm in Manduca) relative to eupyrene sperm, these evolutionarily novel and highly abundant proteins are candidates for possessing apyrene-specific functions. Lastly, comparative genomic analyses of testis-expressed, ovary-expressed and sperm genes identified a concentration of novel sperm proteins shared amongst Lepidoptera of potential relevance to the evolutionary origin of heteromorphic spermatogenesis. As the first published Lepidopteran sperm proteome, this whole-cell proteomic characterisation will facilitate future evolutionary genetic and developmental studies of heteromorphic sperm production and parasperm function. Furthermore, the analyses presented here provide useful annotation information regarding sex-biased gene expression, novel Lepidopteran genes and gene function in the male gamete to complement the newly sequenced and annotated Manduca genome.
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Affiliation(s)
| | - Qian Zhao
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Kirill Borziak
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - James R Walters
- Ecology and Evolutionary Biology, Kansas University, Lawrence, KS, USA
| | - Steve Dorus
- Department of Biology, Syracuse University, Syracuse, NY, USA.
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Pereira-Neves A, Gonzaga L, Menna-Barreto RFS, Benchimol M. Characterisation of 20S Proteasome in Tritrichomonas foetus and Its Role during the Cell Cycle and Transformation into Endoflagellar Form. PLoS One 2015; 10:e0129165. [PMID: 26047503 PMCID: PMC4457923 DOI: 10.1371/journal.pone.0129165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022] Open
Abstract
Proteasomes are intracellular complexes that control selective protein degradation in organisms ranging from Archaea to higher eukaryotes. These structures have multiple proteolytic activities that are required for cell differentiation, replication and maintaining cellular homeostasis. Here, we document the presence of the 20S proteasome in the protist parasite Tritrichomonas foetus. Complementary techniques, such as a combination of whole genome sequencing technologies, bioinformatics algorithms, cell fractionation and biochemistry and microscopy approaches were used to characterise the 20S proteasome of T. foetus. The 14 homologues of the typical eukaryotic proteasome subunits were identified in the T. foetus genome. Alignment analyses showed that the main regulatory and catalytic domains of the proteasome were conserved in the predicted amino acid sequences from T. foetus-proteasome subunits. Immunofluorescence assays using an anti-proteasome antibody revealed a labelling distributed throughout the cytosol as punctate cytoplasmic structures and in the perinuclear region. Electron microscopy of a T. foetus-proteasome-enriched fraction confirmed the presence of particles that resembled the typical eukaryotic 20S proteasome. Fluorogenic assays using specific peptidyl substrates detected presence of the three typical peptidase activities of eukaryotic proteasomes in T. foetus. As expected, these peptidase activities were inhibited by lactacystin, a well-known specific proteasome inhibitor, and were not affected by inhibitors of serine or cysteine proteases. During the transformation of T. foetus to endoflagellar form (EFF), also known as pseudocyst, we observed correlations between the EFF formation rates, increases in the proteasome activities and reduced levels of ubiquitin-protein conjugates. The growth, cell cycle and EFF transformation of T. foetus were inhibited after treatment with lactacystin in a dose-dependent manner. Lactacystin treatment also resulted in an accumulation of ubiquitinated proteins and caused increase in the amount of endoplasmic reticulum membranes in the parasite. Taken together, our results suggest that the ubiquitin-proteasome pathway is required for cell cycle and EFF transformation in T. foetus.
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MESH Headings
- Acetylcysteine/analogs & derivatives
- Acetylcysteine/pharmacology
- Amino Acid Sequence
- Blotting, Western
- Cell Cycle
- Cysteine Proteinase Inhibitors/pharmacology
- Endoplasmic Reticulum/drug effects
- Endoplasmic Reticulum/metabolism
- Endoplasmic Reticulum/ultrastructure
- Flagella/metabolism
- Flagella/ultrastructure
- Life Cycle Stages/drug effects
- Microscopy, Electron, Scanning
- Microscopy, Electron, Transmission
- Microscopy, Fluorescence
- Molecular Sequence Data
- Phylogeny
- Proteasome Endopeptidase Complex/classification
- Proteasome Endopeptidase Complex/genetics
- Proteasome Endopeptidase Complex/metabolism
- Protein Subunits/antagonists & inhibitors
- Protein Subunits/genetics
- Protein Subunits/metabolism
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- Protozoan Proteins/ultrastructure
- Sequence Homology, Amino Acid
- Spores, Protozoan/drug effects
- Spores, Protozoan/metabolism
- Spores, Protozoan/ultrastructure
- Tritrichomonas foetus/genetics
- Tritrichomonas foetus/growth & development
- Tritrichomonas foetus/metabolism
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Affiliation(s)
- Antonio Pereira-Neves
- Programa de Pós-graduação em Ciências Morfológicas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Fiocruz, Centro de Pesquisa Aggeu Magalhães, Departamento de Microbiologia, Laboratório de Microbiologia e Biologia Celular, Recife, PE, Brazil
| | - Luiz Gonzaga
- Laboratório Nacional de Computação Cientifica (LNCC/MCT), Petrópolis, RJ, Brazil
| | | | - Marlene Benchimol
- Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- UNIGRANRIO- Universidade do Grande Rio, Duque de Caxias, RJ, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- * E-mail:
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Gu ZC, Enenkel C. Proteasome assembly. Cell Mol Life Sci 2014; 71:4729-45. [PMID: 25107634 PMCID: PMC11113775 DOI: 10.1007/s00018-014-1699-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
In eukaryotic cells, proteasomes are highly conserved protease complexes and eliminate unwanted proteins which are marked by poly-ubiquitin chains for degradation. The 26S proteasome consists of the proteolytic core particle, the 20S proteasome, and the 19S regulatory particle, which are composed of 14 and 19 different subunits, respectively. Proteasomes are the second-most abundant protein complexes and are continuously assembled from inactive precursor complexes in proliferating cells. The modular concept of proteasome assembly was recognized in prokaryotic ancestors and applies to eukaryotic successors. The efficiency and fidelity of eukaryotic proteasome assembly is achieved by several proteasome-dedicated chaperones that initiate subunit incorporation and control the quality of proteasome assemblies by transiently interacting with proteasome precursors. It is important to understand the mechanism of proteasome assembly as the proteasome has key functions in the turnover of short-lived proteins regulating diverse biological processes.
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Affiliation(s)
- Zhu Chao Gu
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
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Ubiquitin-proteasome system in spermatogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 759:181-213. [PMID: 25030765 DOI: 10.1007/978-1-4939-0817-2_9] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Spermatogenesis represents a complex succession of cell division and differentiation events resulting in the continuous formation of spermatozoa. Such a complex program requires precise expression of enzymes and structural proteins which is effected not only by regulation of gene transcription and translation, but also by targeted protein degradation. In this chapter, we review current knowledge about the role of the ubiquitin-proteasome system in spermatogenesis, describing both proteolytic and non-proteolytic functions of ubiquitination. Ubiquitination plays essential roles in the establishment of both spermatogonial stem cells and differentiating spermatogonia from gonocytes. It also plays critical roles in several key processes during meiosis such as genetic recombination and sex chromosome silencing. Finally, in spermiogenesis, we summarize current knowledge of the role of the ubiquitin-proteasome system in nucleosome removal and establishment of key structures in the mature spermatid. Many mechanisms remain to be precisely defined, but present knowledge indicates that research in this area has significant potential to translate into benefits that will address problems in both human and animal reproduction.
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25
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Kniepert A, Groettrup M. The unique functions of tissue-specific proteasomes. Trends Biochem Sci 2013; 39:17-24. [PMID: 24286712 DOI: 10.1016/j.tibs.2013.10.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/24/2013] [Accepted: 10/28/2013] [Indexed: 11/26/2022]
Abstract
The 26S proteasome is the main protease in eukaryotes. Proteolysis occurs within the cylindrical 20S proteasome that is constitutively expressed in most tissues. However, three tissue-specific versions of the 20S proteasome have been discovered to date. The immunoproteasome is optimized to process antigens and it directs the differentiation of T helper (Th) cells. The thymoproteasome is selectively expressed in cortical epithelial cells of the thymus where it plays an essential role in the positive selection of T lymphocytes. Finally, the spermatoproteasome is found in the testes where it is required during spermatogenesis. Here, we outline how tissue-specific proteasomes adapt to functional needs in their respective tissues and how their selective inhibition may be used to interfere with autoimmune diseases and cancer.
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Affiliation(s)
- Andrea Kniepert
- Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcus Groettrup
- Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany; Biotechnology Institute Thurgau at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland.
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Basiri ML, Blachon S, Chim YCF, Avidor-Reiss T. Imaging centrosomes in fly testes. J Vis Exp 2013:e50938. [PMID: 24084634 DOI: 10.3791/50938] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Centrosomes are conserved microtubule-based organelles whose structure and function change dramatically throughout the cell cycle and cell differentiation. Centrosomes are essential to determine the cell division axis during mitosis and to nucleate cilia during interphase. The identity of the proteins that mediate these dynamic changes remains only partially known, and the function of many of the proteins that have been implicated in these processes is still rudimentary. Recent work has shown that Drosophila spermatogenesis provides a powerful system to identify new proteins critical for centrosome function and formation as well as to gain insight into the particular function of known players in centrosome-related processes. Drosophila is an established genetic model organism where mutants in centrosomal genes can be readily obtained and easily analyzed. Furthermore, recent advances in the sensitivity and resolution of light microscopy and the development of robust genetically tagged centrosomal markers have transformed the ability to use Drosophila testes as a simple and accessible model system to study centrosomes. This paper describes the use of genetically-tagged centrosomal markers to perform genetic screens for new centrosomal mutants and to gain insight into the specific function of newly identified genes.
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Serino G, Pick E. Duplication and familial promiscuity within the proteasome lid and COP9 signalosome kin complexes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 203-204:89-97. [PMID: 23415332 DOI: 10.1016/j.plantsci.2012.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Revised: 12/28/2012] [Accepted: 12/29/2012] [Indexed: 05/13/2023]
Abstract
Two paralogous complexes, the proteasome lid and the COP9 signalosome (CSN), have diverged from a common ancestor; yet fulfill distinctive roles within the ubiquitin-proteasome sphere. The CSN regulates the largest family of E3 ubiquitin ligases, called CRLs (Cullin-RING ubiquitin Ligases), while the lid is a subcomplex of the 26S proteasome, a proteolytic machinery responsible for the degradation of ubiquitinated proteins. Remarkably, in many organisms, several subunits of both complexes are duplicated, a circumstance that can hypothetically increase the number of different complexes that can be formed. Duplication, however, is not the only complexity trait within the lid and the CSN, because many of their subunits are not fully committed only to one of the two complexes, but they are able to associate with both. Indeed, their corresponding mutants have features that can be due to the absence of more than one complex. This could be simply explained by the subunits being able to carry an identical function within more than one paralogous complex or by the subunits having a certain level of promiscuity, i.e. being able to carry more than one function, depending on the complex they are associating with. Recent data show that both options are possible and, although their functional relevance still needs to be fully uncovered, evidence is accumulating, which indicates a promiscuous trading of paralogous subunits, and suggests that this may occur transiently, and/or in response to particular environmental conditions.
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Affiliation(s)
- Giovanna Serino
- Istituto Pasteur- Fondazione Cenci-Bolognetti, Department of Biology and Biotechnology, Sapienza Università di Roma, piazzale Aldo Moro 5, 00185 Rome, Italy.
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Lindsley DL, Roote J, Kennison JA. Anent the genomics of spermatogenesis in Drosophila melanogaster. PLoS One 2013; 8:e55915. [PMID: 23409089 PMCID: PMC3567030 DOI: 10.1371/journal.pone.0055915] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/04/2013] [Indexed: 01/09/2023] Open
Abstract
An appreciable fraction of the Drosophila melanogaster genome is dedicated to male fertility. One approach to characterizing this subset of the genome is through the study of male-sterile mutations. We studied the relation between vital and male-fertility genes in three large autosomal regions that were saturated for lethal and male-sterile mutations. The majority of male-sterile mutations affect genes that are exclusively expressed in males. These genes are required only for male fertility, and several mutant alleles of each such gene were encountered. A few male-sterile mutations were alleles of vital genes that are expressed in both males and females. About one-fifth of the genes in Drosophila melanogaster show male-specific expression in adults. Although some earlier studies found a paucity of genes on the X chromosome showing male-biased expression, we did not find any significant differences between the X chromosome and the autosomes either in the relative frequencies of mutations to male sterility or in the frequencies of genes with male-specific expression in adults. Our results suggest that as much as 25% of the Drosophila genome may be dedicated to male fertility.
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Affiliation(s)
- Dan L. Lindsley
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, California, United States of America
| | - John Roote
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - James A. Kennison
- Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Baker RH, Narechania A, Johns PM, Wilkinson GS. Gene duplication, tissue-specific gene expression and sexual conflict in stalk-eyed flies (Diopsidae). Philos Trans R Soc Lond B Biol Sci 2012; 367:2357-75. [PMID: 22777023 PMCID: PMC3391427 DOI: 10.1098/rstb.2011.0287] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Gene duplication provides an essential source of novel genetic material to facilitate rapid morphological evolution. Traits involved in reproduction and sexual dimorphism represent some of the fastest evolving traits in nature, and gene duplication is intricately involved in the origin and evolution of these traits. Here, we review genomic research on stalk-eyed flies (Diopsidae) that has been used to examine the extent of gene duplication and its role in the genetic architecture of sexual dimorphism. Stalk-eyed flies are remarkable because of the elongation of the head into long stalks, with the eyes and antenna laterally displaced at the ends of these stalks. Many species are strongly sexually dimorphic for eyespan, and these flies have become a model system for studying sexual selection. Using both expressed sequence tag and next-generation sequencing, we have established an extensive database of gene expression in the developing eye-antennal imaginal disc, the adult head and testes. Duplicated genes exhibit narrower expression patterns than non-duplicated genes, and the testes, in particular, provide an abundant source of gene duplication. Within somatic tissue, duplicated genes are more likely to be differentially expressed between the sexes, suggesting gene duplication may provide a mechanism for resolving sexual conflict.
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Affiliation(s)
- Richard H Baker
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA.
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Dorus S, Skerget S, Karr TL. Proteomic discovery of diverse immunity molecules in mammalian spermatozoa. Syst Biol Reprod Med 2012; 58:218-28. [DOI: 10.3109/19396368.2012.700442] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Sloan RS, Swanson CI, Gavilano L, Smith KN, Malek PY, Snow-Smith M, Duronio RJ, Key SCS. Characterization of null and hypomorphic alleles of the Drosophila l(2)dtl/cdt2 gene: Larval lethality and male fertility. Fly (Austin) 2012; 6:173-83. [PMID: 22722696 DOI: 10.4161/fly.20247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The Drosophila lethal(2)denticleless (l(2)dtl) gene was originally reported as essential for embryogenesis and formation of the rows of tiny hairs on the larval ventral cuticle known as denticle belts. It is now well-established that l(2)dtl (also called cdt2) encodes a subunit of a Cullin 4-based E3 ubiquitin ligase complex that targets a number of key cell cycle regulatory proteins, including p21, Cdt1, E2F1 and Set8, to prevent replication defects and maintain cell cycle control. To investigate the role of l(2)dtl/cdt2 during development, we characterized existing l(2)dtl/cdt2 mutants and generated new deletion alleles, using P-element excision mutagenesis. Surprisingly, homozygous l(2)dtl/cdt2 mutant embryos developed beyond embryogenesis, had intact denticle belts, and lacked an observable embryonic replication defect. These mutants died during larval stages, affirming that loss of l(2)dtl/cdt2 function is lethal. Our data show that L(2)dtl/Cdt2 is maternally deposited, remains nuclear throughout the cell cycle, and has a previously unreported, elevated expression in the developing gonads. We also find that E2f1 regulates l(2)dtl/cdt2 expression during embryogenesis, possibly via several highly conserved putative E2f1 binding sites near the l(2)dtl/cdt2 promoter. Finally, hypomorphic allele combinations of the l(2)dtl/cdt2 gene result in a novel phenotype: viable, low-fertility males. We conclude that "denticleless" is a misnomer, but that l(2)dtl/cdt2 is an essential gene for Drosophila development.
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Affiliation(s)
- Roketa S Sloan
- Department of Biology, North Carolina Central University, Durham, NC USA
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32
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Yano H, Yamamoto-Hino M, Awano W, Aoki-Kinoshita KF, Tsuda-Sakurai K, Okano H, Goto S. Identification of proteasome components required for apical localization of Chaoptin using functional genomics. J Neurogenet 2012; 26:53-63. [PMID: 22417167 DOI: 10.3109/01677063.2012.661497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Abstract: the distinct localization of membrane proteins with regard to cell polarity is crucial for the structure and function of various organs in multicellular organisms. However, the molecules and mechanisms that regulate protein localization to particular subcellular domains are still largely unknown. To identify the genes involved in regulation of protein localization, the authors performed a large-scale screen using a Drosophila RNA interference (RNAi) library, by which Drosophila genes could be knocked down in a tissue- and stage-specific manner. Drosophila photoreceptor cells have a morphologically distinct apicobasal polarity, along which Chaoptin (Chp), a glycosylphosphatidylinositol (GPI)-anchored membrane protein, and the Na (+) , K(+) -ATPase are localized to the apical and basolateral domains, respectively. By examining the subcellular localization of these proteins, the authors identified 106 genes whose knockdown resulted in mislocalization of Chp and Na(+) , K(+) -ATPase. Gene ontology analysis revealed that the knockdown of proteasome components resulted in mislocalization of Chp to the basolateral plasma membrane. These results suggest that the proteasome is involved, directly or indirectly, in selective localization of Chp to the apical plasma membrane of Drosophila photoreceptor cells.
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Affiliation(s)
- Hiroyuki Yano
- Research Group of Glycobiology and Glycotechnology , Tokyo , Japan
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Abstract
Males and females share most of the same genes, so selection in one sex will typically produce a correlated response in the other sex. Yet, the sexes have evolved to differ in a multitude of behavioral, morphological, and physiological traits. How did this sexual dimorphism evolve despite the presence of a common underlying genome? We investigated the potential role of gene duplication in the evolution of sexual dimorphism. Because duplication events provide extra genetic material, the sexes each might use this redundancy to facilitate sex-specific gene expression, permitting the evolution of dimorphism. We investigated this hypothesis at the genome-wide level in Drosophila melanogaster, using the presence of sex-biased expression as a proxy for the sex-specific specialization of gene function. We expected that if sexually antagonistic selection is a potent force acting upon individual genes, duplication will result in paralog families whose members differ in sex-biased expression. Gene members of the same duplicate family can have different expression patterns in males versus females. In particular, duplicate pairs containing a male-biased gene are found more frequently than expected, in agreement with previous studies. Furthermore, when the singleton ortholog is unbiased, duplication appears to allow one of the paralog copies to acquire male-biased expression. Conversely, female-biased expression is not common among duplicates; fewer duplicate genes are expressed in the female-soma and ovaries than in the male-soma and testes. Expression divergence exists more in older than in younger duplicates pairs, but expression divergence does not correlate with protein sequence divergence. Finally, genomic proximity may have an effect on whether paralogs differ in sex-biased expression. We conclude that the data are consistent with a role of gene duplication in fostering male-biased, but not female-biased, gene expression, thereby aiding the evolution of sexual dimorphism.
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Affiliation(s)
- Minyoung J Wyman
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S. A protein complex network of Drosophila melanogaster. Cell 2011; 147:690-703. [PMID: 22036573 DOI: 10.1016/j.cell.2011.08.047] [Citation(s) in RCA: 465] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 07/14/2011] [Accepted: 08/19/2011] [Indexed: 01/24/2023]
Abstract
Determining the composition of protein complexes is an essential step toward understanding the cell as an integrated system. Using coaffinity purification coupled to mass spectrometry analysis, we examined protein associations involving nearly 5,000 individual, FLAG-HA epitope-tagged Drosophila proteins. Stringent analysis of these data, based on a statistical framework designed to define individual protein-protein interactions, led to the generation of a Drosophila protein interaction map (DPiM) encompassing 556 protein complexes. The high quality of the DPiM and its usefulness as a paradigm for metazoan proteomes are apparent from the recovery of many known complexes, significant enrichment for shared functional attributes, and validation in human cells. The DPiM defines potential novel members for several important protein complexes and assigns functional links to 586 protein-coding genes lacking previous experimental annotation. The DPiM represents, to our knowledge, the largest metazoan protein complex map and provides a valuable resource for analysis of protein complex evolution.
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Affiliation(s)
- K G Guruharsha
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Zhan Z, Ding Y, Zhao R, Zhang Y, Yu H, Zhou Q, Yang S, Xiang H, Wang W. Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan. Mol Biol Evol 2011; 29:1407-16. [PMID: 22135190 DOI: 10.1093/molbev/msr299] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cost of reproduction is a pivotal trade-off with various biological processes during the evolution of organisms. However, the genes and molecular mechanisms underlying the evolution of balancing reproductive capacity and its cost are still largely unknown. Here, we present a comprehensive study on the evolution, expression, and biological functions of a newly evolved pair of X-linked polyubiquitin tandemly duplicated genes, CG32744 and CG11700, of which the duplication event occurred in Drosophila melanogaster lineage after the split from D. simulans clade. We found that CG32744 retains conserved polyubiquitin-coding sequences across Drosophila species and is ubiquitously expressed, whereas CG11700 has accumulated numerous amino acid changes and shows a male-specific expression pattern. Null mutants of CG11700 have a higher male fecundity but shorter lifespan, whereas its overexpression decreases male fecundity. In contrast, the null mutants of the peptide-conserved CG32744 do not exhibit such phenotypes. These results suggest that CG11700 might have experienced neofunctionalization and evolved important functions in the trade-off between male fecundity and lifespan and that CG32744 likely has retained the ancestral function.
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Affiliation(s)
- Zubing Zhan
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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36
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37
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Yokota N, Kataoka Y, Hashii N, Kawasaki N, Sawada H. Sperm-specific C-terminal processing of the proteasome PSMA1/α6 subunit. Biochem Biophys Res Commun 2011; 410:809-15. [DOI: 10.1016/j.bbrc.2011.06.069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 06/09/2011] [Indexed: 12/19/2022]
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38
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Gallach M, Betrán E. Intralocus sexual conflict resolved through gene duplication. Trends Ecol Evol 2011; 26:222-8. [PMID: 21397976 DOI: 10.1016/j.tree.2011.02.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 11/27/2022]
Abstract
Gene duplication is mainly recognized by its primary role in the origin of new genes and functions. However, the idea that gene duplication can be a central player in resolving sexual genetic conflicts through its potential to generate sex-biased and sex-specifically expressed genes, has been almost entirely overlooked. We review recent data and theory that support gene duplication as a theoretically predicted and experimentally supported means of resolving intralocus sexual antagonism. We believe that this role is probably the consequence of sexual conflict for housekeeping genes that are required in males and females, and which are expressed in sexually dimorphic tissues (i.e. where sexually antagonistic selection is exerted). We think that these genes cannot evolve tissue-specific expression unless they duplicate.
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Affiliation(s)
- Miguel Gallach
- Department of Biology, University of Texas at Arlington, 501 S. Nedderman Drive, Arlington, TX, USA
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39
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Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution. Proc Natl Acad Sci U S A 2010; 107:20992-7. [PMID: 21098295 DOI: 10.1073/pnas.1015530107] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The structure of the 26S proteasome from Schizosaccharomyces pombe has been determined to a resolution of 9.1 Å by cryoelectron microscopy and single particle analysis. In addition, chemical cross-linking in conjunction with mass spectrometry has been used to identify numerous residue pairs in close proximity to each other, providing an array of spatial restraints. Taken together these data clarify the topology of the AAA-ATPase module in the 19S regulatory particle and its spatial relationship to the α-ring of the 20S core particle. Image classification and variance analysis reveal a belt of high "activity" surrounding the AAA-ATPase module which is tentatively assigned to the reversible association of proteasome interacting proteins and the conformational heterogeneity among the particles. An integrated model is presented which sheds light on the early steps of protein degradation by the 26S complex.
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40
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Gallach M, Chandrasekaran C, Betrán E. Analyses of nuclearly encoded mitochondrial genes suggest gene duplication as a mechanism for resolving intralocus sexually antagonistic conflict in Drosophila. Genome Biol Evol 2010; 2:835-50. [PMID: 21037198 PMCID: PMC2995371 DOI: 10.1093/gbe/evq069] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gene duplication is probably the most important mechanism for generating new gene functions. However, gene duplication has been overlooked as a potentially effective way to resolve genetic conflicts. Here, we analyze the entire set of Drosophila melanogaster nuclearly encoded mitochondrial duplicate genes and show that both RNA- and DNA-mediated mitochondrial gene duplications exhibit an unexpectedly high rate of relocation (change in location between parental and duplicated gene) as well as an extreme tendency to avoid the X chromosome. These trends are likely related to our observation that relocated genes tend to have testis-specific expression. We also infer that these trends hold across the entire Drosophila genus. Importantly, analyses of gene ontology and functional interaction networks show that there is an overrepresentation of energy production-related functions in these mitochondrial duplicates. We discuss different hypotheses to explain our results and conclude that our findings substantiate the hypothesis that gene duplication for male germline function is likely a mechanism to resolve intralocus sexually antagonistic conflicts that we propose are common in testis. In the case of nuclearly encoded mitochondrial duplicates, our hypothesis is that past sexually antagonistic conflict related to mitochondrial energy function in Drosophila was resolved by gene duplication.
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Affiliation(s)
- Miguel Gallach
- Department of Biology, University of Texas at Arlington, USA
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41
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Zhang N, Liang J, Tian Y, Yuan L, Wu L, Miao S, Zong S, Wang L. A novel testis-specific GTPase serves as a link to proteasome biogenesis: functional characterization of RhoS/RSA-14-44 in spermatogenesis. Mol Biol Cell 2010; 21:4312-24. [PMID: 20980621 PMCID: PMC3002385 DOI: 10.1091/mbc.e10-04-0310] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We functionally characterized RhoS/RSA-14-44 as a new member of Rho GTPase subfamily in spermatogenesis, which provides a direct link between Rho family GTPase and the proteasome biogenesis. Most Rho family GTPases serve as key molecular switches in a wide spectrum of biological processes. An increasing number of studies have expanded their roles to the spermatogenesis. Several members of Rho family have been confirmed to be essential for mammalian spermatogenesis, but the precise roles of this family in male reproduction have not been well studied yet. Here we report a surprising function of an atypical and testis-specific Rho GTPase, RSA-14-44 in spermatogenesis. Featured by unique structural and expressional patterns, RSA-14-44 is distinguished from three canonical members of Rho cluster. Thus, we define RSA-14-44 as a new member of Rho GTPases family and rename it RhoS (Rho in spermatogenic cells). RhoS associates with PSMB5, a catalytic subunit of the proteasome, in a series of stage-specific spermatogenic cells. More importantly, RhoS does not directly modulate the cellular proteasome activity, but participates in regulating the stability of “unincorporated” PSMB5 precursors. Meanwhile, our data demonstrate that the activation of RhoS is prerequisite for negatively regulating the stability of PSMB5 precursors. Therefore, our finding uncovers a direct and functional connection between the Rho GTPase family and the pathway of proteasome biogenesis and provide new clues for deciphering the secrets of spermatogenesis.
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Affiliation(s)
- Ning Zhang
- Chinese Academy of Medical Sciences, Peking Union Medical College, Tsinghua University, Beijing, China
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42
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Meisel RP, Hilldorfer BB, Koch JL, Lockton S, Schaeffer SW. Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Mol Biol Evol 2010; 27:1963-78. [PMID: 20351054 DOI: 10.1093/molbev/msq085] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Drosophila X chromosomes are disproportionate sources of duplicated genes, and these duplications are usually the result of retrotransposition of X-linked genes to the autosomes. The excess duplication is thought to be driven by natural selection for two reasons: X chromosomes are inactivated during spermatogenesis, and the derived copies of retroposed duplications tend to be testis expressed. Therefore, autosomal derived copies of retroposed genes provide a mechanism for their X-linked paralogs to "escape" X inactivation. Once these duplications have fixed, they may then be selected for male-specific functions. Throughout the evolution of the Drosophila genus, autosomes have fused with X chromosomes along multiple lineages giving rise to neo-X chromosomes. There has also been excess duplication from the two independent neo-X chromosomes that have been examined--one that occurred prior to the common ancestor of the willistoni species group and another that occurred along the lineage leading to Drosophila pseudoobscura. To determine what role natural selection plays in the evolution of genes duplicated from the D. pseudoobscura neo-X chromosome, we analyzed DNA sequence divergence between paralogs, polymorphism within each copy, and the expression profiles of these duplicated genes. We found that the derived copies of all duplicated genes have elevated nonsynonymous polymorphism, suggesting that they are under relaxed selective constraints. The derived copies also tend to have testis- or male-biased expression profiles regardless of their chromosome of origin. Genes duplicated from the neo-X chromosome appear to be under less constraints than those duplicated from other chromosome arms. We also find more evidence for historical adaptive evolution in genes duplicated from the neo-X chromosome, suggesting that they are under a unique selection regime in which elevated nonsynonymous polymorphism provides a large reservoir of functional variants, some of which are fixed by natural selection.
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Affiliation(s)
- Richard P Meisel
- Intercollege Graduate Program in Genetics, The Pennsylvania State University, PA, USA.
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43
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Sorourian M, Betrán E. Turnover and lineage-specific broadening of the transcription start site in a testis-specific retrogene. Fly (Austin) 2010; 4:3-11. [PMID: 20160503 DOI: 10.4161/fly.4.1.11136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Proteasomes are large multisubunit complexes responsible for regulated protein degradation. Made of a core particle (20S) and regulatory caps (19S), proteasomal proteins are encoded by at least 33 genes, of which 12 have been shown to have testis-specific isoforms in Drosophila melanogaster. Pros28.1A (also known as Prosalpha4T1), a young retroduplicate copy of Pros28.1 (also known as Prosalpha4), is one of these isoforms. It is present in the D. melanogaster subgroup and was previously shown to be testis-specific in D. melanogaster. Here, we show its testis-specific transcription in all D. melanogaster subgroup species. Due to this conserved pattern of expression in the species harboring this insertion, we initially expected that a regulatory region common to these species evolved prior to the speciation event. We determined that the region driving testis expression in D. melanogaster is not far from the coding region (within 272 bp upstream of the ATG). However, different Transcription Start Sites (TSSs) are used in D. melanogaster and D. simulans, and a "broad" transcription start site is used in D. yakuba. These results suggest one of the following scenarios: (1) there is a conserved motif in the 5' region of the gene that can be used as an upstream or downstream element or at different distance depending on the species; (2) different species evolved diverse regulatory sequences for the same pattern of expression (i.e., "TSS turnover"); or (3) the transcription start site can be broad or narrow depending on the species. This work reveals the difficulties of studying gene regulation in one species and extrapolating those findings to close relatives.
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Affiliation(s)
- Mehran Sorourian
- Department of Biology, University of Texas at Arlington, TX, USA
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