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Sánchez-Bellver L, Férriz-Gordillo A, Carrillo-Pz M, Rabanal L, Garcia-Gonzalo FR, Marfany G. The Deubiquitinating Enzyme USP48 Interacts with the Retinal Degeneration-Associated Proteins UNC119a and ARL3. Int J Mol Sci 2022; 23:ijms232012527. [PMID: 36293380 PMCID: PMC9603860 DOI: 10.3390/ijms232012527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins related to the ubiquitin-proteasome system play an important role during the differentiation and ciliogenesis of photoreceptor cells. Mutations in several genes involved in ubiquitination and proteostasis have been identified as causative of inherited retinal dystrophies (IRDs) and ciliopathies. USP48 is a deubiquitinating enzyme whose role in the retina is still unexplored although previous studies indicate its relevance for neurosensory organs. In this work, we describe that a pool of endogenous USP48 localises to the basal body in retinal cells and provide data that supports the function of USP48 in the photoreceptor cilium. We also demonstrate that USP48 interacts with the IRD-associated proteins ARL3 and UNC119a, and stabilise their protein levels using different mechanisms. Our results suggest that USP48 may act in the regulation/stabilisation of key ciliary proteins for photoreceptor function, in the modulation of intracellular protein transport, and in ciliary trafficking to the photoreceptor outer segment.
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Affiliation(s)
- Laura Sánchez-Bellver
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Andrea Férriz-Gordillo
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Marc Carrillo-Pz
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Laura Rabanal
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - Francesc R. Garcia-Gonzalo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, 28029 Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC), 28029 Madrid, Spain
- Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina-Institut de Recerca Sant Joan de Déu (IBUB-IRSJD), Universitat de Barcelona, 08028 Barcelona, Spain
- DBGen Ocular Genomics, 08028 Barcelona, Spain
- Correspondence:
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Altered retinal structure and function in Spinocerebellar ataxia type 3. Neurobiol Dis 2022; 170:105774. [DOI: 10.1016/j.nbd.2022.105774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 01/13/2023] Open
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Appelbaum T, Murgiano L, Becker D, Santana E, Aguirre GD. Candidate Genetic Modifiers for RPGR Retinal Degeneration. Invest Ophthalmol Vis Sci 2021; 61:20. [PMID: 33326016 PMCID: PMC7745631 DOI: 10.1167/iovs.61.14.20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Purpose To define genetic variants associated with variable severity of X-linked progressive retinal atrophy 1 (XLPRA1) caused by a five-nucleotide deletion in canine RPGR exon ORF15. Methods A genome-wide association study (GWAS) was performed in XLPRA1 phenotype informative pedigree. Whole genome sequencing (WGS) was used for mutational analysis of genes within the candidate genomic region. Retinas of normal and mutant dogs were used for gene expression, gene structure, and RNA duplex analyses. Results GWAS followed by haplotype phasing identified an approximately 4.6 Mb candidate genomic interval on CFA31 containing seven protein-coding genes expressed in retina (ROBO1, ROBO2, RBM11, NRIP1, HSPA13, SAMSN1, and USP25). Furthermore, we identified and characterized two novel lncRNAs, ROBO1-AS and ROBO2-AS, that display overlapping gene organization with axon guidance pathway genes ROBO1 and ROBO2, respectively, producing sense-antisense gene pairs. Notably, ROBO1-AS and ROBO2-AS act in cis to form lncRNA/mRNA duplexes with ROBO1 and ROBO2, respectively, suggesting important roles for these lncRNAs in the ROBO regulatory network. A subsequent WGS identified candidate genes within the genomic region on CFA31 that might be implicated in modifying severity of XLPRA1. This approach led to discovery of genetic variants in ROBO1, ROBO1-AS, ROBO2-AS, and USP25 that are strongly associated with the XLPRA1 moderate phenotype. Conclusions The study provides new insights into the genetic basis of phenotypic variation in severity of RPGRorf15-associated retinal degeneration. Our findings suggest an important role for ROBO pathways in disease progression further expanding on our previously reported changes of ROBO1 expression in XLPRA1 retinas.
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Affiliation(s)
- Tatyana Appelbaum
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Leonardo Murgiano
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Doreen Becker
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States.,Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf, Germany
| | - Evelyn Santana
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Gustavo D Aguirre
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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Piedade WP, Famulski JK. E3 ubiquitin ligase-mediated regulation of vertebrate ocular development; new insights into the function of SIAH enzymes. Biochem Soc Trans 2021; 49:327-340. [PMID: 33616626 PMCID: PMC7924998 DOI: 10.1042/bst20200613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 01/18/2023]
Abstract
Developmental regulation of the vertebrate visual system has been a focus of investigation for generations as understanding this critical time period has direct implications on our understanding of congenital blinding disease. The majority of studies to date have focused on transcriptional regulation mediated by morphogen gradients and signaling pathways. However, recent studies of post translational regulation during ocular development have shed light on the role of the ubiquitin proteasome system (UPS). This rather ubiquitous yet highly diverse system is well known for regulating protein function and localization as well as stability via targeting for degradation by the 26S proteasome. Work from many model organisms has recently identified UPS activity during various milestones of ocular development including retinal morphogenesis, retinal ganglion cell function as well as photoreceptor homeostasis. In particular work from flies and zebrafish has highlighted the role of the E3 ligase enzyme family, Seven in Absentia Homologue (Siah) during these events. In this review, we summarize the current understanding of UPS activity during Drosophila and vertebrate ocular development, with a major focus on recent findings correlating Siah E3 ligase activity with two major developmental stages of vertebrate ocular development, retinal morphogenesis and photoreceptor specification and survival.
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Toulis V, García-Monclús S, de la Peña-Ramírez C, Arenas-Galnares R, Abril JF, Todi SV, Khan N, Garanto A, Costa MDC, Marfany G. The Deubiquitinating Enzyme Ataxin-3 Regulates Ciliogenesis and Phagocytosis in the Retina. Cell Rep 2020; 33:108360. [PMID: 33176149 PMCID: PMC8738964 DOI: 10.1016/j.celrep.2020.108360] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/04/2020] [Accepted: 10/17/2020] [Indexed: 01/07/2023] Open
Abstract
Expansion of a CAG repeat in ATXN3 causes the dominant polyglutamine disease spinocerebellar ataxia type 3 (SCA3), yet the physiological role of ATXN3 remains unclear. Here, we focus on unveiling the function of Ataxin-3 (ATXN3) in the retina, a neurological organ amenable to morphological and physiological studies. Depletion of Atxn3 in zebrafish and mice causes morphological and functional retinal alterations and, more precisely, photoreceptor cilium and outer segment elongation, cone opsin mislocalization, and cone hyperexcitation. ATXN3 localizes at the basal body and axoneme of the cilium, supporting its role in regulating ciliary length. Abrogation of Atxn3 expression causes decreased levels of the regulatory protein KEAP1 in the retina and delayed phagosome maturation in the retinal pigment epithelium. We propose that ATXN3 regulates two relevant biological processes in the retina, namely, ciliogenesis and phagocytosis, by modulating microtubule polymerization and microtubule-dependent retrograde transport, thus positing ATXN3 as a causative or modifier gene in retinal/macular dystrophies. Toulis et al. show that depletion of Atxn3 causes retinal morphological and electrophysiological alterations, as well as diminished phagocytosis in vivo and in vitro. ATXN3 regulates retinal ciliogenesis and phagocytosis through the KEAP1-SQSTM1-HDAC6-acetylated tubulin pathway by modulating microtubule polymerization and microtubule-dependent retrograde transport.
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Affiliation(s)
- Vasileios Toulis
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain; CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain; Department of Neurology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sílvia García-Monclús
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain
| | - Carlos de la Peña-Ramírez
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain
| | - Rodrigo Arenas-Galnares
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain; Institute of Biomedicine (IBUB, IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
| | - Josep F Abril
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain; Institute of Biomedicine (IBUB, IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Neurology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Naheed Khan
- Department of Ophthalmology and Visual Sciences, W. K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | - Alejandro Garanto
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain; Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maria do Carmo Costa
- Department of Neurology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain; CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain; Institute of Biomedicine (IBUB, IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain.
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Toulis V, Marfany G. By the Tips of Your Cilia: Ciliogenesis in the Retina and the Ubiquitin-Proteasome System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:303-310. [PMID: 32274763 DOI: 10.1007/978-3-030-38266-7_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Primary cilia are microtubule-based sensory organelles that are involved in the organization of numerous key signals during development and in differentiated tissue homeostasis. In fact, the formation and resorption of cilia highly depends on the cell cycle phase in replicative cells, and the ubiquitin proteasome pathway (UPS) proteins, such as E3 ligases and deubiquitinating enzymes, promote microtubule assembly and disassembly by regulating the degradation/availability of ciliary regulatory proteins. Also, many differentiated tissues display cilia, and mutations in genes encoding ciliary proteins are associated with several human pathologies, named ciliopathies, which are multi-organ rare diseases. The retina is one of the organs most affected by ciliary gene mutations because photoreceptors are ciliated cells. Photoreception and phototransduction occur in the outer segment, a highly specialized neurosensory cilium. In this review, we focus on the function of UPS proteins in ciliogenesis and cilia length control in replicative cells and compare it with the scanty data on the identified UPS genes that cause syndromic and non-syndromic inherited retinal disorders. Clearly, further work using animal models and gene-edited mutants of ciliary genes in cells and organoids will widen the landscape of UPS involvement in ciliogenesis and cilia homeostasis.
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Affiliation(s)
- Vasileios Toulis
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain.,CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain. .,CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain. .,Institut de Biomedicina (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain.
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Esquerdo-Barragán M, Brooks MJ, Toulis V, Swaroop A, Marfany G. Expression of deubiquitinating enzyme genes in the developing mammal retina. Mol Vis 2019; 25:800-813. [PMID: 31819342 PMCID: PMC6887694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/29/2019] [Indexed: 11/18/2022] Open
Abstract
Purpose Genes involved in the development and differentiation of the mammalian retina are also associated with inherited retinal dystrophies (IRDs) and age-related macular degeneration. Transcriptional regulation of retinal cell differentiation has been addressed by genetic and transcriptomic studies. Much less is known about the posttranslational regulation of key regulatory proteins, although mutations in some genes involved in ubiquitination and proteostasis-E3 ligases and deubiquitinating enzymes (DUBs)-cause IRDs. This study intends to provide new data on DUB gene expression during different developmental stages of mouse and human fetal retinas. Methods We performed a comprehensive transcriptomic analysis of all the annotated human and mouse DUBs (87) in the developing mouse retina at several embryonic and postnatal time points compared with the transcriptome of the fetal human retina. An integrated comparison of data from transcriptomics, reported chromatin immunoprecipitation sequencing (ChIP-seq) of CRX and NRL transcription factors, and the phenotypic retinal alterations in different animal models is presented. Results Several DUB genes are differentially expressed during the development of the mouse and human retinas in relation to proliferation or differentiation stages. Some DUB genes appear to be distinctly expressed during the differentiation stages of rod and cone photoreceptor cells, and their expression is altered in mouse knockout models of relevant photoreceptor transcription factors. We complemented this RNA-sequencing (RNA-seq) analysis with other reported expression and phenotypic data to underscore the involvement of DUBs in cell fate decision and photoreceptor differentiation. Conclusions The present results highlight a short list of potential DUB candidates for retinal disorders, which require further study.
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Affiliation(s)
- Mariona Esquerdo-Barragán
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain,Institut de Biomedicina (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
| | - Matthew J. Brooks
- Neurobiology Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Vasileios Toulis
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain,Institut de Biomedicina (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain,CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
| | - Anand Swaroop
- Neurobiology Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Avda. Diagonal 643, Universitat de Barcelona, Barcelona 08028, Spain,Institut de Biomedicina (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain,CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
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Zachariah S, Gray DA. Deubiquitinating Enzymes in Model Systems and Therapy: Redundancy and Compensation Have Implications. Bioessays 2019; 41:e1900112. [DOI: 10.1002/bies.201900112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/06/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Sarah Zachariah
- Centre for Cancer TherapeuticsOttawa Hospital Research Institute 501 Smyth Box 926 Ottawa ON K1H 8L6 Canada
- Department of Biochemistry, Microbiology and ImmunologyUniversity of Ottawa 451 Smyth Rd Ottawa ON K1H 8M5 Canada
| | - Douglas A. Gray
- Centre for Cancer TherapeuticsOttawa Hospital Research Institute 501 Smyth Box 926 Ottawa ON K1H 8L6 Canada
- Department of Biochemistry, Microbiology and ImmunologyUniversity of Ottawa 451 Smyth Rd Ottawa ON K1H 8M5 Canada
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Vlasschaert C, Cook D, Xia X, Gray DA. The evolution and functional diversification of the deubiquitinating enzyme superfamily. Genome Biol Evol 2017; 9:558-573. [PMID: 28177072 PMCID: PMC5381560 DOI: 10.1093/gbe/evx020] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/18/2017] [Accepted: 02/04/2017] [Indexed: 12/16/2022] Open
Abstract
Ubiquitin and ubiquitin-like molecules are attached to and removed from cellular proteins in a dynamic and highly regulated manner. Deubiquitinating enzymes are critical to this process, and the genetic catalogue of deubiquitinating enzymes expanded greatly over the course of evolution. Extensive functional redundancy has been noted among the 93 members of the human deubiquitinating enzyme (DUB) superfamily. This is especially true of genes that were generated by duplication (termed paralogs) as they often retain considerable sequence similarity. Because complete redundancy in systems should be eliminated by selective pressure, we theorized that many overlapping DUBs must have significant and unique spatiotemporal roles that can be evaluated in an evolutionary context. We have determined the evolutionary history of the entire class of deubiquitinating enzymes, including the sequence and means of duplication for all paralogous pairs. To establish their uniqueness, we have investigated cell-type specificity in developmental and adult contexts, and have investigated the coemergence of substrates from the same duplication events. Our analysis has revealed examples of DUB gene subfunctionalization, neofunctionalization, and nonfunctionalization.
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Affiliation(s)
- Caitlyn Vlasschaert
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario, Canada
- The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ontario, Canada
| | - David Cook
- The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ontario, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
| | - Douglas A. Gray
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ontario, Canada
- The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
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