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Mirra S, García-Arroyo R, B Domènech E, Gavaldà-Navarro A, Herrera-Úbeda C, Oliva C, Garcia-Fernàndez J, Artuch R, Villarroya F, Marfany G. CERKL, a retinal dystrophy gene, regulates mitochondrial function and dynamics in the mammalian retina. Neurobiol Dis 2021; 156:105405. [PMID: 34048907 DOI: 10.1016/j.nbd.2021.105405] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/06/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022] Open
Abstract
The retina is a highly active metabolic organ that displays a particular vulnerability to genetic and environmental factors causing stress and homeostatic imbalance. Mitochondria constitute a bioenergetic hub that coordinates stress response and cellular homeostasis, therefore structural and functional regulation of the mitochondrial dynamic network is essential for the mammalian retina. CERKL (ceramide kinase like) is a retinal degeneration gene whose mutations cause Retinitis Pigmentosa in humans, a visual disorder characterized by photoreceptors neurodegeneration and progressive vision loss. CERKL produces multiple isoforms with a dynamic subcellular localization. Here we show that a pool of CERKL isoforms localizes at mitochondria in mouse retinal ganglion cells. The depletion of CERKL levels in CerklKD/KO(knockdown/knockout) mouse retinas cause increase of autophagy, mitochondrial fragmentation, alteration of mitochondrial distribution, and dysfunction of mitochondrial-dependent bioenergetics and metabolism. Our results support CERKL as a regulator of autophagy and mitochondrial biology in the mammalian retina.
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Affiliation(s)
- Serena Mirra
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine (IBUB), Faculty of Biology, University of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona- Institut de Recerca Hospital Sant Joan de Déu, IBUB-IRSJD, Barcelona, Spain.
| | - Rocío García-Arroyo
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine (IBUB), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Elena B Domènech
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine (IBUB), Faculty of Biology, University of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Aleix Gavaldà-Navarro
- Institut de Biomedicina de la Universitat de Barcelona- Institut de Recerca Hospital Sant Joan de Déu, IBUB-IRSJD, Barcelona, Spain; Department of Biochemistry and Molecular Biomedicine, Barcelona, Spain; CIBEROBN, Instituto de Salud Carlos III, Spain
| | - Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine (IBUB), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Clara Oliva
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Spain
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine (IBUB), Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Rafael Artuch
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain; Clinical Biochemistry Department, Hospital Sant Joan de Déu, Spain
| | - Francesc Villarroya
- Institut de Biomedicina de la Universitat de Barcelona- Institut de Recerca Hospital Sant Joan de Déu, IBUB-IRSJD, Barcelona, Spain; Department of Biochemistry and Molecular Biomedicine, Barcelona, Spain; CIBEROBN, Instituto de Salud Carlos III, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics and Institute of Biomedicine (IBUB), Faculty of Biology, University of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona- Institut de Recerca Hospital Sant Joan de Déu, IBUB-IRSJD, Barcelona, Spain.
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2
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Domènech EB, Andrés R, López-Iniesta MJ, Mirra S, García-Arroyo R, Milla S, Sava F, Andilla J, Loza-Álvarez P, de la Villa P, Gonzàlez-Duarte R, Marfany G. A New Cerkl Mouse Model Generated by CRISPR-Cas9 Shows Progressive Retinal Degeneration and Altered Morphological and Electrophysiological Phenotype. Invest Ophthalmol Vis Sci 2020; 61:14. [PMID: 32658961 PMCID: PMC7425692 DOI: 10.1167/iovs.61.8.14] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/14/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose Close to 100 genes cause retinitis pigmentosa, a Mendelian rare disease that affects 1 out of 4000 people worldwide. Mutations in the ceramide kinase-like gene (CERKL) are a prevalent cause of autosomal recessive cause retinitis pigmentosa and cone-rod dystrophy, but the functional role of this gene in the retina has yet to be fully determined. We aimed to generate a mouse model that resembles the phenotypic traits of patients carrying CERKL mutations to undertake functional studies and assay therapeutic approaches. Methods The Cerkl locus has been deleted (around 97 kb of genomic DNA) by gene editing using the CRISPR-Cas9 D10A nickase. Because the deletion of the Cerkl locus is lethal in mice in homozygosis, a double heterozygote mouse model with less than 10% residual Cerkl expression has been generated. The phenotypic alterations of the retina of this new model have been characterized at the morphological and electrophysiological levels. Results This CerklKD/KO model shows retinal degeneration, with a decreased number of cones and progressive photoreceptor loss, poorly stacked photoreceptor outer segment membranes, defective retinal pigment epithelium phagocytosis, and altered electrophysiological recordings in aged retinas. Conclusions To our knowledge, this is the first Cerkl mouse model to mimic many of the phenotypic traits, including the slow but progressive retinal degeneration, shown by human patients carrying CERKL mutations. This useful model will provide unprecedented insights into the retinal molecular pathways altered in these patients and will contribute to the design of effective treatments.
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Affiliation(s)
- Elena B. Domènech
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- CIBERER/ISCIII, University of Barcelona, Barcelona, Spain
| | - Rosa Andrés
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- CIBERER/ISCIII, University of Barcelona, Barcelona, Spain
| | - M. José López-Iniesta
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Serena Mirra
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- CIBERER/ISCIII, University of Barcelona, Barcelona, Spain
| | - Rocío García-Arroyo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Santiago Milla
- Department of Systems Biology, University of Alcalá, Madrid, Spain
| | - Florentina Sava
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Jordi Andilla
- ICFO–The Institute of Photonic Sciences, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pablo Loza-Álvarez
- ICFO–The Institute of Photonic Sciences, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pedro de la Villa
- Department of Systems Biology, University of Alcalá, Madrid, Spain
- Ramón y Cajal Institute for Health Research, Madrid, Spain
| | - Roser Gonzàlez-Duarte
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- CIBERER/ISCIII, University of Barcelona, Barcelona, Spain
- DBGen Ocular Genomics, Barcelona, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
- CIBERER/ISCIII, University of Barcelona, Barcelona, Spain
- DBGen Ocular Genomics, Barcelona, Spain
- Institute of Biomedicine, University of Barcelona, Barcelona, Spain
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Hu X, Lu Z, Yu S, Reilly J, Liu F, Jia D, Qin Y, Han S, Liu X, Qu Z, Lv Y, Li J, Huang Y, Jiang T, Jia H, Wang Q, Liu J, Shu X, Tang Z, Liu M. CERKL regulates autophagy via the NAD-dependent deacetylase SIRT1. Autophagy 2019; 15:453-465. [PMID: 30205735 PMCID: PMC6351130 DOI: 10.1080/15548627.2018.1520548] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 08/18/2018] [Accepted: 08/22/2018] [Indexed: 01/07/2023] Open
Abstract
Macroautophagy/autophagy is an important intracellular mechanism for the maintenance of cellular homeostasis. Here we show that the CERKL (ceramide kinase like) gene, a retinal degeneration (RD) pathogenic gene, plays a critical role in regulating autophagy by stabilizing SIRT1. In vitro and in vivo, suppressing CERKL results in impaired autophagy. SIRT1 is one of the main regulators of acetylation/deacetylation in autophagy. In CERKL-depleted retinas and cells, SIRT1 is downregulated. ATG5 and ATG7, 2 essential components of autophagy, show a higher degree of acetylation in CERKL-depleted cells. Overexpression of SIRT1 rescues autophagy in CERKL-depleted cells, whereas CERKL loses its function of regulating autophagy in SIRT1-depleted cells, and overexpression of CERKL upregulates SIRT1. Finally, we show that CERKL directly interacts with SIRT1, and may regulate its phosphorylation at Ser27 to stabilize SIRT1. These results show that CERKL is an important regulator of autophagy and it plays this role by stabilizing the deacetylase SIRT1.
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Affiliation(s)
- Xuebin Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Zhaojing Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - James Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Danna Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Yayun Qin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Shanshan Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Zhen Qu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Jingzhen Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Tao Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Haibo Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Qing Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Jingyu Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
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Azab B, Barham R, Ali D, Dardas Z, Rashdan L, Bijawi M, Maswadi R, Awidi A, Jafar H, Abu-Ameerh M, Al-Bdour M, Amr S, Awidi A. Novel CERKL variant in consanguineous Jordanian pedigrees with inherited retinal dystrophies. Can J Ophthalmol 2019; 54:51-59. [DOI: 10.1016/j.jcjo.2018.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/24/2018] [Accepted: 02/27/2018] [Indexed: 01/02/2023]
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Kim J, Tsuruta F, Okajima T, Yano S, Sato B, Chiba T. KLHL7 promotes TUT1 ubiquitination associated with nucleolar integrity: Implications for retinitis pigmentosa. Biochem Biophys Res Commun 2017; 494:220-226. [PMID: 29032201 DOI: 10.1016/j.bbrc.2017.10.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/10/2017] [Indexed: 01/06/2023]
Abstract
Kelch-like protein 7 (KLHL7) is a component of Cul3-based Cullin-RING ubiquitin ligase. Recent studies have revealed that mutations in klhl7 gene cause several disorders, such as retinitis pigmentosa (RP). Although KLHL7 is considered to be crucial for regulating the protein homeostasis, little is known about its biological functions. In this study, we report that KLHL7 increases terminal uridylyl transferase 1 (TUT1) ubiquitination involved in nucleolar integrity. TUT1 is normally localized in nucleolus; however, expression of KLHL7 facilitates a vulnerability of nucleolar integrity, followed by a decrease of TUT1 localization in nucleolus. On the other hand, pathogenic KLHL7 mutants, which causes an onset of RP, have little effect on both nucleolar integrity and TUT1 localization. Finally, KLHL7 increases TUT1 ubiquitination levels. Taken together, these results imply that KLHL7 is a novel regulator of nucleolus associated with TUT1 ubiquitination. Our study may provide a valuable information to elucidate a pathogenic mechanism of RP.
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Affiliation(s)
- Jaehyun Kim
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Fuminori Tsuruta
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Tomomi Okajima
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Sarasa Yano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Ban Sato
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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6
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Yu S, Li C, Biswas L, Hu X, Liu F, Reilly J, Liu X, Liu Y, Huang Y, Lu Z, Han S, Wang L, Yu Liu J, Jiang T, Shu X, Wong F, Tang Z, Liu M. CERKL gene knockout disturbs photoreceptor outer segment phagocytosis and causes rod-cone dystrophy in zebrafish. Hum Mol Genet 2017; 26:2335-2345. [PMID: 28398482 DOI: 10.1093/hmg/ddx137] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 04/04/2017] [Indexed: 11/13/2022] Open
Abstract
In humans, CERKL mutations cause widespread retinal degeneration: early dysfunction and loss of rod and cone photoreceptors in the outer retina and, progressively, death of cells in the inner retina. Despite intensive efforts, the function of CERKL remains obscure and studies in animal models have failed to clarify the disease mechanism of CERKL mutations. To address this gap in knowledge, we have generated a stable CERKL knockout zebrafish model by TALEN technology and a 7bp deletion in CERKL cDNA that caused the premature termination of CERKL. These CERKL-/- animals showed progressive degeneration of photoreceptor outer segments (OSs) and increased apoptosis of retinal cells, including those in the outer and inner retinal layers. Additionally, we confirmed by immunofluorescence and western-blot that rod degeneration in CERKL-/- zebrafish occurred earlier and was more significant than that in cone cells. Accumulation of shed OSs in the interphotoreceptor matrix was observed by transmission election microscopy (TEM). This suggested that CERKL may regulate the phagocytosis of OSs by the retinal pigment epithelium (RPE). We further found that the phagocytosis-associated protein MERTK was significantly reduced in CERKL-/- zebrafish. Additionally, in ARPE-19 cell lines, knockdown of CERKL also decreased the mRNA and protein level of MERTK, as well as the ox-POS phagocytosis. We conclude that CERKL deficiency in zebrafish may cause rod-cone dystrophy, but not cone-rod dystrophy, while interfering with the phagocytosis function of RPE associated with down-regulation of the expression of MERTK.
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Affiliation(s)
- Shanshan Yu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Chang Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Lincoln Biswas
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4?0BA, UK
| | - Xuebin Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - James Reilly
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4?0BA, UK
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Ying Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Zhaojing Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Shanshan Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Lei Wang
- Department of Pathology & Lab Medicine, University of Cincinnati Medical Center, Cincinnati, OH 45267, USA
| | - Jing Yu Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Tao Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4?0BA, UK
| | - Fulton Wong
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China
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Uyar B, Weatheritt RJ, Dinkel H, Davey NE, Gibson TJ. Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? MOLECULAR BIOSYSTEMS 2014; 10:2626-42. [PMID: 25057855 PMCID: PMC4306509 DOI: 10.1039/c4mb00290c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/11/2014] [Indexed: 01/09/2023]
Abstract
Disease mutations are traditionally thought to impair protein functionality by disrupting the folded globular structure of proteins. However, 22% of human disease mutations occur in natively unstructured segments of proteins known as intrinsically disordered regions (IDRs). This therefore implicates defective IDR functionality in various human diseases including cancer. The functionality of IDRs is partly attributable to short linear motifs (SLiMs), but it remains an open question how much defects in SLiMs contribute to human diseases. A proteome-wide comparison of the distribution of missense mutations from disease and non-disease mutation datasets revealed that, in IDRs, disease mutations are more likely to occur within SLiMs than neutral missense mutations. Moreover, compared to neutral missense mutations, disease mutations more frequently impact functionally important residues of SLiMs, cause changes in the physicochemical properties of SLiMs, and disrupt more SLiM-mediated interactions. Analysis of these mutations resulted in a comprehensive list of experimentally validated or predicted SLiMs disrupted in disease. Furthermore, this in-depth analysis suggests that 'prostate cancer pathway' is particularly enriched for proteins with disease-related SLiMs. The contribution of mutations in SLiMs to disease may currently appear small when compared to mutations in globular domains. However, our analysis of mutations in predicted SLiMs suggests that this contribution might be more substantial. Therefore, when analysing the functional impact of mutations on proteins, SLiMs in proteins should not be neglected. Our results suggest that an increased focus on SLiMs in the coming decades will improve our understanding of human diseases and aid in the development of targeted treatments.
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Affiliation(s)
- Bora Uyar
- Structural and Computational Biology Unit , European Molecular Biology Laboratory , Meyerhofstrasse 1 , 69117 , Heidelberg , Germany . ;
| | - Robert J. Weatheritt
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Hills Road , Cambridge CB2 0QH , UK
- Banting and Best Department of Medical Research and Donnelly Centre , University of Toronto , Toronto , Ontario M5S 3E1 , Canada
| | - Holger Dinkel
- Structural and Computational Biology Unit , European Molecular Biology Laboratory , Meyerhofstrasse 1 , 69117 , Heidelberg , Germany . ;
| | - Norman E. Davey
- Structural and Computational Biology Unit , European Molecular Biology Laboratory , Meyerhofstrasse 1 , 69117 , Heidelberg , Germany . ;
- Department of Physiology , University of California, San Francisco , San Francisco , California , USA
| | - Toby J. Gibson
- Structural and Computational Biology Unit , European Molecular Biology Laboratory , Meyerhofstrasse 1 , 69117 , Heidelberg , Germany . ;
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8
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Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation. Chem Rev 2014; 114:6733-78. [DOI: 10.1021/cr400585q] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kim Van Roey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Holger Dinkel
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Seiler
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aidan Budd
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J. Gibson
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Norman E. Davey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department
of Physiology, University of California, San Francisco, San Francisco, California 94143, United States
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9
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CERKL, a retinal disease gene, encodes an mRNA-binding protein that localizes in compact and untranslated mRNPs associated with microtubules. PLoS One 2014; 9:e87898. [PMID: 24498393 PMCID: PMC3912138 DOI: 10.1371/journal.pone.0087898] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/30/2013] [Indexed: 11/25/2022] Open
Abstract
The function of CERKL (CERamide Kinase Like), a causative gene of retinitis pigmentosa and cone-rod dystrophy, still awaits characterization. To approach its cellular role we have investigated the subcellular localization and interaction partners of the full length CERKL isoform, CERKLa of 532 amino acids, in different cell lines, including a photoreceptor-derived cell line. We demonstrate that CERKLa is a main component of compact and untranslated mRNPs and that associates with other RNP complexes such as stress granules, P-bodies and polysomes. CERKLa is a protein that binds through its N-terminus to mRNAs and interacts with other mRNA-binding proteins like eIF3B, PABP, HSP70 and RPS3. Except for eIF3B, these interactions depend on the integrity of mRNAs but not of ribosomes. Interestingly, the C125W CERKLa pathological mutant does not interact with eIF3B and is absent from these complexes. Compact mRNPs containing CERKLa also associate with microtubules and are found in neurites of neural differentiated cells. These localizations had not been reported previously for any member of the retinal disorders gene family and should be considered when investigating the pathogenic mechanisms and therapeutical approaches in these diseases.
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10
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Riera M, Burguera D, Garcia-Fernàndez J, Gonzàlez-Duarte R. CERKL knockdown causes retinal degeneration in zebrafish. PLoS One 2013; 8:e64048. [PMID: 23671706 PMCID: PMC3650063 DOI: 10.1371/journal.pone.0064048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 04/08/2013] [Indexed: 12/21/2022] Open
Abstract
The human CERKL gene is responsible for common and severe forms of retinal dystrophies. Despite intense in vitro studies at the molecular and cellular level and in vivo analyses of the retina of murine knockout models, CERKL function remains unknown. In this study, we aimed to approach the developmental and functional features of cerkl in Danio rerio within an Evo-Devo framework. We show that gene expression increases from early developmental stages until the formation of the retina in the optic cup. Unlike the high mRNA-CERKL isoform multiplicity shown in mammals, the moderate transcriptional complexity in fish facilitates phenotypic studies derived from gene silencing. Moreover, of relevance to pathogenicity, teleost CERKL shares the two main human protein isoforms. Morpholino injection has been used to generate a cerkl knockdown zebrafish model. The morphant phenotype results in abnormal eye development with lamination defects, failure to develop photoreceptor outer segments, increased apoptosis of retinal cells and small eyes. Our data support that zebrafish Cerkl does not interfere with proliferation and neural differentiation during early developmental stages but is relevant for survival and protection of the retinal tissue. Overall, we propose that this zebrafish model is a powerful tool to unveil CERKL contribution to human retinal degeneration.
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Affiliation(s)
- Marina Riera
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
- CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Demian Burguera
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Jordi Garcia-Fernàndez
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Roser Gonzàlez-Duarte
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
- CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
- * E-mail:
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11
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Garanto A, Mandal NA, Egido-Gabás M, Marfany G, Fabriàs G, Anderson RE, Casas J, Gonzàlez-Duarte R. Specific sphingolipid content decrease in Cerkl knockdown mouse retinas. Exp Eye Res 2013; 110:96-106. [PMID: 23501591 DOI: 10.1016/j.exer.2013.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/19/2013] [Accepted: 03/04/2013] [Indexed: 01/12/2023]
Abstract
Sphingolipids (SPLs) are finely tuned structural compounds and bioactive molecules involved in membrane fluidity and cellular homeostasis. The core sphingolipid, ceramide (CER), and its derivatives, regulate several crucial processes in neuronal cells, among them cell differentiation, cell-cell interactions, membrane conductance, synaptic transmission, and apoptosis. Mutations in Ceramide Kinase-Like (CERKL) cause autosomal recessive Retinitis Pigmentosa and Cone Rod Dystrophy. The presence of a conserved lipid kinase domain and the overall similarity with CERK suggested that CERKL might play a role in the SPL metabolism as a CER kinase. Unfortunately, CERKL function and substrate(s), as well as its contribution to the retinal etiopathology, remain as yet unknown. In this work we aimed to characterize the mouse retinal sphingolipidome by UPLC-TOF to first, thoroughly investigate the SPL composition of the murine retina, compare it to our Cerkl -/- model, and finally assess new possible CERKL substrates by phosphorus quantification and protein-lipid overlay. Our results showed a consistent and notable decrease of the retinal SPL content (mainly ranging from 30% to 60%) in the Cerkl -/- compared to WT retinas, which was particularly evident in the glucosyl/galactosyl ceramide species (Glc/GalCer) whereas the phospholipids and neutral lipids remained unaltered. Moreover, evidence in favor of CERKL binding to GlcCer, GalCer and sphingomyelin has been gathered. Altogether, these results highlight the involvement of CERKL in the SPL metabolism, question its role as a kinase, and open new scenarios concerning its function.
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Affiliation(s)
- Alejandro Garanto
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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12
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Mandal NA, Tran JTA, Saadi A, Rahman AK, Huynh TP, Klein WH, Cho JH. Expression and localization of CERKL in the mammalian retina, its response to light-stress, and relationship with NeuroD1 gene. Exp Eye Res 2012; 106:24-33. [PMID: 23142158 DOI: 10.1016/j.exer.2012.10.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 01/30/2023]
Abstract
Mutations in the Ceramide kinase like (CERKL) gene are associated with retinitis pigmentosa (RP26) and cone-rod dystrophy. CERKL is homologous to Ceramide kinase (CERK), and its function is still unknown. The purpose of this study was to test the expression and distribution of this gene and its protein in rat and in mouse tissues, in light-stressed rat retinas and in the retinas of NeuroD1 knock-out mice to understand the role of CERKL in the retina. Expression of Cerkl and Cerk mRNA was determined by quantitative RT-PCR. Expression of the protein was determined by Western blotting with anti-CERKL antibody. Localization of the protein was determined by using immunofluorescence microscopy. With qRT-PCR, we revealed that the relative mRNA expression of Cerkl was the highest in the retina among all the rat tissue tested; it was >10-fold higher than in the brain. On the other hand, Cerk has ubiquitous expression and its relative abundance is >2 fold of Cerkl in the retina. Cerkl was expressed minimally in the developing mouse eyes and reached a peak at retinal maturity at 2 months. Western blots of retinal tissues revealed two major CERKL protein bands: 59 kDa (C1) and 37 kDa (C2). However, only C2 CERKL was found in the rat retinal rod outer segment (ROS) at level of that was not changed in light vs. dark adaptation. In the light-stressed retina, expression of Cerkl mRNA increased significantly, which was reflected in only on C2 CERKL protein. The CERKL protein localized prominently to the ganglion cells, inner nuclear layers (INL), retinal pigment epithelial (RPE) cells, and photoreceptor inner segments in the retinal sections. Nuclear localization of CERKL was not affected in RPE, INL and the ganglion cell layers in the light-stressed retina; however, the perinuclear and outer segment locations appear to be altered. In the NeuroD1 knock-out mouse retina, the expression of Cerkl mRNA and protein decreased and that decrease also pertains to C2 CERKL. In conclusion, the retina had the highest level of Cerkl mRNA and protein expression, which reached its maximum in the adult retina; CERKL localized to ROS and RPE cells and the light-adaptation did not change the level of CERKL in ROS; light-stress induced Cerkl expression in the retina; and its expression decreased in NeuroD1 knock-out retina. Thus, CERKL may be important for the stress responses and protection of photoreceptor cells.
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Affiliation(s)
- Nawajes A Mandal
- Department of Ophthalmology, OUHSC, Dean A. McGee Eye Institute, Oklahoma City, OK 73104, United States.
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13
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Garanto A, Vicente-Tejedor J, Riera M, de la Villa P, Gonzàlez-Duarte R, Blanco R, Marfany G. Targeted knockdown of Cerkl, a retinal dystrophy gene, causes mild affectation of the retinal ganglion cell layer. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1258-69. [PMID: 22549043 DOI: 10.1016/j.bbadis.2012.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 11/28/2022]
Abstract
In order to approach the function of the retinal dystrophy CERKL gene we generated a novel knockout mouse model by cre-mediated targeted deletion of the Cerkl first exon and proximal promoter. The excised genomic region (2.3kb) encompassed the first Cerkl exon, upstream sequences including the proximal promoter and the initial segment of the first intron. The Cerkl-/- mice were viable and fertile. The targeted Cerkl deletion resulted in a knockdown more than a knockout model, given that alternative promoters (unreported at that time) directed basal expression of Cerkl (35%). In situ hybridizations and immunohistochemistry showed that this remnant expression was moderate in the photoreceptors and weak in the ganglion and inner cell layers. Morphological characterization of the Cerkl-/- retinas did not show any gross structural changes, even at 12 months of age. However, some clear and consistent signals of gliosis and retinal stress were detected by the statistically significant increase of i) the glial fibrillary antigen protein (GFAP) expression, and ii) apoptosis, as detected by TUNEL. Remarkably, consistent non-progressive perturbation (from birth up to 12 months of age) of ganglion cells was supported by the decrease of the Brn3a marker expression as well as the reduced oscillatory potentials in the electroretinographic recordings. In conclusion, the Cerkl-/- knockdown shows a mild retinal phenotype, with increased levels of cellular stress and apoptosis indicators, and clear signs of functional alteration at the ganglion cell layer, but no detectable morphological changes.
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14
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Li Y, Shao Y, Tong Y, Shen T, Zhang J, Li Y, Gu H, Li F. Nucleo-cytoplasmic shuttling of PAK4 modulates β-catenin intracellular translocation and signaling. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1823:465-75. [PMID: 22173096 DOI: 10.1016/j.bbamcr.2011.11.013] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 11/08/2011] [Accepted: 11/29/2011] [Indexed: 01/15/2023]
Abstract
The canonical Wnt/β-catenin signaling pathway plays a central role in development and cancer. The p21-activated kinase 4 (PAK4) involves in a wide range of cellular processes, including cytoskeletal reorganization, cell proliferation, gene transcription and oncogenic transformation. However, the cross talk between the Wnt and PAK4 signaling pathways is poorly understood. Here, we show that PAK4 is a nucleo-cytoplasmic shuttling protein, containing three nuclear export signals (NESs) and two nuclear localization signals (NLSs). PAK4 is exported by the chromosome region maintenance-1 (CRM-1)-dependent pathway and is imported into the nucleus in an importin α5-dependent manner. PAK4 interacts with and phosphorylates β-catenin on Ser675, which promotes the TCF/LEF transcriptional activity and stabilizes β-catenin through inhibition of its degradation. Moreover, nuclear import of PAK4 accompanies with the nuclear import of β-catenin and increased TCF/LEF transcriptional activity. We further demonstrated that PAK4 associates with the TCF/LEF transcriptional complex by ChIP assays. These findings uncover a novel role for PAK4 in modulating intracellular translocation and signaling of β-catenin.
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Affiliation(s)
- Yan Li
- Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, China Medical University, Shenyang, PR China
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15
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Bornancin F. Ceramide kinase: the first decade. Cell Signal 2010; 23:999-1008. [PMID: 21111813 DOI: 10.1016/j.cellsig.2010.11.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 11/16/2010] [Accepted: 11/16/2010] [Indexed: 11/20/2022]
Abstract
It has been some 20 years since the initial discovery of ceramide 1-phosphate (C1P) and nearly a decade since ceramide kinase (CERK) was cloned. Many studies have shown that C1P is important for membrane biology and for the regulation of membrane-bound proteins, and the CERK enzyme has appeared to be tightly regulated in order to control both ceramide levels and production of C1P. Furthermore, C1P made by CERK has emerged as a genuine signalling entity. However, it represents only part of the C1P pool that is available in the cell, therefore suggesting that alternative unknown C1P-producing mechanisms may also play a role. Recent technological developments for measuring complex sphingolipids in biological samples, together with the availability of Cerk-deficient animals as well as potent CERK inhibitors, have now provided new grounds for investigating C1P biology further. Here, we will review the current understanding of CERK and C1P in terms of biochemistry and functional implications, with particular attention to C1P produced by CERK.
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Affiliation(s)
- Frédéric Bornancin
- Novartis Institutes for BioMedical Research, CH-4056 Basle, Switzerland.
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16
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Rotstein NP, Miranda GE, Abrahan CE, German OL. Regulating survival and development in the retina: key roles for simple sphingolipids. J Lipid Res 2010; 51:1247-62. [PMID: 20100817 PMCID: PMC3035489 DOI: 10.1194/jlr.r003442] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 01/25/2010] [Indexed: 12/28/2022] Open
Abstract
Many sphingolipids have key functions in the regulation of crucial cellular processes. Ceramide (Cer) and sphingosine (Sph) induce growth arrest and cell death in multiple situations of cellular stress. On the contrary, sphingosine-1-phosphate (S1P), the product of Sph phosphorylation, promotes proliferation, differentiation, and survival in different cell systems. This review summarizes the roles of these simple sphingolipids in different tissues and then analyzes their possible functions in the retina. Alterations in proliferation, neovascularization, differentiation, and cell death are critical in major retina diseases and collective evidence points to a role for sphingolipids in these processes. Cer induces inflammation and apoptosis in endothelial and retinal pigmented epithelium cells, leading to several retinopathies. S1P can prevent this death but also promotes cell proliferation that might lead to neovascularization and fibrosis. Recent data support Cer and Sph as crucial mediators in the induction of photoreceptor apoptosis in diverse models of oxidative damage and neurodegeneration, and suggest that regulating their metabolism can prevent this death. New evidence proposes a central role for S1P controlling photoreceptor survival and differentiation. Finally, this review discusses the ability of trophic factors to regulate sphingolipid metabolism and transactivate S1P signaling pathways to control survival and development in retina photoreceptors.
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Affiliation(s)
- Nora P Rotstein
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del Sur-CONICET, Bahía Blanca, Buenos Aires, Argentina.
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17
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Gault CR, Obeid LM, Hannun YA. An overview of sphingolipid metabolism: from synthesis to breakdown. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 688:1-23. [PMID: 20919643 DOI: 10.1007/978-1-4419-6741-1_1] [Citation(s) in RCA: 703] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Sphingolipids constitute a class of lipids defined by their eighteen carbon amino-alcohol backbones which are synthesized in the ER from nonsphingolipid precursors. Modification of this basic structure is what gives rise to the vast family of sphingolipids that play significant roles in membrane biology and provide many bioactive metabolites that regulate cell function. Despite the diversity of structure and function of sphingolipids, their creation and destruction are governed by common synthetic and catabolic pathways. In this regard, sphingolipid metabolism can be imagined as an array of interconnected networks that diverge from a single common entry point and converge into a single common breakdown pathway. In their simplest forms, sphingosine, phytosphingosine and dihydrosphingosine serve as the backbones upon which further complexity is achieved. For example, phosphorylation of the C1 hydroxyl group yields the final breakdown products and/or the important signaling molecules sphingosine-1-phosphate, phytosphingosine-1-phosphate and dihydrosphingosine-1-phosphate, respectively. On the other hand, acylation of sphingosine, phytosphingosine, or dihydrosphingosine with one of several possible acyl CoA molecules through the action of distinct ceramide synthases produces the molecules defined as ceramide, phytoceramide, or dihydroceramide. Ceramide, due to the differing acyl CoAs that can be used to produce it, is technically a class of molecules rather than a single molecule and therefore may have different biological functions depending on the acyl chain it is composed of. At the apex of complexity is the group of lipids known as glycosphingolipids (GSL) which contain dozens of different sphingolipid species differing by both the order and type of sugar residues attached to their headgroups. Since these molecules are produced from ceramide precursors, they too may have differences in their acyl chain composition, revealing an additional layer of variation. The glycosphingolipids are divided broadly into two categories: glucosphingolipids and galactosphingolipids. The glucosphingolipids depend initially on the enzyme glucosylceramide synthase (GCS) which attaches glucose as the first residue to the C1 hydroxyl position. Galactosphingolipids, on the other hand, are generated from galactosylceramide synthase (GalCerS), an evolutionarily dissimilar enzyme from GCS. Glycosphingolipids are further divided based upon further modification by various glycosyltransferases which increases the potential variation in lipid species by several fold. Far more abundant are the sphingomyelin species which are produced in parallel with glycosphingolipids, however they are defined by a phosphocholine headgroup rather than the addition of sugar residues. Although sphingomyelin species all share a common headgroup, they too are produced from a variety of ceramide species and therefore can have differing acyl chains attached to their C-2 amino groups. Whether or not the differing acyl chain lengths in SMs dictate unique functions or important biophysical distinctions has not yet been established. Understanding the function of all the existing glycosphingolipids and sphingomyelin species will be a major undertaking in the future since the tools to study and measure these species are only beginning to be developed (see Fig 1 for an illustrated depiction of the various sphingolipid structures). The simple sphingolipids serve both as the precursors and the breakdown products of the more complex ones. Importantly, in recent decades, these simple sphingolipids have gained attention for having significant signaling and regulatory roles within cells. In addition, many tools have emerged to measure the levels of simple sphingolipids and therefore have become the focus of even more intense study in recent years. With this thought in mind, this chapter will pay tribute to the complex sphingolipids, but focus on the regulation of simple sphingolipid metabolism.
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Affiliation(s)
- Christopher R Gault
- Department of Biochemistry, Medical University of South Carolina, Charleston, South Carolina 29425, USA
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Rovina P, Schanzer A, Graf C, Mechtcheriakova D, Jaritz M, Bornancin F. Subcellular localization of ceramide kinase and ceramide kinase-like protein requires interplay of their Pleckstrin Homology domain-containing N-terminal regions together with C-terminal domains. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:1023-30. [PMID: 19501188 DOI: 10.1016/j.bbalip.2009.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/15/2009] [Accepted: 05/29/2009] [Indexed: 01/14/2023]
Abstract
Ceramide kinase (CERK) and the ceramide kinase-like protein (CERKL), two related members of the diacylglycerol kinase family, are ill-defined at the molecular level. In particular, what determines their distinctive subcellular localization is not well understood. Here we show that the Pleckstrin Homology (PH) domain of CERK, which is required for Golgi complex localization, can substitute for the N-terminal region of CERKL and allow for wild-type CERKL localization, which is typified by nucleolar accumulation. This demonstrates that determinants for localization of these two enzymes do not lie solely in their PH domain-containing N-terminal regions. Moreover, we present evidence for a previously unrecognized participation of CERK distal sequences in structural stability, localization and activity of the full-length protein. Progressive deletion of CERK and CERKL from the C-terminus revealed similar sequential organization in both proteins, with nuclear import signals in their N-terminal part, and nuclear export signals in their C-terminal part. Furthermore, mutagenesis of individual cysteine residues of a CERK-specific CXXXCXXC motif severely compromised both exportation of CERK from the nucleus and its association with the Golgi complex. Altogether, this work identifies conserved domains in CERK and CERKL as well as new determinants for their subcellular localization. It further suggests a nucleocytoplasmic shuttling mechanism for both proteins that may be defective in CERKL mutant proteins responsible for retinal degenerative diseases.
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Affiliation(s)
- Philipp Rovina
- Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
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Graf C, Niwa S, Müller M, Kinzel B, Bornancin F. Wild-type levels of ceramide and ceramide-1-phosphate in the retina of ceramide kinase-like-deficient mice. Biochem Biophys Res Commun 2008; 373:159-63. [PMID: 18555012 DOI: 10.1016/j.bbrc.2008.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 06/04/2008] [Indexed: 11/18/2022]
Abstract
Ceramide kinase-like (CerkL) is the most recently identified member of the sphingolipid metabolizing enzyme family. This protein is believed to have ceramide kinase (CerK) activity; however, this has not been clarified yet. We generated CerkL-deficient (CerkL(-/-)) mice, measured ceramide (Cer) and ceramide-1-phosphate (C1P) levels in isolated retina, and compared them to levels measured in Cerk(-/-) and WT retinas. We also labeled CerkL(-/-), Cerk(-/-), and WT retinas with (33)P orthophosphate to measure and compare de novo phosphorylation of Cer. Whereas Cerk(-/-) retinas displayed decreased C1P and enhanced Cer, and lacked the capacity to phosphorylate Cer, CerkL(-/-) retinas were indistinguishable from WT retinas with regard to Cer and C1P levels, and in their ability to phosphorylate Cer. Altogether, our results do not support the hypothesis that CerkL is a second CerK enzyme impacting on Cer levels in the retina. CerkL, if active enzymatically, might use a novel, not yet described, lipid substrate.
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Affiliation(s)
- Christine Graf
- Novartis Institutes for BioMedical Research, Brunnerstrasse 59, A-1235 Vienna, Austria
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Kinetics of the ceramide kinase inhibitor K1, a suppressor of mast-cell activation. Biosci Biotechnol Biochem 2007; 71:2581-4. [PMID: 17928690 DOI: 10.1271/bbb.70308] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In a previous study, we synthesized a novel inhibitor of ceramide kinase, K1. In this study, we determined that inhibition by K1 is non-competitive and that four intact six-membered rings are important to the inhibitory activity. Furthermore, we identified an effective in vivo concentration for K1, at which it did not influence any cellular lipid synthesis other than that of ceramide 1-phosphate (C1P) using RBL-2H3 cells, and found that K1 suppressed the activation of mast cells.
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