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Sikora J, Dovero S, Kinet R, Arotcarena ML, Bohic S, Bezard E, Fernagut PO, Dehay B. Nigral ATP13A2 depletion induces Parkinson's disease-related neurodegeneration in a pilot study in non-human primates. NPJ Parkinsons Dis 2024; 10:141. [PMID: 39090150 PMCID: PMC11294619 DOI: 10.1038/s41531-024-00757-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
Lysosomal impairment is strongly implicated in Parkinson's disease (PD). Among the several PD-linked genes, the ATP13A2 gene, associated with the PARK9 locus, encodes a transmembrane lysosomal P5-type ATPase. Mutations in the ATP13A2 gene were primarily identified as the cause of Kufor-Rakeb syndrome (KRS), a juvenile-onset form of PD. Subsequently, an increasing list of several mutations has been described. These mutations result in truncation of the ATP13A2 protein, leading to a loss of function but surprisingly causing heterogeneity and variability in the clinical symptoms associated with different brain pathologies. In vitro studies show that its loss compromises lysosomal function, contributing to cell death. To understand the role of ATP13A2 dysfunction in disease, we disrupted its expression through a viral vector-based approach in nonhuman primates. Here, in this pilot study, we injected bilaterally into the substantia nigra of macaques, a lentiviral vector expressing an ATP13A2 small hairpin RNA. Animals were terminated five months later, and brains were harvested and compared with historical non-injected control brains to evaluate cerebral pathological markers known to be affected in KRS and PD. We characterised the pattern of dopaminergic loss in the striatum and the substantia nigra, the regional distribution of α-synuclein immunoreactivity in several brain structures, and its pathological status (i.e., S129 phosphorylation), the accumulation of heavy metals in nigral sections and occurrence of lysosomal dysfunction. This proof-of-concept experiment highlights the potential value of lentivirus-mediated ATP13A2 silencing to induce significant and ongoing degeneration in the nigrostriatal pathway, α-synuclein pathology, and iron accumulation in nonhuman primates.
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Affiliation(s)
- Joanna Sikora
- Univ. Bordeaux, CNRS, IMN, Bordeaux, France
- Univ. De Poitiers, INSERM, LNEC, Poitiers, France
| | | | - Rémi Kinet
- Univ. Bordeaux, CNRS, IMN, Bordeaux, France
| | | | - Sylvain Bohic
- Univ. Grenoble Alpes, Synchrotron Radiation for Biomedicine (STROBE), Grenoble, France
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2
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Garg V, Geurten BRH. Diving deep: zebrafish models in motor neuron degeneration research. Front Neurosci 2024; 18:1424025. [PMID: 38966756 PMCID: PMC11222423 DOI: 10.3389/fnins.2024.1424025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 05/30/2024] [Indexed: 07/06/2024] Open
Abstract
In the dynamic landscape of biomedical science, the pursuit of effective treatments for motor neuron disorders like hereditary spastic paraplegia (HSP), amyotrophic lateral sclerosis (ALS), and spinal muscular atrophy (SMA) remains a key priority. Central to this endeavor is the development of robust animal models, with the zebrafish emerging as a prime candidate. Exhibiting embryonic transparency, a swift life cycle, and significant genetic and neuroanatomical congruencies with humans, zebrafish offer substantial potential for research. Despite the difference in locomotion-zebrafish undulate while humans use limbs, the zebrafish presents relevant phenotypic parallels to human motor control disorders, providing valuable insights into neurodegenerative diseases. This review explores the zebrafish's inherent traits and how they facilitate profound insights into the complex behavioral and cellular phenotypes associated with these disorders. Furthermore, we examine recent advancements in high-throughput drug screening using the zebrafish model, a promising avenue for identifying therapeutically potent compounds.
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Affiliation(s)
- Vranda Garg
- Department of Cellular Neurobiology, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
- Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
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3
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Heins-Marroquin U, Singh RR, Perathoner S, Gavotto F, Merino Ruiz C, Patraskaki M, Gomez-Giro G, Kleine Borgmann F, Meyer M, Carpentier A, Warmoes MO, Jäger C, Mittelbronn M, Schwamborn JC, Cordero-Maldonado ML, Crawford AD, Schymanski EL, Linster CL. CLN3 deficiency leads to neurological and metabolic perturbations during early development. Life Sci Alliance 2024; 7:e202302057. [PMID: 38195117 PMCID: PMC10776888 DOI: 10.26508/lsa.202302057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Juvenile neuronal ceroid lipofuscinosis (or Batten disease) is an autosomal recessive, rare neurodegenerative disorder that affects mainly children above the age of 5 yr and is most commonly caused by mutations in the highly conserved CLN3 gene. Here, we generated cln3 morphants and stable mutant lines in zebrafish. Although neither morphant nor mutant cln3 larvae showed any obvious developmental or morphological defects, behavioral phenotyping of the mutant larvae revealed hyposensitivity to abrupt light changes and hypersensitivity to pro-convulsive drugs. Importantly, in-depth metabolomics and lipidomics analyses revealed significant accumulation of several glycerophosphodiesters (GPDs) and cholesteryl esters, and a global decrease in bis(monoacylglycero)phosphate species, two of which (GPDs and bis(monoacylglycero)phosphates) were previously proposed as potential biomarkers for CLN3 disease based on independent studies in other organisms. We could also demonstrate GPD accumulation in human-induced pluripotent stem cell-derived cerebral organoids carrying a pathogenic variant for CLN3 Our models revealed that GPDs accumulate at very early stages of life in the absence of functional CLN3 and highlight glycerophosphoinositol and BMP as promising biomarker candidates for pre-symptomatic CLN3 disease.
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Affiliation(s)
- Ursula Heins-Marroquin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Randolph R Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- https://ror.org/00hj8s172 Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Simon Perathoner
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Floriane Gavotto
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carla Merino Ruiz
- Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
- Biosfer Teslab SL, Reus, Spain
| | - Myrto Patraskaki
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Gemma Gomez-Giro
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Felix Kleine Borgmann
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Melanie Meyer
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Anaïs Carpentier
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Marc O Warmoes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Science and Medicine (DLSM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Institute for Orphan Drug Discovery, Bremerhaven, Germany
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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4
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Dang T, Cao WJ, Zhao R, Lu M, Hu G, Qiao C. ATP13A2 protects dopaminergic neurons in Parkinson's disease: from biology to pathology. J Biomed Res 2022; 36:98-108. [PMID: 35387901 PMCID: PMC9002154 DOI: 10.7555/jbr.36.20220001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As a late endosomal/lysosomal transport protein of the P5-type, ATP13A2 is capable of removing the abnormal accumulation of α-synuclein, which maintains the homeostasis of metal ions and polyamines in the central nervous system. Furthermore, ATP13A2 regulates the normal function of several organelles such as lysosomes, endoplasmic reticulum (ER) and mitochondria, and maintains the normal physiological activity of neural cells. Especially, ATP13A2 protects dopaminergic (DA) neurons against environmental or genetically induced Parkinson's disease (PD). As we all know, PD is a neurodegenerative disease characterized by the loss of DA neurons in the substantia nigra pars compacta. An increasing number of studies have reported that the loss-of-function of ATP13A2 affects normal physiological processes of various organelles, leading to abnormalities and the death of DA neurons. Previous studies in our laboratory have also shown that ATP13A2 deletion intensifies the neuroinflammatory response induced by astrocytes, thus inducing DA neuronal injury. In addition to elucidating the normal structure and function of ATP13A2, this review summarized the pathological mechanisms of ATP13A2 mutations leading to PD in existing literature studies, deepening the understanding of ATP13A2 in the pathological process of PD and other related neurodegenerative diseases. This review provides inspiration for investigators to explore the essential regulatory role of ATP13A2 in PD in the future.
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Affiliation(s)
- Tao Dang
- Department of Clinical Pharmacy, the Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.,College of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wen-Jing Cao
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan 411100, China
| | - Rong Zhao
- Department of Clinical Pharmacy, the Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Ming Lu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Gang Hu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Chen Qiao
- Department of Clinical Pharmacy, the Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.,College of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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Zhao W, Guo F, Kong L, Liu J, Hong X, Jiang Z, Song H, Cui X, Ruan J, Liu X. Yeast YPK9 deficiency results in shortened replicative lifespan and sensitivity to hydrogen peroxide. Biogerontology 2021; 22:547-563. [PMID: 34524607 DOI: 10.1007/s10522-021-09935-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022]
Abstract
YPK9/YOR291W of Saccharomyces cerevisiae encodes a vacuolar membrane protein. Previous research has suggested that Ypk9p is similar to the yeast P5-type ATPase Spf1p and that it plays a role in the sequestration of heavy metals. In addition, bioinformatics analysis has suggested that Ypk9p is a homolog of human ATP13A2, which encodes a protein of the subfamily of P5 ATPases. However, no specific function of Ypk9p has been described to date. In this study, we found, for the first time, that YPK9 is involved in the oxidative stress response and modulation of the replicative lifespan (RLS). We found that YPK9 deficiency confers sensitivity to the oxidative stress inducer hydrogen peroxide accompanied by increased intracellular ROS levels, decreased mitochondrial membrane potential, abnormal mitochondrial function, and increased incidence of early apoptosis in budding yeast. More importantly, YPK9 deficiency can lead to a shortened RLS. In addition, we found that overexpression of the catalase-encoding gene CTA1 can reverse the phenotypic abnormalities of the ypk9Δ yeast strain. Collectively, these findings highlight the involvement of Ypk9p in the oxidative stress response and modulation of RLS.
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Affiliation(s)
- Wei Zhao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Fang Guo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Lingyue Kong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Jiaxin Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Xiaoshan Hong
- Institute of Gynecology, Women and Children's Hospital of Guangdong Province, Guangzhou, 511442, China
| | - Zhiwen Jiang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Haochang Song
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Xiaojing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Jie Ruan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China.
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China.
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China.
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China.
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Bastioli G, Regoni M, Cazzaniga F, De Luca CMG, Bistaffa E, Zanetti L, Moda F, Valtorta F, Sassone J. Animal Models of Autosomal Recessive Parkinsonism. Biomedicines 2021; 9:biomedicines9070812. [PMID: 34356877 PMCID: PMC8301401 DOI: 10.3390/biomedicines9070812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s disease (PD) is the most common neurodegenerative movement disorder. The neuropathological hallmark of the disease is the loss of dopamine neurons of the substantia nigra pars compacta. The clinical manifestations of PD are bradykinesia, rigidity, resting tremors and postural instability. PD patients often display non-motor symptoms such as depression, anxiety, weakness, sleep disturbances and cognitive disorders. Although, in 90% of cases, PD has a sporadic onset of unknown etiology, highly penetrant rare genetic mutations in many genes have been linked with typical familial PD. Understanding the mechanisms behind the DA neuron death in these Mendelian forms may help to illuminate the pathogenesis of DA neuron degeneration in the more common forms of PD. A key step in the identification of the molecular pathways underlying DA neuron death, and in the development of therapeutic strategies, is the creation and characterization of animal models that faithfully recapitulate the human disease. In this review, we outline the current status of PD modeling using mouse, rat and non-mammalian models, focusing on animal models for autosomal recessive PD.
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Affiliation(s)
- Guendalina Bastioli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy; (G.B.); (M.R.); (L.Z.); (F.V.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Maria Regoni
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy; (G.B.); (M.R.); (L.Z.); (F.V.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Federico Cazzaniga
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (F.C.); (C.M.G.D.L.); (E.B.); (F.M.)
| | - Chiara Maria Giulia De Luca
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (F.C.); (C.M.G.D.L.); (E.B.); (F.M.)
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati, 34136 Trieste, Italy
| | - Edoardo Bistaffa
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (F.C.); (C.M.G.D.L.); (E.B.); (F.M.)
| | - Letizia Zanetti
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy; (G.B.); (M.R.); (L.Z.); (F.V.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Fabio Moda
- Division of Neurology 5 and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy; (F.C.); (C.M.G.D.L.); (E.B.); (F.M.)
| | - Flavia Valtorta
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy; (G.B.); (M.R.); (L.Z.); (F.V.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Jenny Sassone
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy; (G.B.); (M.R.); (L.Z.); (F.V.)
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, 20132 Milan, Italy
- Correspondence:
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7
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Zheng K, Li T. Prediction of ATPase cation transporting 13A2 molecule in Petromyzon marinus and pan-cancer analysis into human tumors from an evolutionary perspective. Immunogenetics 2021; 73:277-289. [PMID: 33743014 DOI: 10.1007/s00251-021-01216-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/11/2021] [Indexed: 11/30/2022]
Abstract
The ATPase cation transporting 13A2 protein (ATP13A2), which maintains the homeostasis of mitochondria and lysosomes, plays a significant role in human neurodegenerative diseases and cancer. Through constructing a lamprey proteome database, employing multiple sequence alignment and phylogenetic analysis, 5 ATP13A2 proteins from Petromyzon marinus (Pm-ATP13A2) were identified based on the evolutionary perspective. The motif and domain analysis showed that the ATP13A2 protein was conserved. The multiple phosphorylation sites and transmembrane structures highlighted the characteristics of ATP13A2 as the P-ATPase-V cation transporting protein. Based on the information provided by the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, this study was conducted as a preliminary investigation of the carcinogenic effects of the ATP13A2 gene in a variety of tumors. The ATP13A2 was strongly expressed in most tumors, except in two types of nervous system tumors glioblastoma multiforme (GBM) and brain lower grade glioma (LGG). Moreover, the expression of ATP13A2 was strongly correlated with the prognosis of tumor patients. The high expression of ATP13A2 was obviously related to the poor prognosis of LGG. The poor prognosis of LGG patients may affect the ATP13A2 expression through the immune cells and radiotherapy. Also, cancer-related fibroblast infiltration was observed. All in all, this work offers more insights into the molecular evolution of the ATP13A2 protein and facilitates the understanding of the carcinogenic effects of the ATP13A2 in different tumors. Our discussion also promotes the study into the successful evolution of the vertebrate brain and the mechanism of clinical brain-related diseases.
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Affiliation(s)
- Kaifeng Zheng
- College of Life Sciences, Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China.
| | - Tiesong Li
- College of Life Sciences, Lamprey Research Center, Liaoning Normal University, Dalian, 116081, China.
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Nagamatsu ST, Coutouné N, José J, Fiamenghi MB, Pereira GAG, Oliveira JVDC, Carazzolle MF. Ethanol production process driving changes on industrial strains. FEMS Yeast Res 2021; 21:6070656. [PMID: 33417685 DOI: 10.1093/femsyr/foaa071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Ethanol production has key differences between the two largest producing countries of this biofuel, Brazil and the USA, such as feedstock source, sugar concentration and ethanol titers in industrial fermentation. Therefore, it is highly probable that these specificities have led to genome adaptation of the Saccharomyces cerevisiae strains employed in each process to tolerate different environments. In order to identify particular adaptations, in this work, we have compared the genomes of industrial yeast strains widely used to produce ethanol from sugarcane, corn and sweet sorghum, and also two laboratory strains as reference. The genes were predicted and then 4524 single-copy orthologous were selected to build the phylogenetic tree. We found that the geographic location and industrial process were shown as the main evolutionary drivers: for sugarcane fermentation, positive selection was identified for metal homeostasis and stress response genes, whereas genes involved in membrane modeling have been connected with corn fermentation. In addition, the corn specialized strain Ethanol Red showed an increased number of copies of MAL31, a gene encoding a maltose transporter. In summary, our work can help to guide new strain chassis selection for engineering strategies, to produce more robust strains for biofuel production and other industrial applications.
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Affiliation(s)
- Sheila Tiemi Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Natalia Coutouné
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Juliana José
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Mateus Bernabe Fiamenghi
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
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9
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Soczewka P, Flis K, Tribouillard-Tanvier D, di Rago JP, Santos CN, Menezes R, Kaminska J, Zoladek T. Flavonoids as Potential Drugs for VPS13-Dependent Rare Neurodegenerative Diseases. Genes (Basel) 2020; 11:E828. [PMID: 32708255 PMCID: PMC7397310 DOI: 10.3390/genes11070828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/06/2020] [Accepted: 07/17/2020] [Indexed: 12/30/2022] Open
Abstract
Several rare neurodegenerative diseases, including chorea acanthocytosis, are caused by mutations in the VPS13A-D genes. Only symptomatic treatments for these diseases are available. Saccharomyces cerevisiae contains a unique VPS13 gene and the yeast vps13Δ mutant has been proven as a suitable model for drug tests. A library of drugs and an in-house library of natural compounds and their derivatives were screened for molecules preventing the growth defect of vps13Δ cells on medium with sodium dodecyl sulfate (SDS). Seven polyphenols, including the iron-binding flavone luteolin, were identified. The structure-activity relationship and molecular mechanisms underlying the action of luteolin were characterized. The FET4 gene, which encodes an iron transporter, was found to be a multicopy suppressor of vps13Δ, pointing out the importance of iron in response to SDS stress. The growth defect of vps13Δ in SDS-supplemented medium was also alleviated by the addition of iron salts. Suppression did not involve cell antioxidant responses, as chemical antioxidants were not active. Our findings support that luteolin and iron may target the same cellular process, possibly the synthesis of sphingolipids. Unveiling the mechanisms of action of chemical and genetic suppressors of vps13Δ may help to better understand VPS13A-D-dependent pathogenesis and to develop novel therapeutic strategies.
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Affiliation(s)
- Piotr Soczewka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (P.S.); (K.F.); (J.K.)
| | - Krzysztof Flis
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (P.S.); (K.F.); (J.K.)
| | - Déborah Tribouillard-Tanvier
- CNRS, Institut de Biochimie et Génétique Cellulaires, Bordeaux University, CEDEX, 33077 Bordeaux, France; (D.T.-T.); (J.-P.d.R.)
- Institut National de la Santé et de la Recherche Médicale INSERM, 33077 Bordeaux, France
| | - Jean-Paul di Rago
- CNRS, Institut de Biochimie et Génétique Cellulaires, Bordeaux University, CEDEX, 33077 Bordeaux, France; (D.T.-T.); (J.-P.d.R.)
| | - Cláudia N. Santos
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal; (C.N.S.); (R.M.)
- CEDOC—Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana n° 6, 6-A Edifício CEDOC II, 1150-082 Lisboa, Portugal
| | - Regina Menezes
- Instituto de Biologia Experimental e Tecnológica, Av. República, Qta. do Marquês, 2780-157 Oeiras, Portugal; (C.N.S.); (R.M.)
- CEDOC—Chronic Diseases Research Center, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana n° 6, 6-A Edifício CEDOC II, 1150-082 Lisboa, Portugal
| | - Joanna Kaminska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (P.S.); (K.F.); (J.K.)
| | - Teresa Zoladek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (P.S.); (K.F.); (J.K.)
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