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Chithra Y, Dey G, Ghose V, Chandramohan V, Gowthami N, Vasudev V, Srinivas Bharath MM. Mitochondrial Complex I Inhibition in Dopaminergic Neurons Causes Altered Protein Profile and Protein Oxidation: Implications for Parkinson's disease. Neurochem Res 2023:10.1007/s11064-023-03907-x. [PMID: 36964824 DOI: 10.1007/s11064-023-03907-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/25/2023] [Accepted: 03/03/2023] [Indexed: 03/26/2023]
Abstract
Mitochondrial dysfunction and oxidative stress are critical to neurodegeneration in Parkinson's disease (PD). Mitochondrial dysfunction in PD entails inhibition of the mitochondrial complex I (CI) in the dopaminergic neurons of substantia nigra. The events contributing to CI inhibition and downstream pathways are not completely elucidated. We conducted proteomic analysis in a dopaminergic neuronal cell line exposed individually to neurotoxic CI inhibitors: rotenone (Rot), paraquat (Pq) and 1-methyl-4-phenylpyridinium (MPP+). Mass spectrometry (MS) revealed the involvement of biological processes including cell death pathways, structural changes and metabolic processes among others, most of which were common across all models. The proteomic changes induced by Pq were significantly higher than those induced by Rot and MPP+. Altered metabolic processes included downregulated mitochondrial proteins such as CI subunits. MS of CI isolated from the models revealed oxidative post-translational modifications with Tryptophan (Trp) oxidation as the predominant modification. Further, 62 peptides in 22 subunits of CI revealed Trp oxidation with 16 subunits common across toxins. NDUFV1 subunit had the greatest number of oxidized Trp and Rot model displayed the highest number of Trp oxidation events compared to the other models. Molecular dynamics simulation (MDS) of NDUFV1 revealed that oxidized Trp 433 altered the local conformation thereby changing the distance between the Fe-S clusters, Fe-S 301(N1a) to Fe-S 502 (N3) and Fe-S 802 (N4) to Fe-S 801 (N5), potentially affecting the efficiency of electron transfer. The events triggered by the neurotoxins represent CI damage, mitochondrial dysfunction and neurodegeneration in PD.
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Affiliation(s)
- Yogeshachar Chithra
- Department of Bioscience, P.G. Center, Hemagangotri, University of Mysore, Hassan, Karnataka, 573220, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore, 560066, India
| | - Vivek Ghose
- Manipal Academy of Higher Education, Udupi, Karnataka, 576104, India
| | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka, 572103, India
| | - Niya Gowthami
- Department of Clinical Psychopharmacology and Neurotoxicology, National Institute of Mental Health and Neurosciences (NIMHANS), No. 2900, Hosur Road, Lakkasandra, Bangalore, 560029, India
| | - V Vasudev
- Department of Bioscience, P.G. Center, Hemagangotri, University of Mysore, Hassan, Karnataka, 573220, India
| | - M M Srinivas Bharath
- Department of Clinical Psychopharmacology and Neurotoxicology, National Institute of Mental Health and Neurosciences (NIMHANS), No. 2900, Hosur Road, Lakkasandra, Bangalore, 560029, India.
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Amate-García G, Ballesta-Martínez MJ, Serrano-Lorenzo P, Garrido-Moraga R, González-Quintana A, Blázquez A, Rubio JC, García-Consuegra I, Arenas J, Ugalde C, Morán M, Guillén-Navarro E, Martín MA. A Novel Mutation Associated with Neonatal Lethal Cardiomyopathy Leads to an Alternative Transcript Expression in the X-Linked Complex I NDUFB11 Gene. Int J Mol Sci 2023; 24:ijms24021743. [PMID: 36675256 PMCID: PMC9865986 DOI: 10.3390/ijms24021743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
We report a neonatal patient with hypertrophic cardiomyopathy (HCM), lactic acidosis and isolated complex I deficiency. Using a customized next-generation sequencing panel, we identified a novel hemizygous variant c.338G>A in the X-linked NDUFB11 gene that encodes the NADH: ubiquinone oxidoreductase subunit B11 of the mitochondrial respiratory chain (MRC) complex I (CI). Molecular and functional assays performed in the proband’s target tissues—skeletal and heart muscle—showed biochemical disturbances of the MRC, suggesting a pathogenic role for this variant. In silico analyses initially predicted an amino acid missense change p.(Arg113Lys) in the NDUFB11 CI subunit. However, we showed that the molecular effect of the c.338G>A variant, which is located at the last nucleotide of exon 2 of the NDUFB11 gene in the canonical ‘short’ transcript (sized 462 bp), instead causes a splicing defect triggering the up-regulation of the expression of an alternative ‘long’ transcript (sized 492 bp) that can also be detected in the control individuals. Our results support the hypothesis that the canonical ‘short’ transcript is required for the proper NDUFB11 protein synthesis, which is essential for optimal CI assembly and activity, whereas the longer alternative transcript seems to represent a non-functional, unprocessed splicing intermediate. Our results highlight the importance of characterizing the molecular effect of new variants in the affected patient’s tissues to demonstrate their pathogenicity and association with the clinical phenotypes.
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Affiliation(s)
- Guillermo Amate-García
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - María Juliana Ballesta-Martínez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120 Murcia, Spain
| | - Pablo Serrano-Lorenzo
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Rocío Garrido-Moraga
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Adrián González-Quintana
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Alberto Blázquez
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Juan C. Rubio
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Inés García-Consuegra
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Joaquín Arenas
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Cristina Ugalde
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - María Morán
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Encarnación Guillén-Navarro
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB) Pascual Parrilla, 30120 Murcia, Spain
- Facultad de Medicina, Universidad de Murcia, 30120 Murcia, Spain
| | - Miguel A. Martín
- Grupo de Enfermedades Mitocondriales y Neuromusculares, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Servicio de Genética, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
- Correspondence:
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Alkhaldi HA, Phan DH, Vik SB. Analysis of Human Clinical Mutations of Mitochondrial ND1 in a Bacterial Model System for Complex I. Life (Basel) 2022; 12:1934. [PMID: 36431069 PMCID: PMC9696053 DOI: 10.3390/life12111934] [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: 10/18/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
The most common causes of mitochondrial dysfunction and disease include mutations in subunits and assembly factors of Complex I. Numerous mutations in the mitochondrial gene ND1 have been identified in humans. Currently, a bacterial model system provides the only method for rapid construction and analysis of mutations in homologs of human ND1. In this report, we have identified nine mutations in human ND1 that are reported to be pathogenic and are located at subunit interfaces. Our hypothesis was that these mutations would disrupt Complex I assembly. Seventeen mutations were constructed in the homologous nuoH gene in an E. coli model system. In addition to the clinical mutations, alanine substitutions were constructed in order to distinguish between a deleterious effect from the introduction of the mutant residue and the loss of the original residue. The mutations were moved to an expression vector containing all thirteen genes of the E. coli nuo operon coding for Complex I. Membrane vesicles were prepared and rates of deamino-NADH oxidase activity and proton translocation were measured. Samples were also tested for assembly by native gel electrophoresis and for expression of NuoH by immunoblotting. A range of outcomes was observed: Mutations at four of the sites allow normal assembly with moderate activity (50−76% of wild type). Mutations at the other sites disrupt assembly and/or activity, and in some cases the outcomes depend upon the amino acid introduced. In general, the outcomes are consistent with the proposed pathogenicity in humans.
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Affiliation(s)
| | | | - Steven B. Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
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Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Int J Mol Sci 2021; 22:8325. [PMID: 34361091 PMCID: PMC8348117 DOI: 10.3390/ijms22158325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Paola Zanfardino
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Stefano Doccini
- IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy;
| | | | - Vittoria Petruzzella
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
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Accessory Subunits of the Matrix Arm of Mitochondrial Complex I with a Focus on Subunit NDUFS4 and Its Role in Complex I Function and Assembly. Life (Basel) 2021; 11:life11050455. [PMID: 34069703 PMCID: PMC8161149 DOI: 10.3390/life11050455] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/19/2022] Open
Abstract
NADH:ubiquinone-oxidoreductase (complex I) is the largest membrane protein complex of the respiratory chain. Complex I couples electron transfer to vectorial proton translocation across the inner mitochondrial membrane. The L shaped structure of complex I is divided into a membrane arm and a matrix arm. Fourteen central subunits are conserved throughout species, while some 30 accessory subunits are typically found in eukaryotes. Complex I dysfunction is associated with mutations in the nuclear and mitochondrial genome, resulting in a broad spectrum of neuromuscular and neurodegenerative diseases. Accessory subunit NDUFS4 in the matrix arm is a hot spot for mutations causing Leigh or Leigh-like syndrome. In this review, we focus on accessory subunits of the matrix arm and discuss recent reports on the function of accessory subunit NDUFS4 and its interplay with NDUFS6, NDUFA12, and assembly factor NDUFAF2 in complex I assembly.
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