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Pinto M, Vempati UD, Diaz F, Peralta S, Moraes CT. Ablation of Cytochrome c in Adult Forebrain Neurons Impairs Oxidative Phosphorylation Without Detectable Apoptosis. Mol Neurobiol 2018; 56:3722-3735. [PMID: 30191381 DOI: 10.1007/s12035-018-1335-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/27/2018] [Indexed: 01/27/2023]
Abstract
Cytochrome c (Cyt c), a heme-containing mitochondrial protein, has a critical function in both respiration and apoptosis. Consistent with these vital functions, somatic Cyt c mouse knockout is embryonic lethal. In order to investigate the sensitivity of postnatal neurons to Cyt c depletion, we developed a neuron-specific conditional knockout model. Neuron-specific Cyt c KO mouse (nCytcKO) was created by crossing the floxed Cyt c mouse with a CamKIIα-cre transgenic mouse, which deletes the floxed alleles postnatally. nCytcKO mice were normal at birth but developed an abnormal phenotype starting at 8 weeks of age with weight loss, tremor, decreased sensorimotor coordination, and sudden death between 12 and 16 weeks. Histological analysis did not show major neuronal degeneration. Analyses of oxidative phosphorylation showed a specific reduction in complex IV levels. Markers of oxidative stress were also increased. This novel model showed that neuronal complex IV is destabilized in the absence of Cyt c. It also showed that ablation of Cyt c in neurons leads to severe behavioral abnormalities and premature death without detectable neuronal loss, suggesting that neurons have the potential to survive for extended periods of time without a functional OXPHOS.
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Affiliation(s)
- Milena Pinto
- Department of Neurology, Miller School of Medicine Miami, University of Miami, 1420 NW 9th Avenue, TSL Building, Rm. 231, Miami, FL, 33136, USA.
| | - Uma D Vempati
- Department of Neurology, Miller School of Medicine Miami, University of Miami, 1420 NW 9th Avenue, TSL Building, Rm. 231, Miami, FL, 33136, USA
- Neuroscience Program, Miller School of Medicine Miami, University of Miami, 1420 NW 9th Avenue, TSL Building, Rm. 231, Miami, FL, 33136, USA
| | - Francisca Diaz
- Department of Neurology, Miller School of Medicine Miami, University of Miami, 1420 NW 9th Avenue, TSL Building, Rm. 231, Miami, FL, 33136, USA
| | - Susana Peralta
- Department of Neurology, Miller School of Medicine Miami, University of Miami, 1420 NW 9th Avenue, TSL Building, Rm. 231, Miami, FL, 33136, USA
| | - Carlos T Moraes
- Department of Neurology, Miller School of Medicine Miami, University of Miami, 1420 NW 9th Avenue, TSL Building, Rm. 231, Miami, FL, 33136, USA.
- Neuroscience Program, Miller School of Medicine Miami, University of Miami, 1420 NW 9th Avenue, TSL Building, Rm. 231, Miami, FL, 33136, USA.
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Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. CLO: The cell line ontology. J Biomed Semantics 2014; 5:37. [PMID: 25852852 PMCID: PMC4387853 DOI: 10.1186/2041-1480-5-37] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 06/24/2014] [Indexed: 01/07/2023] Open
Abstract
Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.
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Affiliation(s)
- Sirarat Sarntivijai
- US Food and Drug Administration, Silver Spring, MD, USA ; University of Michigan, Ann Arbor, MI, USA
| | - Yu Lin
- University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | - Chao Pang
- University Medical Center Groningen, Groningen, Netherlands
| | - James Malone
- European Molecular Biology Laboratory, (EMBL-EBI), Hinxton, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, (EMBL-EBI), Hinxton, UK
| | - Yue Liu
- University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | | | - Jie Zheng
- University of Pennsylvania, Philadelphia, USA
| | | | - Bjoern Peters
- La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | | | | | | | | | - Yongqun He
- University of Michigan, Ann Arbor, MI, USA
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Abeyruwan S, Vempati UD, Küçük-McGinty H, Visser U, Koleti A, Mir A, Sakurai K, Chung C, Bittker JA, Clemons PA, Brudz S, Siripala A, Morales AJ, Romacker M, Twomey D, Bureeva S, Lemmon V, Schürer SC. Evolving BioAssay Ontology (BAO): modularization, integration and applications. J Biomed Semantics 2014; 5:S5. [PMID: 25093074 PMCID: PMC4108877 DOI: 10.1186/2041-1480-5-s1-s5] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and datasets.
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Affiliation(s)
- Saminda Abeyruwan
- Department of Computer Science, University of Miami, 1365 Memorial Drive, 33146 Coral Gables, FL, USA
| | - Uma D Vempati
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, 33146 Coral Gables, FL, USA
| | - Hande Küçük-McGinty
- Department of Computer Science, University of Miami, 1365 Memorial Drive, 33146 Coral Gables, FL, USA
| | - Ubbo Visser
- Department of Computer Science, University of Miami, 1365 Memorial Drive, 33146 Coral Gables, FL, USA
| | - Amar Koleti
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, 33146 Coral Gables, FL, USA
| | - Ahsan Mir
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, 33146 Coral Gables, FL, USA
| | - Kunie Sakurai
- The Miami Project to Cure Paralysis, 1095 NW 14th Terrace, 33136 Miami, FL, USA
| | - Caty Chung
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, 33146 Coral Gables, FL, USA
| | | | | | - Steve Brudz
- 7 Cambridge Center, Cambridge, MA 02142, MA, USA
| | - Anosha Siripala
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, 02139 Cambridge, MA, USA
| | - Arturo J Morales
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, 02139 Cambridge, MA, USA
| | - Martin Romacker
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, 02139 Cambridge, MA, USA
| | - David Twomey
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, 02139 Cambridge, MA, USA
| | - Svetlana Bureeva
- Thomson Reuters, 5901 Priestly Drive, Suite 200, 92008 Carlsbad, CA, USA
| | - Vance Lemmon
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, 33146 Coral Gables, FL, USA ; The Miami Project to Cure Paralysis, 1095 NW 14th Terrace, 33136 Miami, FL, USA
| | - Stephan C Schürer
- Center for Computational Science, University of Miami, 1320 S. Dixie Highway, Gables One Tower, 33146 Coral Gables, FL, USA ; Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, 1120 NW 14th Street, CRB 650 (M-857), 33136 Miami, FL, USA
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Vempati UD, Chung C, Mader C, Koleti A, Datar N, Vidović D, Wrobel D, Erickson S, Muhlich JL, Berriz G, Benes CH, Subramanian A, Pillai A, Shamu CE, Schürer SC. Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). J Biomol Screen 2014; 19:803-16. [PMID: 24518066 PMCID: PMC7723305 DOI: 10.1177/1087057114522514] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/13/2014] [Indexed: 01/15/2023]
Abstract
The National Institutes of Health Library of Integrated Network-based Cellular Signatures (LINCS) program is generating extensive multidimensional data sets, including biochemical, genome-wide transcriptional, and phenotypic cellular response signatures to a variety of small-molecule and genetic perturbations with the goal of creating a sustainable, widely applicable, and readily accessible systems biology knowledge resource. Integration and analysis of diverse LINCS data sets depend on the availability of sufficient metadata to describe the assays and screening results and on their syntactic, structural, and semantic consistency. Here we report metadata specifications for the most important molecular and cellular components and recommend them for adoption beyond the LINCS project. We focus on the minimum required information to model LINCS assays and results based on a number of use cases, and we recommend controlled terminologies and ontologies to annotate assays with syntactic consistency and semantic integrity. We also report specifications for a simple annotation format (SAF) to describe assays and screening results based on our metadata specifications with explicit controlled vocabularies. SAF specifically serves to programmatically access and exchange LINCS data as a prerequisite for a distributed information management infrastructure. We applied the metadata specifications to annotate large numbers of LINCS cell lines, proteins, and small molecules. The resources generated and presented here are freely available.
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Affiliation(s)
- Uma D Vempati
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Caty Chung
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Chris Mader
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Amar Koleti
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Nakul Datar
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Dušica Vidović
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - David Wrobel
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, USA
| | - Sean Erickson
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, USA
| | - Jeremy L Muhlich
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Gabriel Berriz
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Cyril H Benes
- Center for Molecular Therapeutics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Ajay Pillai
- National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Caroline E Shamu
- ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, USA Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephan C Schürer
- Center for Computational Science, University of Miami, Miami, FL, USA Department of Molecular and Cellular Pharmacology, University of Miami, Miami, Florida, USA
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de Souza A, Bittker JA, Lahr DL, Brudz S, Chatwin S, Oprea TI, Waller A, Yang JJ, Southall N, Guha R, Schürer SC, Vempati UD, Southern MR, Dawson ES, Clemons PA, Chung TDY. An Overview of the Challenges in Designing, Integrating, and Delivering BARD: A Public Chemical-Biology Resource and Query Portal for Multiple Organizations, Locations, and Disciplines. ACTA ACUST UNITED AC 2014; 19:614-27. [PMID: 24441647 DOI: 10.1177/1087057113517139] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/22/2013] [Indexed: 01/15/2023]
Abstract
Recent industry-academic partnerships involve collaboration among disciplines, locations, and organizations using publicly funded "open-access" and proprietary commercial data sources. These require the effective integration of chemical and biological information from diverse data sources, which presents key informatics, personnel, and organizational challenges. The BioAssay Research Database (BARD) was conceived to address these challenges and serve as a community-wide resource and intuitive web portal for public-sector chemical-biology data. Its initial focus is to enable scientists to more effectively use the National Institutes of Health Roadmap Molecular Libraries Program (MLP) data generated from the 3-year pilot and 6-year production phases of the Molecular Libraries Probe Production Centers Network (MLPCN), which is currently in its final year. BARD evolves the current data standards through structured assay and result annotations that leverage BioAssay Ontology and other industry-standard ontologies, and a core hierarchy of assay definition terms and data standards defined specifically for small-molecule assay data. We initially focused on migrating the highest-value MLP data into BARD and bringing it up to this new standard. We review the technical and organizational challenges overcome by the interdisciplinary BARD team, veterans of public- and private-sector data-integration projects, who are collaborating to describe (functional specifications), design (technical specifications), and implement this next-generation software solution.
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Affiliation(s)
| | | | - David L Lahr
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steve Brudz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Simon Chatwin
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Tudor I Oprea
- University of New Mexico Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Anna Waller
- University of New Mexico Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jeremy J Yang
- University of New Mexico Center for Molecular Discovery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Noel Southall
- NIH Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Rajarshi Guha
- NIH Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Stephan C Schürer
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Uma D Vempati
- Center for Computational Science, University of Miami, Miami, FL, USA
| | - Mark R Southern
- The Translational Research Institute, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Dawson
- The Vanderbilt Specialized Chemistry Center for Accelerated Probe Development, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Thomas D Y Chung
- Conrad Prebys Center for Chemical Genomics, Sanford
- Burnham Medical Research Institute, La Jolla, CA, USA
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Vempati UD, Przydzial MJ, Chung C, Abeyruwan S, Mir A, Sakurai K, Visser U, Lemmon VP, Schürer SC. Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). PLoS One 2012; 7:e49198. [PMID: 23155465 PMCID: PMC3498356 DOI: 10.1371/journal.pone.0049198] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 10/04/2012] [Indexed: 11/30/2022] Open
Abstract
Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO). BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.
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Affiliation(s)
- Uma D. Vempati
- Center for Computational Science, University of Miami, Miami, Florida, United States of America
| | - Magdalena J. Przydzial
- Center for Computational Science, University of Miami, Miami, Florida, United States of America
| | - Caty Chung
- Center for Computational Science, University of Miami, Miami, Florida, United States of America
| | - Saminda Abeyruwan
- Department of Computer Science, University of Miami, Miami, Florida, United States of America
| | - Ahsan Mir
- Center for Computational Science, University of Miami, Miami, Florida, United States of America
| | - Kunie Sakurai
- Center for Computational Science, University of Miami, Miami, Florida, United States of America
| | - Ubbo Visser
- Department of Computer Science, University of Miami, Miami, Florida, United States of America
| | - Vance P. Lemmon
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, Miami, Florida, United States of America
| | - Stephan C. Schürer
- Center for Computational Science, University of Miami, Miami, Florida, United States of America
- Department of Molecular and Cellular Pharmacology, University of Miami, Miami, Florida, United States of America
- * E-mail:
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Torraco A, Diaz F, Vempati UD, Moraes CT. Mouse models of oxidative phosphorylation defects: powerful tools to study the pathobiology of mitochondrial diseases. Biochim Biophys Acta 2009; 1793:171-80. [PMID: 18601959 PMCID: PMC2652735 DOI: 10.1016/j.bbamcr.2008.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 05/28/2008] [Accepted: 06/04/2008] [Indexed: 01/14/2023]
Abstract
Defects in the oxidative phosphorylation system (OXPHOS) are responsible for a group of extremely heterogeneous and pleiotropic pathologies commonly known as mitochondrial diseases. Although many mutations have been found to be responsible for OXPHOS defects, their pathogenetic mechanisms are still poorly understood. An important contribution to investigate the in vivo function of several mitochondrial proteins and their role in mitochondrial dysfunction, has been provided by mouse models. Thanks to their genetic and physiologic similarity to humans, mouse models represent a powerful tool to investigate the impact of pathological mutations on metabolic pathways. In this review we discuss the main mouse models of mitochondrial disease developed, focusing on the ones that directly affect the OXPHOS system.
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Affiliation(s)
- Alessandra Torraco
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Uma D. Vempati
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Carlos T. Moraes
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
- Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
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Vempati UD, Han X, Moraes CT. Lack of cytochrome c in mouse fibroblasts disrupts assembly/stability of respiratory complexes I and IV. J Biol Chem 2008; 284:4383-91. [PMID: 19075019 DOI: 10.1074/jbc.m805972200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c (cyt c) is a heme-containing protein that participates in electron transport in the respiratory chain and as a signaling molecule in the apoptotic cascade. Here we addressed the effect of removing mammalian cyt c on the integrity of the respiratory complexes in mammalian cells. Mitochondria from cyt c knockout mouse cells lacked fully assembled complexes I and IV and had reduced levels of complex III. A redox-deficient mutant of cyt c was unable to rescue the levels of complexes I and IV. We found that cyt c is associated with both complex IV and respiratory supercomplexes, providing a potential mechanism for the requirement for cyt c in the assembly/stability of complex IV.
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Affiliation(s)
- Uma D Vempati
- Department of Neurology and Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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9
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Vempati UD, Torraco A, Moraes CT. Mouse models of oxidative phosphorylation dysfunction and disease. Methods 2008; 46:241-7. [PMID: 18848991 PMCID: PMC2652743 DOI: 10.1016/j.ymeth.2008.09.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 08/28/2008] [Accepted: 09/12/2008] [Indexed: 11/23/2022] Open
Abstract
Oxidative phosphorylation (OXPHOS) deficiency results in a number of human diseases, affecting at least one in 5000 of the general population. Altering the function of genes by mutations are central to our understanding their function. Prior to the development of gene targeting, this approach was limited to rare spontaneous mutations that resulted in a phenotype. Since its discovery, targeted mutagenesis of the mouse germline has proved to be a powerful approach to understand the in vivo function of genes. Gene targeting has yielded remarkable understanding of the role of several gene products in the OXPHOS system. We provide a "tool box" of mouse models with OXPHOS defects that could be used to answer diverse scientific questions.
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Affiliation(s)
| | | | - Carlos T. Moraes
- Department of Neurology, University of Miami, USA
- Department of Cell Biology & Anatomy, University of Miami, USA
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Vempati UD, Diaz F, Barrientos A, Narisawa S, Mian AM, Millán JL, Boise LH, Moraes CT. Role of cytochrome C in apoptosis: increased sensitivity to tumor necrosis factor alpha is associated with respiratory defects but not with lack of cytochrome C release. Mol Cell Biol 2007; 27:1771-83. [PMID: 17210651 PMCID: PMC1820455 DOI: 10.1128/mcb.00287-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the role of cytochrome c in apoptosis is well established, details of its participation in signaling pathways in vivo are not completely understood. The knockout for the somatic isoform of cytochrome c caused embryonic lethality in mice, but derived embryonic fibroblasts were shown to be resistant to apoptosis induced by agents known to trigger the intrinsic apoptotic pathway. In contrast, these cells were reported to be hypersensitive to tumor necrosis factor alpha (TNF-alpha)-induced apoptosis, which signals through the extrinsic pathway. Surprisingly, we found that this cell line (CRL 2613) respired at close to normal levels because of an aberrant activation of a testis isoform of cytochrome c, which, albeit expressed at low levels, was able to replace the somatic isoform for respiration and apoptosis. To produce a bona fide cytochrome c knockout, we developed a mouse knockout for both the testis and somatic isoforms of cytochrome c. The mouse was made viable by the introduction of a ubiquitously expressed cytochrome c transgene flanked by loxP sites. Lung fibroblasts in which the transgene was deleted showed no cytochrome c expression, no respiration, and resistance to agents that activate the intrinsic and to a lesser but significant extent also the extrinsic pathways. Comparison of these cells with lines with a defective oxidative phosphorylation system showed that cells with defective respiration have increased sensitivity to TNF-alpha-induced apoptosis, but this process was still amplified by cytochrome c. These studies underscore the importance of oxidative phosphorylation and apoptosome function to both the intrinsic and extrinsic apoptotic pathways.
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Affiliation(s)
- Uma D Vempati
- University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA.
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Abstract
Transforming Growth Factor-beta (TGF-beta) and their receptors have been characterized from many organisms. Two TGF-beta signaling receptors called Type I and II have been described for various ligands of the superfamily from organisms ranging from Drosophila to humans. In Xenopus laevis, TGF-beta2 and 5 have been reported and presumably, play important roles during early development. Several Type I and type II receptors for many ligands of the TGF-beta superfamily except TGF-beta type II receptor (TbetaIIR), have been characterized in Xenopus laevis. A chemical cross linking experiment using iodinated TGF-beta1 and -beta5, revealed four specific binding proteins on XTC cells. In order to understand the TGF-beta involvement during Xenopus development, a TGF-beta type II receptor (XTbetaIIR) has been isolated from a XTC cDNA library. XTbetaIIR was a partial cDNA lacking a portion of the signal peptide. The sequence analysis and homology comparison with the human TbetaIIR revealed 67% amino acid similarity in the extra cellular domain, 60% similarity in the transmembrane domain and 87% similarity in the cytoplasmic kinase domain, suggesting that XTbetaIIR is a putative TGF-beta type II receptor. In addition, the consensus amino acid motif for serine threonine receptor kinases was also present. Further, a dominant negative expression construct lacking the cytoplasmic kinase domain (engineered with the signal peptide from human TGF-beta type II receptor), was able to abolish TGF-beta mediated induction of a luciferase reporter plasmid, in a transient cell transfection assay. This substantiates the notion that XTbetaIIR cDNA can act as a receptor for TGF-beta. RT-PCR analysis using RNA isolated from various developmental stages of Xenopus laevis revealed expression of this gene in all the early stages of development and in the adult organs, except in stages 46/48.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cross-Linking Reagents
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Gene Expression Regulation, Developmental
- Humans
- Luciferases/genetics
- Luciferases/metabolism
- Molecular Sequence Data
- Protein Kinases/genetics
- Protein Serine-Threonine Kinases
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, Transforming Growth Factor-beta Type II
- Receptors, Transforming Growth Factor beta/chemistry
- Receptors, Transforming Growth Factor beta/genetics
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transforming Growth Factor beta/chemistry
- Tumor Cells, Cultured
- Xenopus laevis/embryology
- Xenopus laevis/genetics
- Xenopus laevis/growth & development
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Affiliation(s)
- S M Dhanasekaran
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560 012, India
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12
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Abstract
Members of the transforming growth factor-beta (TGF-beta) superfamily play various roles during development in both vertebrates and invertebrates. Two isoforms, TGF-beta2 and -beta5, have been isolated from Xenopus laevis. We describe here the localization of TGF-beta5 mRNA in early embryos of X. laevis, assessed by whole-mount in situ hybridization. The first detectable expression of TGF-beta5 was seen in the stage 14 embryo at the posterior tip of notochord, which continued to later stages, accompanied by the expression in bilateral regions of posterior wall in the tail region next to the notochord. At later stages, transient expression was seen in the cement gland (around stage 21) and in the somites (stages 24-27). In addition, expression was present in the branchial arches (stage 29-36) and olfactory placodes (stage 36).
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Affiliation(s)
- P Kondaiah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, -560 012, Bangalore, India.
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13
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Vempati UD, Kondaiah P. Molecular organization of the gene encoding Xenopus laevis transforming growth factor-beta 5. Biochem Mol Biol Int 1998; 45:997-1003. [PMID: 9739464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transforming growth factor-beta s (TGF-beta s) are multifunctional polypeptides, known to influence proliferation and differentiation of many cell types. TGF-beta 5 cDNA was cloned from Xenopus laevis and this isoform is unique to the amphibians. Here, we report the isolation and characterization of the TGF-beta 5 genomic clones to determine the structure of TGF-beta 5 gene. The gene consists of seven exons and all intron-exon boundaries follow the GT-AG consensus. The organization of TGF-beta 5 gene was identical to that of the mammalian TGF-beta isoforms, with the exception of position of the first splice junction. We determined the size of TGF-beta 5 gene to be approximately 20 kb.
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Affiliation(s)
- U D Vempati
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
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14
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Abstract
Transforming growth factors-beta are potent regulators of cellular proliferation, differentiation and morphogenesis. 2.41 kb of the 5' flanking region of the transforming growth factor-beta 5 (TGF-beta 5) gene has been isolated from a Xenopus laevis genomic library and sequenced. The transcription start site of this gene was determined by 5' RACE method. Promoter activity was demonstrated by transient transfection experiments using luciferase reporter gene constructs in XTC cells. A number of putative recognition sites for transcription factors were found in the 5' flanking region of the TGF-beta 5 gene.
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Affiliation(s)
- U D Vempati
- Indian Institute of Science, Department of Molecular Reproduction, Development and Genetics, Bangalore, India
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