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Hooper CM, Castleden IR, Tanz SK, Grasso SV, Millar AH. Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1346:67-89. [PMID: 35113396 DOI: 10.1007/978-3-030-80352-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?
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Affiliation(s)
- Cornelia M Hooper
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Ian R Castleden
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sandra K Tanz
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Sally V Grasso
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - A Harvey Millar
- The Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
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Hammond MJ, Nenarokova A, Butenko A, Zoltner M, Dobáková EL, Field MC, Lukeš J. A Uniquely Complex Mitochondrial Proteome from Euglena gracilis. Mol Biol Evol 2020; 37:2173-2191. [PMID: 32159766 PMCID: PMC7403612 DOI: 10.1093/molbev/msaa061] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Euglena gracilis is a metabolically flexible, photosynthetic, and adaptable free-living protist of considerable environmental importance and biotechnological value. By label-free liquid chromatography tandem mass spectrometry, a total of 1,786 proteins were identified from the E. gracilis purified mitochondria, representing one of the largest mitochondrial proteomes so far described. Despite this apparent complexity, protein machinery responsible for the extensive RNA editing, splicing, and processing in the sister clades diplonemids and kinetoplastids is absent. This strongly suggests that the complex mechanisms of mitochondrial gene expression in diplonemids and kinetoplastids occurred late in euglenozoan evolution, arising independently. By contrast, the alternative oxidase pathway and numerous ribosomal subunits presumed to be specific for parasitic trypanosomes are present in E. gracilis. We investigated the evolution of unexplored protein families, including import complexes, cristae formation proteins, and translation termination factors, as well as canonical and unique metabolic pathways. We additionally compare this mitoproteome with the transcriptome of Eutreptiella gymnastica, illuminating conserved features of Euglenida mitochondria as well as those exclusive to E. gracilis. This is the first mitochondrial proteome of a free-living protist from the Excavata and one of few available for protists as a whole. This study alters our views of the evolution of the mitochondrion and indicates early emergence of complexity within euglenozoan mitochondria, independent of parasitism.
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Affiliation(s)
- Michael J Hammond
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
| | - Anna Nenarokova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Anzhelika Butenko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Eva Lacová Dobáková
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
| | - Mark C Field
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Budweis, Czech Republic
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Nithya V. SubmitoLoc: Identification of mitochondrial sub cellular locations of proteins using support vector machine. Bioinformation 2019; 15:863-868. [PMID: 32256006 PMCID: PMC7088428 DOI: 10.6026/97320630015863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 11/23/2022] Open
Abstract
Mitochondria are important sub-cellular organelles in eukaryotes. Defects in mitochondrial system lead to a variety of disease. Therefore, detailed knowledge of mitochondrial proteome is vital to understand mitochondrial system and their function. Sequence databases contain large number of mitochondrial proteins but they are mostly not annotated. In this study, we developed a support vector machine approach, SubmitoLoc, to predict mitochondrial sub cellular locations of proteins based on various sequence derived properties. We evaluated the predictor using 10-fold cross validation. Our method achieved 88.56 % accuracy using all features. Average sensitivity and specificity for four-subclass prediction is 85.37% and 87.25% respectively. High prediction accuracy suggests that SubmitoLoc will be useful for researchers studying mitochondrial biology and drug discovery.
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Affiliation(s)
- Varadharaju Nithya
- Department of Animal Health Management, Alagappa University, Karaikudi-630003, India
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Abstract
Candida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolism. Mitochondria, which have a central metabolic role, have undergone many lineage-specific adaptations in association with their eukaryotic host. A screen for lineage-specific genes identified seven such genes specific to the CTG clade of fungi, of which C. albicans is a member. Each is required for respiratory growth and is integral to expression of complex I, III, or IV of the electron transport chain. Two genes, NUO3 and NUO4, encode supernumerary subunits of complex I, whereas NUE1 and NUE2 have nonstructural roles in expression of complex I. Similarly, the other three genes have nonstructural roles in expression of complex III (QCE1) or complex IV (COE1 and COE2). In addition to these novel additions, an alternative functional assignment was found for the mitochondrial protein encoded by MNE1 MNE1 was required for complex I expression in C. albicans, whereas the distantly related Saccharomyces cerevisiae ortholog participates in expression of complex III. Phenotypic analysis of deletion mutants showed that fermentative metabolism is unable to support optimal growth rates or yields of C. albicans However, yeast-hypha morphogenesis, an important virulence attribute, did not require respiratory metabolism under hypoxic conditions. The inability to respire also resulted in hypersensitivity to the antifungal fluconazole and in attenuated virulence in a Galleria mellonella infection model. The results show that lineage-specific adaptations have occurred in C. albicans mitochondria and highlight the significance of respiratory metabolism in the pathobiology of C. albicans IMPORTANCE Candida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolic behavior, and mitochondria have a central role in that metabolism. Mitochondria have undergone many evolutionary changes, which include lineage-specific adaptations in association with their eukaryotic host. Seven lineage-specific genes required for electron transport chain function were identified in the CTG clade of fungi, of which C. albicans is a member. Additionally, examination of several highly diverged orthologs encoding mitochondrial proteins demonstrated functional reassignment for one of these. Deficits imparted by deletion of these genes revealed the critical role of respiration in virulence attributes of the fungus and highlight important evolutionary adaptations in C. albicans metabolism.
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Mustafa G, Komatsu S. Insights into the Response of Soybean Mitochondrial Proteins to Various Sizes of Aluminum Oxide Nanoparticles under Flooding Stress. J Proteome Res 2016; 15:4464-4475. [PMID: 27780359 DOI: 10.1021/acs.jproteome.6b00572] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid developments in nanotechnology have led to the increasing use of nanoparticles (NPs) in the agricultural sector. For possible interactions between NPs and crops under flooding stress to be investigated, the molecular mechanisms in soybeans affected by exposure to various sizes of Al2O3 NPs were analyzed using a proteomic technique. In plants exposed to 30-60 nm Al2O3 NPs, the length of the root including hypocotyl was increased, and proteins related to glycolysis were suppressed. Exposure to 30-60 nm Al2O3 NPs mediated the scavenging activity of cells by regulating the ascorbate/glutathione pathway. Hierarchical clustering analysis indicated that ribosomal proteins were also increased upon exposure to flooding-stressed plants with 30-60 nm Al2O3 NPs. Mitochondrion was the target organelle of Al2O3 NPs under flooding-stress conditions. Mitochondrial proteomic analysis revealed that the abundance of voltage-dependent anion channel protein was increased upon exposure to flooding-stressed soybeans with 135 nm Al2O3 NPs, indicating the permeability of the mitochondrial membrane was increased. Furthermore, isocitrate dehydrogenase was increased upon exposure of plants to 5 nm Al2O3 NPs under flooding conditions. These results suggest that Al2O3 NPs of various sizes affect mitochondrial proteins under flooding stress by regulating membrane permeability and tricarboxylic acid cycle activity.
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Affiliation(s)
- Ghazala Mustafa
- Graduate School of Life and Environmental Science, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Science, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
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Gaona-López C, Julián-Sánchez A, Riveros-Rosas H. Diversity and Evolutionary Analysis of Iron-Containing (Type-III) Alcohol Dehydrogenases in Eukaryotes. PLoS One 2016; 11:e0166851. [PMID: 27893862 PMCID: PMC5125639 DOI: 10.1371/journal.pone.0166851] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/05/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alcohol dehydrogenase (ADH) activity is widely distributed in the three domains of life. Currently, there are three non-homologous NAD(P)+-dependent ADH families reported: Type I ADH comprises Zn-dependent ADHs; type II ADH comprises short-chain ADHs described first in Drosophila; and, type III ADH comprises iron-containing ADHs (FeADHs). These three families arose independently throughout evolution and possess different structures and mechanisms of reaction. While types I and II ADHs have been extensively studied, analyses about the evolution and diversity of (type III) FeADHs have not been published yet. Therefore in this work, a phylogenetic analysis of FeADHs was performed to get insights into the evolution of this protein family, as well as explore the diversity of FeADHs in eukaryotes. PRINCIPAL FINDINGS Results showed that FeADHs from eukaryotes are distributed in thirteen protein subfamilies, eight of them possessing protein sequences distributed in the three domains of life. Interestingly, none of these protein subfamilies possess protein sequences found simultaneously in animals, plants and fungi. Many FeADHs are activated by or contain Fe2+, but many others bind to a variety of metals, or even lack of metal cofactor. Animal FeADHs are found in just one protein subfamily, the hydroxyacid-oxoacid transhydrogenase (HOT) subfamily, which includes protein sequences widely distributed in fungi, but not in plants), and in several taxa from lower eukaryotes, bacteria and archaea. Fungi FeADHs are found mainly in two subfamilies: HOT and maleylacetate reductase (MAR), but some can be found also in other three different protein subfamilies. Plant FeADHs are found only in chlorophyta but not in higher plants, and are distributed in three different protein subfamilies. CONCLUSIONS/SIGNIFICANCE FeADHs are a diverse and ancient protein family that shares a common 3D scaffold with a patchy distribution in eukaryotes. The majority of sequenced FeADHs from eukaryotes are distributed in just two subfamilies, HOT and MAR (found mainly in animals and fungi). These two subfamilies comprise almost 85% of all sequenced FeADHs in eukaryotes.
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Affiliation(s)
- Carlos Gaona-López
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Adriana Julián-Sánchez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM). Cd. Universitaria, Ciudad de México, México
- * E-mail:
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Abstract
Apoptosis triggered by ricin toxin (RT) has previously been associated with certain cellular organellar compartments, but the diversity in the composition of the organellar proteins remains unclear. Here, we applied a shotgun proteomics strategy to examine the differential expression of proteins in the mitochondria, nuclei, and cytoplasm of HeLa cells treated and not treated with RT. Data were combined with a global bioinformatics analysis and experimental confirmations. A total of 3107 proteins were identified. Bioinformatics predictors (Proteome Analyst, WoLF PSORT, TargetP, MitoPred, Nucleo, MultiLoc, and k-nearest neighbor) and a Bayesian model that integrated these predictors were used to predict the locations of 1349 distinct organellar proteins. Our data indicate that the Bayesian model was more efficient than the individual implementation of these predictors. Additionally, a Biomolecular Interaction Network (BIN) analysis was used to identify 149 BIN subnetworks. Our experimental confirmations indicate that certain apoptosis-related proteins (e.g. cytochrome c, enolase, lamin B, Bax, and Drp1) were found to be translocated and had variable expression levels. These results provide new insights for the systematic understanding of RT-induced apoptosis responses.
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Affiliation(s)
- Peng Liao
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, People's Republic of China Institute of Military Veterinary Science, Academy of Military Medical Science, Changchun, Jilin Province, People's Republic of China
| | - Yunhu Li
- Hunan Biological and Electromechanical Polytechnic, The Party and Government Office, Changsha, Hunan Province, People's Republic of China
| | - Hongyang Li
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, People's Republic of China
| | - Wensen Liu
- Institute of Military Veterinary Science, Academy of Military Medical Science, Changchun, Jilin Province, People's Republic of China
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Kamal AHM, Komatsu S. Involvement of Reactive Oxygen Species and Mitochondrial Proteins in Biophoton Emission in Roots of Soybean Plants under Flooding Stress. J Proteome Res 2015; 14:2219-36. [PMID: 25806999 DOI: 10.1021/acs.jproteome.5b00007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To understand the mechanism of biophoton emission, ROS and mitochondrial proteins were analyzed in soybean plants under flooding stress. Enzyme activity and biophoton emission were increased in the flooding stress samples when assayed in reaction mixes specific for antioxidant enzymes and reactive oxygen species; although the level of the hydroxyl radicals was increased at day 4 (2 days of flooding) compared to nonflooding at day 4, the emission of biophotons did not change. Mitochondria were isolated and purified from the roots of soybean plants grown under flooding stress by using a Percoll gradient, and proteins were analyzed by a gel-free proteomic technique. Out of the 98 mitochondrial proteins that significantly changed abundance under flooding stress, 47 increased and 51 decreased at day 4. The mitochondrial enzymes fumarase, glutathione-S-transferase, and aldehyde dehydrogenase increased at day 4 in protein abundance and enzyme activity. Enzyme activity and biophoton emission decreased at day 4 by the assay of lipoxygenase under stress. Aconitase, acyl CoA oxidase, succinate dehydrogenase, and NADH ubiquinone dehydrogenase were up-regulated at the transcription level. These results indicate that oxidation and peroxide scavenging might lead to biophoton emission and oxidative damage in the roots of soybean plants under flooding stress.
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Affiliation(s)
- Abu Hena Mostafa Kamal
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan
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Negi S, Pandey S, Srinivasan SM, Mohammed A, Guda C. LocSigDB: a database of protein localization signals. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav003. [PMID: 25725059 PMCID: PMC4343182 DOI: 10.1093/database/bav003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/
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Affiliation(s)
- Simarjeet Negi
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sanjit Pandey
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Satish M Srinivasan
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Akram Mohammed
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA Department of Genetics, Cell Biology and Anatomy, Bioinformatics and Systems Biology Core, Department of Biochemistry and Molecular Biology, Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Ding H, Li D. Identification of mitochondrial proteins of malaria parasite using analysis of variance. Amino Acids 2014; 47:329-33. [DOI: 10.1007/s00726-014-1862-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
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Candat A, Paszkiewicz G, Neveu M, Gautier R, Logan DC, Avelange-Macherel MH, Macherel D. The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress. THE PLANT CELL 2014; 26:3148-66. [PMID: 25005920 PMCID: PMC4145138 DOI: 10.1105/tpc.114.127316] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress.
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Affiliation(s)
- Adrien Candat
- Université d'Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
| | - Gaël Paszkiewicz
- Université d'Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
| | - Martine Neveu
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
| | - Romain Gautier
- Institut de Pharmacologie Moléculaire et Cellulaire, Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7275, F-06560 Valbonne, France
| | - David C Logan
- Université d'Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
| | | | - David Macherel
- Université d'Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
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Pan R, Kaur N, Hu J. The Arabidopsis mitochondrial membrane-bound ubiquitin protease UBP27 contributes to mitochondrial morphogenesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:1047-59. [PMID: 24707813 DOI: 10.1111/tpj.12532] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 03/28/2014] [Accepted: 04/01/2014] [Indexed: 05/13/2023]
Abstract
Mitochondria are essential organelles with dynamic morphology and function. Post-translational modifications (PTMs), which include protein ubiquitination, are critically involved in animal and yeast mitochondrial dynamics. How PTMs contribute to plant mitochondrial dynamics is just beginning to be elucidated, and mitochondrial enzymes involved in ubiquitination have not been reported from plants. In this study, we identified an Arabidopsis mitochondrial localized ubiquitin protease, UBP27, through a screen that combined bioinformatics and fluorescent fusion protein targeting analysis. We characterized UBP27 with respect to its membrane topology and enzymatic activities, and analysed the mitochondrial morphological changes in UBP27T-DNA insertion mutants and overexpression lines. We have shown that UBP27 is embedded in the mitochondrial outer membrane with an Nin -Cout orientation and possesses ubiquitin protease activities in vitro. UBP27 demonstrates similar sub-cellular localization, domain structure, membrane topology and enzymatic activities with two mitochondrial deubiquitinases, yeast ScUBP16 and human HsUSP30, which indicated that these proteins are functional orthologues in eukaryotes. Although loss-of-function mutants of UBP27 do not show obvious phenotypes in plant growth and mitochondrial morphology, UBP27 overexpression can change mitochondrial morphology from rod to spherical shape and reduce the mitochondrial association of dynamin-related protein 3 (DRP3) proteins, large GTPases that serve as the main mitochondrial fission factors. Thus, our study has uncovered a plant ubiquitin protease that plays a role in mitochondrial morphogenesis possibly through modulation of the function of organelle division proteins.
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Affiliation(s)
- Ronghui Pan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
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Lim S, Smith K, Stroud D, Compton A, Tucker E, Dasvarma A, Gandolfo L, Marum J, McKenzie M, Peters H, Mowat D, Procopis P, Wilcken B, Christodoulou J, Brown G, Ryan M, Bahlo M, Thorburn D. A founder mutation in PET100 causes isolated complex IV deficiency in Lebanese individuals with Leigh syndrome. Am J Hum Genet 2014; 94:209-22. [PMID: 24462369 DOI: 10.1016/j.ajhg.2013.12.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/18/2013] [Indexed: 12/30/2022] Open
Abstract
Leigh syndrome (LS) is a severe neurodegenerative disorder with characteristic bilateral lesions, typically in the brainstem and basal ganglia. It usually presents in infancy and is genetically heterogeneous, but most individuals with mitochondrial complex IV (or cytochrome c oxidase) deficiency have mutations in the biogenesis factor SURF1. We studied eight complex IV-deficient LS individuals from six families of Lebanese origin. They differed from individuals with SURF1 mutations in having seizures as a prominent feature. Complementation analysis suggested they had mutation(s) in the same gene but targeted massively parallel sequencing (MPS) of 1,034 genes encoding known mitochondrial proteins failed to identify a likely candidate. Linkage and haplotype analyses mapped the location of the gene to chromosome 19 and targeted MPS of the linkage region identified a homozygous c.3G>C (p.Met1?) mutation in C19orf79. Abolishing the initiation codon could potentially still allow initiation at a downstream methionine residue but we showed that this would not result in a functional protein. We confirmed that mutation of this gene was causative by lentiviral-mediated phenotypic correction. C19orf79 was recently renamed PET100 and predicted to encode a complex IV biogenesis factor. We showed that it is located in the mitochondrial inner membrane and forms a ∼300 kDa subcomplex with complex IV subunits. Previous proteomic analyses of mitochondria had overlooked PET100 because its small size was below the cutoff for annotating bona fide proteins. The mutation was estimated to have arisen at least 520 years ago, explaining how the families could have different religions and different geographic origins within Lebanon.
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Liu L, Zhang Z, Mei Q, Chen M. PSI: a comprehensive and integrative approach for accurate plant subcellular localization prediction. PLoS One 2013; 8:e75826. [PMID: 24194827 PMCID: PMC3806775 DOI: 10.1371/journal.pone.0075826] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 08/19/2013] [Indexed: 12/03/2022] Open
Abstract
Predicting the subcellular localization of proteins conquers the major drawbacks of high-throughput localization experiments that are costly and time-consuming. However, current subcellular localization predictors are limited in scope and accuracy. In particular, most predictors perform well on certain locations or with certain data sets while poorly on others. Here, we present PSI, a novel high accuracy web server for plant subcellular localization prediction. PSI derives the wisdom of multiple specialized predictors via a joint-approach of group decision making strategy and machine learning methods to give an integrated best result. The overall accuracy obtained (up to 93.4%) was higher than best individual (CELLO) by ∼10.7%. The precision of each predicable subcellular location (more than 80%) far exceeds that of the individual predictors. It can also deal with multi-localization proteins. PSI is expected to be a powerful tool in protein location engineering as well as in plant sciences, while the strategy employed could be applied to other integrative problems. A user-friendly web server, PSI, has been developed for free access at http://bis.zju.edu.cn/psi/.
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Affiliation(s)
- Lili Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zijun Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qian Mei
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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15
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Manna S, Le P, Barth C. A unique mitochondrial transcription factor B protein in Dictyostelium discoideum. PLoS One 2013; 8:e70614. [PMID: 23923009 PMCID: PMC3724811 DOI: 10.1371/journal.pone.0070614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022] Open
Abstract
Unlike their bacteriophage homologs, mitochondrial RNA polymerases require the assistance of transcription factors in order to transcribe mitochondrial DNA efficiently. The transcription factor A family has been shown to be important for transcription of the human mitochondrial DNA, with some of its regulatory activity located in its extended C-terminal tail. The mitochondrial transcription factor B family often has functions not only in transcription, but also in mitochondrial rRNA modification, a hallmark of its α-proteobacterial origin. We have identified and characterised a mitochondrial transcription factor B homolog in the soil dwelling cellular slime mould Dictyostelium discoideum, an organism widely established as a model for studying eukaryotic cell biology. Using in bacterio functional assays, we demonstrate that the mitochondrial transcription factor B homolog not only functions as a mitochondrial transcription factor, but that it also has a role in rRNA methylation. Additionally, we show that the transcriptional activation properties of the D. discoideum protein are located in its extended C-terminal tail, a feature not seen before in the mitochondrial transcription factor B family, but reminiscent of the human mitochondrial transcription factor A. This report contributes to our current understanding of the complexities of mitochondrial transcription, and its evolution in eukaryotes.
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Affiliation(s)
- Sam Manna
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Phuong Le
- Tokyo Metropolitan University, Department of Biological Science, Tokyo, Japan
| | - Christian Barth
- Department of Microbiology, La Trobe University, Melbourne, Victoria, Australia
- * E-mail:
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16
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New putative chloroplast vesicle transport components and cargo proteins revealed using a bioinformatics approach: an Arabidopsis model. PLoS One 2013; 8:e59898. [PMID: 23573218 PMCID: PMC3613420 DOI: 10.1371/journal.pone.0059898] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/19/2013] [Indexed: 11/23/2022] Open
Abstract
Proteins and lipids are known to be transported to targeted cytosolic compartments in vesicles. A similar system in chloroplasts is suggested to transfer lipids from the inner envelope to the thylakoids. However, little is known about both possible cargo proteins and the proteins required to build a functional vesicle transport system in chloroplasts. A few components have been suggested, but only one (CPSAR1) has a verified location in chloroplast vesicles. This protein is localized in the donor membrane (envelope) and vesicles, but not in the target membrane (thylakoids) suggesting it plays a similar role to a cytosolic homologue, Sar1, in the secretory pathway. Thus, we hypothesized that there may be more similarities, in addition to lipid transport, between the vesicle transport systems in the cytosol and chloroplast, i.e. similar vesicle transport components, possible cargo proteins and receptors. Therefore, using a bioinformatics approach we searched for putative chloroplast components in the model plant Arabidopsis thaliana, corresponding mainly to components of the cytosolic vesicle transport system that may act in coordination with previously proposed COPII chloroplast homologues. We found several additional possible components, supporting the notion of a fully functional vesicle transport system in chloroplasts. Moreover, we found motifs in thylakoid-located proteins similar to those of COPII vesicle cargo proteins, supporting the hypothesis that chloroplast vesicles may transport thylakoid proteins from the envelope to the thylakoid membrane. Several putative cargo proteins are involved in photosynthesis, thus we propose the existence of a novel thylakoid protein pathway that is important for construction and maintenance of the photosynthetic machinery.
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17
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Rai A, Tzvetkov N, Manstein DJ. Functional dissection of the dictyostelium discoideum dynamin B mitochondrial targeting sequence. PLoS One 2013; 8:e56975. [PMID: 23437285 PMCID: PMC3578813 DOI: 10.1371/journal.pone.0056975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/16/2013] [Indexed: 12/05/2022] Open
Abstract
Most mitochondrial proteins are nuclear encoded and synthesized in the cytosol with an N-terminal mitochondrial targeting sequence or presequence for subsequent import into mitochondria. Here, we describe the proteolytic processing and inner membrane potential-dependent translocation of a dynamin family member by the Dictyostelium discoideum mitochondrial import system. Our results show that the unusual D. discoideum dynamin B presequence is removed through a processing mechanism that is common for mitochondrial matrix proteins. We identified a minimal segment of the dynamin B presequence containing seven lysine residues. This 47-residue region is, in combination with consensus matrix protease cleavage sites, necessary and sufficient for mitochondrial targeting. The correct positioning of these lysine residues plays a critical role for the proper processing and mitochondrial import of dynamin B in D. discoideum. Fluorescent proteins tagged with the dynamin B presequence or presequence regions supporting mitochondrial import in D. discoideum are imported with similar efficiency into the mitochondrial matrix of mammalian cells, indicating that the basic mechanisms underlying mitochondrial protein import are highly conserved from amoebozoa to mammalia.
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Affiliation(s)
- Amrita Rai
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Nikolay Tzvetkov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Dietmar J. Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
- * E-mail:
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18
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Zhang X, Shen Y, Ding G, Tian Y, Liu Z, Li B, Wang Y, Jiang C. TFPP: an SVM-based tool for recognizing flagellar proteins in Trypanosoma brucei. PLoS One 2013; 8:e54032. [PMID: 23349782 PMCID: PMC3547966 DOI: 10.1371/journal.pone.0054032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/07/2012] [Indexed: 11/18/2022] Open
Abstract
Trypanosoma brucei is a unicellular flagellated eukaryotic parasite that causes African trypanosomiasis in human and domestic animals with devastating health and economic consequences. Recent studies have revealed the important roles of the single flagellum of T. brucei in many aspects, especially that the flagellar motility is required for the viability of the bloodstream form T. brucei, suggesting that impairment of the flagellar function may provide a promising cure for African sleeping sickness. Knowing the flagellum proteome is crucial to study the molecular mechanism of the flagellar functions. Here we present a novel computational method for identifying flagellar proteins in T. brucei, called trypanosome flagellar protein predictor (TFPP). TFPP was developed based on a list of selected discriminating features derived from protein sequences, and could predict flagellar proteins with ∼92% specificity at a ∼84% sensitivity rate. Applied to the whole T. brucei proteome, TFPP reveals 811 more flagellar proteins with high confidence, suggesting that the flagellar proteome covers ∼10% of the whole proteome. Comparison of the expression profiles of the whole T. brucei proteome at three typical life cycle stages found that ∼45% of the flagellar proteins were significantly changed in expression levels between the three life cycle stages, indicating life cycle stage-specific regulation of flagellar functions in T. brucei. Overall, our study demonstrated that TFPP is highly effective in identifying flagellar proteins and could provide opportunities to study the trypanosome flagellar proteome systematically. Furthermore, the web server for TFPP can be freely accessed at http:/wukong.tongji.edu.cn/tfpp.
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Affiliation(s)
- Xiaobai Zhang
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail: (XZ); (CJ)
| | - Yuefeng Shen
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guitao Ding
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yi Tian
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhenping Liu
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Bing Li
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yun Wang
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Cizhong Jiang
- Department of Bioinformatics, the School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail: (XZ); (CJ)
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19
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Wojtovich AP, Smith CO, Haynes CM, Nehrke KW, Brookes PS. Physiological consequences of complex II inhibition for aging, disease, and the mKATP channel. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:598-611. [PMID: 23291191 DOI: 10.1016/j.bbabio.2012.12.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 12/14/2012] [Accepted: 12/17/2012] [Indexed: 12/21/2022]
Abstract
In recent years, it has become apparent that there exist several roles for respiratory complex II beyond metabolism. These include: (i) succinate signaling, (ii) reactive oxygen species (ROS) generation, (iii) ischemic preconditioning, (iv) various disease states and aging, and (v) a role in the function of the mitochondrial ATP-sensitive K(+) (mKATP) channel. This review will address the involvement of complex II in each of these areas, with a focus on how complex II regulates or may be involved in the assembly of the mKATP. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Andrew P Wojtovich
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
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20
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Tanz SK, Castleden I, Hooper CM, Vacher M, Small I, Millar HA. SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. Nucleic Acids Res 2013; 41:D1185-91. [PMID: 23180787 PMCID: PMC3531127 DOI: 10.1093/nar/gks1151] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 12/27/2022] Open
Abstract
The subcellular location database for Arabidopsis proteins (SUBA3, http://suba.plantenergy.uwa.edu.au) combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization and protein-protein interaction (PPI) datasets with subcellular targeting calls from 22 prediction programs. More than 14 500 new experimental locations have been added since its first release in 2007. Overall, nearly 650 000 new calls of subcellular location for 35 388 non-redundant Arabidopsis proteins are included (almost six times the information in the previous SUBA version). A re-designed interface makes the SUBA3 site more intuitive and easier to use than earlier versions and provides powerful options to search for PPIs within the context of cell compartmentation. SUBA3 also includes detailed localization information for reference organelle datasets and incorporates green fluorescent protein (GFP) images for many proteins. To determine as objectively as possible where a particular protein is located, we have developed SUBAcon, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein's location in the cell. The probabilities of subcellular location for each protein are provided and displayed as a pictographic heat map of a plant cell in SUBA3.
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Affiliation(s)
- Sandra K. Tanz
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Ian Castleden
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Cornelia M. Hooper
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Michael Vacher
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Ian Small
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
| | - Harvey A. Millar
- Centre of Excellence in Computational Systems Biology, ARC Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis on Biomolecular Networks (CABiN), The University of Western Australia, Perth, WA 6009, Australia
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21
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Abstract
The central dogma states that DNA is transcribed to generate RNA and that the mRNA components are then translated to generate proteins; a simple statement that completely belies the complexities of gene expression. Post-transcriptional regulation alone has many points of control, including changes in the stability, translatability or susceptibility to degradation of RNA species, where both cis- and trans-acting elements will play a role in the outcome. The present review concentrates on just one aspect of this complicated process, which ultimately regulates the protein production in cells, or more specifically what governs RNA catabolism in a particular subcompartment of human cells: the mitochondrion.
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22
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The human MSH5 (MutS Homolog 5) protein localizes to mitochondria and protects the mitochondrial genome from oxidative damage. Mitochondrion 2012; 12:654-65. [DOI: 10.1016/j.mito.2012.07.111] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 07/14/2012] [Accepted: 07/20/2012] [Indexed: 01/07/2023]
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23
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Mackiewicz P, Bodył A, Gagat P. Possible import routes of proteins into the cyanobacterial endosymbionts/plastids of Paulinella chromatophora. Theory Biosci 2011; 131:1-18. [PMID: 22209953 PMCID: PMC3334493 DOI: 10.1007/s12064-011-0147-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 12/13/2011] [Indexed: 01/13/2023]
Abstract
The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active and deeply integrated cyanobacterial endosymbionts acquired ~60 million years ago. Recent genomic analyses of P. chromatophora have revealed the loss of many essential genes from the endosymbiont's genome, and have identified more than 30 genes that have been transferred to the host cell's nucleus through endosymbiotic gene transfer (EGT). This indicates that, similar to classical primary plastids, Paulinella endosymbionts have evolved a transport system to import their nuclear-encoded proteins. To deduce how these proteins are transported, we searched for potential targeting signals in genes for 10 EGT-derived proteins. Our analyses indicate that five proteins carry potential signal peptides, implying they are targeted via the host endomembrane system. One sequence encodes a mitochondrial-like transit peptide, which suggests an import pathway involving a channel protein residing in the outer membrane of the endosymbiont. No N-terminal targeting signals were identified in the four other genes, but their encoded proteins could utilize non-classical targeting signals contained internally or in C-terminal regions. Several amino acids more often found in the Paulinella EGT-derived proteins than in their ancestral set (proteins still encoded in the endosymbiont genome) could constitute such signals. Characteristic features of the EGT-derived proteins are low molecular weight and nearly neutral charge, which both could be adaptations to enhance passage through the peptidoglycan wall present in the intermembrane space of the endosymbiont's envelope. Our results suggest that Paulinella endosymbionts/plastids have evolved several different import routes, as has been shown in classical primary plastids.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, ul. Przybyszewskiego 63/77, 51-148 Wrocław, Poland.
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24
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Szabò I, Leanza L, Gulbins E, Zoratti M. Physiology of potassium channels in the inner membrane of mitochondria. Pflugers Arch 2011; 463:231-46. [PMID: 22089812 DOI: 10.1007/s00424-011-1058-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 10/30/2011] [Indexed: 02/06/2023]
Abstract
The inner membrane of the ATP-producing organelles of endosymbiotic origin, mitochondria, has long been considered to be poorly permeable to cations and anions, since the strict control of inner mitochondrial membrane permeability is crucial for efficient ATP synthesis. Over the past 30 years, however, it has become clear that various ion channels--along with antiporters and uniporters--are present in the mitochondrial inner membrane, although at rather low abundance. These channels are important for energy supply, and some are a decisive factor in determining whether a cell lives or dies. Their electrophysiological and pharmacological characterisations have contributed importantly to the ongoing elucidation of their pathophysiological roles. This review gives an overview of recent advances in our understanding of the functions of the mitochondrial potassium channels identified so far. Open issues concerning the possible molecular entities giving rise to the observed activities and channel protein targeting to mitochondria are also discussed.
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Affiliation(s)
- Ildikò Szabò
- Department of Biology, University of Padova, Padova, Italy.
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25
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Identification of a de novo thymidylate biosynthesis pathway in mammalian mitochondria. Proc Natl Acad Sci U S A 2011; 108:15163-8. [PMID: 21876188 DOI: 10.1073/pnas.1103623108] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The de novo and salvage dTTP pathways are essential for maintaining cellular dTTP pools to ensure the faithful replication of both mitochondrial and nuclear DNA. Disregulation of dTTP pools results in mitochondrial dysfunction and nuclear genome instability due to an increase in uracil misincorporation. In this study, we identified a de novo dTMP synthesis pathway in mammalian mitochondria. Mitochondria purified from wild-type Chinese hamster ovary (CHO) cells and HepG2 cells converted dUMP to dTMP in the presence of NADPH and serine, through the activities of mitochondrial serine hydroxymethyltransferase (SHMT2), thymidylate synthase (TYMS), and a novel human mitochondrial dihydrofolate reductase (DHFR) previously thought to be a pseudogene known as dihydrofolate reductase-like protein 1 (DHFRL1). Human DHFRL1, SHMT2, and TYMS were localized to mitochondrial matrix and inner membrane, confirming the presence of this pathway in mitochondria. Knockdown of DHFRL1 using siRNA eliminated DHFR activity in mitochondria. DHFRL1 expression in CHO glyC, a previously uncharacterized mutant glycine auxotrophic cell line, rescued the glycine auxotrophy. De novo thymidylate synthesis activity was diminished in mitochondria isolated from glyA CHO cells that lack SHMT2 activity, as well as mitochondria isolated from wild-type CHO cells treated with methotrexate, a DHFR inhibitor. De novo thymidylate synthesis in mitochondria prevents uracil accumulation in mitochondrial DNA (mtDNA), as uracil levels in mtDNA isolated from glyA CHO cells was 40% higher than observed in mtDNA isolated from wild-type CHO cells. These data indicate that unlike other nucleotides, de novo dTMP synthesis occurs within mitochondria and is essential for mtDNA integrity.
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26
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Delage L, Leblanc C, Nyvall Collén P, Gschloessl B, Oudot MP, Sterck L, Poulain J, Aury JM, Cock JM. In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus. PLoS One 2011; 6:e19540. [PMID: 21611166 PMCID: PMC3097184 DOI: 10.1371/journal.pone.0019540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/31/2011] [Indexed: 01/24/2023] Open
Abstract
The acquisition of mitochondria was a key event in eukaryote evolution. The aim of this study was to identify homologues of the components of the mitochondrial protein import machinery in the brown alga Ectocarpus and to use this information to investigate the evolutionary history of this fundamental cellular process. Detailed searches were carried out both for components of the protein import system and for related peptidases. Comparative and phylogenetic analyses were used to investigate the evolution of mitochondrial proteins during eukaryote diversification. Key observations include phylogenetic evidence for very ancient origins for many protein import components (Tim21, Tim50, for example) and indications of differences between the outer membrane receptors that recognize the mitochondrial targeting signals, suggesting replacement, rearrangement and/or emergence of new components across the major eukaryotic lineages. Overall, the mitochondrial protein import components analysed in this study confirmed a high level of conservation during evolution, indicating that most are derived from very ancient, ancestral proteins. Several of the protein import components identified in Ectocarpus, such as Tim21, Tim50 and metaxin, have also been found in other stramenopiles and this study suggests an early origin during the evolution of the eukaryotes.
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Affiliation(s)
- Ludovic Delage
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Catherine Leblanc
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Pi Nyvall Collén
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Bernhard Gschloessl
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
| | - Marie-Pierre Oudot
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lieven Sterck
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Julie Poulain
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, Evry, France
- Centre National de la Recherche Scientifique, UMR 8030, Evry, France
- Université d'Evry, Evry, France
| | - J. Mark Cock
- Université Pierre et Marie Curie, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Roscoff, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Roscoff, France
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27
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Hernández-Tobías A, Julián-Sánchez A, Piña E, Riveros-Rosas H. Natural alcohol exposure: Is ethanol the main substrate for alcohol dehydrogenases in animals? Chem Biol Interact 2011; 191:14-25. [DOI: 10.1016/j.cbi.2011.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 01/30/2023]
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28
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Low JSW, Tao Q, Ng KM, Goh HK, Shu XS, Woo WL, Ambinder RF, Srivastava G, Shamay M, Chan ATC, Popescu NC, Hsieh WS. A novel isoform of the 8p22 tumor suppressor gene DLC1 suppresses tumor growth and is frequently silenced in multiple common tumors. Oncogene 2011; 30:1923-35. [PMID: 21217778 PMCID: PMC3385516 DOI: 10.1038/onc.2010.576] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 11/15/2010] [Accepted: 11/15/2010] [Indexed: 12/18/2022]
Abstract
The critical 8p22 tumor suppressor deleted in liver cancer 1 (DLC1) is frequently inactivated by aberrant CpG methylation and/or genetic deletion and implicated in tumorigeneses of multiple tumor types. Here, we report the identification and characterization of its new isoform, DLC1 isoform 4 (DLC1-i4). This novel isoform encodes an 1125-aa (amino acid) protein with distinct N-terminus as compared with other known DLC1 isoforms. Similar to other isoforms, DLC1-i4 is expressed ubiquitously in normal tissues and immortalized normal epithelial cells, suggesting a role as a major DLC1 transcript. However, differential expression of the four DLC1 isoforms is found in tumor cell lines: Isoform 1 (longest) and 3 (short thus probably nonfunctional) share a promoter and are silenced in almost all cancer and immortalized cell lines, whereas isoform 2 and 4 utilize different promoters and are frequently downregulated. DLC1-i4 is significantly downregulated in multiple carcinoma cell lines, including 2/4 nasopharyngeal, 8/16 (50%) esophageal, 4/16 (25%) gastric, 6/9 (67%) breast, 3/4 colorectal, 4/4 cervical and 2/8(25%) lung carcinoma cell lines. The functional DLC1-i4 promoter is within a CpG island and is activated by wild-type p53. CpG methylation of the DLC1-i4 promoter is associated with its silencing in tumor cells and was detected in 38-100% of multiple primary tumors. Treatment with 5-aza-2'-deoxycytidine or genetic double knockout of DNMT1 and DNMT3B led to demethylation of the promoter and reactivation of its expression, indicating a predominantly epigenetic mechanism of silencing. Ectopic expression of DLC1-i4 in silenced tumor cells strongly inhibited their growth and colony formation. Thus, we identified a new isoform of DLC1 with tumor suppressive function. The differential expression of various DLC1 isoforms suggests interplay in modulating the complex activities of DLC1 during carcinogenesis.
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Affiliation(s)
- JSW Low
- Division of Biomedical Sciences, Johns Hopkins Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Q Tao
- Division of Biomedical Sciences, Johns Hopkins Singapore, Singapore
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Cancer Epigenetics Laboratory, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - KM Ng
- Cancer Epigenetics Laboratory, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - HK Goh
- Division of Biomedical Sciences, Johns Hopkins Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - X-S Shu
- Cancer Epigenetics Laboratory, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - WL Woo
- Division of Biomedical Sciences, Johns Hopkins Singapore, Singapore
| | - RF Ambinder
- Division of Biomedical Sciences, Johns Hopkins Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - G Srivastava
- Department of Pathology, University of Hong Kong, Hong Kong
| | - M Shamay
- Division of Biomedical Sciences, Johns Hopkins Singapore, Singapore
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - ATC Chan
- Cancer Epigenetics Laboratory, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - NC Popescu
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - W-S Hsieh
- Division of Biomedical Sciences, Johns Hopkins Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Jia C, Liu T, Chang AK, Zhai Y. Prediction of mitochondrial proteins of malaria parasite using bi-profile Bayes feature extraction. Biochimie 2011; 93:778-82. [DOI: 10.1016/j.biochi.2011.01.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 01/22/2011] [Indexed: 11/26/2022]
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30
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Panwar B, Raghava GPS. Predicting sub-cellular localization of tRNA synthetases from their primary structures. Amino Acids 2011; 42:1703-13. [DOI: 10.1007/s00726-011-0872-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 02/21/2011] [Indexed: 11/25/2022]
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31
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Lee YH, Tan HT, Chung MCM. Subcellular fractionation methods and strategies for proteomics. Proteomics 2010; 10:3935-56. [DOI: 10.1002/pmic.201000289] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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32
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Zhang X, Cui J, Nilsson D, Gunasekera K, Chanfon A, Song X, Wang H, Xu Y, Ochsenreiter T. The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development. Nucleic Acids Res 2010; 38:7378-87. [PMID: 20660476 PMCID: PMC2995047 DOI: 10.1093/nar/gkq618] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
It has long been known that trypanosomes regulate mitochondrial biogenesis during the life cycle of the parasite; however, the mitochondrial protein inventory (MitoCarta) and its regulation remain unknown. We present a novel computational method for genome-wide prediction of mitochondrial proteins using a support vector machine-based classifier with ∼90% prediction accuracy. Using this method, we predicted the mitochondrial localization of 468 proteins with high confidence and have experimentally verified the localization of a subset of these proteins. We then applied a recently developed parallel sequencing technology to determine the expression profiles and the splicing patterns of a total of 1065 predicted MitoCarta transcripts during the development of the parasite, and showed that 435 of the transcripts significantly changed their expressions while 630 remain unchanged in any of the three life stages analyzed. Furthermore, we identified 298 alternatively splicing events, a small subset of which could lead to dual localization of the corresponding proteins.
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Affiliation(s)
- Xiaobai Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, Jiangsu 210016 China
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33
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Haselier A, Akbari H, Weth A, Baumgartner W, Frentzen M. Two closely related genes of Arabidopsis encode plastidial cytidinediphosphate diacylglycerol synthases essential for photoautotrophic growth. PLANT PHYSIOLOGY 2010; 153:1372-84. [PMID: 20442275 PMCID: PMC2899908 DOI: 10.1104/pp.110.156422] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 05/01/2010] [Indexed: 05/23/2023]
Abstract
Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the formation of cytidinediphosphate diacylglycerol, an essential precursor of anionic phosphoglycerolipids like phosphatidylglycerol or -inositol. In plant cells, CDS isozymes are located in plastids, mitochondria, and microsomes. Here, we show that these isozymes are encoded by five genes in Arabidopsis (Arabidopsis thaliana). Alternative translation initiation or alternative splicing of CDS2 and CDS4 transcripts can result in up to 10 isoforms. Most of the cDNAs encoding the various plant isoforms were functionally expressed in yeast and rescued the nonviable phenotype of the mutant strain lacking CDS activity. The closely related genes CDS4 and CDS5 were found to encode plastidial isozymes with similar catalytic properties. Inactivation of both genes was required to obtain Arabidopsis mutant lines with a visible phenotype, suggesting that the genes have redundant functions. Analysis of these Arabidopsis mutants provided further independent evidence for the importance of plastidial phosphatidylglycerol for structure and function of thylakoid membranes and, hence, for photoautotrophic growth.
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Affiliation(s)
- André Haselier
- Unit of Botany, Institute for Biology I , Rheinisch-Westfälische Technische Hochschule Aachen University, 52056 Aachen, Germany.
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34
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Chang HW, Chuang LY, Cheng YH, Gu DL, Huang HW, Yang CH. An introduction to mitochondrial informatics. Methods Mol Biol 2010; 628:259-74. [PMID: 20238086 DOI: 10.1007/978-1-60327-367-1_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this chapter, we review the public resources available for human mitochondrial DNA and protein related bioinformatics, with a special focus on mitochondrial single nucleotide polymorphisms (mtSNPs). We also review our own freeware tool V-MitoSNP, giving an overview of its implementation and program workflow. Apart from these, we review several protocols for the graphic input of genes, keywords, gene searching by sequence, mtSNP searching by sequence, restriction enzyme mining, primer design, and virtual electrophoresis for PCR-RFLP genotyping. Some databases with similar function are integrated and compared.
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Affiliation(s)
- Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, Center of Excellence for Environmental Medicine, Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
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35
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Wojtovich AP, Williams DM, Karcz MK, Lopes CMB, Gray DA, Nehrke KW, Brookes PS. A novel mitochondrial K(ATP) channel assay. Circ Res 2010; 106:1190-6. [PMID: 20185796 DOI: 10.1161/circresaha.109.215400] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE The mitochondrial ATP sensitive potassium channel (mK(ATP)) is implicated in cardioprotection by ischemic preconditioning (IPC), but the molecular identity of the channel remains controversial. The validity of current methods to assay mK(ATP) activity is disputed. OBJECTIVE We sought to develop novel methods to assay mK(ATP) activity and its regulation. METHODS AND RESULTS Using a thallium (Tl(+))-sensitive fluorophore, we developed a novel Tl(+) flux based assay for mK(ATP) activity, and used this assay probe several aspects of mK(ATP) function. The following key observations were made. (1) Time-dependent run down of mK(ATP) activity was reversed by phosphatidylinositol-4,5-bisphosphate (PIP(2)). (2) Dose responses of mK(ATP) to nucleotides revealed a UDP EC(50) of approximately 20 micromol/L and an ATP IC(50) of approximately 5 micromol/L. (3) The antidepressant fluoxetine (Prozac) inhibited mK(ATP) (IC(50)=2.4 micromol/L). Fluoxetine also blocked cardioprotection triggered by IPC, but did not block protection triggered by a mK(ATP)-independent stimulus. The related antidepressant zimelidine was without effect on either mK(ATP) or IPC. CONCLUSIONS The Tl(+) flux mK(ATP) assay was validated by correlation with a classical mK(ATP) channel osmotic swelling assay (R(2)=0.855). The pharmacological profile of mK(ATP) (response to ATP, UDP, PIP(2), and fluoxetine) is consistent with that of an inward rectifying K(+) channel (K(IR)) and is somewhat closer to that of the K(IR)6.2 than the K(IR)6.1 isoform. The effect of fluoxetine on mK(ATP)-dependent cardioprotection has implications for the growing use of antidepressants in patients who may benefit from preconditioning.
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Affiliation(s)
- Andrew P Wojtovich
- Department of Pharmacology, University of Rochester Medical Center, 601 Elmwood Ave, Rochester, NY 14642, USA
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36
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Park S, Yang JS, Jang SK, Kim S. Construction of functional interaction networks through consensus localization predictions of the human proteome. J Proteome Res 2009; 8:3367-76. [PMID: 19415893 DOI: 10.1021/pr900018z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Characterizing the subcellular localization of a protein provides a key clue for understanding protein function. However, different protein localization prediction programs often deliver conflicting results regarding the localization of the same protein. As the number of available localization prediction programs continues to grow, there is a need for a consensus prediction approach. To address this need, we developed a consensus localization prediction method called ConLoc based on a large-scale, systematic integration of 13 available programs that make predictions for five major subcellular localizations (cytosol, extracellular, mitochondria, nucleus, and plasma membrane). The ability of ConLoc to accurately predict protein localization was substantially better than existing programs. Using ConLoc prediction, we built a localization-guided functional interaction network of the human proteome and mapped known disease associations within this network. We found a high degree of shared disease associations among functionally interacting proteins that are localized to the same cellular compartment. Thus, the use of consensus localization prediction, such as ConLoc, is a new approach for the identification of novel disease associated genes.
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Affiliation(s)
- Solip Park
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 790-784, Korea
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37
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Desler C, Suravajhala P, Sanderhoff M, Rasmussen M, Rasmussen LJ. In Silico screening for functional candidates amongst hypothetical proteins. BMC Bioinformatics 2009; 10:289. [PMID: 19754976 PMCID: PMC2758874 DOI: 10.1186/1471-2105-10-289] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 09/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The definition of a hypothetical protein is a protein that is predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation. Hypothetical proteins constitute a substantial fraction of proteomes of human as well as of other eukaryotes. With the general belief that the majority of hypothetical proteins are the product of pseudogenes, it is essential to have a tool with the ability of pinpointing the minority of hypothetical proteins with a high probability of being expressed. RESULTS Here, we present an in silico selection strategy where eukaryotic hypothetical proteins are sorted according to two criteria that can be reliably identified in silico: the presence of subcellular targeting signals and presence of characterized protein domains. To validate the selection strategy we applied it on a database of human hypothetical proteins dating to 2006 and compared the proteins predicted to be expressed by our selecting strategy, with their status in 2008. For the comparison we focused on mitochondrial proteins, since considerable amounts of research have focused on this field in between 2006 and 2008. Therefore, many proteins, defined as hypothetical in 2006, have later been characterized as mitochondrial. CONCLUSION Among the total amount of human proteins hypothetical in 2006, 21% have later been experimentally characterized and 6% of those have been shown to have a role in a mitochondrial context. In contrast, among the selected hypothetical proteins from the 2006 dataset, predicted by our strategy to have a mitochondrial role, 53-62% have later been experimentally characterized, and 85% of these have actually been assigned a role in mitochondria by 2008.Therefore our in silico selection strategy can be used to select the most promising candidates for subsequent in vitro and in vivo analyses.
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Affiliation(s)
- Claus Desler
- Department of Science, Systems and Models, Roskilde University, DK-4000 Roskilde, Denmark.
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38
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Li J, Cai T, Wu P, Cui Z, Chen X, Hou J, Xie Z, Xue P, Shi L, Liu P, Yates JR, Yang F. Proteomic analysis of mitochondria from Caenorhabditis elegans. Proteomics 2009; 9:4539-53. [DOI: 10.1002/pmic.200900101] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Lefort N, Yi Z, Bowen B, Glancy B, De Filippis EA, Mapes R, Hwang H, Flynn CR, Willis WT, Civitarese A, Højlund K, Mandarino LJ. Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS. J Proteomics 2009; 72:1046-60. [PMID: 19567276 DOI: 10.1016/j.jprot.2009.06.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 06/12/2009] [Accepted: 06/20/2009] [Indexed: 10/20/2022]
Abstract
Mitochondria can be isolated from skeletal muscle in a manner that preserves tightly coupled bioenergetic function in vitro. The purpose of this study was to characterize the composition of such preparations using a proteomics approach. Mitochondria isolated from human vastus lateralis biopsies were functional as evidenced by their response to carbohydrate and fat-derived fuels. Using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS, 823 unique proteins were detected, and 487 of these were assigned to the mitochondrion, including the newly characterized SIRT5, MitoNEET and RDH13. Proteins detected included 9 of the 13 mitochondrial DNA-encoded proteins and 86 of 104 electron transport chain (ETC) and ETC-related proteins. In addition, 59 of 78 proteins of the 55S mitoribosome, several TIM and TOM proteins and cell death proteins were present. This study presents an efficient method for future qualitative assessments of proteins from functional isolated mitochondria from small samples of healthy and diseased skeletal muscle.
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Affiliation(s)
- Natalie Lefort
- Center for Metabolic Biology, Arizona State University, Tempe, AZ, USA
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40
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HSPB7 is a SC35 speckle resident small heat shock protein. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1793:1343-53. [PMID: 19464326 DOI: 10.1016/j.bbamcr.2009.05.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 05/13/2009] [Accepted: 05/15/2009] [Indexed: 01/15/2023]
Abstract
BACKGROUND The HSPB family is one of the more diverse families within the group of HSP families. Some members have chaperone-like activities and/or play a role in cytoskeletal stabilization. Some members also show a dynamic, stress-induced translocation to SC35 splicing speckles. If and how these features are interrelated and if they are shared by all members are yet unknown. METHODS Tissue expression data and interaction and co-regulated gene expression data of the human HSPB members was analyzed using bioinformatics. Using a gene expression library, sub-cellular distribution of the diverse members was analyzed by confocal microscopy. Chaperone activity was measured using a cellular luciferase refolding assay. RESULTS Online databases did not accurately predict the sub-cellular distribution of all the HSPB members. A novel and non-predicted finding was that HSPB7 constitutively localized to SC35 splicing speckles, driven by its N-terminus. Unlike HSPB1 and HSPB5, that chaperoned heat unfolded substrates and kept them folding competent, HSPB7 did not support refolding. CONCLUSION Our data suggest a non-chaperone-like role of HSPB7 at SC35 speckles. GENERAL SIGNIFICANCE The functional divergence between HSPB members seems larger than previously expected and also includes non-canonical members lacking classical chaperone-like functions.
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Miyakawa I, Okamuro A, Kinsky S, Visacka K, Tomaska L, Nosek J. Mitochondrial nucleoids from the yeast Candida parapsilosis: expansion of the repertoire of proteins associated with mitochondrial DNA. MICROBIOLOGY-SGM 2009; 155:1558-1568. [PMID: 19383705 DOI: 10.1099/mic.0.027474-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecules of mitochondrial DNA (mtDNA) are packed into nucleic acid-protein complexes termed mitochondrial nucleoids (mt-nucleoids). In this study, we analysed mt-nucleoids of the yeast Candida parapsilosis, which harbours a linear form of the mitochondrial genome. To identify conserved as well as specific features of mt-nucleoids in this species, we employed two strategies for analysis of their components. First, we investigated the protein composition of mt-nucleoids isolated from C. parapsilosis mitochondria, determined N-terminal amino acid sequences of 14 proteins associated with the mt-nucleoids and identified corresponding genes. Next, we complemented the list of mt-nucleoid components with additional candidates identified in the complete genome sequence of C. parapsilosis as homologues of Saccharomyces cerevisiae mt-nucleoid proteins. Our approach revealed several known mt-nucleoid proteins as well as additional components that expand the repertoire of proteins associated with these cytological structures. In particular, we identified and purified the protein Gcf1, which is abundant in the mt-nucleoids and exhibits structural features in common with the mtDNA packaging protein Abf2 from S. cerevisiae. We demonstrate that Gcf1p co-localizes with mtDNA, has DNA-binding activity in vitro, and is able to stabilize mtDNA in the S. cerevisiae Deltaabf2 mutant, all of which points to a role in the maintenance of the C. parapsilosis mitochondrial genome. Importantly, in contrast to Abf2p, in silico analysis of Gcf1p predicted the presence of a coiled-coil domain and a single high-mobility group (HMG) box, suggesting that it represents a novel type of mitochondrial HMG protein.
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Affiliation(s)
- Isamu Miyakawa
- Department of Physics, Biology, and Informatics, Faculty of Science, Yamaguchi University, Yamaguchi 753-8512, Japan
| | - Akira Okamuro
- Department of Physics, Biology, and Informatics, Faculty of Science, Yamaguchi University, Yamaguchi 753-8512, Japan
| | - Slavomir Kinsky
- Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Katarina Visacka
- Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Lubomir Tomaska
- Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
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Zeng YH, Guo YZ, Xiao RQ, Yang L, Yu LZ, Li ML. Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach. J Theor Biol 2009; 259:366-72. [PMID: 19341746 DOI: 10.1016/j.jtbi.2009.03.028] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2008] [Revised: 02/25/2009] [Accepted: 03/13/2009] [Indexed: 12/20/2022]
Abstract
The submitochondria location of a mitochondrial protein is very important for further understanding the structure and function of this protein. Hence, it is of great practical significance to develop an automated and reliable method for timely identifying the submitochondria locations of novel mitochondrial proteins. In this study, a sequence-based algorithm combining the augmented Chou's pseudo amino acid composition (Chou's PseAA) based on auto covariance (AC) is developed to predict protein submitochondria locations and membrane protein types in mitochondria inner membrane. The model fully considers the sequence-order effects between residues a certain distance apart in the sequence by AC combined with eight representative descriptors for both common proteins and membrane proteins. As a result of jackknife cross-validation tests, the method for submitochondria location prediction yields the accuracies of 91.8%, 96.4% and 66.1% for inner membrane, matrix, and outer membrane, respectively. The total accuracy is 89.7%. When predicting membrane protein types in mitochondria inner membrane, the method achieves the prediction performance with the accuracies of 98.4%, 64.3% and 86.7% for multi-pass inner membrane, single-pass inner membrane, and matrix side inner membrane, where the total accuracy is 93.6%. The overall performance of our method is better than the achievements of the previous studies. So our method can be an effective supplementary tool for future proteomics studies. The prediction software and all data sets used in this article are freely available at http://chemlab.scu.edu.cn/Predict_subMITO/index.htm.
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Affiliation(s)
- Yu-hong Zeng
- College of Chemistry, Sichuan University, Chengdu 610064, PR China.
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Gaston D, Tsaousis AD, Roger AJ. Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data. Methods Enzymol 2009; 457:21-47. [PMID: 19426860 DOI: 10.1016/s0076-6879(09)05002-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In eukaryotes, determination of the subcellular location of a novel protein encoded in genomic or transcriptomic data provides useful clues as to its possible function. However, experimental localization studies are expensive and time-consuming. As a result, accurate in silico prediction of subcellular localization from sequence data alone is an extremely important field of study in bioinformatics. This is especially so as genomic studies expand beyond model system organisms to encompass the full diversity of eukaryotes. Here we review some of the more commonly used programs for prediction of proteins that function in mitochondria, or mitochondrion-related organelles in diverse eukaryotic lineages and provide recommendations on how to apply these methods. Furthermore, we compare the predictive performance of these programs on a mixed set of mitochondrial and non-mitochondrial proteins. Although N-terminal targeting peptide prediction programs tend to have the highest accuracy, they cannot be effectively used for partial coding sequences derived from high-throughput expressed sequence tag surveys where data for the N-terminus of the encoded protein is often missing. Therefore methods that do not rely on the presence of an N-terminal targeting sequence alone are extremely useful, especially for expressed sequence tag data. The best strategy for classification of unknown proteins is to use multiple programs, incorporating a variety of prediction strategies, and closely examine the predictions with an understanding of how each of those programs will likely handle the data.
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Affiliation(s)
- Daniel Gaston
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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44
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GeneDistiller--distilling candidate genes from linkage intervals. PLoS One 2008; 3:e3874. [PMID: 19057649 PMCID: PMC2587712 DOI: 10.1371/journal.pone.0003874] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 11/10/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Linkage studies often yield intervals containing several hundred positional candidate genes. Different manual or automatic approaches exist for the determination of the gene most likely to cause the disease. While the manual search is very flexible and takes advantage of the researchers' background knowledge and intuition, it may be very cumbersome to collect and study the relevant data. Automatic solutions on the other hand usually focus on certain models, remain "black boxes" and do not offer the same degree of flexibility. METHODOLOGY We have developed a web-based application that combines the advantages of both approaches. Information from various data sources such as gene-phenotype associations, gene expression patterns and protein-protein interactions was integrated into a central database. Researchers can select which information for the genes within a candidate interval or for single genes shall be displayed. Genes can also interactively be filtered, sorted and prioritised according to criteria derived from the background knowledge and preconception of the disease under scrutiny. CONCLUSIONS GeneDistiller provides knowledge-driven, fully interactive and intuitive access to multiple data sources. It displays maximum relevant information, while saving the user from drowning in the flood of data. A typical query takes less than two seconds, thus allowing an interactive and explorative approach to the hunt for the candidate gene. ACCESS GeneDistiller can be freely accessed at http://www.genedistiller.org.
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van Grinsven KWA, van Hellemond JJ, Tielens AGM. Acetate:succinate CoA-transferase in the anaerobic mitochondria of Fasciola hepatica. Mol Biochem Parasitol 2008; 164:74-9. [PMID: 19103231 DOI: 10.1016/j.molbiopara.2008.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 11/12/2008] [Accepted: 11/20/2008] [Indexed: 11/16/2022]
Abstract
Fasciola hepatica contains anaerobically functioning mitochondria that produce acetate and propionate, the main endproducts excreted by this parasite. The final reactions in the pathways leading to these endproducts are performed by acetate:succinate CoA-transferase (ASCT) and propionate:succinate CoA-transferase (PSCT), respectively. The enzymes catalysing these essential reactions in anaerobic mitochondria are still not characterized, nor are the corresponding genes identified. Here we describe the identification of the gene that codes for the F. hepatica ASCT. The F. hepatica gene was heterologously expressed and studies on the corresponding enzyme activity showed that the enzyme is indeed a transferase and uses a ping-pong bi-bi reaction mechanism, like most other known CoA-transferases. This F. hepatica CoA-transferase was shown to be a true transferase and not a hydrolase, as it needs an acceptor for optimal activity. Our studies demonstrated that the F. hepatica ASCT can use other CoA-acceptors than succinate, such as propionate, acetate and butyrate, and is in fact a short-chain acyl-CoA-transferase. We further showed that this F. hepatica CoA-transferase can also catalyze the PSCT reaction, which is responsible for the production of propionate. Analysis of the amino acid sequence of F. hepatica clearly indicated the presence of a mitochondrial targeting sequence, and in CHO cells the enzyme is indeed present in the mitochondrial fraction. F. hepatica ASCT is the first ASCT identified in anaerobic mitochondria. It is homologous to the hydrogenosomal ASCT we earlier identified in Trichomonas vaginalis, but not to the ASCT present in the aerobic mitochondria of Trypanosoma brucei.
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Affiliation(s)
- Koen W A van Grinsven
- Department of Biochemistry, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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PGAM5 tethers a ternary complex containing Keap1 and Nrf2 to mitochondria. Exp Cell Res 2008; 314:1789-803. [PMID: 18387606 DOI: 10.1016/j.yexcr.2008.02.014] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2007] [Revised: 01/21/2008] [Accepted: 02/21/2008] [Indexed: 11/23/2022]
Abstract
Eukaryote cells balance production of reactive oxygen species (ROS) with levels of anti-oxidant enzyme activity to maintain cellular redox homeostasis. Mitochondria are a major source of ROS, while many anti-oxidant genes are regulated by the Nrf2 transcription factor. Keap1, a redox-regulated substrate adaptor for a cullin-based ubiquitin ligase, targets Nrf2 for proteosome-mediated degradation and represses Nrf2-dependent gene expression. We have previously identified a member of the phosphoglycerate mutase family, PGAM5, as a Keap1-binding protein. In this report, we demonstrate that PGAM5 is targeted to the outer membrane of mitochondria by an N-terminal mitochondrial-localization sequence. Furthermore, we provide evidence that PGAM5 forms a ternary complex containing both Keap1 and Nrf2, in which the dimeric Keap1 protein simultaneously binds both PGAM5 and Nrf2 through their conserved E(S/T)GE motifs. Knockdown of either Keap1 or PGAM5 activates Nrf2-dependent gene expression. We suggest that this ternary complex provides a molecular framework for understanding how nuclear anti-oxidant gene expression is regulated in response to changes in mitochondrial function(s).
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Tamura T, Akutsu T. Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinformatics 2007; 8:466. [PMID: 18047679 PMCID: PMC2220007 DOI: 10.1186/1471-2105-8-466] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2007] [Accepted: 11/30/2007] [Indexed: 12/03/2022] Open
Abstract
Background Subcellular location prediction of proteins is an important and well-studied problem in bioinformatics. This is a problem of predicting which part in a cell a given protein is transported to, where an amino acid sequence of the protein is given as an input. This problem is becoming more important since information on subcellular location is helpful for annotation of proteins and genes and the number of complete genomes is rapidly increasing. Since existing predictors are based on various heuristics, it is important to develop a simple method with high prediction accuracies. Results In this paper, we propose a novel and general predicting method by combining techniques for sequence alignment and feature vectors based on amino acid composition. We implemented this method with support vector machines on plant data sets extracted from the TargetP database. Through fivefold cross validation tests, the obtained overall accuracies and average MCC were 0.9096 and 0.8655 respectively. We also applied our method to other datasets including that of WoLF PSORT. Conclusion Although there is a predictor which uses the information of gene ontology and yields higher accuracy than ours, our accuracies are higher than existing predictors which use only sequence information. Since such information as gene ontology can be obtained only for known proteins, our predictor is considered to be useful for subcellular location prediction of newly-discovered proteins. Furthermore, the idea of combination of alignment and amino acid frequency is novel and general so that it may be applied to other problems in bioinformatics. Our method for plant is also implemented as a web-system and available on .
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Affiliation(s)
- Takeyuki Tamura
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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van Grinsven KWA, Rosnowsky S, van Weelden SWH, Pütz S, van der Giezen M, Martin W, van Hellemond JJ, Tielens AGM, Henze K. Acetate:succinate CoA-transferase in the hydrogenosomes of Trichomonas vaginalis: identification and characterization. J Biol Chem 2007; 283:1411-1418. [PMID: 18024431 DOI: 10.1074/jbc.m702528200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acetate:succinate CoA-transferases (ASCT) are acetate-producing enzymes in hydrogenosomes, anaerobically functioning mitochondria and in the aerobically functioning mitochondria of trypanosomatids. Although acetate is produced in the hydrogenosomes of a number of anaerobic microbial eukaryotes such as Trichomonas vaginalis, no acetate producing enzyme has ever been identified in these organelles. Acetate production is the last unidentified enzymatic reaction of hydrogenosomal carbohydrate metabolism. We identified a gene encoding an enzyme for acetate production in the genome of the hydrogenosome-containing protozoan parasite T. vaginalis. This gene shows high similarity to Saccharomyces cerevisiae acetyl-CoA hydrolase and Clostridium kluyveri succinyl-CoA:CoA-transferase. Here we demonstrate that this protein is expressed and is present in the hydrogenosomes where it functions as the T. vaginalis acetate:succinate CoA-transferase (TvASCT). Heterologous expression of TvASCT in CHO cells resulted in the expression of an active ASCT. Furthermore, homologous overexpression of the TvASCT gene in T. vaginalis resulted in an equivalent increase in ASCT activity. It was shown that the CoA transferase activity is succinate-dependent. These results demonstrate that this acetyl-CoA hydrolase/transferase homolog functions as the hydrogenosomal ASCT of T. vaginalis. This is the first hydrogenosomal acetate-producing enzyme to be identified. Interestingly, TvASCT does not share any similarity with the mitochondrial ASCT from Trypanosoma brucei, the only other eukaryotic succinate-dependent acetyl-CoA-transferase identified so far. The trichomonad enzyme clearly belongs to a distinct class of acetate:succinate CoA-transferases. Apparently, two completely different enzymes for succinate-dependent acetate production have evolved independently in ATP-generating organelles.
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Affiliation(s)
- Koen W A van Grinsven
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Silke Rosnowsky
- Institute of Botany III, Heinrich Heine University, Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Susanne W H van Weelden
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands
| | - Simone Pütz
- Institute of Botany III, Heinrich Heine University, Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Mark van der Giezen
- Centre for Eukaryotic Evolutionary Microbiology, School of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - William Martin
- Institute of Botany III, Heinrich Heine University, Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Jaap J van Hellemond
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands; Department of Medical Microbiology & Infectious Diseases, ErasmusMC University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Aloysius G M Tielens
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM Utrecht, The Netherlands; Department of Medical Microbiology & Infectious Diseases, ErasmusMC University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Katrin Henze
- Institute of Botany III, Heinrich Heine University, Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
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Kessler D, Papatheodorou P, Stratmann T, Dian EA, Hartmann-Fatu C, Rassow J, Bayer P, Mueller JW. The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae. BMC Biol 2007; 5:37. [PMID: 17875217 PMCID: PMC2031878 DOI: 10.1186/1741-7007-5-37] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 09/17/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The parvulin-type peptidyl prolyl cis/trans isomerase Par14 is highly conserved in all metazoans. The recently identified parvulin Par17 contains an additional N-terminal domain whose occurrence and function was the focus of the present study. RESULTS Based on the observation that the human genome encodes Par17, but bovine and rodent genomes do not, Par17 exon sequences from 10 different primate species were cloned and sequenced. Par17 is encoded in the genomes of Hominidae species including humans, but is absent from other mammalian species. In contrast to Par14, endogenous Par17 was found in mitochondrial and membrane fractions of human cell lysates. Fluorescence of EGFP fusions of Par17, but not Par14, co-localized with mitochondrial staining. Par14 and Par17 associated with isolated human, rat and yeast mitochondria at low salt concentrations, but only the Par17 mitochondrial association was resistant to higher salt concentrations. Par17 was imported into mitochondria in a time and membrane potential-dependent manner, where it reached the mitochondrial matrix. Moreover, Par17 was shown to bind to double-stranded DNA under physiological salt conditions. CONCLUSION Taken together, the DNA binding parvulin Par17 is targeted to the mitochondrial matrix by the most recently evolved mitochondrial prepeptide known to date, thus adding a novel protein constituent to the mitochondrial proteome of Hominidae.
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Affiliation(s)
- Daniel Kessler
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Tina Stratmann
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elke Andrea Dian
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Cristina Hartmann-Fatu
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joachim Rassow
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Jonathan Wolf Mueller
- Department of Structural and Medicinal Biochemistry, Center for Medical Biotechnology – ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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Kawasaki I, Hanazawa M, Gengyo-Ando K, Mitani S, Maruyama I, Iino Y. ASB-1, a germline-specific isoform of mitochondrial ATP synthase b subunit, is required to maintain the rate of germline development in Caenorhabditis elegans. Mech Dev 2007; 124:237-51. [PMID: 17223323 DOI: 10.1016/j.mod.2006.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2006] [Revised: 11/24/2006] [Accepted: 11/26/2006] [Indexed: 10/23/2022]
Abstract
The developmental timing of all types of cells must be synchronized and spatially coordinated to achieve the organized development of a multicellular organism. Previously, we found RNAi of asb-1, encoding a germline-specific isoform of mitochondrial ATP synthase b subunit, caused 100% penetrant sterility in Caenorhabditis elegans. ATP synthase is one of the five complexes of the mitochondrial respiratory chain, and defects in some of the components of the chain are known to slow the growth and extend the lifespan of worms. We found that development of asb-1 mutant germ line was not arrested at any stage, but did slow to half the rate of wild type, whereas the rate of somatic development was the same in asb-1 mutants as that of wild type, indicating that asb-1 is required to maintain the rate of germline development but has no effect on somatic development. Among ATP synthase subunit genes, RNAi of asg-1, encoding a germline-specific isoform of the g subunit, also caused asb-1-like sterility, indicating that some other germline-specific components are also required to maintain the rate of germline development. Both asb-1 and asg-1 are located on autosomes while they possess counterparts, asb-2 and asg-2, respectively, on X chromosome, which are both required for somatic development. Chromosomal locations of the genes may be the basis of the segregation of germline/somatic functions of each gene, as were demonstrated for other autosomal/X-linked duplicated gene pairs.
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Affiliation(s)
- Ichiro Kawasaki
- Molecular Genetics Research Laboratory, University of Tokyo, Science Building No. 7, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
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