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Anoar S, Woodling NS, Niccoli T. Mitochondria Dysfunction in Frontotemporal Dementia/Amyotrophic Lateral Sclerosis: Lessons From Drosophila Models. Front Neurosci 2021; 15:786076. [PMID: 34899176 PMCID: PMC8652125 DOI: 10.3389/fnins.2021.786076] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by declining motor and cognitive functions. Even though these diseases present with distinct sets of symptoms, FTD and ALS are two extremes of the same disease spectrum, as they show considerable overlap in genetic, clinical and neuropathological features. Among these overlapping features, mitochondrial dysfunction is associated with both FTD and ALS. Recent studies have shown that cells derived from patients' induced pluripotent stem cells (iPSC)s display mitochondrial abnormalities, and similar abnormalities have been observed in a number of animal disease models. Drosophila models have been widely used to study FTD and ALS because of their rapid generation time and extensive set of genetic tools. A wide array of fly models have been developed to elucidate the molecular mechanisms of toxicity for mutations associated with FTD/ALS. Fly models have been often instrumental in understanding the role of disease associated mutations in mitochondria biology. In this review, we discuss how mutations associated with FTD/ALS disrupt mitochondrial function, and we review how the use of Drosophila models has been pivotal to our current knowledge in this field.
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Affiliation(s)
- Sharifah Anoar
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
| | - Nathaniel S Woodling
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
| | - Teresa Niccoli
- Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, United Kingdom
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2
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Yan J, Xie Y, Wang F, Chen Y, Zhang J, Dou Z, Gan L, Li H, Si J, Sun C, Di C, Zhang H. Carbon ion combined with tigecycline inhibits lung cancer cell proliferation by inducing mitochondrial dysfunction. Life Sci 2020; 263:118586. [PMID: 33065148 DOI: 10.1016/j.lfs.2020.118586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023]
Abstract
AIMS Mitochondrial dysfunction is receiving considerable attention due to irreplaceable biological function of mitochondria. Ionizing radiation and tigecycline (TIG) alone can cause mitochondrial dysfunction, playing important role in tumor therapy. However, prior studies fail to investigate combined mechanism of carbon ion irradiation (IR) and TIG on tumor proliferation inhibition. The study aimed to explore the combined effects of both on autophagy and apoptosis. MATERIALS AND METHODS NSCLC cells A549 and H1299 were treated with carbon ion, TIG, or both. Cell survival rate, autophagy, apoptosis, expression of mitochondrial signaling proteins were determined by clone formation assay, immunofluorescence of LC3B, flow cytometry and western blotting, respectively; ATP content, mitochondrial membrane potential (MMP) and Ca2+ level in mitochondria were used to assessed mitochondrial function. KEY FINDINGS Results showed IR combined TIG inhibited cells proliferation by increasing apoptosis in both cells and enhancing autophagy in H1299 cells. Additionally, combination treatment induced the most severe mitochondrial dysfunction by sharply reducing ATP, MMP and increasing Ca2+ level of mitochondria. Up-regulation and down-regulation of mitochondrial translation proteins (EF-Tu, GFM1 and MRPS12) expression affected apoptosis and autophagy, while the level of p-mTOR was consistent with their expression in both cell types. In A549 cells, p-AMPK level decreased while p-Akt and p-mTOR increased after combination treatment. SIGNIFICANCE Overall, our results showed that p-Akt and p-AMPK antagonistically targeted p-mTOR to regulate mitochondrial translation proteins to affect autophagy and apoptosis. Furthermore, this study suggests that combination of carbon ion and TIG is a potential therapeutic option against tumors.
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Affiliation(s)
- Junfang Yan
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China; Graduate School of University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yi Xie
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Fang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China; Graduate School of University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yuhong Chen
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China; Graduate School of University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jinhua Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China; Graduate School of University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhihui Dou
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China; Graduate School of University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lu Gan
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China; Graduate School of University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hongyan Li
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Jing Si
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Chao Sun
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Cuixia Di
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China
| | - Hong Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, 509 Nanchang Road, Lanzhou 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, Gansu, China; Key Laboratory of Heavy Ion Radiation Medicine of Gansu Province, Lanzhou, Gansu, China.
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3
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Han X, Wang Z, Wang W, Bai R, Zhao P, Shang J. Screening on human hepatoma cell line HepG-2 nucleus and cytoplasm protein after CDK2 silencing by RNAi. Cytotechnology 2014; 66:567-74. [PMID: 24801578 DOI: 10.1007/s10616-013-9604-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/08/2013] [Indexed: 11/30/2022] Open
Abstract
The activation of phase-specific cyclin-dependent kinases is associated with ordered cell cycle transitions. Among the mammalian Cdks, Cdk2 is essential for liver cancer cell proliferation. The related cycling protein CDK2 was analyzed by 2D-gel and MALDI-TOF/TOF MS mass assay in liver cancer cells, which CDK2 was silenced. The results showed four significantly different spots in cell ribonucleoprotein (similar to ribosomal protein S12, chaperonin 10-related protein, beta-actin and zinc finger protein 276) and four in plasmosin (aldolase A protein, hCG, anonymous protein and tubulin, gamma complex associated protein 2). In the plasmosin, aldolase A catalyzes the production of tublin and actin. Together they regulate the cell cycle and arrest the cell in the S phage. In the cell ribonucleoprotein, proteins with homology to ribosomal protein S12 and chaperonin 10 play a similar role in cell cycle regulation.
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Affiliation(s)
- Xiaofang Han
- Department of Clinical Laboratory, Inner Mongolia People's Hospital, Hohhot, 010018, People's Republic of China
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4
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Hubal MJ, Reich KA, De Biase A, Bilbie C, Clarkson PM, Hoffman EP, Thompson PD. Transcriptional deficits in oxidative phosphorylation with statin myopathy. Muscle Nerve 2011; 44:393-401. [DOI: 10.1002/mus.22081] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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5
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Han MJ, Chiu DT, Koc EC. Regulation of mitochondrial ribosomal protein S29 (MRPS29) expression by a 5'-upstream open reading frame. Mitochondrion 2010; 10:274-83. [PMID: 20079882 DOI: 10.1016/j.mito.2009.12.150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 11/25/2009] [Accepted: 12/23/2009] [Indexed: 10/20/2022]
Abstract
Mitochondrial ribosomal protein S29 (MRPS29) is a mitochondrial pro-apoptotic protein also known as death associated protein 3 (DAP3). Over-expression of MRPS29 has been reported to induce apoptosis in several different human cell lines while conferring resistance in glioma and Ataxia telangiectasia cells. These two contradictory reports led us to investigate the MRPS29-induced apoptosis further. Cyber searches of the EST databases revealed the presence of a splice variant of MRPS29 mRNA containing an upstream open reading frame (uORF) at the 5' untranslated region (UTR). In this study, we confirmed the presence of this uORF using real-time RT-PCR and investigated its role in MRPS29 expression.
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Affiliation(s)
- Min-Joon Han
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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6
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Zheng S, Chen L. A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res 2009; 37:e75. [PMID: 19417075 PMCID: PMC2691848 DOI: 10.1093/nar/gkp282] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 04/13/2009] [Accepted: 04/14/2009] [Indexed: 11/19/2022] Open
Abstract
The complexity of mammalian transcriptomes is compounded by alternative splicing which allows one gene to produce multiple transcript isoforms. However, transcriptome comparison has been limited to differential analysis at the gene level instead of the individual transcript isoform level. High-throughput sequencing technologies and high-resolution tiling arrays provide an unprecedented opportunity to compare transcriptomes at the level of individual splice variants. However, sequence read coverage or probe intensity at each position may represent a family of splice variants instead of one single isoform. Here we propose a hierarchical Bayesian model, BASIS (Bayesian Analysis of Splicing IsoformS), to infer the differential expression level of each transcript isoform in response to two conditions. A latent variable was introduced to perform direct statistical selection of differentially expressed isoforms. Model parameters were inferred based on an ergodic Markov chain generated by our Gibbs sampler. BASIS has the ability to borrow information across different probes (or positions) from the same genes and different genes. BASIS can handle the heteroskedasticity of probe intensity or sequence read coverage. We applied BASIS to a human tiling-array data set and a mouse RNA-seq data set. Some of the predictions were validated by quantitative real-time RT-PCR experiments.
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Affiliation(s)
- Sika Zheng
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095 and Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Liang Chen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095 and Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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7
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Zanotto E, Shah ZH, Jacobs HT. The bidirectional promoter of two genes for the mitochondrial translational apparatus in mouse is regulated by an array of CCAAT boxes interacting with the transcription factor NF-Y. Nucleic Acids Res 2006; 35:664-77. [PMID: 17179180 PMCID: PMC1802594 DOI: 10.1093/nar/gkl1037] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The genes for mitoribosomal protein S12 (Mrps12) and mitochondrial seryl-tRNA ligase (Sarsm and Sars2) are oppositely transcribed from a conserved promoter region of <200 bp in both human and mouse. Using a dual reporter vector we identified an array of 4 CCAAT box elements required for efficient transcription of the two genes in cultured mouse 3T3 cells, and for enforcing directionality in favour of Mrps12. Electrophoretic mobility shift assay (EMSA) and in vivo footprinting confirmed the importance of these promoter elements as sites of protein-binding, and EMSA supershift and chromatin immunoprecipitation (ChIP) assays identified NF-Y as the key transcription factor involved, revealing a common pattern of protein–DNA interactions in all tissues tested (liver, brain, heart, kidney and 3T3 cells). The inherently bidirectional activity of NF-Y makes it an especially suitable factor to govern promoters of this class, whose expression is linked to cell proliferation.
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Affiliation(s)
- Ernesto Zanotto
- Institute of Medical Technology & Tampere University Hospital, FI-33014 University of TampereFinland
| | - Zahid H. Shah
- Institute of Medical Technology & Tampere University Hospital, FI-33014 University of TampereFinland
| | - Howard T. Jacobs
- Institute of Medical Technology & Tampere University Hospital, FI-33014 University of TampereFinland
- Institute of Biomedical and Life Sciences, University of GlasgowGlasgow G12 8QQ, Scotland, UK
- To whom correspondence should be addressed. Tel: +35 8335517731; Fax: +35 832157710;
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8
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Abstract
Members of the Wnt gene family play important roles in the regulation of a number of basic developmental processes. Because Wnt is such a potent morphogen, its expression must be controlled tightly and precisely. While many review papers focused on Wnt signaling downstream of the receptor, this review addresses regulations of Wnt itself on several levels, including the transcriptional level, RNA splicing, the post-transcriptional level, the translational level, and the post-translational level. It is these multiple, precise and tight regulations that guarantee that Wnts function correctly both temporally and spatially.
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Affiliation(s)
- Qi Tian
- Department of Pathology, Oregon Health Sciences University, School of Medicine, Portland, OR 97239, USA.
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9
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Tselykh TV, Roos C, Heino TI. The mitochondrial ribosome-specific MrpL55 protein is essential in Drosophila and dynamically required during development. Exp Cell Res 2005; 307:354-66. [PMID: 15894314 DOI: 10.1016/j.yexcr.2005.03.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2004] [Revised: 03/22/2005] [Accepted: 03/24/2005] [Indexed: 10/25/2022]
Abstract
We report on the essential Drosophila mRpL55 gene conserved exclusively in metazoans. Null mRpL55 mutants did not grow after hatching, moved slowly and died as first instar larvae. MrpL55 is similar to mammalian MRPL55, a protein that, in a large-scale mass spectrometry study, has been found as a mitoribosome-specific large subunit protein. We showed that MrpL55 was localised to the mitochondrion in S2 cells and tissues and was enriched in cells with a higher protein synthesis activity. The MrpL55 protein contains a KOW-like motif present in proteins with a role in transcriptional anti-termination and regulation of translation. Modulation of mRpL55 expression level is critical for development. Somatic clonal analysis showed that MrpL55 was not required in larval eye imaginal discs but required in pupal discs apparently during the second mitotic wave. Therefore, our results showed that the MrpL55 protein acts dynamically in the cell during development. We propose that MrpL55 is involved in Drosophila mitochondrial biogenesis and G2/M phase cell cycle progression.
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MESH Headings
- Amino Acid Motifs/genetics
- Amino Acid Sequence
- Animals
- Animals, Genetically Modified
- Cell Line
- Cloning, Molecular
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila Proteins/physiology
- Drosophila melanogaster/embryology
- Drosophila melanogaster/growth & development
- Drosophila melanogaster/physiology
- Eye/cytology
- Eye/growth & development
- Female
- Gene Deletion
- Gene Expression/genetics
- Gene Expression Regulation, Developmental
- Humans
- Immunohistochemistry
- Larva/genetics
- Larva/growth & development
- Mitochondria/chemistry
- Mitochondria/metabolism
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Mitochondrial Proteins/physiology
- Molecular Sequence Data
- Mutation
- Nematoda/genetics
- Oogenesis/physiology
- Phenotype
- Protein Structure, Secondary
- RNA, Messenger, Stored/analysis
- RNA, Messenger, Stored/physiology
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/physiology
- Recombination, Genetic/genetics
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomal Proteins/physiology
- Salivary Glands/cytology
- Salivary Glands/metabolism
- Sequence Homology, Amino Acid
- Subcellular Fractions/chemistry
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Affiliation(s)
- Timofey V Tselykh
- Institute of Biotechnology, Developmental Biology Program, University of Helsinki, FIN-00014 Helsinki, Finland.
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10
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Dalziel AC, Moore SE, Moyes CD. Mitochondrial enzyme content in the muscles of high-performance fish: evolution and variation among fiber types. Am J Physiol Regul Integr Comp Physiol 2005; 288:R163-72. [PMID: 15374817 DOI: 10.1152/ajpregu.00152.2004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Muscle mitochondrial content varies widely among fiber types and species. We investigated the origins of variation in the activity of the mitochondrial enzyme citrate synthase (CS), an index of mitochondrial abundance, among fiber types and species of high-performance fish (tunas and billfishes). CS activities varied up to 30-fold among muscles: lowest in billfish white muscle and highest in billfish heater organ. Among species, CS activities of red, white, and cardiac muscles of three tuna species were twofold greater than the homologous muscles of two billfish species. Because comparisons of CS amino acid sequences deduced from a combination of PCR methods argue against clade-specific differences in catalytic properties, CS activity reflects CS content among these five species. To assess the bases of these differences in CS activity, we looked at the relationship between CS activity (U/g muscle), nuclear content (DNA/g muscle), and CS transcript levels (CS mRNA/g RNA). Muscle CS activity differed by 10- to 30-fold when expressed per gram of muscle but only threefold when expressed per milligram of DNA. Thus it is nuclear DNA content, not fiber-type differences, in CS gene expression that may be the main determinant of CS activity in muscle. Conversely, evolutionary (tunas vs. billfishes) differences in CS arise from differences in posttranscriptional regulation, based on relationships between CS enzyme levels and CS mRNA assessed by quantitative competitive RT-PCR. These data argue that fiber-type differences can arise without major differences in fiber-type-specific regulation of the CS gene, whereas evolutionary differences may be largely due to posttranscriptional regulation.
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Affiliation(s)
- Anne C Dalziel
- Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6
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11
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Takeuchi N, Ueda T. Down-regulation of the mitochondrial translation system during terminal differentiation of HL-60 cells by 12-O-tetradecanoyl-1-phorbol-13-acetate: comparison with the cytoplasmic translation system. J Biol Chem 2003; 278:45318-24. [PMID: 12952954 DOI: 10.1074/jbc.m307620200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial (mt) biogenesis depends on both the nuclear and mt genomes, and a coordination of these two genetic systems is necessary for proper cell functioning. Little is known about the regulatory mechanisms of mt translation or about the expression of mt translation factors. Here, we studied the expression of mt translation factors during 12-O-tetradecanoyl-1-phorbol-13-acetate (TPA)-induced terminal differentiation of HL-60 cells. For all mt translation factors investigated, mRNA expression was markedly down-regulated in a coordinate and specific manner, whereas mRNA levels for the cytoplasmic translation factors showed only a slight reduction. An actinomycin D chase study and nuclear run-on assay revealed that the TPA-induced decrease in mt elongation factor Tu (EF-Tumt) mRNA mainly results from decreased mRNA stability. Polysome analysis showed that there was no significant translational control of mt translation factor (EF-Tumt, ribosomal proteins L7/L12mt and S12mt) mRNA expression during differentiation. Thus, the decreased protein level of one of these mt translation factors (EF-Tumt) simply reflects its decreased mRNA level. It was also demonstrated by pulse labeling of mt translation products that the down-regulation of mt translational activity is actually associated with down-regulated mt translation factor expression during cellular differentiation. Our results illustrate that the regulatory mechanisms of mt translational activity upon terminal differentiation (in response to the growth arrest) is different to that of the cytoplasmic system, where the control of mRNA translational efficiency of major translation factors is the central mechanism for their down-regulation.
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Affiliation(s)
- Nono Takeuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FSB-401, 5-1-5, Kashiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan.
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12
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Abstract
Mitochondrial tRNA gene mutations, including heteroplasmic deletions that eliminate one or more tRNAs, as well as point mutations that may be either hetero- or homoplasmic, are associated with a wide spectrum of human diseases. These range from rare syndromic disorders to cases of commoner conditions such as sensorineural deafness or cardiomyopathy. The disease spectrum of mutations in a given gene, or even a single mutation, may vary, but some patterns are evident, for example the prominence of cardiomyopathy resulting from tRNAIle defects, or of MERFF-like disease from tRNALys defects. Molecular studies of many laboratories have reached a consensus on molecular mechanisms associated with these mutations. Although precise details vary, loss of translational function of the affected tRNA(s) seems to be the final outcome, whether by impaired pre-tRNA processing, half-life, base-modification or aminoacylation. However, a mechanistic understanding of the consequences of this for the assembly and function of the mitochondrial OXPHOS complexes and for the physiological functions of the affected tissues is still a distant prospect. This review presents some views of possible downstream consequences of specific tRNA deficiencies.
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Affiliation(s)
- Howard T Jacobs
- Institute of Medical Technology, Tampere University Hospital, University of Tampere, Finland.
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13
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Pesole G, Liuni S, Grillo G, Licciulli F, Mignone F, Gissi C, Saccone C. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res 2002; 30:335-40. [PMID: 11752330 PMCID: PMC99102 DOI: 10.1093/nar/30.1.335] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5' and 3' untranslated sequences of eukaryotic mRNAs cleaned from redundancy. UTRdb entries are enriched with specialized information not present in the primary databases including the presence of nucleotide sequence patterns already demonstrated by experimental analysis to have some functional role. All these patterns have been collected in the UTRsite database so that it is possible to search any input sequence for the presence of annotated functional motifs. Furthermore, UTRdb entries have been annotated for the presence of repetitive elements. All Internet resources we implemented for retrieval and functional analysis of 5'- and 3'-UTRs of eukaryotic mRNAs are accessible at http://bighost.area.ba.cnr.it/BIG/UTRHome/.
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Affiliation(s)
- Graziano Pesole
- Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, via Celoria 26, 20133 Milano, Italy.
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14
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Koc EC, Burkhart W, Blackburn K, Moyer MB, Schlatzer DM, Moseley A, Spremulli LL. The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present. J Biol Chem 2001; 276:43958-69. [PMID: 11551941 DOI: 10.1074/jbc.m106510200] [Citation(s) in RCA: 211] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Identification of all the protein components of the large subunit (39 S) of the mammalian mitochondrial ribosome has been achieved by carrying out proteolytic digestions of whole 39 S subunits followed by analysis of the resultant peptides by liquid chromatography and mass spectrometry. Peptide sequence information was used to search the human EST data bases and complete coding sequences were assembled. The human mitochondrial 39 S subunit has 48 distinct proteins. Twenty eight of these are homologs of the Escherichia coli 50 S ribosomal proteins L1, L2, L3, L4, L7/L12, L9, L10, L11, L13, L14, L15, L16, L17, L18, L19, L20, L21, L22, L23, L24, L27, L28, L30, L32, L33, L34, L35, and L36. Almost all of these proteins have homologs in Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae mitochondrial ribosomes. No mitochondrial homologs to prokaryotic ribosomal proteins L5, L6, L25, L29, and L31 could be found either in the peptides obtained or by analysis of the available data bases. The remaining 20 proteins present in the 39 S subunits are specific to mitochondrial ribosomes. Proteins in this group have no apparent homologs in bacterial, chloroplast, archaebacterial, or cytosolic ribosomes. All but two of the proteins has a clear homolog in D. melanogaster while all can be found in the genome of C. elegans. Ten of the 20 mitochondrial specific 39 S proteins have homologs in S. cerevisiae. Homologs of 2 of these new classes of ribosomal proteins could be identified in the Arabidopsis thaliana genome.
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Affiliation(s)
- E C Koc
- Department of Chemistry and Campus Box 3290, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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15
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Toivonen JM, O'Dell KM, Petit N, Irvine SC, Knight GK, Lehtonen M, Longmuir M, Luoto K, Touraille S, Wang Z, Alziari S, Shah ZH, Jacobs HT. Technical knockout, a Drosophila model of mitochondrial deafness. Genetics 2001; 159:241-54. [PMID: 11560901 PMCID: PMC1461776 DOI: 10.1093/genetics/159.1.241] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mutations in mtDNA-encoded components of the mitochondrial translational apparatus are associated with diverse pathological states in humans, notably sensorineural deafness. To develop animal models of such disorders, we have manipulated the nuclear gene for mitochondrial ribosomal protein S12 in Drosophila (technical knockout, tko). The prototypic mutant tko(25t) exhibits developmental delay, bang sensitivity, impaired male courtship, and defective response to sound. On the basis of a transgenic reversion test, these phenotypes are attributable to a single substitution (L85H) at a conserved residue of the tko protein. The mutant is hypersensitive to doxycyclin, an antibiotic that selectively inhibits mitochondrial protein synthesis, and mutant larvae have greatly diminished activities of mitochondrial redox enzymes and decreased levels of mitochondrial small-subunit rRNA. A second mutation in the tko gene, Q116K, which is predicted to impair the accuracy of mitochondrial translation, results in the completely different phenotype of recessive female sterility, based on three independent transgenic insertions. We infer that the tko(25t) mutant provides a model of mitochondrial hearing impairment resulting from a quantitative deficiency of mitochondrial translational capacity.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Anti-Bacterial Agents/pharmacology
- Blotting, Northern
- Blotting, Southern
- Cell Nucleus/genetics
- Cloning, Molecular
- Crosses, Genetic
- DNA, Mitochondrial/genetics
- Deafness/genetics
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Doxycycline/pharmacology
- Drosophila/genetics
- Drosophila/physiology
- Female
- Humans
- Infertility, Female/genetics
- Male
- Mitochondria/metabolism
- Models, Genetic
- Mutation
- Oligonucleotides/metabolism
- Oxidation-Reduction
- Phenotype
- Polymerase Chain Reaction
- Protein Biosynthesis
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/physiology
- Sequence Analysis, DNA
- Sound
- Time Factors
- Transgenes
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Affiliation(s)
- J M Toivonen
- Institute of Medical Technology & Tampere University Hospital, FIN-33014 University of Tampere, Finland
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16
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Kenmochi N, Suzuki T, Uechi T, Magoori M, Kuniba M, Higa S, Watanabe K, Tanaka T. The human mitochondrial ribosomal protein genes: mapping of 54 genes to the chromosomes and implications for human disorders. Genomics 2001; 77:65-70. [PMID: 11543634 DOI: 10.1006/geno.2001.6622] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mitochondria possess their own translational machinery, which is composed of components distinct from their cytoplasmic counterparts. To investigate the possible involvement of mitochondrial ribosomal defects in human disease, we mapped nuclear genes that encode mitochondrial ribosomal proteins (MRPs). We generated sequence-tagged sites (STSs) of individual MRP genes that were able to be detected by PCR. They were placed on an STS content map of the human genome by typing of radiation hybrid panels. We located 54 MRP genes on the STS-content map and assigned these genes to cytogenetic bands of the human chromosomes. Although mitochondria are thought to have originated from bacteria, in which the genes encoding ribosomal proteins are clustered into operons, the mapped MRP genes are widely dispersed throughout the genome, suggesting that transfer of each MRP gene to the nuclear genome occurred individually. We compared the assigned positions with candidate regions for mendelian disorders and found certain genes that might be involved in particular diseases. This map provides a basis for studying possible roles of MRP defects in mitochondrial disorders.
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Affiliation(s)
- N Kenmochi
- Department of Biochemistry, School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.
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17
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Cavdar Koc E, Burkhart W, Blackburn K, Moseley A, Spremulli LL. The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present. J Biol Chem 2001; 276:19363-74. [PMID: 11279123 DOI: 10.1074/jbc.m100727200] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Identification of all the protein components of the small subunit (28 S) of the mammalian mitochondrial ribosome has been achieved by carrying out proteolytic digestions of whole 28 S subunits followed by analysis of the resultant peptides by liquid chromatography and tandem mass spectrometry (LC/MS/MS). Peptide sequence information was used to search the human EST data bases and complete coding sequences of the proteins were assembled. The human mitochondrial ribosome has 29 distinct proteins in the small subunit. Fourteen of this group of proteins are homologs of the Escherichia coli 30 S ribosomal proteins S2, S5, S6, S7, S9, S10, S11, S12, S14, S15, S16, S17, S18, and S21. All of these proteins have homologs in Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae mitochondrial ribosomes. Surprisingly, three variants of ribosomal protein S18 are found in the mammalian and D. melanogaster mitochondrial ribosomes while C. elegans has two S18 homologs. The S18 homologs tend to be more closely related to chloroplast S18s than to prokaryotic S18s. No mitochondrial homologs to prokaryotic ribosomal proteins S1, S3, S4, S8, S13, S19, and S20 could be found in the peptides obtained from the whole 28 S subunit digests or by analysis of the available data bases. The remaining 15 proteins present in mammalian mitochondrial 28 S subunits (MRP-S22 through MRP-S36) are specific to mitochondrial ribosomes. Proteins in this group have no apparent homologs in bacterial, chloroplast, archaebacterial, or cytosolic ribosomes. All but two of these proteins have a clear homolog in D. melanogaster while all but three can be found in the genome of C. elegans. Five of the mitochondrial specific ribosomal proteins have homologs in S. cerevisiae.
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Affiliation(s)
- E Cavdar Koc
- Department of Chemistry and Campus Box 3290, University of North Carolina, Chapel Hill, North Carolina, 27599-3290, USA
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18
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Koc EC, Burkhart W, Blackburn K, Koc H, Moseley A, Spremulli LL. Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approach. Protein Sci 2001; 10:471-81. [PMID: 11344316 PMCID: PMC2374141 DOI: 10.1110/ps.35301] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Proteins in the small subunit of the mammalian mitochondrial ribosome were separated by two-dimensional polyacrylamide gel electrophoresis. Four individual proteins were subjected to in-gel Endoprotease Lys-C digestion. The sequences of selected proteolytic peptides were obtained by electrospray tandem mass spectrometry. Peptide sequences obtained from in-gel digestion of individual spots were used to screen human, mouse, and rat expressed sequence tag databases, and complete consensus cDNAs for these species were deduced in silico. The corresponding protein sequences were characterized by comparison to known ribosomal proteins in protein databases. Four different classes of mammalian mitochondrial small subunit ribosomal proteins were identified. Only two of these proteins have significant sequence similarities to ribosomal proteins from prokaryotes. These proteins are homologs to Escherichia coli S9 and S5 proteins. The presence of these newly identified mitochondrial ribosomal proteins are also investigated in the Drosophila melanogaster, Caenorhabditis elegans, and in the genomes of several fungi.
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Affiliation(s)
- E C Koc
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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19
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Garesse R, Vallejo CG. Animal mitochondrial biogenesis and function: a regulatory cross-talk between two genomes. Gene 2001; 263:1-16. [PMID: 11223238 DOI: 10.1016/s0378-1119(00)00582-5] [Citation(s) in RCA: 223] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mitochondria play a pivotal role in cell physiology, producing the cellular energy and other essential metabolites as well as controlling apoptosis by integrating numerous death signals. The biogenesis of the oxidative phosphorylation system (OXPHOS) depends on the coordinated expression of two genomes, nuclear and mitochondrial. As a consequence, the control of mitochondrial biogenesis and function depends on extremely complex processes that require a variety of well orchestrated regulatory mechanisms. It is now clear that in order to provide cells with the correct number of structural and functional differentiated mitochondria, a variety of intracellular and extracellular signals including hormones and environmental stimuli need to be integrated. During the last few years a considerable effort has been devoted to study the factors that regulate mtDNA replication and transcription as well as the expression of nuclear-encoded mitochondrial genes in physiological and pathological conditions. Although still in their infancy, these studies are starting to provide the molecular basis that will allow to understand the mechanisms involved in the nucleo-mitochondrial communication, a cross-talk essential for cell life and death.
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Affiliation(s)
- R Garesse
- Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid, Arturo Duperier, 4, 28029 Madrid, Spain.
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20
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Koc EC, Burkhart W, Blackburn K, Moseley A, Koc H, Spremulli LL. A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. J Biol Chem 2000; 275:32585-91. [PMID: 10938081 DOI: 10.1074/jbc.m003596200] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mammalian mitochondrial small subunit ribosomal proteins were separated by two-dimensional polyacrylamide gel electrophoresis. The proteins in six individual spots were subjected to in-gel tryptic digestion. Peptides were separated by capillary liquid chromatography, and the sequences of selected peptides were obtained by electrospray tandem mass spectrometry. The peptide sequences obtained were used to screen human expressed sequence tag data bases, and complete consensus cDNAs were assembled. Mammalian mitochondrial small subunit ribosomal proteins from six different classes of ribosomal proteins were identified. Only two of these proteins have significant sequence similarities to ribosomal proteins from prokaryotes. These proteins correspond to Escherichia coli S10 and S14. Homologs of two human mitochondrial proteins not found in prokaryotes were observed in the genomes of Drosophila melanogaster and Caenorhabditis elegans. A homolog of one of these proteins was observed in D. melanogaster but not in C. elegans, while a homolog of the other was present in C. elegans but not in D. melanogaster. A homolog of one of the ribosomal proteins not found in prokaryotes was tentatively identified in the yeast genome. This latter protein is the first reported example of a ribosomal protein that is shared by mitochondrial ribosomes from lower and higher eukaryotes that does not have a homolog in prokaryotes.
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Affiliation(s)
- E C Koc
- Department of Chemistry and School of Public Health, Environmental Science and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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