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Tan S, Zhang X, Guo X, Pan G, Yan L, Ding Z, Li R, Wang D, Yan Y, Dong Z, Li T. DAP3 promotes mitochondrial activity and tumour progression in hepatocellular carcinoma by regulating MT-ND5 expression. Cell Death Dis 2024; 15:540. [PMID: 39080251 PMCID: PMC11289107 DOI: 10.1038/s41419-024-06912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
Cancer cells often exhibit fragmented mitochondria and dysregulated mitochondrial dynamics, but the underlying mechanism remains elusive. Here, we found that the mitochondrial protein death-associated protein 3 (DAP3) is localized to mitochondria and promotes the progression of hepatocellular carcinoma (HCC) by regulating mitochondrial function. DAP3 can promote the proliferation, migration, and invasion of HCC cells in vitro and in vivo by increasing mitochondrial respiration, inducing the epithelial-mesenchymal transition (EMT), and slowing cellular senescence. Mechanistically, DAP3 can increase mitochondrial complex I activity in HCC cells by regulating the translation and expression of MT-ND5. The phosphorylation of DAP3 at Ser185 mediated by AKT is the key event mediating the mitochondrial localization and function of DAP3 in HCC cells. In addition, the DAP3 expression in HCC samples is inversely correlated with patient survival. Our results revealed a mechanism by which DAP3 promotes mitochondrial function and HCC progression by regulating MT-ND5 translation and expression, indicating that DAP3 may be a therapeutic target for HCC.
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Affiliation(s)
- Siyu Tan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xiao Zhang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Xiaowei Guo
- Key Laboratory for Experimental Teratology of Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province and Department of Immunology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guoqiang Pan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Lunjie Yan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Ziniu Ding
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Ruizhe Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Dongxu Wang
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Yuchuan Yan
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Zhaoru Dong
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China.
| | - Tao Li
- Department of General Surgery, Qilu Hospital, Shandong University, Jinan, 250012, China.
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Dass S, Mather MW, Morrisey JM, Ling L, Vaidya AB, Ke H. Transcriptional changes in Plasmodium falciparum upon conditional knock down of mitochondrial ribosomal proteins RSM22 and L23. PLoS One 2022; 17:e0274993. [PMID: 36201550 PMCID: PMC9536634 DOI: 10.1371/journal.pone.0274993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/07/2022] [Indexed: 11/23/2022] Open
Abstract
The mitochondrion of malaria parasites is an attractive antimalarial drug target, which require mitoribosomes to translate genes encoded in the mitochondrial (mt) DNA. Plasmodium mitoribosomes are composed of highly fragmented ribosomal RNA (rRNA) encoded in the mtDNA. All mitoribosomal proteins (MRPs) and other assembly factors are encoded in the nuclear genome. Here, we have studied one putative assembly factor, RSM22 (Pf3D7_1027200) and one large subunit (LSU) MRP, L23 (Pf3D7_1239100) in Plasmodium falciparum. We show that both proteins localize to the mitochondrion. Conditional knock down (KD) of PfRSM22 or PfMRPL23 leads to reduced cytochrome bc1 complex activity and increased sensitivity to bc1 inhibitors such as atovaquone and ELQ-300. Using RNA sequencing as a tool, we reveal the transcriptomic changes of nuclear and mitochondrial genomes upon KD of these two proteins. In the early phase of KD, while most mt rRNAs and transcripts of putative MRPs were downregulated in the absence of PfRSM22, many mt rRNAs and several MRPs were upregulated after KD of PfMRPL23. The contrast effects in the early phase of KD likely suggests non-redundant roles of PfRSM22 and PfMRPL23 in the assembly of P. falciparum mitoribosomes. At the late time points of KD, loss of PfRSM22 and PfMRPL23 caused defects in many essential metabolic pathways and transcripts related to essential mitochondrial functions, leading to parasite death. In addition, we enlist mitochondrial proteins of unknown function that are likely novel Plasmodium MRPs based on their structural similarity to known MRPs as well as their expression profiles in KD parasites.
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Affiliation(s)
- Swati Dass
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael W. Mather
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joanne M. Morrisey
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Liqin Ling
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Akhil B. Vaidya
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Hangjun Ke
- Center for Molecular Parasitology, Department of Microbiology and Immunology Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
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Galindo LJ, Torruella G, López-García P, Ciobanu M, Gutiérrez-Preciado A, Karpov SA, Moreira D. Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies. Syst Biol 2022:6651083. [PMID: 35900180 DOI: 10.1093/sysbio/syac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/12/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the 'Opisthosporidia hypothesis'). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the 'Aphelida+Fungi hypothesis'). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (A. insulamus and A. tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida+Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favour of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia.
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Affiliation(s)
- Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Maria Ciobanu
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Ana Gutiérrez-Preciado
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Sergey A Karpov
- Zoological Institute RAS, Universitetskaya emb. 1, and St Petersburg State University, Universitetskaya emb. 7/9, St Petersburg 199034, Russia
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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4
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Alam J, Rahman FT, Sah-Teli SK, Venkatesan R, Koski MK, Autio KJ, Hiltunen JK, Kastaniotis AJ. Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae. Acta Crystallogr D Struct Biol 2021; 77:840-853. [PMID: 34076597 PMCID: PMC8171064 DOI: 10.1107/s2059798321004149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/17/2021] [Indexed: 12/04/2022] Open
Abstract
Rsm22-family proteins are conserved putative SAM-dependent methyltransferases with important functions in mitochondrial translation. Here, the results of a comparative bioinformatics analysis of Rsm22-type proteins are presented, the expression, biophysical characterization and crystallization of Saccharomyces cerevisiae Rsm22 are reported, a low-resolution SAXS structure of the protein is revealed, and SAM-dependent RNA methyl transferase activity of the protein is demonstrated. The Saccharomyces cerevisiae Rsm22 protein (Sc-Rsm22), encoded by the nuclear RSM22 (systematic name YKL155c) gene, is a distant homologue of Rsm22 from Trypanosoma brucei (Tb-Rsm22) and METTL17 from mouse (Mm-METTL17). All three proteins have been shown to be associated with mitochondrial gene expression, and Sc-Rsm22 has been documented to be essential for mitochondrial respiration. The Sc-Rsm22 protein comprises a polypeptide of molecular weight 72.2 kDa that is predicted to harbor an N-terminal mitochondrial targeting sequence. The precise physiological function of Rsm22-family proteins is unknown, and no structural information has been available for Sc-Rsm22 to date. In this study, Sc-Rsm22 was expressed and purified in monomeric and dimeric forms, their folding was confirmed by circular-dichroism analyses and their low-resolution structures were determined using a small-angle X-ray scattering (SAXS) approach. The solution structure of the monomeric form of Sc-Rsm22 revealed an elongated three-domain arrangement, which differs from the shape of Tb-Rsm22 in its complex with the mitochondrial small ribosomal subunit in T. brucei (PDB entry 6sg9). A bioinformatic analysis revealed that the core domain in the middle (Leu117–Asp462 in Sc-Rsm22) resembles the corresponding region in Tb-Rsm22, including a Rossmann-like methyltransferase fold followed by a zinc-finger-like structure. The latter structure is not present in this position in other methyltransferases and is therefore a unique structural motif for this family. The first half of the C-terminal domain is likely to form an OB-fold, which is typically found in RNA-binding proteins and is also seen in the Tb-Rsm22 structure. In contrast, the N-terminal domain of Sc-Rsm22 is predicted to be fully α-helical and shares no sequence similarity with other family members. Functional studies demonstrated that the monomeric variant of Sc-Rsm22 methylates mitochondrial tRNAs in vitro. These data suggest that Sc-Rsm22 is a new and unique member of the RNA methyltransferases that is important for mitochondrial protein synthesis.
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Affiliation(s)
- Jahangir Alam
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, FIN-90220 Oulu, Finland
| | - Farah Tazkera Rahman
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, FIN-90220 Oulu, Finland
| | - Shiv K Sah-Teli
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, FIN-90220 Oulu, Finland
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, FIN-90220 Oulu, Finland
| | | | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, FIN-90220 Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, FIN-90220 Oulu, Finland
| | - Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7B, FIN-90220 Oulu, Finland
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5
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Saurer M, Ramrath DJF, Niemann M, Calderaro S, Prange C, Mattei S, Scaiola A, Leitner A, Bieri P, Horn EK, Leibundgut M, Boehringer D, Schneider A, Ban N. Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery. Science 2020; 365:1144-1149. [PMID: 31515389 DOI: 10.1126/science.aaw5570] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 07/02/2019] [Accepted: 08/04/2019] [Indexed: 01/02/2023]
Abstract
Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in Trypanosoma brucei involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo-electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which we identified 34 factors that interact with immature ribosomal RNA (rRNA) and recognize its functionally important regions. The assembly proceeds through large-scale conformational changes in rRNA coupled with successive incorporation of mitoribosomal proteins, providing an example for the complexity of the ribosomal assembly process in mitochondria.
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Affiliation(s)
- Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - David J F Ramrath
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Moritz Niemann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Salvatore Calderaro
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Céline Prange
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Simone Mattei
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Alain Scaiola
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Otto-Stern-Weg 3, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Philipp Bieri
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Elke K Horn
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland.
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6
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Single-Gene Deletions Contributing to Loss of Heterozygosity in Saccharomyces cerevisiae: Genome-Wide Screens and Reproducibility. G3-GENES GENOMES GENETICS 2019; 9:2835-2850. [PMID: 31270132 PMCID: PMC6723133 DOI: 10.1534/g3.119.400429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Loss of heterozygosity (LOH) is a phenomenon commonly observed in cancers; the loss of chromosomal regions can be both causal and indicative of underlying genome instability. Yeast has long been used as a model organism to study genetic mechanisms difficult to study in mammalian cells. Studying gene deletions leading to increased LOH in yeast aids our understanding of the processes involved, and guides exploration into the etiology of LOH in cancers. Yet, before in-depth mechanistic studies can occur, candidate genes of interest must be identified. Utilizing the heterozygous Saccharomyces cerevisiae deletion collection (≈ 6500 strains), 217 genes whose disruption leads to increased LOH events at the endogenously heterozygous mating type locus were identified. Our investigation to refine this list of genes to candidates with the most definite impact on LOH includes: secondary testing for LOH impact at an additional locus, gene ontology analysis to determine common gene characteristics, and positional gene enrichment studies to identify chromosomal regions important in LOH events. Further, we conducted extensive comparisons of our data to screens with similar, but distinct methodologies, to further distinguish genes that are more likely to be true contributors to instability due to their reproducibility, and not just identified due to the stochastic nature of LOH. Finally, we selected nine candidate genes and quantitatively measured their impact on LOH as a benchmark for the impact of genes identified in our study. Our data add to the existing body of work and strengthen the evidence of single-gene knockdowns contributing to genome instability.
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Desai N, Brown A, Amunts A, Ramakrishnan V. The structure of the yeast mitochondrial ribosome. Science 2017; 355:528-531. [PMID: 28154081 DOI: 10.1126/science.aal2415] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/05/2017] [Indexed: 01/02/2023]
Abstract
Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms. The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeast-specific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded messenger RNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation.
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Affiliation(s)
- Nirupa Desai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alan Brown
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alexey Amunts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.,SciLifeLab, Stockholm University, SE-106 91 Stockholm, Sweden
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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8
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RSM22, mtYsxC and PNKD-like proteins are required for mitochondrial translation in Trypanosoma brucei. Mitochondrion 2017; 34:67-74. [DOI: 10.1016/j.mito.2017.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/07/2016] [Accepted: 01/10/2017] [Indexed: 11/20/2022]
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Abstract
Mitochondria play fundamental roles in the regulation of life and death of eukaryotic cells. They mediate aerobic energy conversion through the oxidative phosphorylation (OXPHOS) system, and harbor and control the intrinsic pathway of apoptosis. As a descendant of a bacterial endosymbiont, mitochondria retain a vestige of their original genome (mtDNA), and its corresponding full gene expression machinery. Proteins encoded in the mtDNA, all components of the multimeric OXPHOS enzymes, are synthesized in specialized mitochondrial ribosomes (mitoribosomes). Mitoribosomes are therefore essential in the regulation of cellular respiration. Additionally, an increasing body of literature has been reporting an alternative role for several mitochondrial ribosomal proteins as apoptosis-inducing factors. No surprisingly, the expression of genes encoding for mitoribosomal proteins, mitoribosome assembly factors and mitochondrial translation factors is modified in numerous cancers, a trait that has been linked to tumorigenesis and metastasis. In this article, we will review the current knowledge regarding the dual function of mitoribosome components in protein synthesis and apoptosis and their association with cancer susceptibility and development. We will also highlight recent developments in targeting mitochondrial ribosomes for the treatment of cancer.
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10
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Kowalec P, Fronk J, Kurlandzka A. The Irr1/Scc3 protein implicated in chromosome segregation in Saccharomyces cerevisiae has a dual nuclear-cytoplasmic localization. Cell Div 2017; 12:1. [PMID: 28077952 PMCID: PMC5223379 DOI: 10.1186/s13008-016-0027-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Correct chromosome segregation depends on the sister chromatid cohesion complex. The essential, evolutionarily conserved regulatory protein Irr1/Scc3, is responsible for the complex loading onto DNA and for its removal. We found that, unexpectedly, Irr1 is present not only in the nucleus but also in the cytoplasm. RESULTS We show that Irr1 protein is enriched in the cytoplasm upon arrest of yeast cells in G1 phase following nitrogen starvation, diauxic shift or α-factor action, and also during normal cell cycle. Despite the presence of numerous Crm1-dependent export signals, the cytoplasmic pool of Irr1 is not derived through export from the nucleus but instead is simply retained in the cytoplasm. Cytoplasmic Irr1 interacts with the Imi1 protein implicated in glutathione homeostasis and mitochondrial integrity. CONCLUSIONS Besides regulation of the sister chromatid cohesion complex in the nucleus Irr1 appears to have an additional role in the cytoplasm, possibly through interaction with the cytoplasmic protein Imi1.
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Affiliation(s)
- Piotr Kowalec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Jan Fronk
- Department of Molecular Biology, Faculty of Biology, Institute of Biochemistry, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Kurlandzka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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11
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Caslavka Zempel KE, Vashisht AA, Barshop WD, Wohlschlegel JA, Clarke SG. Determining the Mitochondrial Methyl Proteome in Saccharomyces cerevisiae using Heavy Methyl SILAC. J Proteome Res 2016; 15:4436-4451. [PMID: 27696855 DOI: 10.1021/acs.jproteome.6b00521] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Methylation is a common and abundant post-translational modification. High-throughput proteomic investigations have reported many methylation sites from complex mixtures of proteins. The lack of consistency between parallel studies, resulting from both false positives and missed identifications, suggests problems with both over-reporting and under-reporting methylation sites. However, isotope labeling can be used effectively to address the issue of false-positives, and fractionation of proteins can increase the probability of identifying methylation sites in lower abundance. Here we have adapted heavy methyl SILAC to analyze fractions of the budding yeast Saccharomyces cerevisiae under respiratory conditions to allow for the production of mitochondria, an organelle whose proteins are often overlooked in larger methyl proteome studies. We have found 12 methylation sites on 11 mitochondrial proteins as well as an additional 14 methylation sites on 9 proteins that are nonmitochondrial. Of these methylation sites, 20 sites have not been previously reported. This study represents the first characterization of the yeast mitochondrial methyl proteome and the second proteomic investigation of global mitochondrial methylation to date in any organism.
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Affiliation(s)
- Katelyn E Caslavka Zempel
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - Ajay A Vashisht
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - William D Barshop
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - James A Wohlschlegel
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute and ‡Department of Biological Chemistry and the David Geffen School of Medicine, UCLA , Los Angeles, California 90095, United States
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12
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Sun X, Wang Z, Guo X, Li H, Gu Z. Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains. PLoS One 2016; 11:e0153523. [PMID: 27077367 PMCID: PMC4831757 DOI: 10.1371/journal.pone.0153523] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/30/2016] [Indexed: 11/19/2022] Open
Abstract
Evolution of gene regulation has been proposed to play an important role in environmental adaptation. Exploring mechanisms underlying coordinated evolutionary changes at various levels of gene regulation could shed new light on how organism adapt in nature. In this study, we focused on regulatory differences between a laboratory Saccharomyces cerevisiae strain BY4742 and a pathogenic S. cerevisiae strain, YJM789. The two strains diverge in many features, including growth rate, morphology, high temperature tolerance, and pathogenicity. Our RNA-Seq and ribosomal footprint profiling data showed that gene expression differences are pervasive, and genes functioning in mitochondria are mostly divergent between the two strains at both transcriptional and translational levels. Combining functional genomics data from other yeast strains, we further demonstrated that significant divergence of expression for genes functioning in the electron transport chain (ETC) was likely caused by differential expression of a transcriptional factor, HAP4, and that post-transcriptional regulation mediated by an RNA-binding protein, PUF3, likely led to expression divergence for genes involved in mitochondrial translation. We also explored mito-nuclear interactions via mitochondrial DNA replacement between strains. Although the two mitochondrial genomes harbor substantial sequence divergence, neither growth nor gene expression were affected by mitochondrial DNA replacement in both fermentative and respiratory growth media, indicating compatible mitochondrial and nuclear genomes between these two strains in the tested conditions. Collectively, we used mitochondrial functions as an example to demonstrate for the first time that evolution at both transcriptional and post-transcriptional levels could lead to coordinated regulatory changes underlying strain specific functional variations.
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Affiliation(s)
- Xuepeng Sun
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Zhe Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America
| | - Xiaoxian Guo
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America
| | - Hongye Li
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America
- * E-mail:
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13
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Du P, Yuan B, Cao J, Zhao J, Ding L, Chen L, Ying S, Jiang L, Lin J, Xu X, Cheng L, Ye Q. Methyltransferase-like 17 physically and functionally interacts with estrogen receptors. IUBMB Life 2015; 67:861-8. [PMID: 26488768 DOI: 10.1002/iub.1444] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 10/03/2015] [Indexed: 02/06/2023]
Abstract
Estrogen exerts its physiological and pathological functions through two estrogen receptors (ERs), ERα and ERβ, which act as transcription factors. Coregulators, including coactivators and corepressors, have been shown to be crucial for regulation of ER transcriptional activity. Although many coregulators have been identified to regulate activities of ERs, novel coregulators are still needed to be investigated. Here, we show that human methyltransferase-like 17 (METTL17), whose function is unknown, physically interacts with ERα and ERβ, and functionally acts as a coactivator for ERs. METTL17 interacts with ER in vitro and in yeast and mammalian cells. Activation function-1 (AF1) and AF2 domains of ERs are responsible for the interaction between METTL17 and ERs. Knockdown of METTL17 reduces transcriptional activities of ERα and ERβ in breast cancer cells, whereas METTL17 overexpression increases ERα and ERβ transcriptional activities. Inhibition of METTL17 expression decreases mRNA and protein levels of ER target genes, including PR, cathepsin D, and pS2. Moreover, METTL17 knockdown reduces breast cancer cell growth. These results indicate that METTL17 is a novel coactivator of ERs and may play a role in breast tumorigenesis.
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Affiliation(s)
- Peiyun Du
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Bin Yuan
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Jia Cao
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Jing Zhao
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Lihua Ding
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Lihan Chen
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Sunyang Ying
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Lina Jiang
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Jiajia Lin
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Xiaojie Xu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Long Cheng
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
| | - Qinong Ye
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing, People's Republic of China
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The Stationary-Phase Cells of Saccharomyces cerevisiae Display Dynamic Actin Filaments Required for Processes Extending Chronological Life Span. Mol Cell Biol 2015; 35:3892-908. [PMID: 26351139 DOI: 10.1128/mcb.00811-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 08/31/2015] [Indexed: 11/20/2022] Open
Abstract
Stationary-growth-phase Saccharomyces cerevisiae yeast cultures consist of nondividing cells that undergo chronological aging. For their successful survival, the turnover of proteins and organelles, ensured by autophagy and the activation of mitochondria, is performed. Some of these processes are engaged in by the actin cytoskeleton. In S. cerevisiae stationary-phase cells, F actin has been shown to form static aggregates named actin bodies, subsequently cited to be markers of quiescence. Our in vivo analyses revealed that stationary-phase cultures contain cells with dynamic actin filaments, besides the cells with static actin bodies. The cells with dynamic actin displayed active endocytosis and autophagy and well-developed mitochondrial networks. Even more, stationary-phase cell cultures grown under calorie restriction predominantly contained cells with actin cables, confirming that the presence of actin cables is linked to successful adaptation to stationary phase. Cells with actin bodies were inactive in endocytosis and autophagy and displayed aberrations in mitochondrial networks. Notably, cells of the respiratory activity-deficient cox4Δ strain displayed the same mitochondrial aberrations and actin bodies only. Additionally, our results indicate that mitochondrial dysfunction precedes the formation of actin bodies and the appearance of actin bodies corresponds to decreased cell fitness. We conclude that the F-actin status reflects the extent of damage that arises from exponential growth.
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15
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Bennett L, Kittas A, Liu S, Papageorgiou LG, Tsoka S. Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PLoS One 2014; 9:e112821. [PMID: 25412367 PMCID: PMC4239042 DOI: 10.1371/journal.pone.0112821] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 10/15/2014] [Indexed: 12/05/2022] Open
Abstract
Community structure detection has proven to be important in revealing the underlying properties of complex networks. The standard problem, where a partition of disjoint communities is sought, has been continually adapted to offer more realistic models of interactions in these systems. Here, a two-step procedure is outlined for exploring the concept of overlapping communities. First, a hard partition is detected by employing existing methodologies. We then propose a novel mixed integer non linear programming (MINLP) model, known as OverMod, which transforms disjoint communities to overlapping. The procedure is evaluated through its application to protein-protein interaction (PPI) networks of the rat, E. coli, yeast and human organisms. Connector nodes of hard partitions exhibit topological and functional properties indicative of their suitability as candidates for multiple module membership. OverMod identifies two types of connector nodes, inter and intra-connector, each with their own particular characteristics pertaining to their topological and functional role in the organisation of the network. Inter-connector proteins are shown to be highly conserved proteins participating in pathways that control essential cellular processes, such as proliferation, differentiation and apoptosis and their differences with intra-connectors is highlighted. Many of these proteins are shown to possess multiple roles of distinct nature through their participation in different network modules, setting them apart from proteins that are simply ‘hubs’, i.e. proteins with many interaction partners but with a more specific biochemical role.
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Affiliation(s)
- Laura Bennett
- Centre for Process Systems Engineering, Department of Chemical Engineering, UCL (University College London), Torrington Place, WC1E 7JE, London, United Kingdom
| | - Aristotelis Kittas
- Department of Informatics, King's College London, Strand, WC2R 2LS, London, United Kingdom
| | - Songsong Liu
- Centre for Process Systems Engineering, Department of Chemical Engineering, UCL (University College London), Torrington Place, WC1E 7JE, London, United Kingdom
| | - Lazaros G. Papageorgiou
- Centre for Process Systems Engineering, Department of Chemical Engineering, UCL (University College London), Torrington Place, WC1E 7JE, London, United Kingdom
| | - Sophia Tsoka
- Department of Informatics, King's College London, Strand, WC2R 2LS, London, United Kingdom
- * E-mail:
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16
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Grimm C, Böhl L, Osiewacz HD. Overexpression of Pa_1_10620 encoding a mitochondrial Podospora anserina protein with homology to superoxide dismutases and ribosomal proteins leads to lifespan extension. Curr Genet 2014; 61:73-86. [PMID: 25151510 DOI: 10.1007/s00294-014-0446-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/01/2014] [Accepted: 08/17/2014] [Indexed: 11/27/2022]
Abstract
In biological systems, reactive oxygen species (ROS) represent 'double edged swords': as signaling molecules they are essential for proper development, as reactive agents they cause molecular damage and adverse effects like degeneration and aging. A well-coordinated control of ROS is therefore of key importance. Superoxide dismutases (SODs) are enzymes active in the detoxification of superoxide. The number of isoforms of these proteins varies among species. Here we report the characterization of the putative protein encoded by Pa_1_10620 that has been previously annotated to code for a mitochondrial ribosomal protein but shares also sequence domains with SODs. We report that the gene is transcribed in P. anserina cultures of all ages and that the encoded protein localizes to mitochondria. In strains overexpressing Pa_1_10620 in a genetic background in which PaSod3, the mitochondrial MnSOD of P. anserina, is deleted, no SOD activity could be identified in isolated mitochondria. However, overexpression of the gene leads to lifespan extension suggesting a pro-survival function of the protein in P. anserina.
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Affiliation(s)
- Carolin Grimm
- Faculty for Biosciences and Cluster of Excellence Frankfurt 'Macromolecular Complexes', Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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17
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Woellhaf MW, Hansen KG, Garth C, Herrmann JM. Import of ribosomal proteins into yeast mitochondria. Biochem Cell Biol 2014; 92:489-98. [PMID: 24943357 DOI: 10.1139/bcb-2014-0029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial ribosomes of baker's yeast contain at least 78 protein subunits. All but one of these proteins are nuclear-encoded, synthesized on cytosolic ribosomes, and imported into the matrix for biogenesis. The import of matrix proteins typically relies on N-terminal mitochondrial targeting sequences that form positively charged amphipathic helices. Interestingly, the N-terminal regions of many ribosomal proteins do not closely match the characteristics of matrix targeting sequences, suggesting that the import processes of these proteins might deviate to some extent from the general import route. So far, the biogenesis of only two ribosomal proteins, Mrpl32 and Mrp10, was studied experimentally and indeed showed surprising differences to the import of other preproteins. In this review article we summarize the current knowledge on the transport of proteins into the mitochondrial matrix, and thereby specifically focus on proteins of the mitochondrial ribosome.
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Affiliation(s)
- Michael W Woellhaf
- a Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663 Kaiserslautern, Germany
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18
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Jia Y, Ye L, Ji K, Zhang L, Hargest R, Ji J, Jiang WG. Death-associated protein-3, DAP-3, correlates with preoperative chemotherapy effectiveness and prognosis of gastric cancer patients following perioperative chemotherapy and radical gastrectomy. Br J Cancer 2013; 110:421-9. [PMID: 24300973 PMCID: PMC3899757 DOI: 10.1038/bjc.2013.712] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/18/2013] [Accepted: 10/21/2013] [Indexed: 11/09/2022] Open
Abstract
Background: DAP3 is a member of the death-associated protein (DAP) family and is characterised by proapoptotic function. It is involved in both exogenous and endogenous apoptotic pathways. In our previous studies, apoptotic level was found to be correlated with the effectiveness of preoperative chemotherapy. The effectiveness of preoperative chemotherapy was also associated with the overall effectiveness of the combined therapy and prognosis. The present study aimed to investigate the role of DAP3 in the evaluation of preoperative chemotherapy effectiveness and its ability to predict prognosis in gastric cancer. Methods: Quantitative PCR and immunohistochemistry staining were performed in 87 patients who received combined therapy. Knockdown of DAP3 was conducted in gastric cancer cell lines to investigate its impact on cell growth, migration, adhesion and invasion. Tolerance to chemotherapy agents was determined by assessing apoptosis and caspase-3. Results: Higher DAP3 expression in gastric tumours was correlated with better prognosis. Knockdown of DAP3 expression promoted cell migration and enhanced resistance to chemotherapy by inhibiting apoptosis. Conclusion: DAP3 is a potential molecular marker for response to preoperative chemotherapy and for predicting prognosis in gastric cancer patients treated with neoadjuvant chemotherapy and gastrectomy.
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Affiliation(s)
- Y Jia
- 1] Cardiff University-Peking University School of Oncology Joint Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [2] Metastasis and Angiogenesis Research Group, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [3] Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, No. 52, Haidian District, Beijing 100142, China
| | - L Ye
- 1] Cardiff University-Peking University School of Oncology Joint Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [2] Metastasis and Angiogenesis Research Group, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - K Ji
- 1] Cardiff University-Peking University School of Oncology Joint Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [2] Metastasis and Angiogenesis Research Group, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - L Zhang
- 1] Cardiff University-Peking University School of Oncology Joint Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [2] Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, No. 52, Haidian District, Beijing 100142, China
| | - R Hargest
- 1] Cardiff University-Peking University School of Oncology Joint Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [2] Metastasis and Angiogenesis Research Group, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - J Ji
- 1] Cardiff University-Peking University School of Oncology Joint Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [2] Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, No. 52, Haidian District, Beijing 100142, China
| | - W G Jiang
- 1] Cardiff University-Peking University School of Oncology Joint Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK [2] Metastasis and Angiogenesis Research Group, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
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19
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Rhein VF, Carroll J, Ding S, Fearnley IM, Walker JE. NDUFAF7 methylates arginine 85 in the NDUFS2 subunit of human complex I. J Biol Chem 2013; 288:33016-26. [PMID: 24089531 PMCID: PMC3829151 DOI: 10.1074/jbc.m113.518803] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complex I (NADH ubiquinone oxidoreductase) in mammalian mitochondria is an L-shaped assembly of 44 subunits. One arm is embedded in the inner membrane with the other protruding ∼100 Å into the matrix of the organelle. The extrinsic arm contains binding sites for NADH and the primary electron acceptor FMN, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking FMN to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction between the arms. The membrane arm contains four antiporter-like domains, probably energetically coupled to the quinone site and involved in pumping protons from the matrix into the intermembrane space contributing to the proton motive force. Complex I is put together from preassembled subcomplexes. Their compositions have been characterized partially, and at least 12 extrinsic assembly factor proteins are required for the assembly of the complex. One such factor, NDUFAF7, is predicted to belong to the family of S-adenosylmethionine-dependent methyltransferases characterized by the presence in their structures of a seven-β-strand protein fold. In the present study, the presence of NDUFAF7 in the mitochondrial matrix has been confirmed, and it has been demonstrated that it is a protein methylase that symmetrically dimethylates the ω-NG,NG′ atoms of residue Arg-85 in the NDUFS2 subunit of complex I. This methylation step occurs early in the assembly of complex I and probably stabilizes a 400-kDa subcomplex that forms the initial nucleus of the peripheral arm and its juncture with the membrane arm.
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Affiliation(s)
- Virginie F Rhein
- From the Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom
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20
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Franck WL, Gokce E, Oh Y, Muddiman DC, Dean RA. Temporal analysis of the magnaporthe oryzae proteome during conidial germination and cyclic AMP (cAMP)-mediated appressorium formation. Mol Cell Proteomics 2013; 12:2249-65. [PMID: 23665591 PMCID: PMC3734583 DOI: 10.1074/mcp.m112.025874] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/09/2013] [Indexed: 11/06/2022] Open
Abstract
Rice blast disease caused by Magnaporthe oryzae is one of the most serious threats to global rice production. During the earliest stages of rice infection, M. oryzae conidia germinate on the leaf surface and form a specialized infection structure termed the appressorium. The development of the appressorium represents the first critical stage of infectious development. A total of 3200 unique proteins were identified by nanoLC-MS/MS in a temporal study of conidial germination and cAMP-induced appressorium formation in M. oryzae. Using spectral counting based label free quantification, observed changes in relative protein abundance during the developmental process revealed changes in the cell wall biosynthetic machinery, transport functions, and production of extracellular proteins in developing appressoria. One hundred and sixty-six up-regulated and 208 down-regulated proteins were identified in response to cAMP treatment. Proteomic analysis of a cAMP-dependent protein kinase A mutant that is compromised in the ability to form appressoria identified proteins whose developmental regulation is dependent on cAMP signaling. Selected reaction monitoring was used for absolute quantification of four regulated proteins to validate the global proteomics data and confirmed the germination or appressorium specific regulation of these proteins. Finally, a comparison of the proteome and transcriptome was performed and revealed little correlation between transcript and protein regulation. A subset of regulated proteins were identified whose transcripts show similar regulation patterns and include many of the most strongly regulated proteins indicating a central role in appressorium formation. A temporal quantitative RT-PCR analysis confirmed a strong correlation between transcript and protein abundance for some but not all genes. Collectively, the data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity.
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Affiliation(s)
| | - Emine Gokce
- §W.M. Keck Fourier Transform-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27606
| | - Yeonyee Oh
- From the ‡Center for Integrated Fungal Research
| | - David C. Muddiman
- §W.M. Keck Fourier Transform-ICR Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 27606
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21
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Abstract
Motivation: Biological networks change in response to genetic and environmental cues. Changes are reflected in the abundances of biomolecules, the composition of protein complexes and other descriptors of the biological state. Methods to infer the dynamic state of a cell would have great value for understanding how cells change over time to accomplish biological goals. Results: A new method predicts the dynamic state of protein complexes in a cell, with protein expression inferred from transcription profile time courses and protein complexes inferred by joint analysis of protein co-expression and protein–protein interaction maps. Two algorithmic advances are presented: a new method, DHAC (Dynamical Hierarchical Agglomerative Clustering), for clustering time-evolving networks; and a companion method, MATCH-EM, for matching corresponding clusters across time points. With link prediction as an objective assessment metric, DHAC provides a substantial advance over existing clustering methods. An application to the yeast metabolic cycle demonstrates how waves of gene expression correspond to individual protein complexes. Our results suggest regulatory mechanisms for assembling the mitochondrial ribosome and illustrate dynamic changes in the components of the nuclear pore. Availability: All source code and data are available under the Boost Software License as supplementary material, at www.baderzone.org, and at sourceforge.net/projects/dhacdist Contact: joel.bader@jhu.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yongjin Park
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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22
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Shah AN, Cadinu D, Henke RM, Xin X, Dastidar RG, Zhang L. Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance. Physiol Genomics 2011; 43:855-72. [PMID: 21586670 DOI: 10.1152/physiolgenomics.00232.2010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hypoxia is a widely occurring condition experienced by diverse organisms under numerous physiological and disease conditions. To probe the molecular mechanisms underlying hypoxia responses and tolerance, we performed a genome-wide screen to identify mutants with enhanced hypoxia tolerance in the model eukaryote, the yeast Saccharomyces cerevisiae. Yeast provides an excellent model for genomic and proteomic studies of hypoxia. We identified five genes whose deletion significantly enhanced hypoxia tolerance. They are RAI1, NSR1, BUD21, RPL20A, and RSM22, all of which encode functions involved in ribosome biogenesis. Further analysis of the deletion mutants showed that they minimized hypoxia-induced changes in polyribosome profiles and protein synthesis. Strikingly, proteomic analysis by using the iTRAQ profiling technology showed that a substantially fewer number of proteins were changed in response to hypoxia in the deletion mutants, compared with the parent strain. Computational analysis of the iTRAQ data indicated that the activities of a group of regulators were regulated by hypoxia in the wild-type parent cells, but such regulation appeared to be diminished in the deletion strains. These results show that the deletion of one of the genes involved in ribosome biogenesis leads to the reversal of hypoxia-induced changes in gene expression and related regulators. They suggest that modifying ribosomal function is an effective mechanism to minimize hypoxia-induced specific protein changes and to confer hypoxia tolerance. These results may have broad implications in understanding hypoxia responses and tolerance in diverse eukaryotes ranging from yeast to humans.
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Affiliation(s)
- Ajit N Shah
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75080, USA
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23
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Desmond E, Brochier-Armanet C, Forterre P, Gribaldo S. On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes. Res Microbiol 2011; 162:53-70. [DOI: 10.1016/j.resmic.2010.10.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 10/04/2010] [Indexed: 12/31/2022]
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24
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Harada T, Iwai A, Miyazaki T. Identification of DELE, a novel DAP3-binding protein which is crucial for death receptor-mediated apoptosis induction. Apoptosis 2010; 15:1247-55. [DOI: 10.1007/s10495-010-0519-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Koc E, Haque M, Spremulli L. Current Views of the Structure of the Mammalian Mitochondrial Ribosome. Isr J Chem 2010. [DOI: 10.1002/ijch.201000002] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Lambou K, Lamarre C, Beau R, Dufour N, Latge JP. Functional analysis of the superoxide dismutase family inAspergillus fumigatus. Mol Microbiol 2010; 75:910-23. [DOI: 10.1111/j.1365-2958.2009.07024.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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27
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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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28
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Markov DA, Savkina M, Anikin M, Del Campo M, Ecker K, Lambowitz AM, De Gnore JP, McAllister WT. Identification of proteins associated with the yeast mitochondrial RNA polymerase by tandem affinity purification. Yeast 2009; 26:423-40. [PMID: 19536766 PMCID: PMC2896726 DOI: 10.1002/yea.1672] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The abundance of mitochondrial (mt) transcripts varies under different conditions, and is thought to depend upon rates of transcription initiation, transcription termination/attenuation and RNA processing/degradation. The requirement to maintain the balance between RNA synthesis and processing may involve coordination between these processes; however, little is known about factors that regulate the activity of mtRNA polymerase (mtRNAP). Recent attempts to identify mtRNAP–protein interactions in yeast by means of a generalized tandem affinity purification (TAP) protocol were not successful, most likely because they involved a C-terminal mtRNAP–TAP fusion (which is incompatible with mtRNAP function) and because of the use of whole-cell solubilization protocols that did not preserve the integrity of mt protein complexes. Based upon the structure of T7 RNAP (to which mtRNAPs show high sequence similarity), we identified positions in yeast mtRNAP that allow insertion of a small affinity tag, confirmed the mature N-terminus, constructed a functional N-terminal TAP–mtRNAP fusion, pulled down associated proteins, and identified them by LC–MS–MS. Among the proteins found in the pull-down were a DEAD-box protein (Mss116p) and an RNA-binding protein (Pet127p). Previous genetic experiments suggested a role for these proteins in linking transcription and RNA degradation, in that a defect in the mt degradadosome could be suppressed by overexpression of either of these proteins or, independently, by mutations in either mtRNAP or its initiation factor Mtf1p. Further, we found that Mss116p inhibits transcription by mtRNAP in vitro in a steady-state reaction. Our results support the hypothesis that Mss116p and Pet127p are involved in modulation of mtRNAP activity. Copyright © 2009 John Wiley & Sons, Ltd.
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Affiliation(s)
- Dmitriy A Markov
- Departments of Cell Biology, University of Medicine and Dentistry of New Jersey, Stratford, USA.
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29
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Simons SP, McLellan TJ, Aeed PA, Zaniewski RP, Desbonnet CR, Wondrack LM, Marr ES, Subashi TA, Dougherty TJ, Xu Z, Wang IK, LeMotte PK, Maguire BA. Purification of the large ribosomal subunit via its association with the small subunit. Anal Biochem 2009; 395:77-85. [PMID: 19646947 DOI: 10.1016/j.ab.2009.07.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 07/24/2009] [Accepted: 07/27/2009] [Indexed: 11/17/2022]
Abstract
We have developed an affinity purification of the large ribosomal subunit from Deinococcus radiodurans that exploits its association with FLAG-tagged 30S subunits. Thus, capture is indirect so that no modification of the 50S is required and elution is achieved under mild conditions (low magnesium) that disrupt the association, avoiding the addition of competitor ligands or coelution of common contaminants. Efficient purification of highly pure 50S is achieved, and the chromatography simultaneously sorts the 50S into three classes according to their association status (unassociated, loosely associated, or tightly associated), improving homogeneity.
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MESH Headings
- Bacterial Proteins/analysis
- Centrifugation, Density Gradient
- Chromatography, Affinity
- Chromatography, High Pressure Liquid
- Cloning, Molecular
- Databases, Protein
- Deinococcus/ultrastructure
- Gene Expression
- Magnesium Chloride
- Oligopeptides
- Peptide Fragments/analysis
- Peptides/genetics
- RNA, Bacterial/analysis
- RNA, Ribosomal/analysis
- Recombinant Fusion Proteins
- Ribosomal Proteins/analysis
- Ribosomal Proteins/genetics
- Ribosome Subunits, Large, Bacterial/chemistry
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Small, Bacterial/genetics
- Ribosome Subunits, Small, Bacterial/metabolism
- Spectrometry, Mass, Electrospray Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Samuel P Simons
- Department of Exploratory Medicinal Sciences, Pfizer Global Research and Development, Groton, CT 06340, USA
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30
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Heeren G, Rinnerthaler M, Laun P, von Seyerl P, Kössler S, Klinger H, Hager M, Bogengruber E, Jarolim S, Simon-Nobbe B, Schüller C, Carmona-Gutierrez D, Breitenbach-Koller L, Mück C, Jansen-Dürr P, Criollo A, Kroemer G, Madeo F, Breitenbach M. The mitochondrial ribosomal protein of the large subunit, Afo1p, determines cellular longevity through mitochondrial back-signaling via TOR1. Aging (Albany NY) 2009; 1:622-36. [PMID: 20157544 PMCID: PMC2806038 DOI: 10.18632/aging.100065] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/10/2009] [Indexed: 11/25/2022]
Abstract
Yeast
mother cell-specific aging constitutes a model of replicative aging as it
occurs in stem cell populations of higher eukaryotes. Here, we present a
new long-lived yeast deletion mutation,afo1 (for aging factor one),
that confers a 60% increase in replicative lifespan. AFO1/MRPL25
codes for a protein that is contained in the large subunit of the
mitochondrial ribosome. Double mutant experiments indicate that the
longevity-increasing action of the afo1 mutation is independent of
mitochondrial translation, yet involves the cytoplasmic Tor1p as well as
the growth-controlling transcription factor Sfp1p. In their final cell
cycle, the long-lived mutant cells do show the phenotypes of yeast
apoptosis indicating that the longevity of the mutant is not caused by an
inability to undergo programmed cell death. Furthermore, the afo1 mutation
displays high resistance against oxidants. Despite the respiratory
deficiency the mutant has paradoxical increase in growth rate compared to
generic petite mutants. A comparison of the single and double mutant
strains for afo1 and fob1 shows that the longevity phenotype
of afo1 is independent of the formation of ERCs (ribosomal DNA
minicircles). AFO1/MRPL25 function establishes a new connection
between mitochondria, metabolism and aging.
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Affiliation(s)
- Gino Heeren
- Department of Cell Biology, Division of Genetics, University of Salzburg, 5020 Salzburg, Austria
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31
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Miller JL, Koc H, Koc EC. Identification of phosphorylation sites in mammalian mitochondrial ribosomal protein DAP3. Protein Sci 2008; 17:251-60. [PMID: 18227431 DOI: 10.1110/ps.073185608] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Mammalian mitochondrial ribosomes synthesize 13 proteins that are essential for oxidative phosphorylation. In addition to their role in protein synthesis, some of the mitochondrial ribosomal proteins have acquired functions in other cellular processes such as apoptosis. Death-associated protein 3 (DAP3), also referred to as mitochondrial ribosomal protein S29 (MRP-S29), is a GTP-binding pro-apoptotic protein located in the small subunit of the ribosome. Previous studies have shown that phosphorylation is one of the most likely regulatory mechanisms for DAP3 function in apoptosis and may be in protein synthesis; however, no phosphorylation sites were identified. In this study, we have investigated the phosphorylation status of ribosomal DAP3 and mapped the phosphorylation sites by tandem mass spectrometry. Mitochondrial ribosomal DAP3 is phosphorylated at Ser215 or Thr216, Ser220, Ser251 or Ser252, and Ser280. In addition, phosphorylation of recombinant DAP3 by Protein kinase A and Protein kinase Cdelta at residues that are endogenously phosphorylated in ribosomal DAP3 suggests both of these kinases as potential candidates responsible for the in vivo phosphorylation of DAP3 in mammalian mitochondria. Interestingly, the majority of the phosphorylation sites detected in our study are clustered around the highly conserved GTP-binding motifs, speculating on the significance of these residues on protein conformation and activity. Site-directed mutagenesis studies on selected phosphorylation sites were performed to determine the effect of phosphorylation on cell proliferation and PARP cleavage as indication of caspase activation. Overall, our findings suggest DAP3, a mitochondrial ribosomal small subunit protein, is a novel phosphorylated target.
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Affiliation(s)
- Jennifer L Miller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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32
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Zíková A, Panigrahi AK, Dalley RA, Acestor N, Anupama A, Ogata Y, Myler PJ, Stuart K. Trypanosoma brucei mitochondrial ribosomes: affinity purification and component identification by mass spectrometry. Mol Cell Proteomics 2008; 7:1286-96. [PMID: 18364347 DOI: 10.1074/mcp.m700490-mcp200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although eukaryotic mitochondrial (mt) ribosomes evolved from a putative prokaryotic ancestor their compositions vary considerably among organisms. We determined the protein composition of tandem affinity-purified Trypanosoma brucei mt ribosomes by mass spectrometry and identified 133 proteins of which 77 were associated with the large subunit and 56 were associated with the small subunit. Comparisons with bacterial and mammalian mt ribosomal proteins identified T. brucei mt homologs of L2-4, L7/12, L9, L11, L13-17, L20-24, L27-30, L33, L38, L43, L46, L47, L49, L52, S5, S6, S8, S9, S11, S15-18, S29, and S34, although the degree of conservation varied widely. Sequence characteristics of some of the component proteins indicated apparent functions in rRNA modification and processing, protein assembly, and mitochondrial metabolism implying possible additional roles for these proteins. Nevertheless most of the identified proteins have no homology outside Kinetoplastida implying very low conservation and/or a divergent function in kinetoplastid mitochondria.
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Affiliation(s)
- Alena Zíková
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
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33
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Pham TK, Wright PC. Proteomic Analysis of Calcium Alginate-Immobilized Saccharomyces cerevisiae under High-Gravity Fermentation Conditions. J Proteome Res 2008; 7:515-25. [DOI: 10.1021/pr070391h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Trong Khoa Pham
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
| | - Phillip C. Wright
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, U.K
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34
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Smits P, Smeitink JAM, van den Heuvel LP, Huynen MA, Ettema TJG. Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Res 2007; 35:4686-703. [PMID: 17604309 PMCID: PMC1950548 DOI: 10.1093/nar/gkm441] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For production of proteins that are encoded by the mitochondrial genome, mitochondria rely on their own mitochondrial translation system, with the mitoribosome as its central component. Using extensive homology searches, we have reconstructed the evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, revealing an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. We observe large variations in the protein content of mitoribosomes between different eukaryotes, with mammalian mitoribosomes sharing only 74 and 43% of its proteins with yeast and Leishmania mitoribosomes, respectively. We detected many previously unidentified mitochondrial ribosomal proteins (MRPs) and found that several have increased in size compared to their bacterial ancestral counterparts by addition of functional domains. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. Using sensitive profile-profile homology searches, we found hitherto undetected homology between bacterial and eukaryotic ribosomal proteins, as well as between fungal and mammalian ribosomal proteins, detecting two novel human MRPs. These newly detected MRPs constitute, along with evolutionary conserved MRPs, excellent new screening targets for human patients with unresolved mitochondrial oxidative phosphorylation disorders.
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Affiliation(s)
- Paulien Smits
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Jan A. M. Smeitink
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Lambert P. van den Heuvel
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Thijs J. G. Ettema
- Nijmegen Center for Mitochondrial Disorders, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert–Grooteplein-Zuid 10 and Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert-Grooteplein 28, 6525 GA Nijmegen, The Netherlands
- *To whom correspondence should be addressed.
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35
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Chang IF. Mass spectrometry-based proteomic analysis of the epitope-tag affinity purified protein complexes in eukaryotes. Proteomics 2007; 6:6158-66. [PMID: 17072909 DOI: 10.1002/pmic.200600225] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In recent years, MS has been widely used to study protein complex in eukaryotes. The identification of interacting proteins of a particular target protein may help defining protein-protein interaction and proteins of unknown functions. To isolate protein complexes, high-speed ultracentrifugation, sucrose density-gradient centrifugation, and coimmunoprecipitation have been widely used. However, the probability of getting nonspecific binding is comparatively high. Alternatively, by use of one- or two-step (tandem affinity purification) epitope-tag affinity purification, protein complexes can be isolated by affinity or immunoaffinity columns. These epitope-tags include protein A, hexahistidine (His), c-Myc, hemaglutinin (HA), calmodulin-binding protein, FLAG, maltose-binding protein, Strep, etc. The isolated protein complex can then be subjected to protease (i.e., trypsin) digestion followed by an MS analysis for protein identification. An example, the epitope-tag purification of the Arabidopsis cytosolic ribosomes, is addressed in this article to show the success of the application. Several representative protein complexes in eukaryotes been isolated and characterized by use of this approach are listed. In this review, the comparison among different tag systems, validation of interacting relationship, and choices of MS analysis method are addressed. The successful rate, advantages, limitations, and challenges of the epitope-tag purification are also discussed.
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Affiliation(s)
- Ing-Feng Chang
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA.
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36
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Kim HR, Chae HJ, Thomas M, Miyazaki T, Monosov A, Monosov E, Krajewska M, Krajewski S, Reed JC. Mammalian dap3 is an essential gene required for mitochondrial homeostasis in vivo and contributing to the extrinsic pathway for apoptosis. FASEB J 2006; 21:188-96. [PMID: 17135360 DOI: 10.1096/fj.06-6283com] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Death-associated protein-3 (DAP3) is a GTP binding protein previously implicated in both intramitochondrial protein synthesis and apoptosis. To explore the in vivo roles of DAP3, we generated and characterized DAP3-deficient mice. Homozygous dap3-/- embryos died at approximately day 9.5 in utero. The dap3-/- embryos and placentas were markedly shrunken. Embryos had arrested development, displaying severe growth restriction and lack of axial turning. Transmission electron microscopy analysis revealed abnormal, shrunken mitochondria with swollen crystae in dap3-/- embryos. Levels of cytochrome c oxidase-I, a protein encoded in the mitochondrial genome, were reduced in dap3-/- embryos, consistent with a role for DAP3 in intramitochondrial protein synthesis. A requirement for DAP3 in mitochondrial respiration was also revealed by oxygen consumption measurements using cultured cells treated with DAP3-specific small interfering RNA (siRNA). Studies of cultured cells from dap3-/- embryos confirmed a role in apoptosis induced by stimuli that trigger the extrinsic (TNFalpha, TRAIL, anti-Fas antibody) but not intrinsic (mitochondrial) cell death pathway. Thus, DAP3 joins a growing list of bifunctional proteins that play roles in normal mitochondrial physiology and in apoptosis.
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Affiliation(s)
- Hyung-Ryong Kim
- Burnham Institute for Medical Research, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
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37
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Khalimonchuk O, Ott M, Funes S, Ostermann K, Rödel G, Herrmann JM. Sequential processing of a mitochondrial tandem protein: insights into protein import in Schizosaccharomyces pombe. EUKARYOTIC CELL 2006; 5:997-1006. [PMID: 16835444 PMCID: PMC1489288 DOI: 10.1128/ec.00092-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The sequencing of the genome of Schizosaccharomyces pombe revealed the presence of a number of genes encoding tandem proteins, some of which are mitochondrial components. One of these proteins (pre-Rsm22-Cox11) consists of a fusion of Rsm22, a component of the mitochondrial ribosome, and Cox11, a factor required for copper insertion into cytochrome oxidase. Since in Saccharomyces cerevisiae, Cox11 is physically attached to the mitochondrial ribosome, it was suggested that the tandem organization of Rsm22-Cox11 is used to covalently tie the mitochondrial ribosome to Cox11 in S. pombe. We report here that pre-Rsm22-Cox11 is matured in two subsequent processing events. First, the mitochondrial presequence is removed. At a later stage of the import process, the Rsm22 and Cox11 domains are separated by cleavage of the mitochondrial processing peptidase at an internal processing site. In vivo data obtained using a tagged version of pre-Rsm22-Cox11 confirmed the proteolytic separation of Cox11 from the Rsm22 domain. Hence, the tandem organization of pre-Rsm22-Cox11 does not give rise to a persistent fusion protein but rather might be used to increase the import efficiency of Cox11 and/or to coordinate expression levels of Rsm22 and Cox11 in S. pombe.
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38
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Cobine PA, Pierrel F, Winge DR. Copper trafficking to the mitochondrion and assembly of copper metalloenzymes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:759-72. [PMID: 16631971 DOI: 10.1016/j.bbamcr.2006.03.002] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 03/03/2006] [Accepted: 03/05/2006] [Indexed: 11/20/2022]
Abstract
Copper is required within the mitochondrion for the function of two metalloenzymes, cytochrome c oxidase (CcO) and superoxide dismutase (Sod1). Copper metallation of these two enzymes occurs within the mitochondrial intermembrane space and is mediated by metallochaperone proteins. Cox17 is a key copper donor to two accessory proteins, Sco1 and Cox11, to form the two copper centers in the mature CcO complex. Ccs1 is the necessary metallochaperone for the copper metallation of Sod1 in the IMS as well as within the cytoplasm where the bulk of Sod1 resides. Copper ions used in the metallation of CcO and Sod1 appear to be provided by a novel copper pool within the mitochondrial matrix. This review documents copper ion shuttling within the mitochondrion and the proteins that mediate assembly of active CcO and Sod1.
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Affiliation(s)
- Paul A Cobine
- Departments of Medicine and Biochemistry, University of Utah Health Sciences Center, Salt Lake City, UT 84132, USA
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39
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Gan X, Arita K, Isono S, Kitakawa M, Yoshino KI, Yonezawa K, Kato A, Inoue H, Isono K. Identification and comparative analysis of the large subunit mitochondrial ribosomal proteins of Neurospora crassa. FEMS Microbiol Lett 2006; 254:157-64. [PMID: 16451194 DOI: 10.1111/j.1574-6968.2005.00024.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The mitochondrial ribosome (mitoribosome) has highly evolved from its putative prokaryotic ancestor and varies considerably from one organism to another. To gain further insights into its structural and evolutionary characteristics, we have purified and identified individual mitochondrial ribosomal proteins of Neurospora crassa by mass spectrometry and compared them with those of the budding yeast Saccharomyces cerevisiae. Most of the mitochondrial ribosomal proteins of the two fungi are well conserved with each other, although the degree of conservation varies to a large extent. One of the N. crassa mitochondrial ribosomal proteins was found to be homologous to yeast Mhr1p that is involved in homologous DNA recombination and genome maintenance in yeast mitochondria.
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Affiliation(s)
- Xiang Gan
- Department of Biology, Faculty of Science, Kobe University, Kobe, Japan
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40
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Jacques C, Chevrollier A, Loiseau D, Lagoutte L, Savagner F, Malthièry Y, Reynier P. mtDNA controls expression of the Death Associated Protein 3. Exp Cell Res 2006; 312:737-45. [PMID: 16413536 DOI: 10.1016/j.yexcr.2005.11.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 11/13/2005] [Accepted: 11/17/2005] [Indexed: 10/25/2022]
Abstract
The Death Associated Protein 3 (DAP3), a GTP-binding constituent of the small subunit of the mitochondrial ribosome, is implicated in the TNFalpha and IFNgamma apoptotic pathways of the cell and is involved in the maintenance of the mitochondrial network. We have investigated the mitochondrial role of DAP3 by analyzing its mRNA and protein expression in transformed and non-transformed cell lines presenting various levels of mtDNA. The 3 mtDNA-less (rho degrees ) cell lines showed a complete absence of DAP3, whereas the mRNA expression was conserved. In HepG2 cells treated with increasing doses of ddCTP, the depletion of mtDNA was accompanied by the reduced expression of DAP3. However, the expression of the corresponding mRNA was maintained, suggesting the existence of a post-transcriptional mechanism responsible for the depletion of the DAP3. Compared to the parental cells, the 3 rho degrees cell lines displayed partial resistance to staurosporin-induced cell death. The absence of pro-apoptotic DAP3 in these mtDNA-less cells could explain their reduced apoptotic capacity. Our results suggest that the mtDNA content plays a role in cell apoptosis by mediating the expression of DAP3.
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41
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O'Brien TW, O'Brien BJ, Norman RA. Nuclear MRP genes and mitochondrial disease. Gene 2005; 354:147-51. [PMID: 15908146 DOI: 10.1016/j.gene.2005.03.026] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2004] [Revised: 02/21/2005] [Accepted: 03/25/2005] [Indexed: 11/23/2022]
Abstract
The ancestral mitochondrial ribosome (70S) underwent major structural remodeling during the evolution of mammalian mitochondrial ribosomes (55S). Despite the loss of nearly half their RNA, 55S ribosomes are actually larger than bacterial ribosomes because of all the extra proteins they contain. Typical of mammalian mitochondrial ribosomes, the human mitochondrial ribosome is one of the most protein-rich ribosomes, containing several new proteins. One of the new proteins is a novel GTP binding protein, DAP3, that has been implicated in apoptosis. Except for DAP3, the locations of the individual new proteins in the ribosome are unknown. All of the MRPs are encoded by nuclear genes. Mutations or deficiencies of ribosome assembly proteins or other essential proteins are candidates for mitochondrial disease, since the mitochondrial ribosome translates mRNAs for the 13 essential components of the oxidative phosphorylation system. Several of the MRP genes map to loci associated with disorders consistent with impaired oxidative phosphorylation, such as Leigh Syndrome, multiple mitochondrial dysfunctions, and non-syndromic hearing loss. This manuscript reviews the distinctive properties of human mitochondrial ribosomes and ribosomal proteins, and the correlation of MRP3 gene locations with loci associated with disorders of energy metabolism, and provides localization information for one of the unusual proteins contained in human mitochondrial ribosomes, MRPS29.
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Affiliation(s)
- Thomas W O'Brien
- Department of Biochemistry and Molecular Biology, Health Science Center, University of Florida, Gainesville, FL 32610-0245, USA.
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42
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Khalimonchuk O, Rödel G. Biogenesis of cytochrome c oxidase. Mitochondrion 2005; 5:363-88. [PMID: 16199211 DOI: 10.1016/j.mito.2005.08.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Accepted: 08/10/2005] [Indexed: 11/20/2022]
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of electron transport chains in some prokaryotes and in mitochondria, has been characterized in detail over many years. Recently, a number of new data on structural and functional aspects as well as on COX biogenesis emerged. COX biogenesis includes a variety of steps starting from translation to the formation of the mature complex. Each step involves a set of specific factors that assist translation of subunits, their translocation across membranes, insertion of essential cofactors, assembly and final maturation of the enzyme. In this review, we focus on the organization and biogenesis of COX.
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Affiliation(s)
- Oleh Khalimonchuk
- Institut für Genetik, Technische Universität Dresden, 01062 Dresden, Germany
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43
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Williams EH, Bsat N, Bonnefoy N, Butler CA, Fox TD. Alteration of a novel dispensable mitochondrial ribosomal small-subunit protein, Rsm28p, allows translation of defective COX2 mRNAs. EUKARYOTIC CELL 2005; 4:337-45. [PMID: 15701796 PMCID: PMC549345 DOI: 10.1128/ec.4.2.337-345.2005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutations affecting the RNA sequence of the first 10 codons of the Saccharomyces cerevisiae mitochondrial gene COX2 strongly reduce translation of the mRNA, which encodes the precursor of cytochrome c oxidase subunit II. A dominant chromosomal mutation that suppresses these defects is an internal in-frame deletion of 67 codons from the gene YDR494w. Wild-type YDR494w encodes a 361-residue polypeptide with no similarity to proteins of known function. The epitope-tagged product of this gene, now named RSM28, is both peripherally associated with the inner surface of the inner mitochondrial membrane and soluble in the matrix. Epitope-tagged Rsm28p from Triton X-100-solubilized mitochondria sedimented with the small subunit of mitochondrial ribosomes in a sucrose gradient containing 500 mM NH4Cl. Complete deletion of RSM28 caused only a modest decrease in growth on nonfermentable carbon sources in otherwise wild-type strains and enhanced the respiratory defect of the suppressible cox2 mutations. The rsm28 null mutation also reduced translation of an ARG8m reporter sequence inserted at the COX1, COX2, and COX3 mitochondrial loci. We tested the ability of RSM28-1 to suppress a variety of cox2 and cox3 mutations and found that initiation codon mutations in both genes were suppressed. We conclude that Rsm28p is a dispensable small-subunit mitochondrial ribosomal protein previously undetected in systematic investigations of these ribosomes, with a positive role in translation of several mitochondrial mRNAs.
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Affiliation(s)
- Elizabeth H Williams
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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44
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Abstract
Cox11 is an intrinsic mitochondrial membrane protein essential for the assembly of an active cytochrome c oxidase complex. Cox11 is tethered to the mitochondrial inner membrane by a single transmembrane helix. Domain mapping was carried out to determine the functional segments of the Cox11 protein. The C-terminal 189 residue Cu(I)-binding domain is shown to be exposed within the mitochondrial intermembrane space. This orientation was demonstrated by the proteolytic susceptibility of a C-terminal Myc epitope tag in mitoplasts but not intact mitochondria. Fusion of the N terminus of Cox11 to the matrix ribosomal protein Rsm22 results in a functional protein capable of suppressing the respiratory defect of both Deltacox11 cells and Deltarsm22 cells. The functionality of the fusion protein suggests that the Cox11 N terminus projects into the matrix. The fusion of the C-terminal segment of Cox11 to Rsm22 resembles a naturally occurring fusion of Cox11 in Schizosaccharomyces pombe to a sequence homologous to the Saccharomyces cerevisiae Rsm22. Studies on a series of SCO1/COX11 chimeras reveal that the matrix domain of Cox11 lacks a specific function, whereas the Cu(I) binding/donating function requires the yeast Cox11 sequence. The Cu(I)-binding domain from human Cox11 cannot functionally replace the yeast sequence. The copper domain of Cox11 may be an important docking motif for Cox1 or a Cox1-associated protein.
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Affiliation(s)
- Heather S Carr
- University of Utah Health Sciences Center, Salt Lake City, 84132, USA
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45
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Khalimonchuk O, Ostermann K, Rödel G. Evidence for the association of yeast mitochondrial ribosomes with Cox11p, a protein required for the Cu(B) site formation of cytochrome c oxidase. Curr Genet 2005; 47:223-33. [PMID: 15776235 DOI: 10.1007/s00294-005-0569-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Revised: 01/25/2005] [Accepted: 02/20/2005] [Indexed: 11/27/2022]
Abstract
Cytochrome c oxidase is the terminal enzyme of the mitochondrial (mt) respiratory chain. It contains copper ions, which are organized in two centres, Cu(A) and Cu(B). The Cu(A) site of subunit Cox2p is exposed to the mt intermembrane space, while the Cu(B) site of subunit Cox1p is buried in the inner mt membrane. Incorporation of copper into the two centres is crucial for the assembly and activity of the enzyme. Formation of the Cu(B) site is dependent on Cox11p, a copper-binding protein of the mt inner membrane. Here, we experimentally prove that Cox11p possesses a N(in)-C(out) topology, with the C-terminal copper-binding domain exposed in the mt intermembrane space. Furthermore, we provide evidence for the association of Cox11p with the mt translation machinery. We propose a model in which the Cu(B) site is co-translationally formed by a transient interaction between Cox11p and the nascent Cox1p in the intermembrane space.
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Affiliation(s)
- Oleh Khalimonchuk
- Institut für Genetik, Technische Universität Dresden, 01062 Dresden, Germany.
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Chang IF, Szick-Miranda K, Pan S, Bailey-Serres J. Proteomic characterization of evolutionarily conserved and variable proteins of Arabidopsis cytosolic ribosomes. PLANT PHYSIOLOGY 2005; 137:848-62. [PMID: 15734919 PMCID: PMC1065386 DOI: 10.1104/pp.104.053637] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 11/16/2004] [Accepted: 11/23/2004] [Indexed: 05/18/2023]
Abstract
Analysis of 80S ribosomes of Arabidopsis (Arabidopsis thaliana) by use of high-speed centrifugation, sucrose gradient fractionation, one- and two-dimensional gel electrophoresis, liquid chromatography purification, and mass spectrometry (matrix-assisted laser desorption/ionization time-of-flight and electrospray ionization) identified 74 ribosomal proteins (r-proteins), of which 73 are orthologs of rat r-proteins and one is the plant-specific r-protein P3. Thirty small (40S) subunit and 44 large (60S) subunit r-proteins were confirmed. In addition, an ortholog of the mammalian receptor for activated protein kinase C, a tryptophan-aspartic acid-domain repeat protein, was found to be associated with the 40S subunit and polysomes. Based on the prediction that each r-protein is present in a single copy, the mass of the Arabidopsis 80S ribosome was estimated as 3.2 MD (1,159 kD 40S; 2,010 kD 60S), with the 4 single-copy rRNAs (18S, 26S, 5.8S, and 5S) contributing 53% of the mass. Despite strong evolutionary conservation in r-protein composition among eukaryotes, Arabidopsis 80S ribosomes are variable in composition due to distinctions in mass or charge of approximately 25% of the r-proteins. This is a consequence of amino acid sequence divergence within r-protein gene families and posttranslational modification of individual r-proteins (e.g. amino-terminal acetylation, phosphorylation). For example, distinct types of r-proteins S15a and P2 accumulate in ribosomes due to evolutionarily divergence of r-protein genes. Ribosome variation is also due to amino acid sequence divergence and differential phosphorylation of the carboxy terminus of r-protein S6. The role of ribosome heterogeneity in differential mRNA translation is discussed.
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Affiliation(s)
- Ing-Feng Chang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124, USA.
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Williams EH, Perez-Martinez X, Fox TD. MrpL36p, a highly diverged L31 ribosomal protein homolog with additional functional domains in Saccharomyces cerevisiae mitochondria. Genetics 2005; 167:65-75. [PMID: 15166137 PMCID: PMC1470847 DOI: 10.1534/genetics.167.1.65] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translation in mitochondria utilizes a large complement of ribosomal proteins. Many mitochondrial ribosomal components are clearly homologous to eubacterial ribosomal proteins, but others appear unique to the mitochondrial system. A handful of mitochondrial ribosomal proteins appear to be eubacterial in origin but to have evolved additional functional domains. MrpL36p is an essential mitochondrial ribosomal large-subunit component in Saccharomyces cerevisiae. Increased dosage of MRPL36 also has been shown to suppress certain types of translation defects encoded within the mitochondrial COX2 mRNA. A central domain of MrpL36p that is similar to eubacterial ribosomal large-subunit protein L31 is sufficient for general mitochondrial translation but not suppression, and proteins bearing this domain sediment with the ribosomal large subunit in sucrose gradients. In contrast, proteins lacking the L31 domain, but retaining a novel N-terminal sequence and a C-terminal sequence with weak similarity to the Escherichia coli signal recognition particle component Ffh, are sufficient for dosage suppression and do not sediment with the large subunit of the ribosome. Interestingly, the activity of MrpL36p as a dosage suppressor exhibits gene and allele specificity. We propose that MrpL36p represents a highly diverged L31 homolog with derived domains functioning in mRNA selection in yeast mitochondria.
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Affiliation(s)
- Elizabeth H Williams
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA
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Krause-Buchholz U, Schöbel K, Lauffer S, Rödel G. Saccharomyces cerevisiae translational activator Cbs1p is associated with translationally active mitochondrial ribosomes. Biol Chem 2005; 386:407-15. [PMID: 15927884 DOI: 10.1515/bc.2005.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In the yeast Saccharomyces cerevisiae, mitochondrial translation of most, if not all, mitochondrially encoded genes is regulated by an individual set of gene-specific activators. Translation of the COB mRNA encoding cytochrome b requires the function of two nuclearly encoded proteins, Cbs1p and Cbs2p. Genetic data revealed that the 5'-untranslated region of COB mRNA is the target of both proteins. Recently, we provided evidence for an interaction of Cbs2p with mitochondrial ribosomes. We demonstrate here by means of blue native gel electrophoresis, density gradient centrifugation and tandem affinity purification that a portion of Cbs1p is also associated with mitochondrial ribosomes. In addition, we demonstrate that the amount of ribosome-associated Cbs1p is elevated in the presence of chloramphenicol, which is known to stall ribosomes on mRNAs. In the presence of puromycin, which strips off the mRNA and nascent protein chains from ribosomes, Cbs1p is no longer associated with ribosomes. Our data indicate that the observed interaction is mediated by ribosome-bound mRNA, thus restricting the association to ribosomes actively translating cytochrome b.
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Affiliation(s)
- Udo Krause-Buchholz
- Institut für Genetik, Technische Universität Dresden, D-01062 Dresden, Germany.
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Mukamel Z, Kimchi A. Death-associated protein 3 localizes to the mitochondria and is involved in the process of mitochondrial fragmentation during cell death. J Biol Chem 2004; 279:36732-8. [PMID: 15175341 DOI: 10.1074/jbc.m400041200] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Death-associated protein 3 (DAP3) was previously isolated in our laboratory as a positive mediator of cell death. It is a 46-kDa protein containing a GTP binding domain that was shown to be essential for the induction of cell death. DAP3 functions downstream of the receptor signaling complex, and its death-promoting effects depend on caspase activity. Recent reports have suggested that DAP3 is localized to the mitochondria, but no functional significance of this localization has been reported so far. Here, we study the sub-cellular localization and cellular function of human DAP3 (hDAP3). We found that hDAP3 is localized to the mitochondria and, in contrast to cytochrome c, is not released to the cytoplasm following several cell death signals. Overexpression of hDAP3 induced dramatic changes in the mitochondrial structure involving increased fragmentation of the mitochondria. Both the mitochondrial localization of hDAP3 and its GTP-binding activity were essential for the fragmentation. The punctiform mitochondrial morphology was similar to that observed upon treatment of HeLa cells with staurosporine. In fact, reduction of endogenous hDAP3 protein by RNA interference partially attenuated staurosporine-induced mitochondrial fission. Thus, hDAP3 is a necessary component in the molecular pathway that culminates in fragmented mitochondria, probably reflecting its involvement in the fission process. These results, for the first time, provide a specific functional role for hDAP3 in mitochondrial maintenance.
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Affiliation(s)
- Zohar Mukamel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Dziembowski A, Piwowarski J, Hoser R, Minczuk M, Dmochowska A, Siep M, van der Spek H, Grivell L, Stepien PP. The yeast mitochondrial degradosome. Its composition, interplay between RNA helicase and RNase activities and the role in mitochondrial RNA metabolism. J Biol Chem 2003; 278:1603-11. [PMID: 12426313 DOI: 10.1074/jbc.m208287200] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. Previous purifications suggested that it was composed of three subunits. Our results suggest that the degradosome is composed of only two large subunits: an RNase and a RNA helicase encoded by nuclear genes DSS1 and SUV3, respectively, and that it co-purifies with mitochondrial ribosomes. We have found that the purified degradosome has RNA helicase activity that precedes and is essential for exoribonuclease activity of this complex. The degradosome RNase activity is necessary for mitochondrial biogenesis but in vitro the degradosome without RNase activity is still able to unwind RNA. In yeast strains lacking degradosome components there is a strong accumulation of mitochondrial mRNA and rRNA precursors not processed at 3'- and 5'-ends. The observed accumulation of precursors is probably the result of lack of degradation rather than direct inhibition of processing. We suggest that the degradosome is a central part of a mitochondrial RNA surveillance system responsible for degradation of aberrant and unprocessed RNAs.
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Affiliation(s)
- Andrzej Dziembowski
- Department of Genetics, Warsaw University and Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
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