251
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Manuell AL, Yamaguchi K, Haynes PA, Milligan RA, Mayfield SP. Composition and structure of the 80S ribosome from the green alga Chlamydomonas reinhardtii: 80S ribosomes are conserved in plants and animals. J Mol Biol 2005; 351:266-79. [PMID: 16005888 DOI: 10.1016/j.jmb.2005.06.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/31/2005] [Accepted: 06/07/2005] [Indexed: 11/29/2022]
Abstract
We have conducted a proteomic analysis of the 80S cytosolic ribosome from the eukaryotic green alga Chlamydomonas reinhardtii, and accompany this with a cryo-electron microscopy structure of the ribosome. Proteins homologous to all but one rat 40S subunit protein, including a homolog of RACK1, and all but three rat 60S subunit proteins were identified as components of the C. reinhardtii ribosome. Expressed Sequence Tag (EST) evidence and annotation of the completed C. reinhardtii genome identified genes for each of the four proteins not identified by proteomic analysis, showing that algae potentially have a complete set of orthologs to mammalian 80S ribosomal proteins. Presented at 25A, the algal 80S ribosome is very similar in structure to the yeast 80S ribosome, with only minor distinguishable differences. These data show that, although separated by billions of years of evolution, cytosolic ribosomes from photosynthetic organisms are highly conserved with their yeast and animal counterparts.
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Affiliation(s)
- Andrea L Manuell
- Department of Cell Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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252
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Palenzuela L, Hahn NM, Nelson RP, Arno JN, Schobert C, Bethel R, Ostrowski LA, Sharma MR, Datta PP, Agrawal RK, Schwartz JE, Hirano M. Does Linezolid Cause Lactic Acidosis by Inhibiting Mitochondrial Protein Synthesis? Clin Infect Dis 2005; 40:e113-6. [PMID: 15909253 DOI: 10.1086/430441] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 01/25/2005] [Indexed: 11/03/2022] Open
Abstract
Linezolid, an oxazolidinone antibiotic, inhibits bacterial protein synthesis by binding to 23S ribosomal RNA (rRNA). We studied 3 patients who experienced lactic acidosis while receiving linezolid therapy. The toxicity may have been caused by linezolid binding to mitochondrial 16S rRNA. Genetic polymorphisms may have contributed to the toxicity in 2 patients.
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Affiliation(s)
- Lluis Palenzuela
- Department of Neurology, Columbia University College of Physicians and Surgeons, New York, USA
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253
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Taanman JW, Llewelyn Williams S. The Human Mitochondrial Genome. OXIDATIVE STRESS AND DISEASE 2005. [DOI: 10.1201/9781420028843.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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254
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Zhao F, Ohtsuki T, Yamada K, Yoshinari S, Kita K, Watanabe YI, Watanabe K. Isolation and Physiochemical Properties of Protein-Rich Nematode Mitochondrial Ribosomes. Biochemistry 2005; 44:9232-7. [PMID: 15966747 DOI: 10.1021/bi047833c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present study, mitochondrial ribosomes of the nematode Ascaris suum were isolated and their physiochemical properties were compared to ribosomes of Escherichia coli. The sedimentation coefficient and buoyant density of A. suum mitochondrial ribosomes were determined. The sedimentation coefficient of the intact monosome was about 55 S. The buoyant density of formaldehyde-fixed ribosomes in cesium chloride was 1.40 g/cm(3), which suggests that the nematode mitoribosomes have a much higher protein composition than other mitoribosomes. The diffusion coefficients obtained from dynamic light scattering measurements were (1.48 +/- 0.04) x 10(-)(7) cm(2) s(-)(1) for 55 S mitoribosomes and (1.74 +/- 0.04) x 10(-)(7) cm(2) s(-)(1) for the 70 S E. coli monosome. The diameter of mitoribosomes was measured by dynamic light-scattering analysis and electron microscopy. Though the nematode mitoribosome has a larger size than the bacterial ribosome, it does not differ significantly in size from mammalian mitoribosomes.
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Affiliation(s)
- Feng Zhao
- Department of Integrated Biosciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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255
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Nilsson J, Sengupta J, Frank J, Nissen P. Regulation of eukaryotic translation by the RACK1 protein: a platform for signalling molecules on the ribosome. EMBO Rep 2005; 5:1137-41. [PMID: 15577927 PMCID: PMC1299186 DOI: 10.1038/sj.embor.7400291] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Accepted: 09/30/2004] [Indexed: 11/08/2022] Open
Abstract
The receptor for activated C-kinase (RACK1) is a scaffold protein that is able to interact simultaneously with several signalling molecules. It binds to protein kinases and membrane-bound receptors in a regulated fashion. Interestingly, RACK1 is also a constituent of the eukaryotic ribosome, and a recent cryo-electron microscopy study localized it to the head region of the 40S subunit in the vicinity of the messenger RNA (mRNA) exit channel. RACK1 recruits activated protein kinase C to the ribosome, which leads to the stimulation of translation through the phosphorylation of initiation factor 6 and, potentially, of mRNA-associated proteins. RACK1 therefore links signal-transduction pathways directly to the ribosome, which allows translation to be regulated in response to cell stimuli. In addition, the fact that RACK1 associates with membrane-bound receptors indicates that it promotes the docking of ribosomes at sites where local translation is required, such as focal adhesions.
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Affiliation(s)
- Jakob Nilsson
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Jayati Sengupta
- Health Research, Inc., State University of New York at Albany, Empire State Plaza, Albany, New York 12201-0509, USA
| | - Joachim Frank
- Health Research, Inc., State University of New York at Albany, Empire State Plaza, Albany, New York 12201-0509, USA
- Howard Hughes Medical Institute, Wadsworth Center, New York State Department of Health, State University of New York at Albany, Empire State Plaza, Albany, New York 12201-0509, USA
- Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, New York 12201-0509, USA
| | - Poul Nissen
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
- Tel: +45 89425025; Fax: +45 86123178;
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256
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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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257
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Preuss M, Ott M, Funes S, Luirink J, Herrmann JM. Evolution of mitochondrial oxa proteins from bacterial YidC. Inherited and acquired functions of a conserved protein insertion machinery. J Biol Chem 2005; 280:13004-11. [PMID: 15654078 DOI: 10.1074/jbc.m414093200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the Oxa1/YidC family are involved in the biogenesis of membrane proteins. In bacteria, YidC catalyzes the insertion and assembly of proteins of the inner membrane. Mitochondria of animals, fungi, and plants harbor two distant homologues of YidC, Oxa1 and Cox18/Oxa2. Oxa1 plays a pivotal role in the integration of mitochondrial translation products into the inner membrane of mitochondria. It contains a C-terminal ribosome-binding domain that physically interacts with mitochondrial ribosomes to facilitate the co-translational insertion of nascent membrane proteins. The molecular function of Cox18/Oxa2 is not well understood. Employing a functional complementation approach with mitochondria-targeted versions of YidC we show that YidC is able to functionally replace both Oxa1 and Cox18/Oxa2. However, to integrate mitochondrial translation products into the inner membrane of mitochondria, the ribosome-binding domain of Oxa1 has to be appended onto YidC. On the contrary, the fusion of the ribosome-binding domain onto YidC prevents its ability to complement COX18 mutants suggesting an indispensable post-translational activity of Cox18/Oxa2. Our observations suggest that during evolution of mitochondria from their bacterial ancestors the two descendents of YidC functionally segregated to perform two distinct activities, one co-translational and one post-translational.
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Affiliation(s)
- Marc Preuss
- Institut für Physiologische Chemie, Universität München, Butenandtstrasse 5, 81377 München, Germany
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258
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Habura A, Rosen DR, Bowser SS. Predicted Secondary Structure of the Foraminiferal SSU 3' Major Domain Reveals a Molecular Synapomorphy for Granuloreticulosean Protists. J Eukaryot Microbiol 2004; 51:464-71. [PMID: 15352330 DOI: 10.1111/j.1550-7408.2004.tb00397.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The small subunit ribosomal RNA genes of foraminiferal protists are the largest and most divergent of any eukaryote. We demonstrate that this foraminiferal sequence alteration represents a substantial modification to the small subunit ribosomal RNA structure, including a large (up to 350 nt) novel helix in a very well-conserved portion of the head domain. This modification dates from the beginning of the foraminiferal radiation and, within modern orders, is partially conserved at the sequence level, suggesting that it is a functional part of the ribosome. The pattern of conservation makes it particularly useful for determining lower-taxon relationships in morphologically ambiguous allogromiid foraminifera.
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Affiliation(s)
- Andrea Habura
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA.
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259
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Towpik J, Chaciñska A, Ciesla M, Ginalski K, Boguta M. Mutations in the yeast mrf1 gene encoding mitochondrial release factor inhibit translation on mitochondrial ribosomes. J Biol Chem 2004; 279:14096-103. [PMID: 14734569 DOI: 10.1074/jbc.m312856200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the control of mitochondrial translation in the yeast Saccharomyces cerevisiae has been studied extensively, the mechanism of termination remains obscure. Ten mutations isolated in a genetic screen for read-through of premature stop codons in mitochondrial genes were localized in the chromosomal gene encoding the mitochondrial release factor mRF1. The mrf1-13 and mrf1-780 mutant genes, in contrast to other alleles, caused a non-respiratory phenotype that correlated with decreased expression of mitochondrial genes as well as a reporter ARG8(m) gene inserted into mitochondrial DNA. The steady-state levels of several mitochondrially encoded proteins, but not their mRNAs, were dramatically decreased in mrf1-13 and mrf1-780 cells. Structural models of mRF1 were constructed, allowing localization of residues substituted in the mrf1 mutants and offering an insight into the possible mechanism by which these mutations change the mitochondrial translation termination fidelity. Inhibition of mitochondrial translation in mrf1-13 and mrf1-780 correlated with the three-dimensional localization of the mutated residues close to the PST motif presumably involved in the recognition of stop codons in mitochondrial mRNA.
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Affiliation(s)
- Joanna Towpik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawiñskiego 5A, 02-106 Warsaw, Poland
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260
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Abstract
The recently solved X-ray crystal structures of the ribosome have provided opportunities for studying the molecular basis of translation with a variety of methods including cryo-electron microscopy. The recently solved X-ray crystal structures of the ribosome have provided opportunities for studying the molecular basis of translation with a variety of methods including cryo-electron microscopy - where maps give the first glimpses of ribosomal evolution - and fluorescence spectroscopy techniques.
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Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Health Research, Inc, at the Wadsworth Center and Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA.
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