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Abstract
Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35–40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90–93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.
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Affiliation(s)
- Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
- * E-mail:
| | - Shu-ling Liang
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
| | - Daniel L. Nickrent
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
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2
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Friederich MW, Geddes GC, Wortmann SB, Punnoose A, Wartchow E, Knight KM, Prokisch H, Creadon-Swindell G, Mayr JA, Van Hove JLK. Pathogenic variants in MRPL44 cause infantile cardiomyopathy due to a mitochondrial translation defect. Mol Genet Metab 2021; 133:362-371. [PMID: 34140213 PMCID: PMC8289749 DOI: 10.1016/j.ymgme.2021.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/22/2022]
Abstract
Cardiac dysfunction is a common phenotypic manifestation of primary mitochondrial disease with multiple nuclear and mitochondrial DNA pathogenic variants as a cause, including disorders of mitochondrial translation. To date, five patients have been described with pathogenic variants in MRPL44, encoding the ml44 protein which is part of the large subunit of the mitochondrial ribosome (mitoribosome). Three presented as infants with hypertrophic cardiomyopathy, mild lactic acidosis, and easy fatigue and muscle weakness, whereas two presented in adolescence with myopathy and neurological symptoms. We describe two infants who presented with cardiomyopathy from the neonatal period, failure to thrive, hypoglycemia and in one infant lactic acidosis. A decompensation of the cardiac function in the first year resulted in demise. Exome sequencing identified compound heterozygous variants in the MRPL44 gene including the known pathogenic variant c.467 T > G and two novel pathogenic variants. We document a combined respiratory chain enzyme deficiency with emphasis on complex I and IV, affecting heart muscle tissue more than skeletal muscle or fibroblasts. We show this to be caused by reduced mitochondrial DNA encoded protein synthesis affecting all subunits, and resulting in dysfunction of complex I and IV assembly. The degree of oxidative phosphorylation dysfunction correlated with the impairment of mitochondrial protein synthesis due to different pathogenic variants. These functional studies allow for improved understanding of the pathogenesis of MRPL44-associated mitochondrial disorder.
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Affiliation(s)
- Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Services, Children's Hospital Colorado, Aurora, CO, USA
| | - Gabrielle C Geddes
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Molecular and Medical Genetics, Indiana University, Indianapolis, IN, USA
| | - Saskia B Wortmann
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria; Amalia Children's Hospital, RadboudUMC, Nijmegen, the Netherlands
| | - Ann Punnoose
- Herma Heart Institute, Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Eric Wartchow
- Department of Pathology and Laboratory Services, Children's Hospital Colorado, Aurora, CO, USA
| | - Kaz M Knight
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | | | - Johannes A Mayr
- University Children's Hospital, Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Services, Children's Hospital Colorado, Aurora, CO, USA.
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3
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Abstract
Maintenance of the cellular homeostasis is firmly linked with protein synthesis. Therefore, it is tightly controlled at multiple levels. An advancement in quantitative techniques, mainly over the last decade, shed new light on the regulation of protein production, which pointed the ribosome as a new player. Ribosomes are macromolecular machines that synthesize polypeptide chains using mRNA as a template. The enormous complexity of ribosomes provides many possibilities of changes in their composition and consecutively in their target specificity. However, it is not clear how this specialization is enforced by the cell and which stimuli provoke that diversity. This review presents an overview of currently available knowledge about ribosome heterogeneity, focusing on changes in protein composition, and their role in the control of translation specificity. Importantly, besides the potential advantage of ribosome-mediated regulation of protein synthesis, its failure can play a crucial role in disease development.
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Affiliation(s)
- Karolina Gościńska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Warszawa, Poland
| | - Ulrike Topf
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Department of Genetics, Warszawa, Poland
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4
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Bessa-Silva A, Vallinoto M, Sampaio I, Flores-Villela OA, Smith EN, Sequeira F. The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex. Mol Phylogenet Evol 2019; 145:106723. [PMID: 31891757 DOI: 10.1016/j.ympev.2019.106723] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 12/23/2019] [Accepted: 12/23/2019] [Indexed: 11/19/2022]
Abstract
The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.
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Affiliation(s)
- Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Marcelo Vallinoto
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal.
| | - Iracilda Sampaio
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, 68 600-000 Pará, Brazil
| | - Oscar A Flores-Villela
- Museo de Zoología, Department of Evolutionary Biology, Facultad de Ciencias, Universidad Nacional Autónoma de México, External Circuit of Ciudad Universitaria, Mexico City 04510, Mexico
| | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA; The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Fernando Sequeira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus Agrário de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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Zhang Y, Launay H, Schramm A, Lebrun R, Gontero B. Exploring intrinsically disordered proteins in Chlamydomonas reinhardtii. Sci Rep 2018; 8:6805. [PMID: 29717210 PMCID: PMC5931566 DOI: 10.1038/s41598-018-24772-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/26/2018] [Indexed: 11/14/2022] Open
Abstract
The content of intrinsically disordered protein (IDP) is related to organism complexity, evolution, and regulation. In the Plantae, despite their high complexity, experimental investigation of IDP content is lacking. We identified by mass spectrometry 682 heat-resistant proteins from the green alga, Chlamydomonas reinhardtii. Using a phosphoproteome database, we found that 331 of these proteins are targets of phosphorylation. We analyzed the flexibility propensity of the heat-resistant proteins and their specific features as well as those of predicted IDPs from the same organism. Their mean percentage of disorder was about 20%. Most of the IDPs (~70%) were addressed to other compartments than mitochondrion and chloroplast. Their amino acid composition was biased compared to other classic IDPs. Their molecular functions were diverse; the predominant ones were nucleic acid binding and unfolded protein binding and the less abundant one was catalytic activity. The most represented proteins were ribosomal proteins, proteins associated to flagella, chaperones and histones. We also found CP12, the only experimental IDP from C. reinhardtii that is referenced in disordered protein database. This is the first experimental investigation of IDPs in C. reinhardtii that also combines in silico analysis.
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Affiliation(s)
- Yizhi Zhang
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France
| | - Hélène Launay
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France
| | | | - Régine Lebrun
- Plate-forme Protéomique, Marseille Protéomique (MaP), IBiSA labeled, IMM, FR 3479, CNRS, B.P. 71, 13402, Marseille, Cedex 20, France
| | - Brigitte Gontero
- Aix Marseille Univ, CNRS, BIP, UMR 7281, IMM, 31 Chemin J. Aiguier, 13402, Marseille, Cedex 20, France.
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Jauffrit F, Penel S, Delmotte S, Rey C, de Vienne DM, Gouy M, Charrier JP, Flandrois JP, Brochier-Armanet C. RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics. Mol Biol Evol 2016; 33:2170-2. [PMID: 27189556 DOI: 10.1093/molbev/msw088] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribosomal proteins (r-proteins) are increasingly used as an alternative to ribosomal rRNA for prokaryotic systematics. However, their routine use is difficult because r-proteins are often not or wrongly annotated in complete genome sequences, and there is currently no dedicated exhaustive database of r-proteins. RiboDB aims at fulfilling this gap. This weekly updated comprehensive database allows the fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences. The current version of RiboDB contains 90 r-proteins from 3,750 prokaryotic complete genomes encompassing 38 phyla/major classes and 1,759 different species. RiboDB is accessible at http://ribodb.univ-lyon1.fr and through ACNUC interfaces.
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Affiliation(s)
- Frédéric Jauffrit
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France Technology Research Department, Innovation Unit, bioMérieux SA, Marcy L'Etoile, France
| | - Simon Penel
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Stéphane Delmotte
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Carine Rey
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France Laboratoire de Biologie et de Modélisation de la Cellule, École Normale Supérieure De Lyon, CNRS UMR 5239, UCBL1, IFR128, Lyon, France Master BioSciences, Département de Biologie, École Normale Supérieure de Lyon, Université de Lyon, UCB Lyon1, Lyon, France
| | - Damien M de Vienne
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Manolo Gouy
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | | | - Jean-Pierre Flandrois
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Èvolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
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Liang X, Liu Y, Xie L, Liu X, Wei Y, Zhou X, Zhang S. A ribosomal protein AgRPS3aE from halophilic Aspergillus glaucus confers salt tolerance in heterologous organisms. Int J Mol Sci 2015; 16:3058-70. [PMID: 25642759 PMCID: PMC4346880 DOI: 10.3390/ijms16023058] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 12/30/2014] [Accepted: 01/21/2015] [Indexed: 01/22/2023] Open
Abstract
High salt in soils is one of the abiotic stresses that significantly reduces crop yield, although saline lands are considered potential resources arable for agriculture. Currently, genetic engineering for enhancing salt tolerance is being tested as an efficient and viable strategy for crop improvement. We previously characterized a large subunit of the ribosomal protein RPL44, which is involved in osmotic stress in the extremely halophilic fungus Aspergillus glaucus. Here, we screened another ribosomal protein (AgRPS3aE) that also produced high-salt tolerance in yeast. Bioinformatics analysis indicated that AgRPS3aE encodes a 29.2 kDa small subunit of a ribosomal protein belonging to the RPS3Ae family in eukaryotes. To further confirm its protective function against salinity, we expressed AgRPS3aE in three heterologous systems, the filamentous fungus Magnaporthe oryzae and two model plants Arabidopsis and tobacco. Overexpression of AgRPS3aE in all tested transformants significantly alleviated stress symptoms compared with controls, suggesting that AgRPS3aE functions not only in fungi but also in plants. Considering that ribosomal proteins are housekeeping components in organisms from prokaryotes to eukaryotes, we propose that AgRPS3aE is one of the optimal genes for improving high-salt tolerance in crops.
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Affiliation(s)
- Xilong Liang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yiling Liu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Lixia Xie
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Xiaodan Liu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yi Wei
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Xiaoyang Zhou
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Shihong Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
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Justice NB, Norman A, Brown CT, Singh A, Thomas BC, Banfield JF. Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. BMC Genomics 2014; 15:1107. [PMID: 25511286 PMCID: PMC4378227 DOI: 10.1186/1471-2164-15-1107] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/27/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood. RESULTS Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes. CONCLUSIONS Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.
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Affiliation(s)
- Nicholas B Justice
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA USA
| | - Anders Norman
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
- />Section for Infection Microbiology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Brown
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Andrea Singh
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Brian C Thomas
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
| | - Jillian F Banfield
- />Department of Earth and Planetary Science, University of California, Berkeley, CA 94720 USA
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Ban N, Beckmann R, Cate JHD, Dinman JD, Dragon F, Ellis SR, Lafontaine DLJ, Lindahl L, Liljas A, Lipton JM, McAlear MA, Moore PB, Noller HF, Ortega J, Panse VG, Ramakrishnan V, Spahn CMT, Steitz TA, Tchorzewski M, Tollervey D, Warren AJ, Williamson JR, Wilson D, Yonath A, Yusupov M. A new system for naming ribosomal proteins. Curr Opin Struct Biol 2014; 24:165-9. [PMID: 24524803 DOI: 10.1016/j.sbi.2014.01.002] [Citation(s) in RCA: 407] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A system for naming ribosomal proteins is described that the authors intend to use in the future. They urge others to adopt it. The objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. In the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. It is designed so that new names are similar enough to old names to be easily recognized, but are written in a format that unambiguously identifies them as 'new system' names.
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Affiliation(s)
- Nenad Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 30, 8093 Zurich, Switzerland
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen Str. 25, University of Munich, 81377 Munich, Germany
| | - Jamie H D Cate
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - François Dragon
- Département des sciences biologiques and Centre de recherche BioMed, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Steven R Ellis
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA
| | - Denis L J Lafontaine
- RNA Molecular Biology, FRS/F.N.R.S., Université Libre de Bruxelles, Charleroi Campus, B-6041 Charleroi, Belgium
| | - Lasse Lindahl
- Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Anders Liljas
- Biochemistry and Structural Biology, Lund University, Åkeröv 26, SE-793 Leksand, Sweden.
| | - Jeffrey M Lipton
- Feinstein Institute for Medical Research, 350 Community Dr., Manhasset, NY 11030, USA; Hofstra School of Medicine, 500 Hofstra University, Hempstead, NY 11549, USA
| | - Michael A McAlear
- Molecular Biology and Biochemistry Department, Wesleyan University, 237 Church St., Middletown, CT 06459, USA
| | - Peter B Moore
- Department of Chemistry, Yale University, PO Box 208107, New Haven, CT 06520, USA.
| | - Harry F Noller
- Department of MCD Biology, UCSC, Santa Cruz, CA 94720, USA
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences, DeGroote Institute for Infectious Diseases Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Vikram Govind Panse
- Institute for Biochemistry, ETH Zurich, HPM F12.2, Otto-Stern-Weg 3, CH-8093 Zurich, Switzerland
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christian M T Spahn
- Institut für Medizinsche Physik und Biophysik, Charite-Universitätsmedizin, Ziegelstrass 5-6, 10117 Berlin, Germany
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA
| | - Marek Tchorzewski
- Department of Molecular Biology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - David Tollervey
- Welcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Alan J Warren
- MRC Laboratory of Molecular Biology, Francis Crick Ave., Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - James R Williamson
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Wilson
- Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Ada Yonath
- Structural Biology Department, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, BP10142, Illkirch F-67400, France.
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Tian ZC, Liu GY, Yin H, Luo JX, Guan GQ, Luo J, Xie JR, Shen H, Tian MY, Zheng JF, Yuan XS, Wang FF. RPS8--a new informative DNA marker for phylogeny of Babesia and Theileria parasites in China. PLoS One 2013; 8:e79860. [PMID: 24244571 PMCID: PMC3820542 DOI: 10.1371/journal.pone.0079860] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/25/2013] [Indexed: 11/19/2022] Open
Abstract
Piroplasmosis is a serious debilitating and sometimes fatal disease. Phylogenetic relationships within piroplasmida are complex and remain unclear. We compared the intron–exon structure and DNA sequences of the RPS8 gene from Babesia and Theileria spp. isolates in China. Similar to 18S rDNA, the 40S ribosomal protein S8 gene, RPS8, including both coding and non-coding regions is a useful and novel genetic marker for defining species boundaries and for inferring phylogenies because it tends to have little intra-specific variation but considerable inter-specific difference. However, more samples are needed to verify the usefulness of the RPS8 (coding and non-coding regions) gene as a marker for the phylogenetic position and detection of most Babesia and Theileria species, particularly for some closely related species.
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Affiliation(s)
- Zhan-Cheng Tian
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- * E-mail: (GYL); (ZCT)
| | - Guang-Yuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- * E-mail: (GYL); (ZCT)
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jian-Xun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Gui-Quan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jin Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jun-Ren Xie
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hui Shen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei-Yuan Tian
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jin-feng Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiao-song Yuan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Fang-fang Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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11
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Bog M, Schneider P, Hellwig F, Sachse S, Kochieva EZ, Martyrosian E, Landolt E, Appenroth KJ. Genetic characterization and barcoding of taxa in the genus Wolffia Horkel ex Schleid. (Lemnaceae) as revealed by two plastidic markers and amplified fragment length polymorphism (AFLP). Planta 2013; 237:1-13. [PMID: 23053544 DOI: 10.1007/s00425-012-1777-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 09/14/2012] [Indexed: 05/11/2023]
Abstract
The genus Wolffia of the duckweed family (Lemnaceae) contains the smallest flowering plants. Presently, 11 species are recognized and categorized mainly on the basis of morphology. Because of extreme reduction of structure of all species, molecular methods are especially required for barcoding and identification of species and clones of this genus. We applied AFLP combined with Bayesian analysis of population structure to 66 clones covering all 11 species. Nine clusters were identified: (1) W. angusta and W. microscopica (only one clone), (2) W. arrhiza, (3) W. cylindracea (except one clone that might be a transition form), (4) W. australiana, (5) W. globosa, (6) W. globosa, W. neglecta, and W. borealis, (7) W. brasiliensis, and W. columbiana, (8) W. columbiana, (9) W. elongata. Furthermore, we investigated the sequences of plastidic regions rps16 (54 clones) and rpl16 (55 clones), and identified the following species: W. angusta, W. australiana, W. brasiliensis, W. cylindracea, W. elongata, W. microscopica, and W. neglecta. Wolffia globosa has been separated into two groups by both methods. One group which consists only of clones from North America and East Asia was labelled here "typical W. globosa". The other group of W. globosa, termed operationally "W. neglecta", contains also clones of W. neglecta and shows high similarity to W. borealis. None of the methods recognized W. borealis as a distinct species. Although each clone could be characterized individually by AFLP and plastidic sequences, and most species could be bar-coded, the presently available data are not sufficient to identify all taxa of Wolffia.
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Affiliation(s)
- Manuela Bog
- Institute of Plant Physiology, University of Jena, Dornburger Str. 159, 07743 Jena, Germany
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12
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Stoppel R, Lezhneva L, Schwenkert S, Torabi S, Felder S, Meierhoff K, Westhoff P, Meurer J. Recruitment of a ribosomal release factor for light- and stress-dependent regulation of petB transcript stability in Arabidopsis chloroplasts. Plant Cell 2011; 23:2680-95. [PMID: 21771930 PMCID: PMC3226201 DOI: 10.1105/tpc.111.085324] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 06/17/2011] [Accepted: 07/06/2011] [Indexed: 05/20/2023]
Abstract
Land plant genomes encode four functional ribosomal peptide chain release factors (Prf) of eubacterial origin, two (PrfA and PrfB homologs) for each endosymbiotic organelle. Formerly, we have shown that the Arabidopsis thaliana chloroplast-localized PrfB homolog, PrfB1, is required not only for termination of translation but also for stabilization of UGA stop codon-containing chloroplast transcripts. A previously undiscovered PrfB-like protein, PrfB3, is localized to the chloroplast stroma in a petB RNA-containing complex and found only in vascular plants. Highly conserved positions of introns unequivocally indicate that PrfB3 arose from a duplication of PrfB1. Notably, PrfB3 is lacking the two most important tripeptide motifs characteristic for all eubacterial and organellar PrfB homologs described so far: the stop codon recognition motif SPF and the catalytic center GGQ for peptidyl-tRNA hydrolysis. Complementation studies, as well as functional and molecular analyses of two allelic mutations in Arabidopsis, both of which lead to a specific deficiency of the cytochrome b₆f complex, revealed that PrfB3 is essentially required for photoautotrophic growth. Plastid transcript, polysome, and translation analyses indicate that PrfB3 has been recruited in vascular plants for light- and stress-dependent regulation of stability of 3' processed petB transcripts to adjust cytochrome b₆ levels.
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Affiliation(s)
- Rhea Stoppel
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Lina Lezhneva
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Serena Schwenkert
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Salar Torabi
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
| | - Susanne Felder
- Heinrich-Heine-Universität, Institut für Entwicklungs- und Molekularbiologie der Pflanzen, 40225 Duesseldorf, Germany
| | - Karin Meierhoff
- Heinrich-Heine-Universität, Institut für Entwicklungs- und Molekularbiologie der Pflanzen, 40225 Duesseldorf, Germany
| | - Peter Westhoff
- Heinrich-Heine-Universität, Institut für Entwicklungs- und Molekularbiologie der Pflanzen, 40225 Duesseldorf, Germany
| | - Jörg Meurer
- Biozentrum der Ludwig-Maximilians-Universität, Plant Molecular Biology/Botany, 82152 Planegg-Martinsried, Germany
- Address correspondence to
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13
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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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14
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Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Rückert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005; 33:5691-702. [PMID: 16214803 PMCID: PMC1251668 DOI: 10.1093/nar/gki866] [Citation(s) in RCA: 1424] [Impact Index Per Article: 74.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.
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Affiliation(s)
- Ross Overbeek
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
| | - Tadhg Begley
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY14853, USA
| | - Ralph M. Butler
- Computer Science Dept, Middle Tennessee State UniversityMurfreesboro, TN 37132, USA
| | - Jomuna V. Choudhuri
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | | | - Matthew Cohoon
- Computation Institute, University of ChicagoChicago, IL 60637, USA
| | - Valérie de Crécy-Lagard
- Departments of Microbiology and Cell Science, University of FloridaGainesville, FL 32611, USA
| | - Naryttza Diaz
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | - Terry Disz
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
| | - Robert Edwards
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
- Center for Microbial Sciences, San Diego State UniversitySan Diego, CA 92813, USA
- The Burnham InstituteSan Diego CA 92037, USA
| | - Michael Fonstein
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
- Cleveland BioLabs, Inc.Cleveland, OH 44106, USA
| | - Ed D. Frank
- Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL 60439, USA
| | - Svetlana Gerdes
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
| | - Elizabeth M. Glass
- Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL 60439, USA
| | - Alexander Goesmann
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | - Andrew Hanson
- Department of Horticultural Science, University of FloridaGainesville, FL 32611, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State UniversityPortland, OR 97207, USA
| | - Roy Jensen
- Emerson Hall, University of FloridaPO Box 14425, Gainesville, FL 32604, USA
| | | | - Lutz Krause
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | - Michael Kubal
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
| | - Niels Larsen
- Danish Genome InstituteGustav Wieds vej 10 C, DK-8000 Aarhus C, Denmark
| | - Burkhard Linke
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | - Alice C. McHardy
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | - Folker Meyer
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | - Heiko Neuweger
- Center for Biotechnology, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | - Gary Olsen
- Department of Microbiology, University of Illinois at Urbana-ChampaignUrbana, IL 61801
| | - Robert Olson
- Computation Institute, University of ChicagoChicago, IL 60637, USA
| | - Andrei Osterman
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
- The Burnham InstituteSan Diego CA 92037, USA
| | | | - Gordon D. Pusch
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
| | - Dmitry A. Rodionov
- Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia
| | - Christian Rückert
- International NRW Graduate School in Bioinformatics & Genome Research, Institute for Genome Research, Bielefeld University33594 Bielefeld, Germany, USA
| | | | - Rick Stevens
- Mathematics and Computer Science Division, Argonne National LaboratoryArgonne, IL 60439, USA
- Computation Institute, University of ChicagoChicago, IL 60637, USA
| | - Ines Thiele
- University of CaliforniaSan Diego, CA 92093, USA
| | - Olga Vassieva
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
| | - Yuzhen Ye
- The Burnham InstituteSan Diego CA 92037, USA
| | - Olga Zagnitko
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
| | - Veronika Vonstein
- Fellowship for Interpretation of Genomes15W155 81st Street, Burr Ridge, IL 60527, USA
- To whom correspondence should be addressed. Tel: +1 630 325 4178; Fax: +1 630 325 4179;
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15
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Abstract
Interpreting data from large-scale protein interaction experiments has been a challenging task because of the widespread presence of random false positives. Here, we present a network-based statistical algorithm that overcomes this difficulty and allows us to derive functions of unannotated proteins from large-scale interaction data. Our algorithm uses the insight that if two proteins share significantly larger number of common interaction partners than random, they have close functional associations. Analysis of publicly available data from Saccharomyces cerevisiae reveals >2,800 reliable functional associations, 29% of which involve at least one unannotated protein. By further analyzing these associations, we derive tentative functions for 81 unannotated proteins with high certainty. Our method is not overly sensitive to the false positives present in the data. Even after adding 50% randomly generated interactions to the measured data set, we are able to recover almost all (approximately 89%) of the original associations.
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16
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Milkereit P, Kühn H, Gas N, Tschochner H. The pre-ribosomal network. Nucleic Acids Res 2003; 31:799-804. [PMID: 12560474 PMCID: PMC149187 DOI: 10.1093/nar/gkg165] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2002] [Revised: 10/31/2002] [Accepted: 11/18/2002] [Indexed: 11/14/2022] Open
Abstract
Recent achievements in yeast functional proteomics have significantly advanced our knowledge about ribosome biogenesis. Here, we present a program developed to integrate data from various proteome analyses with cell biological data on components present in the ribosome producing factories. This program allows users to attribute factors to certain complexes and to specific steps of ribosome biogenesis. Thus, it helps to gain novel insights into the complex network involved in maturation of ribosomal subunits. The database can be accessed at the URL http://www.pre-ribosome.de.
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Affiliation(s)
- Philipp Milkereit
- Laboratoire de Biologie Moleculaire Eucaryote, F-32062 Toulouse, France
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17
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Velkov T, Lawen A. Non-ribosomal peptide synthetases as technological platforms for the synthesis of highly modified peptide bioeffectors – Cyclosporin synthetase as a complex example. Biotechnology Annual Review 2003; 9:151-97. [PMID: 14650927 DOI: 10.1016/s1387-2656(03)09002-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Many microbial peptide secondary metabolites possess important medicinal properties, of which the immunosuppressant cyclosporin A is an example. The enormous structural and functional diversity of these low-molecular weight peptides is attributable to their mode of biosynthesis. Peptide secondary metabolites are assembled non-ribosomally by multi-functional enzymes, termed non-ribosomal peptide synthetases. These systems consist of a multi-modular arrangement of the functional domains responsible for the catalysis of the partial reactions of peptide assembly. The extensive homology shared among NRPS systems allows for the generalisation of the knowledge garnered from studies of systems of diverse origins. In this review we shall focus the contemporary knowledge of non-ribosomal peptide biosynthesis on the structure and function of the cyclosporin biosynthetic system, with some emphasis on the re-direction of the biosynthetic potential of this system by combinatorial approaches.
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Affiliation(s)
- Tony Velkov
- Monash University, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, P.O. Box 13D, Melbourne, Victoria 3800, Australia
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18
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Klucar L, Nováková R, Homérová D, Sevcíková B, Turna J, Kormanec J. Phylogenetic analysis of the rplA genes encoding ribosomal protein L1. Folia Microbiol (Praha) 2002; 46:99-106. [PMID: 11501409 DOI: 10.1007/bf02873585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously we have identified the rplA gene encoding ribosomal protein L1 in Streptomyces aureofaciens. Sequence comparison of ribosomal protein L1 among several bacterial genera revealed a high level of conservation. Based on this conservation, these proteins were used as a phylogenetic tool to compare evolutionary relationships among eubacteria and archaebacteria. This phylogenetic analysis of L1 ribosomal proteins including the S. aureofaciens rplA gene product revealed, except similar bacterial groupings, some new evolutionary relationships.
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Affiliation(s)
- L Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, 842 51 Bratislava, Slovakia
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19
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Lin K, Kuang Y, Joseph JS, Kolatkar PR. Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res 2002; 30:2599-607. [PMID: 12034849 PMCID: PMC117187 DOI: 10.1093/nar/30.11.2599] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genomics projects have resulted in a flood of sequence data. Functional annotation currently relies almost exclusively on inter-species sequence comparison and is restricted in cases of limited data from related species and widely divergent sequences with no known homologs. Here, we demonstrate that codon composition, a fusion of codon usage bias and amino acid composition signals, can accurately discriminate, in the absence of sequence homology information, cytoplasmic ribosomal protein genes from all other genes of known function in Saccharomyces cerevisiae, Escherichia coli and Mycobacterium tuberculosis using an implementation of support vector machines, SVM(light). Analysis of these codon composition signals is instructive in determining features that confer individuality to ribosomal protein genes. Each of the sets of positively charged, negatively charged and small hydrophobic residues, as well as codon bias, contribute to their distinctive codon composition profile. The representation of all these signals is sensitively detected, combined and augmented by the SVMs to perform an accurate classification. Of special mention is an obvious outlier, yeast gene RPL22B, highly homologous to RPL22A but employing very different codon usage, perhaps indicating a non-ribosomal function. Finally, we propose that codon composition be used in combination with other attributes in gene/protein classification by supervised machine learning algorithms.
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Affiliation(s)
- Kui Lin
- IMCB-BIC, Institute of Molecular and Cell Biology, 30 Medical Drive, 117609 Singapore
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20
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Skinner DJ, Baker SC, Meister RJ, Broadhvest J, Schneitz K, Gasser CS. The Arabidopsis HUELLENLOS gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein. Plant Cell 2001. [PMID: 11752383 DOI: 10.1105/tpc.13.12.2719] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The HUELLENLOS (HLL) gene participates in patterning and growth of the Arabidopsis ovule. We have isolated the HLL gene and shown that it encodes a protein homologous to the L14 proteins of eubacterial ribosomes. The Arabidopsis genome also includes a highly similar gene, HUELLENLOS PARALOG (HLP), and genes for both cytosolic (L23) and chloroplast ribosome L14 proteins. Phylogenetic analysis shows that HLL and HLP differ significantly from these other two classes of such proteins. HLL and HLP fusions to green fluorescent protein were localized to mitochondria. Ectopic expression of HLP complemented the hll mutant, indicating that HLP and HLL share redundant functions. We conclude that HLL and HLP encode L14 subunits of mitochondrial ribosomes. HLL mRNA was at significantly higher levels than HLP mRNA in pistils, with the opposite pattern in leaves. This differential expression can explain the confinement of effects of hll mutations to gynoecia and ovules. Our elucidation of the nature of HLL shows that metabolic defects can have specific effects on developmental patterning.
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Affiliation(s)
- D J Skinner
- Section of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, California 95616, USA
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21
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Adams KL, Ong HC, Palmer JD. Mitochondrial gene transfer in pieces: fission of the ribosomal protein gene rpl2 and partial or complete gene transfer to the nucleus. Mol Biol Evol 2001; 18:2289-97. [PMID: 11719578 DOI: 10.1093/oxfordjournals.molbev.a003775] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial genes are usually conserved in size in angiosperms. A notable exception is the rpl2 gene, which is considerably shorter in the eudicot Arabidopsis than in the monocot rice. Here, we show that a severely truncated mitochondrial rpl2 gene (termed 5' rpl2) was created by the formation of a premature stop codon early in eudicot evolution. This 5' rpl2 gene was subsequently lost many times from the mitochondrial DNAs of 179 core eudicots surveyed by Southern hybridization. The sequence corresponding to the 3' end of rice rpl2 (termed 3' rpl2) has been lost much more pervasively among the mitochondrial DNAs of core eudicots than has 5' rpl2. Furthermore, where still present in these mitochondrial genomes, 3' rpl2 always appears to be a pseudogene, and there is no evidence that 3' rpl2 was ever a functional mitochondrial gene. An intact and expressed 3' rpl2 gene was discovered in the nucleus of five diverse eudicots (tomato, cotton, Arabidopsis, soybean, and Medicago). In the first three of these species, 5' rpl2 is still present in the mitochondrion, unlike the two legumes, where both parts of rpl2 are present in the nucleus as separate genes. The full-length rpl2 gene has been transferred intact to the nucleus in maize. We propose that the 3' end of rpl2 was functionally transferred to the nucleus early in eudicot evolution, and that this event then permitted the nonsense mutation that gave rise to the mitochondrial 5' rpl2 gene. Once 5' rpl2 was established as a stand-alone mitochondrial gene, it was then lost, and was probably transferred to the nucleus many times. This complex history of gene fission and gene transfer has created four distinct types of rpl2 structures or compartmentalizations in angiosperms: (1) intact rpl2 gene in the mitochondrion, (2) intact gene in the nucleus, (3) split gene, 5' in the mitochondrion and 3' in the nucleus, and (4) split gene, both parts in the nucleus.
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Affiliation(s)
- K L Adams
- Department of Biology, Indiana University, Bloomington, USA.
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22
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Skinner DJ, Baker SC, Meister RJ, Broadhvest J, Schneitz K, Gasser CS. The Arabidopsis HUELLENLOS gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein. Plant Cell 2001; 13:2719-30. [PMID: 11752383 PMCID: PMC139484 DOI: 10.1105/tpc.010323] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2001] [Accepted: 09/17/2001] [Indexed: 05/18/2023]
Abstract
The HUELLENLOS (HLL) gene participates in patterning and growth of the Arabidopsis ovule. We have isolated the HLL gene and shown that it encodes a protein homologous to the L14 proteins of eubacterial ribosomes. The Arabidopsis genome also includes a highly similar gene, HUELLENLOS PARALOG (HLP), and genes for both cytosolic (L23) and chloroplast ribosome L14 proteins. Phylogenetic analysis shows that HLL and HLP differ significantly from these other two classes of such proteins. HLL and HLP fusions to green fluorescent protein were localized to mitochondria. Ectopic expression of HLP complemented the hll mutant, indicating that HLP and HLL share redundant functions. We conclude that HLL and HLP encode L14 subunits of mitochondrial ribosomes. HLL mRNA was at significantly higher levels than HLP mRNA in pistils, with the opposite pattern in leaves. This differential expression can explain the confinement of effects of hll mutations to gynoecia and ovules. Our elucidation of the nature of HLL shows that metabolic defects can have specific effects on developmental patterning.
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Affiliation(s)
- D J Skinner
- Section of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, California 95616, USA
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23
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Niu LL, Fallon AM. The ribosomal protein L34 gene from the mosquito, Aedes albopictus: exon-intron organization, copy number, and potential regulatory elements. Insect Biochem Mol Biol 1999; 29:1105-1117. [PMID: 10612044 DOI: 10.1016/s0965-1748(99)00090-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe the structural analysis of genomic DNA encoding ribosomal protein (rp) L34 from the mosquito, Aedes albopictus. Comparison of genomic DNA sequences encompassing approximately 8 kb with the rpL34 cDNA sequence showed that the gene contains three exons and two introns, encoding a primary transcript with a deduced size of 6196 nucleotides from the transcription start site to the polyadenylation site. Exon 1, which is not translated, measures only 45 bp, and is separated from Exon 2 by a 359 bp intron. Exon 2 measures 78 bp, and contains the AUG translation initiation codon 14 nucleotides downstream of its 5'-end. Downstream of Exon 2 is a 5270 bp intron, followed by the remainder of the coding sequence in Exon 3, which measures 444 bp including the polyadenylation signal. We used a novel PCR-based procedure to obtain 1.7 kb of DNA upstream of the rpL34 gene. Like the previously described Ae. albopictus rpL8 gene and various mammalian rp genes, the DNA immediately upstream of the rpL34 gene lacks the TATA box, and the rpL34 transcription initiation site is embedded in a characteristic polypyrimidine tract. The 5'-flanking DNA contained a number of cis-acting elements that potentially interact with transcription factors characterized by basic domains, zinc-coordinating DNA binding domains, helix-turn-helix motifs, and beta scaffold factors with minor groove contacts. Particularly striking was the conservation of an AP-4 binding site within 100 nucleotides upstream of the transcription initiation site in both Aal-rpL34 and Aal-rpL8 genes. Comparison of Southern hybridization signals using probes from the 5' and 3'-ends of the 5.3 kb second intron and the cDNA suggested that the Ae. albopictus rpL34 gene most likely occurs as a single expressed copy per haploid genome with restriction enzyme polymorphisms in the upstream flanking DNA and the likely presence of one or more pseudogenes.
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Affiliation(s)
- L L Niu
- Department of Entomology, University of Minnesota, St Paul 55108, USA.
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24
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Sano K, Taguchi A, Furumoto H, Uda T, Itoh T. Cloning, sequencing, and characterization of ribosomal protein and RNA polymerase genes from the region analogous to the alpha-operon of escherichia coli in halophilic archaea, halobacterium halobium. Biochem Biophys Res Commun 1999; 264:24-8. [PMID: 10527834 DOI: 10.1006/bbrc.1999.1480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A determination was made of the nucleotide sequence of the 3215-bp region of a ribosomal protein gene cluster (HS13, HS4, HS11, and HeL18), RNA polymerase (RNA poly D), and tRNA genes (tRNAser and tRNAarg) of halophilic Archaea Halobacterium halobium, which is analogous to the alpha-operon of Escherichia coli (tRNAser-HS13-HS4-HS11-RNA poly D-tRNAarg-HeL18). The seven-gene string was preceded by a pseudoknot-like structure similar to the proposed S4 ribosomal protein binding site of the alpha-operon mRNA leader in E. coli. Using an inducible expression system H. halobium HS4 was produced in large amounts in E. coli, and immunoblot analysis showed the S4 to constitute a 21-kDa polypeptide component of the ribosome. Analysis of the deduced amino acids sequence revealed that the HS13, HS4, and HS11 sequences including the RNA polymerase subunit are more similar to their eukaryotic than to their bacterial counterparts. HeL18, located downstream of the gene cluster analogous to the E. coli alpha-operon (S13-S11-S4-RNA poly D-L17), was similar to both the eukaryotic (eL18) and eubacterial ribosomal protein L15 located in the spc-operon, but not to L17 positioned as the terminal gene of the bacterial alpha-operon.
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Affiliation(s)
- K Sano
- School of Bioresources, Hiroshima Prefectural University, Shobara City, Hiroshima, 727-0023, Japan
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25
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Abstract
Ribosomes from the K-12 strain of Escherichia coli were analyzed with good sensitivity and high mass accuracy using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Fifty-five of the 56 subunit proteins were observable. Mass spectral peak locations were consistent with previously reported post-translational modifications involving N-terminal methionine loss, methylation, thiomethylation, and acetylation for all but one case. The speed and accuracy of mass spectrometry make it a good candidate for phylogenetic studies of ribosomes and the observation of posttranslational modifications in other organisms.
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Affiliation(s)
- R J Arnold
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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26
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Mager WH, Planta RJ, Ballesta JG, Lee JC, Mizuta K, Suzuki K, Warner JR, Woolford J. A new nomenclature for the cytoplasmic ribosomal proteins of Saccharomyces cerevisiae. Nucleic Acids Res 1997; 25:4872-5. [PMID: 9396790 PMCID: PMC147144 DOI: 10.1093/nar/25.24.4872] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The availability of the complete sequence of the Saccharomyces cerevisiae genome has allowed a comprehensive analysis of the genes encoding cytoplasmic ribosomal proteins in this organism. On the basis of this complete inventory a new nomenclature for the yeast ribosomal proteins is presented.
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Affiliation(s)
- W H Mager
- Department of Biochemistry and Molecular Biology, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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27
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Abstract
The evolutionary relationships of ribosomal proteins from eubacteria, archaea, eukaryotes, chloroplasts and mitochondria were examined by their degree of conservation, their structural and functional properties and by the occurrence of conserved structural elements. The structural domains formed by the different protein families were studied. The occurrence of monophyletic groups was investigated for each protein family within the archaea. Phylogenetic trees were constructed between these organisms and together with the homologous sequences of the other phylogenetic domains. All organisms belonging to the archaea clearly formed a monophyletic group. The conserved sequence motifs were checked for the potential to form similar secondary structural elements.
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Affiliation(s)
- E C Müller
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.
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28
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Affiliation(s)
- N C Kyrpides
- Department of Microbiology, University of Illnois, Urbana Champaign 61801, USA
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29
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Goddemeier ML, Rensing SA, Feix G. Characterization of a maize ribosomal P2 protein cDNA and phylogenetic analysis of the P1/P2 family of ribosomal proteins. Plant Mol Biol 1996; 30:655-658. [PMID: 8605314 DOI: 10.1007/bf00049340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The nucleotide sequence of a full-length ribosomal P2 protein cDNA from maize was determined and used for a sequence comparison with the P2 and P1 proteins from other organisms. The integration of these data into a phylogenetic tree shows that the P proteins separated into the subspecies P1 and P2 before the eukaryotic kingdoms including plants developed from their ancestor.
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30
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Sorokin A, Serror P, Pujic P, Azevedo V, Ehrlich SD. The Bacillus subtilis chromosome region encoding homologues of the Escherichia coli mssA and rpsA gene products. Microbiology (Reading) 1995; 141 ( Pt 2):311-9. [PMID: 7704259 DOI: 10.1099/13500872-141-2-311] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A gene was found in Bacillus subtilis which encodes a protein highly homologous to the Escherichia coli rpsA gene product, the S1 ribosomal protein. The B. subtilis protein contains the domain responsible for binding to ribosomes and two S1 motifs, instead of four as found in the E. coli protein. The B. subtilis protein is similar in this way to the equivalent protein of plant chloroplast ribosomes, supposed to be the counterpart of E. coli S1. The gene is expressed during vegetative growth in B. subtilis at the transcriptional and translational levels, as judged by Northern hybridization and expression in a translational fusion with a reporter gene. In contrast to the E. coli situation, it can be inactivated without dramatic effects on cell viability. Southern hybridization of the B. subtilis DNA fragment encoding this gene revealed specific homologous fragments in all other Gram-positive bacteria tested. The hybridization pattern with B. stearothermophilus suggests the presence of at least two homologous genes in this bacterium. We show that in B. subtilis the ORF preceding the rpsA homologue encodes a protein which is highly similar to the product of the E. coli mssA gene which is located upstream of rpsA. Again, in contrast to the E. coli situation, where these genes are co-transcribed, in B. subtilis they are separated by a transcription terminator and the mssA homologue is transcribed during sporulation. We suggest that during the evolution very similar structures and genetic organization of these two genes were conserved but acquired different functions in Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- A Sorokin
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Jouy en Josas, France
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31
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Asemota O, Breda C, Sallaud C, el Turk J, de Kozak I, Buffard D, Esnault R, Kondorosi A. Cloning and expression of a cDNA encoding a cytoplasmic L5 ribosomal protein from alfalfa (Medicago sativa L.). Plant Mol Biol 1994; 26:1201-1205. [PMID: 7811977 DOI: 10.1007/bf00040700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A cDNA encoding a putative cytoplasmic ribosomal protein L5 from alfalfa (MsRL5), the first sequence from higher plants, has been characterized. The derived amino acid sequence of 181 residues contains the L5 signature, is 72.2% identical to yeast ribosomal L5 and shares high identity with other RL5 peptides from eukaryotic origin. The sequence does not contain any signal or transit peptide and therefore might be cytoplasmic. In all alfalfa organs examined MsRL5 transcripts were detected at approximately equal levels.
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Affiliation(s)
- O Asemota
- Institut des Sciences Végétales, CNRS, Gif sur Yvette, France
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32
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Abstract
The amino acid sequences of 16 ribosomal proteins from archaebacterium Halobacterium marismortui have been determined by a direct protein chemical method. In addition, amino acid sequences of three proteins, S11, S18, and L25, have been established by DNA sequencing of their genes as well as by protein sequencing. Comparison of their sequences with those of ribosomal proteins from other organisms revealed that proteins S14, S16, S19, and L25 are related to both eukaryotic and eubacterial ribosomal proteins, being more homologous to eukaryotic than eubacterial counterparts, and proteins S12, S15, and L16 are related to only eukaryotic ribosomal proteins. Furthermore, some proteins are found to be similar to only eubacterial proteins, whereas other proteins show no homology to any other known ribosomal proteins. Comparisons of amino acid compositions between halophilic and nonhalophilic ribosomal proteins revealed that halophilic proteins gain aspartic and glutamic acid residues and significantly lose lysine and arginine residues. In addition, halophilic proteins seem to lose isoleucine as compared with Escherichia coli ribosomal proteins.
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Affiliation(s)
- M Kimura
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Germany
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33
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Wada A. Analysis of Escherichia coli ribosomal proteins by an improved two dimensional gel electrophoresis. II. Characterization of four new proteins. J Biochem 1986; 100:1595-605. [PMID: 3553169 DOI: 10.1093/oxfordjournals.jbchem.a121867] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Four new proteins, A, B, C, and D, found in Escherichia coli ribosomes by an improved two dimensional gel electrophoresis were characterized by oxidation, reduction, and carboxymethylation of cysteine residues, and CsCl fractionation. The cysteine contents of proteins A, B, C, and D were determined to be 1 +/- 0, 3 +/- 1, 5 +/- 1, and 0 +/- 0 by carboxymethylation with iodoacetic acid. The components of protein complexes, which formed numerously under non-reducing conditions, were analyzed. Including protein A, B, and C, every ribosomal protein (r-protein) having cysteine residue(s) except unconfirmed S1 was proved to form such complexes with various combinations. The cysteine residue in protein A, in particular, was highly reactive to make intermolecular S-S bridges so that spot A almost disappeared on the second dimension gel under the non-reducing conditions. Proteins B and C shifted their spots by reduction towards upper left side as do all known r-proteins having plural cysteine residues except S1. This suggests that proteins B and C change their conformation by intramolecular S-S bridges. The CsCl density gradient centrifugation of high salt washed 70S ribosomes showed that protein A belonged to the insoluble split proteins, proteins B and C to the core particles, and protein D and a small population of B to the soluble split proteins. The electrophoretic behaviors, CsCl fractionation and stoichiometry of the four new proteins suggested strongly that they were intrinsic ribosomal constituents different from known ribosomal proteins or factors.
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Ohnishi K. Towards a classification of E. coli ribosomal proteins: a hypothetical 'small ribosome' as a primitive protein-synthesizing apparatus. Orig Life 1984; 14:717-24. [PMID: 6379558 DOI: 10.1007/bf00933726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Homologies were searched among the published primary sequences of 51 E. coli ribosomal proteins, partly by 'eye' and partly by computer-assisted methods. By employing Moore and Goodman's alignment statistics for evaluating homology levels, 33 out of these 51 ribosomal proteins has been classified into 9 homology groups, some of which being yet tentative and remaining to be further analyzed. Taking it into consideration that most ribosomal protein genes are clustered at str-stc region, rif region and several other regions, these results strongly suggest that most or all of the contemporary ribosomal proteins must have evolved by repeated gene duplications of very few (or only one) primitive ancestral ribosomal protein gene(s). Thus it is most reasonable to propose that 'a small ribosome' consisting of very few (or only one) ribosomal protein(s) must have existed as a primitive protein-synthesizing apparatus.
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35
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Jue RA, Woodbury NW, Doolittle RF. Sequence homologies among E. coli ribosomal proteins: evidence for evolutionarily related groupings and internal duplications. J Mol Evol 1980; 15:129-48. [PMID: 6995620 DOI: 10.1007/bf01732666] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The complete or partial sequences of 47 E. coli ribosomal proteins described in the literature have been examined by computerized search and matching programs. In contrast to results previously reported by other investigators, sequence homologies were uncovered among some of these ribosomal proteins that are well beyond statistical expectations. Moreover, alignments of the most strongly homologous sequences suggested the existence of a network of family groupings. Several of these proteins also exhibit internal homologies, indicating that they have been elongated by a series of tandem duplications.
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36
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Lelong JC, Maschler R, Crépin M, Jeantet C, Tischendorf GW, Gros F. Function of individual E. coli 30 S ribosomal proteins as determined by in situ immunospecific neutralization: a tentative classification. Biochimie 1979; 61:881-9. [PMID: 93493 DOI: 10.1016/s0300-9084(79)80238-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The accessibility of each 30S subunit protein to their cognate antibodies (IgG or Fabs) having been previously well established, the effect of their in situ specific neutralization by monovalent IgG fragments (FabI) are reported for five reactions: 1) T4 and R17 RNA directed protein synthesis: 2) polyphenylalanine synthesis: 3) enzymatic Phe-tRNA binding in the presence of 30S + 50W subunits: 4) fMet-tRNAf binding to the 30S subunit in the presence of initiation factors IF1, IF2, IF3; 5) coupling with lambda plac DNA transcription of the initial translation step (i.e., interaction of IF3 activated 30S subunits with nascent mRNA, in the absence of tRNA). According to evident similarities in their inhibition pattern concerning the five reactions tested, 30S subunit proteins can be classified in five categories which are discussed in terms of functional topography.
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Abstract
The evolution of ribosomal proteins of about 70 bacterial strains belonging to the family Enterobacteriaceae has been studied by use of previously reported data (S. Osawa, T. Itoh, and E. Otaka, J. Bacteriol. 107:168-178, 1971) and those obtained in this paper. The proximity of the bacteria was quantified by co-chromatographing the differentially labeled ribosomal proteins from two strains on a column of carboxymethyl cellulose in various combinations. The were then classified into 12 groups (=species?) according to their ribosomal protein compositions and were placed in a phylogenic tree.
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