DOCSLIB.ORG

Crystal Structure of Elongation Factor P from Thermus Thermophilus HB8

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Crystal Structure of Elongation Factor P from Thermus Thermophilus HB8 Crystal structure of elongation factor P from Thermus thermophilus HB8 Kyoko Hanawa-Suetsugu*, Shun-ichi Sekine†, Hiroaki Sakai*, Chie Hori-Takemoto*, Takaho Terada*†, Satoru Unzai*‡, Jeremy R. H. Tame*‡, Seiki Kuramitsu†§, Mikako Shirouzu*†, and Shigeyuki Yokoyama*†¶ʈ *RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; †RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan; ‡Protein Design Laboratory, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; §Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; and ¶Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Edited by Paul R. Schimmel, The Scripps Research Institute, La Jolla, CA, and approved May 13, 2004 (received for review December 26, 2003) Translation elongation factor P (EF-P) stimulates ribosomal pepti- other hand, hypusine is not found in bacteria (13). The structures dyltransferase activity. EF-P is conserved in bacteria and is essential of eIF-5A from three Archaea, Methanococcus jannaschii, Py- for cell viability. Eukarya and Archaea have an EF-P homologue, robaculum aerophilum, and Pyrococcus horikoshii, have two eukaryotic initiation factor 5A (eIF-5A). In the present study, we domains, which are composed of several ␤-strands (14–16). determined the crystal structure of EF-P from Thermus thermophi- Crystallizations of EF-P from E. coli and Aquifex aeolicus have lus HB8 at a 1.65-Å resolution. EF-P consists of three ␤-barrel been reported (7, 17). In this article, we report the crystal domains (I, II, and III), whereas eIF-5A has only two domains (N and structure of EF-P from Thermus thermophilus HB8 at a 1.65-Å C domains). Domain I of EF-P is topologically the same as the N resolution. The EF-P structures are ␤-rich and is divided into domain of eIF-5A. On the other hand, EF-P domains II and III share three ␤-barrel domains (domains I, II, and III). Domains II and the same topology as that of the eIF-5A C domain, indicating that III of EF-P share a very similar topology. The structures of domains II and III arose by duplication. Intriguingly, the N-terminal domains I and II of EF-P are superposable on the structures of half of domain II and the C-terminal half of domain III of EF-P have the M. jannaschii, P. aerophilum, and P. horikoshii eIF-5A sequence homologies to the N- and C-terminal halves, respectively, proteins. The overall structure of EF-P is strikingly similar to the of the eIF-5A C domain. The three domains of EF-P are arranged in L-shaped structure of tRNA. BIOCHEMISTRY an ‘‘L’’ shape, with 65- and 53-Å-long arms at an angle of 95°, which is reminiscent of tRNA. Furthermore, most of the EF-P protein Materials and Methods surface is negatively charged. Therefore, EF-P mimics the tRNA Protein Preparation and Crystallization. The DNA fragment encod- shape but uses domain topologies different from those of the ing EF-P, the protein TT0860 (DNA Data Base in Japan, known tRNA-mimicry translation factors. Domain I of EF-P has a accession no. AB103477), was isolated from the T. thermophilus conserved positive charge at its tip, like the eIF-5A N domain. HB8 genome and was cloned into the expression plasmid, pET11a (Novagen). E. coli BL21(DE3) was transformed with the ranslation elongation factor P (EF-P) was found as a protein vector, and T. thermophilus EF-P was overexpressed. The protein Tthat stimulates the peptidyltransferase activity of the 70S was purified by successive chromatography steps on Q Sepharose ribosome in Escherichia coli (1). EF-P enhances dipeptide and HiLoad Superdex 75 columns (Amersham Biosciences). synthesis with N-formylmethionyl-tRNA and puromycin in vitro, Hampton Research Crystal Screen (18) was used to determine suggesting its involvement in the formation of the first peptide the initial crystallization conditions for EF-P. The final crystal- bond of a protein (2). E. coli EF-P is encoded by the efp gene and lization conditions, 100 mM Hepes-Na buffer (pH 7.6) and 1.35 consists of 188 amino acid residues (3). The efp genes are M lithium sulfate at 16°C yielded high-quality crystals suitable universally conserved in Bacteria (4). Gene interruption exper- for x-ray diffraction data collection. They belong to the space ϭ ϭ iments in E. coli revealed that the efp gene is essential for cell group P212121, with unit cell dimensions a 55.8, b 78.4, and viability and is required for protein synthesis (3). The amount of c ϭ 138.9 Å. The crystallographic asymmetric unit contains two Ϸ ͞ EF-P in E. coli cells is 1 10th of that of EF-G; 800–900 nearly identical EF-P monomers. molecules of EF-P exist in a cell, an amount consistent with 1 EF-P per 10 ribosomes (5). Data Collection and Structure Determination. The crystal structure EF-P reportedly binds to both the 30S and 50S ribosomal of EF-P was solved by the multiple isomorphous replacement subunits (6). Antibiotic sensitivity and footprinting studies have method. Three heavy-atom derivatives were prepared by soak- indicated that EF-P binds near the streptomycin-binding site of ing the EF-P crystals for 12 h in reservoir solutions containing the 16S rRNA in the 30S subunit (6). EF-P also interacts with 2 mM potassium tetrachloroaurate (III), 2 mM sodium ethyl- domains II and V of the 23S rRNA, i.e., near the peptidyltrans- mercurithiosalicylate, and 2 mM mersalyl acid, respectively ferase center (PTC) (6, 7). Ribosome reconstitution experiments (Table 1). All the native and heavy-atom derivative data sets have shown that the L16 ribosomal protein or its N-terminal were collected from frozen crystals at 90 K by using synchro- 47-residue fragment was required for EF-P-mediated peptide tron radiation at the SPring-8 beam lines (Hyogo, Japan). The bond synthesis, whereas L11, L15, or L7͞L12 were not (8–10). data were processed with the program HKL2000 (19). Deter- Eukarya and Archaea seem to lack EF-P, although a similar mination of the heavy atom positions and calculation of the function may be mediated by eukaryotic initiation factor 5A (eIF-5A) (4, 6). The eIF-5A protein is composed of Ϸ140 amino Ϸ acid residues and is shorter than EF-P by 40 residues. Com- This paper was submitted directly (Track II) to the PNAS office. plete intracellular depletion of eIF-5A results in cell growth Abbreviations: EF, elongation factor; eIF-5A, eukaryotic initiation factor 5A; rmsd, rms inhibition; however, protein synthesis seems to be only slightly deviation. reduced (11). eIF-5A is a unique cellular protein that contains Data deposition: The atomic coordinates and structure factors have been deposited in the ␧ the unusual amino acid hypusine [N -(4-aminobutyl-2-hydroxy)- Protein Data Bank, www.pdb.org (PDB ID code 1UEB). L-lysine], which is formed by posttranslational modification of a ʈTo whom correspondence should be addressed. E-mail: [email protected]. specific lysine residue. The enzyme that modifies lysine to ac.jp. hypusine in eIF-5A is essential for yeast viability (12). On the © 2004 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0308667101 PNAS ͉ June 29, 2004 ͉ vol. 101 ͉ no. 26 ͉ 9595–9600 Downloaded by guest on October 1, 2021 Table 1. Crystallographic data Native K2AuCl4 EMTS Mersaryl acid Data collection Resolution,* Å 50–1.65 (1.71–4.65) 50–2.37 (2.45–2.37) 50–2.11 (2.19–2.11) 50–2.11 (2.19–2.11) Observed reflections, n 451,416 103,399 133,338 156,921 Unique reflections, n 62,691 21,379 30,131 30,123 Completeness,† % 99.9 (100.0) 98.8 (92.6) 99.9 (99.8) 99.4 (98.8) ‡ Rsym, % 7.7 (49.6) 3.4 (9.1) 5.5 (14.6) 8.1 (26.9) I͞␴(I)§ 26.4 (3.0) 44.9 (22.1) 26.4 (7.9) 18.9 (5.9) Heavy atom refinement and phasing Heavy atom sites, n 111 ¶ Riso, % 6.5 15.0 24.9 Phasing power (centric–acentric)࿣ 0.58–0.75 0.42–0.50 0.33–0.34 Rcullis** 0.69 0.73 0.80 Mean FOM†† 0.46 Refinement Resolution, Å 40–1.65 Reflections, n 62,587 ‡‡ Rcryst, % 21.3 ‡‡ Rfree, % 24.1 Protein atoms, n 2797 Water atoms, n 407 rmsd bonds, Å 0.005 rmsd angles, ° 1.2 rmsd improper angles, ° 0.83 EMTS, sodium ethylmecurithiosalicylate. *Resolution range of the highest shell is listed in parentheses. †Completeness in the highest-resolution shell is listed in parentheses. ‡ Rsym ϭ͚͉Iobs Ϫ͗I͉͚͘͞Iobs, where Iobs is the observed intensity of reflection. Rsym in the highest-resolution shell is listed in parentheses. §I͞␴(I) in the highest-resolution shell is listed in parentheses. ¶ Riso ϭ͚͉Fder Ϫ Fnat͉͚͞Fnat, where Fnat and Fder are the native and derivative structure factor amplitude, respectively. ࿣ ϭ ͚ 2 ͚͞ Ϫ 2 1/2 Phasing power ( FH (FPH(obs) FPH(calc)) ) , where FH represents the calculated heavy atom structure factor amplitude. **Rcullis ϭ͚ʈFPH Ϯ FP͉ Ϫ FH͉͚͉͞FPH Ϯ FP͉. †† Mean figure of merit (FOM) ϭ͗Fbest͞F͘. ‡‡ Rcryst,free ϭ͚͉Fobs Ϫ Fcalc͉͚͞Fobs, where the crystallographic R factor is calculated including and excluding refinement reflections. In each refinement, free reflections consist of 5% of the total number of reflections. multiple isomorphous replacement phases were carried out by and by analytical ultracentrifugation (Optima XL-1, Beckman using the program SOLVE (20).
Load more

Recommended publications
  • Extremozymes of the Hot and Salty Halothermothrix Orenii
    Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry.
    [Show full text]
  • The Status of Natural Resources on the High-Seas
    The status of natural resources on the high-seas Part 1: An environmental perspective Part 2: Legal and political considerations An independent study conducted by: The Southampton Oceanography Centre & Dr. A. Charlotte de Fontaubert The status of natural resources on the high-seas i The status of natural resources on the high-seas Published May 2001 by WWF-World Wide Fund for Nature (Formerly World Wildlife Fund) Gland, Switzerland. Any reproduction in full or in part of this publication must mention the title and credit the above mentioned publisher as the copyright owner. The designation of geographical entities in this book, and the presentation of the material, do not imply the expression of any opinion whatsoever on the part of WWF or IUCN concerning the legal status of any country, territory, or area, or of its authorities, or concerning the delimitation of its frontiers or boundaries. The views expressed in this publication do not necessarily reflect those of WWF or IUCN. Published by: WWF International, Gland, Switzerland IUCN, Gland, Switzerland and Cambridge, UK. Copyright: © text 2001 WWF © 2000 International Union for Conservation of Nature and Natural Resources © All photographs copyright Southampton Oceanography Centre Reproduction of this publication for educational or other non-commercial purposes is authorized without prior written permission from the copyright holder provided the source is fully acknowledged. Reproduction of this publication for resale or other commercial purposes is prohibited without prior written permission of the copyright holder. Citation: WWF/IUCN (2001). The status of natural resources on the high-seas. WWF/IUCN, Gland, Switzerland. Baker, C.M., Bett, B.J., Billett, D.S.M and Rogers, A.D.
    [Show full text]
  • From Thermus Thermophilus HB8
    Crystal Structure of Elongation Factor P from Thermus thermophilus HB8 Genetic information encoded in messenger RNA molecules. Several proteins were found to possess is translated into protein by the ribosome, which is a domain(s) similar to a portion of tRNA, by which they large ribonucleoprotein complex. It has been clarified interact with the ribosome. The C-terminal domain of that diverse proteins called translation factors and elongation factor G (EF-G) has a shape similar to that RNAs are involved in genetic translation. Translation of the anticodon-stem loop in the elongation factor Tu elongation factor P (EF-P) is one of the translation (EF-Tu)• tRNA• GDPNP ternary complex. Release factors and stimulates the first peptidyl transferase factor 2 (RF2) and ribosome recycling factor (RRF) activity of the ribosome [1]. EF-P is conserved in were also found to possess a protruding domain, by bacteria, and is essential for their viability. Eukarya which they are believed to bind to the ribosome A site and Archaea have an EF-P homologue, eukaryotic [3]. In contrast with these factors, the entire structure initiation factor 5A (eIF-5A). of the EF-P mimics the overall shape of the tRNA We succeeded in the determination of the crystal molecule (Fig. 2). In addition, it is notable that EF-P is structure of EF-P from Thermus thermophilus HB8 at an acidic protein and most of its surface is negatively 1.65 Å resolution, using beamline BL45PX [2]. The charged. The overall tRNA-like shape of the EF-P crystallographic asymmetric unit contains two nearly molecule and the charge distribution seem to be identical EF-P monomers (Fig.
    [Show full text]
  • Ribosomal Initiation Complex-Driven Changes in the Stability and Dynamics of Initiation Factor 2 Regulate the Fidelity of Translation Initiation
    Article Ribosomal Initiation Complex-Driven Changes in the Stability and Dynamics of Initiation Factor 2 Regulate the Fidelity of Translation Initiation Jiangning Wang, Kelvin Caban and Ruben L. Gonzalez Jr. Department of Chemistry, Columbia University, 3000 Broadway, MC3126, New York, NY 10027, USA Correspondence to Ruben L. Gonzalez: [email protected] http://dx.doi.org/10.1016/j.jmb.2014.12.025 Edited by S. A. Woodson Abstract Joining of the large, 50S, ribosomal subunit to the small, 30S, ribosomal subunit initiation complex (IC) during bacterial translation initiation is catalyzed by the initiation factor (IF) IF2. Because the rate of subunit joining is coupled to the IF, transfer RNA (tRNA), and mRNA codon compositions of the 30S IC, the subunit joining reaction functions as a kinetic checkpoint that regulates the fidelity of translation initiation. Recent structural studies suggest that the conformational dynamics of the IF2·tRNA sub-complex forming on the intersubunit surface of the 30S IC may play a significant role in the mechanisms that couple the rate of subunit joining to the IF, tRNA, and codon compositions of the 30S IC. To test this hypothesis, we have developed a single-molecule fluorescence resonance energy transfer signal between IF2 and tRNA that has enabled us to monitor the conformational dynamics of the IF2·tRNA sub-complex across a series of 30S ICs. Our results demonstrate that 30S ICs undergoing rapid subunit joining display a high affinity for IF2 and an IF2·tRNA sub-complex that primarily samples a single conformation. In contrast, 30S ICs that undergo slower subunit joining exhibit a decreased affinity for IF2 and/or a change in the conformational dynamics of the IF2·tRNA sub-complex.
    [Show full text]
  • Initiation Factor Eif5b Catalyzes Second GTP-Dependent Step in Eukaryotic Translation Initiation
    Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation Joon H. Lee*†, Tatyana V. Pestova†‡§, Byung-Sik Shin*, Chune Cao*, Sang K. Choi*, and Thomas E. Dever*¶ *Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2716; ‡Department of Microbiology and Immunology, State University of New York Health Science Center, Brooklyn, NY 11203; and §A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia Edited by Harry F. Noller, University of California, Santa Cruz, CA, and approved October 31, 2002 (received for review September 19, 2002) Initiation factors IF2 in bacteria and eIF2 in eukaryotes are GTPases In addition, when nonhydrolyzable GDPNP was substituted Met that bind Met-tRNAi to the small ribosomal subunit. eIF5B, the for GTP, eIF5B catalyzed subunit joining; however, the factor eukaryotic ortholog of IF2, is a GTPase that promotes ribosomal was unable to dissociate from the 80S ribosome after subunit subunit joining. Here we show that eIF5B GTPase activity is re- joining (7). quired for protein synthesis. Mutation of the conserved Asp-759 in To dissect the function of the eIF5B G domain and test the human eIF5B GTP-binding domain to Asn converts eIF5B to an model that two GTP molecules are required in translation XTPase and introduces an XTP requirement for subunit joining and initiation, we mutated conserved residues in the eIF5B G translation initiation. Thus, in contrast to bacteria where the single domain and tested the function of the mutant proteins in GTPase IF2 is sufficient to catalyze translation initiation, eukaryotic translation initiation.
    [Show full text]
  • Access to Electronic Thesis
    Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield.
    [Show full text]
  • And Thermo-Adaptation in Hyperthermophilic Archaea: Identification of Compatible Solutes, Accumulation Profiles, and Biosynthetic Routes in Archaeoglobus Spp
    Universidade Nova de Lisboa Osmo- andInstituto thermo de Tecnologia-adaptation Química e Biológica in hyperthermophilic Archaea: Subtitle Subtitle Luís Pedro Gafeira Gonçalves Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. OH OH OH CDP c c c - CMP O O - PPi O3P P CTP O O O OH OH OH OH OH OH O- C C C O P O O P i Dissertation presented to obtain the Ph.D degree in BiochemistryO O- Instituto de Tecnologia Química e Biológica | Universidade Nova de LisboaP OH O O OH OH OH Oeiras, Luís Pedro Gafeira Gonçalves January, 2008 2008 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. This dissertation was presented to obtain a Ph. D. degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. By Luís Pedro Gafeira Gonçalves Supervised by Prof. Dr. Helena Santos Oeiras, January, 2008 Apoio financeiro da Fundação para a Ciência e Tecnologia (POCI 2010 – Formação Avançada para a Ciência – Medida IV.3) e FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH / BD / 5076 / 2001. ii ACKNOWNLEDGMENTS The work presented in this thesis, would not have been possible without the help, in terms of time and knowledge, of many people, to whom I am extremely grateful. Firstly and mostly, I need to thank my supervisor, Prof. Helena Santos, for her way of thinking science, her knowledge, her rigorous criticism, and her commitment to science.
    [Show full text]
  • Letters to Nature
    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
    [Show full text]
  • Representatives of a Novel Archaeal Phylum Or a Fast-Evolving
    Open Access Research2005BrochieretVolume al. 6, Issue 5, Article R42 Nanoarchaea: representatives of a novel archaeal phylum or a comment fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier*, Simonetta Gribaldo†, Yvan Zivanovic‡, Fabrice Confalonieri‡ and Patrick Forterre†‡ Addresses: *EA EGEE (Evolution, Génomique, Environnement) Université Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo, 13331 Marseille, Cedex 3, France. †Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex ‡ 15, France. Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Celine Brochier. E-mail: [email protected]. Simonetta Gribaldo. E-mail: [email protected] Published: 14 April 2005 Received: 3 December 2004 Revised: 10 February 2005 Genome Biology 2005, 6:R42 (doi:10.1186/gb-2005-6-5-r42) Accepted: 9 March 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/5/R42 reports © 2005 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Placement<p>Anteins from analysis 25of Nanoarcheumarchaeal of the positiongenomes equitans of suggests Nanoarcheum in the that archaeal N. equitans phylogeny inis likethe lyarchaeal to be the phylogeny representative using aof large a fast-evolving dataset of concatenatedeuryarchaeal ribosomalineage.</p>l pro- deposited research Abstract Background: Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis.
    [Show full text]
  • Download Product Insert (PDF)
    PRODUCT INFORMATION eIF4E (human recombinant) Item No. 15137 Overview and Properties Synonyms: eIF-4F 25 kDa subunit, Eukaryotic Translation Initiation Factor 4E, mRNA Cap-binding Protein Source: Recombinant protein expressed in E. coli Amino Acids: 2-217 (full length) Uniprot No.: P06730 Molecular Weight: 25.2 kDa Storage: -80°C (as supplied) Stability: ≥1 year Purity: batch specific (≥55% estimated by SDS-PAGE) Supplied in: 20 mM HEPES, pH 7.5, containing 100 mM potassium chloride, 2 mM DTT, and 10% glycerol Protein Concentration: batch specific mg/ml Image 1 2 3 4 250 kDa · · · · · · · 150 kDa · · · · · · · 100 kDa · · · · · · · 75 kDa · · · · · · · 50 kDa · · · · · · · 37 kDa · · · · · · · 25 kDa · · · · · · · 20 kDa · · · · · · · 15 kDa · · · · · · · Lane 1: MW Markers Lane 2: eIF4E (human recombinant) (4 µg) Lane 3: eIF4E (human recombinant) (2 µg) Lane 4: eIF4E (human recombinant) (1 µg) Representaõve gel image shown; actual purity may vary between each batch. WARNING CAYMAN CHEMICAL THIS PRODUCT IS FOR RESEARCH ONLY - NOT FOR HUMAN OR VETERINARY DIAGNOSTIC OR THERAPEUTIC USE. 1180 EAST ELLSWORTH RD SAFETY DATA ANN ARBOR, MI 48108 · USA This material should be considered hazardous until further information becomes available. Do not ingest, inhale, get in eyes, on skin, or on clothing. Wash thoroughly after handling. Before use, the user must review the complete Safety Data Sheet, which has been sent via email to your institution. PHONE: [800] 364-9897 WARRANTY AND LIMITATION OF REMEDY [734] 971-3335 Buyer agrees to purchase the material subject to Cayman’s Terms and Conditions. Complete Terms and Conditions including Warranty and Limitation of Liability information can be found on our website.
    [Show full text]
  • Translation Initiation Factor Modifications and the Regulation of Protein Synthesis in Apoptotic Cells
    Cell Death and Differentiation (2000) 7, 603 ± 615 ã 2000 Macmillan Publishers Ltd All rights reserved 1350-9047/00 $15.00 www.nature.com/cdd Translation initiation factor modifications and the regulation of protein synthesis in apoptotic cells ,1 1 1 2 MJ Clemens* , M Bushell , IW Jeffrey , VM Pain and Introduction SJ Morley2 Apoptosis is now recognized to be an important physiological 1 Department of Biochemistry and Immunology, Cellular and Molecular process by which cell and tissue growth, differentiation and Sciences Group, St George's Hospital Medical School, Cranmer Terrace, programmes of development are regulated. The molecular London SW17 ORE, UK mechanisms of apoptosis have been the subject of intense 2 Biochemistry Group, School of Biological Sciences, University of Sussex, research in recent years (for reviews see1±5). Cell death is Brighton BN1 9QG, UK induced following the stimulation of specific cell surface * Corresponding author: MJ Clemens, Department of Biochemistry and Immunology, Cellular and Molecular Sciences Group, St George's Hospital receptors such as the CD95 (Apo-1/Fas) antigen or the 6 Medical School, Cranmer Terrace, London SW17 ORE, UK. Tel: +44 20 8725 tumour necrosis factor-a (TNFa) receptor-1 (TNFR-1). It can 5770; Fax: +44 20 8725 2992; E-mail: [email protected] also result from intracellular events such as DNA damage or from a lack of specific growth factors. The relative importance Received 6.12.99; revised 25.1.00; accepted 20.3.00 of these different influences varies between cell types. The Edited by M Piacentini apoptotic process can be divided into a commitment phase and an execution phase.
    [Show full text]
  • Tackling the Methanopyrus Kandleri Paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo†
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Open Access Research2004BrochieretVolume al. 5, Issue 3, Article R17 Archaeal phylogeny based on proteins of the transcription and comment translation machineries: tackling the Methanopyrus kandleri paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo† Addresses: *Equipe Phylogénomique, Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France. †Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Céline Brochier. E-mail: [email protected] Published: 26 February 2004 Received: 14 November 2003 Revised: 5 January 2004 Genome Biology 2004, 5:R17 Accepted: 21 January 2004 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/3/R17 reports © 2004 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. ArchaealPhylogeneticsequencedusingrespectively). two phylogeny concatenated genomes, analysis based it of is datasetsthe now on Archaea proteinspossible consisting has ofto been thetest of transcription alternative mainly14 proteins established approach involv and translationed byes in 16S bytranscription rRNAusing machineries: largesequence andsequence 53comparison.tackling ribosomal datasets. the Methanopyrus Withproteins We theanalyzed accumulation(3,275 archaealkandleri and 6,377 of phyparadox comp positions,logenyletely Abstract deposited research Background: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets.
    [Show full text]