DOCSLIB.ORG

Archaeal Ribosomal Stalk Protein Interacts with Translation Factors in a Nucleotide-Independent Manner Via Its Conserved C Terminus

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Archaeal Ribosomal Stalk Protein Interacts with Translation Factors in a Nucleotide-Independent Manner Via Its Conserved C Terminus Archaeal ribosomal stalk protein interacts with translation factors in a nucleotide-independent manner via its conserved C terminus Naoko Nomuraa, Takayoshi Hondab, Kentaro Babab, Takao Naganumaa,b, Takehito Tanzawaa, Fumio Arisakac, Masanori Nodad, Susumu Uchiyamad, Isao Tanakaa, Min Yaoa,1, and Toshio Uchiumib,1 aFaculty of Advanced Life Science, Hokkaido University, Kita-ku, Kita-10, Nishi-8, Sapporo 060-0810, Japan; bDepartment of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan; cGraduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan; and dDepartment of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan Edited by Harry F. Noller, University of California, Santa Cruz, CA, and approved January 9, 2012 (received for review August 10, 2011) Protein synthesis on the ribosome requires translational GTPase ible hinge region and has a wide range of movement (7, 13). Re- factors to bind to the ribosome in the GTP-bound form, take indi- cently, cryoelectron microscopy (cryo-EM) and X-ray crystallo- vidual actions that are coupled with GTP hydrolysis, and dissociate, graphic analyses have shown that, in the ribosome•elongation usually in the GDP-bound form. The multiple copies of the flexible factor G (EF-G) complex, the globular C-terminal domain of L12 ribosomal stalk protein play an important role in these processes. interacts directly with EF-G through the G′ domain, which is Using biochemical approaches and the stalk protein from a hyper- unique to EF-G (14–16). However, the interaction between L12 thermophilic archaeon, Pyrococcus horikoshii, we here provide evi- and EF-Tu and its contribution to GTP hydrolysis has not been dence that the conserved C terminus of the stalk protein aP1 binds clarified in the crystal structure of the ribosome•EF-Tu complex directly to domain I of the elongation factor aEF-2, irrespective of (17, 18). The analysis of NMR chemical shifts has demonstrated whether aEF-2 is bound to GTP or GDP. Site-directed mutagenesis the presence of interactions between the C-terminal domain of revealed that four hydrophobic amino acids at the C terminus of purified L12 and the translational GTPases EF-G, EF-Tu, initia- BIOCHEMISTRY aP1, Leu-100, 103, 106, and Phe-107, are crucial for the direct bind- tion factor 2 (IF2), and release factor 3 (RF3), which implies that ing. P1 was also found to bind to the initiation factor aIF5B, as well L12 interacts with a structural feature shared by these factors as aEF-1α, but not aIF2γ, via its C terminus. Moreover, analytical (19). The detailed mechanisms of the interactions and their con- ultracentrifugation and gel mobility shift analyses showed that a tributions to the functions of the factors remain unclear. ð Þ ð Þ ð Þ heptameric complex of aP1 and aP0, aP0 aP1 2 aP1 2 aP1 2, can The archaeal L12 (termed aP1 hereafter) and the eukaryotic bind multiple aEF-2 molecules simultaneously, which suggests that P1/P2 stalk proteins are related closely in terms of structure and individual copies of the stalk protein are accessible to the factor. function (20, 21). However, sequence comparisons and small-an- The functional significance of the C terminus of the stalk protein gle X-ray scattering analyses indicate that the archaeal/eukaryotic was also shown using the eukaryotic proteins P1/P2 and P0. It is stalk proteins are not related structurally to bacterial L12, and likely that the conserved C terminus of the stalk proteins of archaea might not be linked evolutionarily either (20). In fact, our recent and eukaryotes can bind to translation factors both before and crystal structure data showed that the mode of dimerization by after GTP hydrolysis. This consistent binding ability of the stalk pro- the N-terminal domain of archaeal aP1 and its binding to aP0 tein may contribute to maintaining high concentrations of transla- are completely different from those of bacterial L12 (9). Whereas tion factors around the ribosome, thus promoting translational the C-terminal domain (CTD) of bacterial L12 is a relatively large efficiency. globular structure that comprises 70 amino acids, the archaeal/ eukaryotic stalk proteins contain a unique and compact C-term- GTPase-associated center ∣ ribosome protein P0 ∣ ribosome protein P1 ∣ inal region that comprises only 20 amino acids (20). It is appar- hyperthermophilic archaeon ently impossible for this 20 amino acid C-terminal region to adopt a conformation that is similar to that of the CTD of the bacterial ajor dynamic steps in translational initiation, elongation, stalk protein. Therefore, even though the archaeal/eukaryotic Mand termination are promoted by the actions of several and bacterial stalk proteins play analogous roles in the GTPase- translational GTPase factors (1–3). During the elongation step, associated events on the ribosome, they show remarkable struc- two elongation factors bind alternately to the ribosome in their tural differences. Thus, to gain a complete understanding of the GTP-bound states. After they have carried out their respective ribosomal stalk, it is important to elucidate the structure-function functions, which are linked to GTP hydrolysis, they then dissoci- relationships in the archaeal/eukaryotic proteins as well as in ate from the ribosome. The large ribosomal subunit contains an their bacterial counterparts. active center, termed the GTPase-associated center or factor- The sequences of the C-terminal region of the stalk protein are binding center, which interacts with the elongation factors (4). highly conserved among archaea/eukaryotes; in particular, the The GTPase-associated center plays a crucial role in the recruit- Leu-Phe sequence at the C terminus is strictly conserved (Fig. S1). ment of translation factors, GTP hydrolysis, and the release of An additional characteristic feature of the archaeal/eukaryotic stalk inorganic phosphate, which is required for the subsequent disso- ciation of the factor. Multiple copies of the acidic ribosomal Author contributions: M.Y. and T.U. designed research; N.N., T.H., K.B., T.N., T.T., F.A., M.N., protein, or so-called stalk protein, are key components of this and S.U. performed research; F.A., S.U., I.T., M.Y., and T.U. analyzed data; and M.Y. and T.U. functional center (5–9). The stalk proteins form homo- or hetero- wrote the paper. dimers, and two or three dimers bind to the ribosome through an The authors declare no conflict of interest. – anchor protein, L10 in bacteria and P0 in eukaryotes (7, 9 12). This article is a PNAS Direct Submission. In the case of bacteria, the structure and function of the stalk 1To whom correspondence may be addressed. E-mail: [email protected] or protein L7/L12 (termed L12 hereafter) is well established. The [email protected]. L12 protein is composed of an N-terminal dimerization domain This article contains supporting information online at www.pnas.org/lookup/suppl/ and a globular C-terminal domain, which is connected by a flex- doi:10.1073/pnas.1112934109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1112934109 PNAS Early Edition ∣ 1of6 Downloaded by guest on September 26, 2021 proteins is that the conserved C-terminal sequence is shared by not and the appearance of a distinct band with lower mobility than only all stalk proteins (aP1 and P1/P2) but also the anchor proteins that of free aEF-2 (Fig. 1 A and B, lanes 2–5). We confirmed that aP0 and P0 (20, 22). Although functional implications of the the shifted band with lower mobility was the aP1•aEF-2 complex C-terminal segments of eukaryotic P0/P1/P2 (23–25) and archaeal by removing this band from the gel and analyzing it by SDS- aP0/aP1 (9) have been reported, their exact role is not yet well un- PAGE and immunoblotting with an anti-aP1 antibody (Fig. S3 A derstood. Here we demonstrate the direct binding of the conserved and B). The complexes of aP1•aEF-2 with GDP (Fig. 1A) and C terminus of aP1 to elongation factors aEF-2 and aEF-1α,and GMPPCP (Fig. 1B) formed very similar patterns on the nonde- initiation factor aIF5B. Surprisingly, the P1 stalk protein showed a naturing gel, which suggested that aP1 binds to aEF-2•GDP and similar ability to bind to both the GTP- and GDP-bound forms of aEF-2•GMPPCP with more or less the same affinity. We also aEF-2, and the P0•P1 complex could bind multiple aEF-2 mole- confirmed that aP1 has a similar ability to bind to aEF-2 in the cules. These characteristics seem to be favorable for efficient trans- absence of any nucleotide as well as in the presence of GTP, lation. 5′-guanylyl imidodiphosphate, or guanosine 5′-O-[γ-thio]tripho- sphate (Fig. S4). Therefore, the binding of aP1 to aEF-2 seems Results to be nucleotide independent. Characteristics of Binding Between Archaeal aP1 and aEF-2. Using mass spectrometry under nondenaturing conditions, we first Structural Elements Involved in aP1•aEF-2 Binding. Considering pre- checked whether purified aEF-2 (with His tag) was free of asso- vious functional data on the archaeal/eukaryotic stalk (9, 23–25), ciated nucleotides (Fig. S2 A and D). The mass of the purified it can be inferred that the C-terminal portion of aP1 contains the 83;914 Æ 1 aEF-2 was determined to be Da, which is slightly site for aEF-2 binding. To confirm this functionality, nondenatur- larger than the calculated mass of aEF-2 on the basis of its amino ing gel analysis was performed after aP1 had been preincubated acid sequence (83,823 Da).
Load more

Recommended publications
  • Regulatory Features of the 5'Untranslated Leader Region Of
    MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Racheal A. Devine Candidate for the Degree Doctor of Philosophy ______________________________________ Mitch Balish, Ph.D., Director ______________________________________ Eileen Bridge, Ph.D., Reader ______________________________________ Rachael Morgan-Kiss, Ph.D., Reader ______________________________________ Xiao-Wen Cheng, Ph.D., Reader ______________________________________ Jack Vaughn, Ph.D., Graduate School Representative ABSTRACT REGULATORY FEATURES OF THE 5’ UNTRANSLATED LEADER REGION OF aroL IN ESCHERICHIA COLI K12 AND THE sRNA, ryhB, IN SHEWANELLA ONEIDENSIS MR-1 by Racheal A. Devine RNA is an important regulator of gene expression within bacterial, eukaryotic, and archaeal cells. This work focuses on two aspects of RNA regulation: the first half investigates the role of regulatory features within the 5’ untranslated leader region (UTR) of the E. coli aroL mRNA and the second half focuses on an sRNA in S. oneidensis MR- 1. The 5’UTR of mRNAs contain information necessary for ribosome recognition and subsequent translation initiation. Translation initiation is a prominent part of gene expression, as it is the rate-limiting step of translation. The 70S ternary initiation complex contains initiator tRNA and the mRNA’s start codon positioned in the P-site of the 70S ribosome. The Shine-Dalgarno (SD) sequence within the 5’UTR of the mRNA is an important feature that helps facilitate the initial interaction between the mRNA and the 30S subunit. Translation of mRNAs lacking an SD has been reported and suggests that alternative mechanisms of mRNA-30S interactions exist. The aroL mRNA contains a short open reading frame within its 5’UTR.
    [Show full text]
  • Archaeal Translation Initiation Revisited: the Initiation Factor 2 and Eukaryotic Initiation Factor 2B ␣-␤-␦ Subunit Families
    Proc. Natl. Acad. Sci. USA Vol. 95, pp. 3726–3730, March 1998 Evolution Archaeal translation initiation revisited: The initiation factor 2 and eukaryotic initiation factor 2B a-b-d subunit families NIKOS C. KYRPIDES* AND CARL R. WOESE Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemical and Life Sciences, MC 110, 407 S. Goodwin, Urbana, IL 61801 Contributed by Carl R. Woese, December 31, 1997 ABSTRACT As the amount of available sequence data bacterial and eukaryotic translation initiation mechanisms, increases, it becomes apparent that our understanding of although mechanistically generally similar, were molecularly translation initiation is far from comprehensive and that unrelated and so had evolved independently. The Methano- prior conclusions concerning the origin of the process are coccus jannaschii genome (7–9), which gave us our first wrong. Contrary to earlier conclusions, key elements of trans- comprehensive look at the componentry of archaeal transla- lation initiation originated at the Universal Ancestor stage, for tion initiation, revealed that archaeal translation initiation homologous counterparts exist in all three primary taxa. showed considerable homology with eukaryotic initiation, Herein, we explore the evolutionary relationships among the which, if anything, reinforced the divide between bacterial components of bacterial initiation factor 2 (IF-2) and eukary- initiation and that seen in the other domains. We recently have otic IF-2 (eIF-2)/eIF-2B, i.e., the initiation factors involved in shown, however, that bacterial translation initiation factor 1 introducing the initiator tRNA into the translation mecha- (IF-1), contrary to previously accepted opinion, is related in nism and performing the first step in the peptide chain sequence to its eukaryotic/archaeal (functional) counterpart, elongation cycle.
    [Show full text]
  • Translation Initiation: Structures, Mechanisms and Evolution
    Quarterly Reviews of Biophysics 37, 3/4 (2004), pp. 197–284. f 2004 Cambridge University Press 197 doi:10.1017/S0033583505004026 Printed in the United Kingdom Translationinitiation: structures, mechanisms and evolution Assen Marintchev and Gerhard Wagner* Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, USA Abstract. Translation, the process of mRNA-encoded protein synthesis, requires a complex apparatus, composed of the ribosome, tRNAs and additional protein factors, including aminoacyl tRNA synthetases. The ribosome provides the platform for proper assembly of mRNA, tRNAs and protein factors and carries the peptidyl-transferase activity. It consists of small and large subunits. The ribosomes are ribonucleoprotein particles with a ribosomal RNA core, to which multiple ribosomal proteins are bound. The sequence and structure of ribosomal RNAs, tRNAs, some of the ribosomal proteins and some of the additional protein factors are conserved in all kingdoms, underlying the common origin of the translation apparatus. Translation can be subdivided into several steps: initiation, elongation, termination and recycling. Of these, initiation is the most complex and the most divergent among the different kingdoms of life. A great amount of new structural, biochemical and genetic information on translation initiation has been accumulated in recent years, which led to the realization that initiation also shows a great degree of conservation throughout evolution. In this review, we summarize the available structural and functional data on translation initiation in the context of evolution, drawing parallels between eubacteria, archaea, and eukaryotes. We will start with an overview of the ribosome structure and of translation in general, placing emphasis on factors and processes with relevance to initiation.
    [Show full text]
  • The Archaeal Dps Nanocage Targets Kidney Proximal Tubules Via Glomerular Filtration
    The Journal of Clinical Investigation RESEARCH ARTICLE The archaeal Dps nanocage targets kidney proximal tubules via glomerular filtration Masaki Uchida,1 Bernhard Maier,2 Hitesh Kumar Waghwani,1 Ekaterina Selivanovitch,1 S. Louise Pay,2 John Avera,1 EJun Yun,1 Ruben M. Sandoval,2 Bruce A. Molitoris,2 Amy Zollman,2 Trevor Douglas,1 and Takashi Hato2 1Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA. 2Department of Medicine, Indiana University Indianapolis, Indianapolis, Indiana, USA. Nature exploits cage-like proteins for a variety of biological purposes, from molecular packaging and cargo delivery to catalysis. These cage-like proteins are of immense importance in nanomedicine due to their propensity to self-assemble from simple identical building blocks to highly ordered architecture and the design flexibility afforded by protein engineering. However, delivery of protein nanocages to the renal tubules remains a major challenge because of the glomerular filtration barrier, which effectively excludes conventional size nanocages. Here, we show that DNA-binding protein from starved cells (Dps) — the extremely small archaeal antioxidant nanocage — is able to cross the glomerular filtration barrier and is endocytosed by the renal proximal tubules. Using a model of endotoxemia, we present an example of the way in which proximal tubule–selective Dps nanocages can limit the degree of endotoxin-induced kidney injury. This was accomplished by amplifying the endogenous antioxidant property of Dps with addition of a dinuclear manganese cluster. Dps is the first-in- class protein cage nanoparticle that can be targeted to renal proximal tubules through glomerular filtration. In addition to its therapeutic potential, chemical and genetic engineering of Dps will offer a nanoplatform to advance our understanding of the physiology and pathophysiology of glomerular filtration and tubular endocytosis.
    [Show full text]
  • Genome-Wide Investigation of Cellular Functions for Trna Nucleus
    Genome-wide Investigation of Cellular Functions for tRNA Nucleus- Cytoplasm Trafficking in the Yeast Saccharomyces cerevisiae DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hui-Yi Chu Graduate Program in Molecular, Cellular and Developmental Biology The Ohio State University 2012 Dissertation Committee: Anita K. Hopper, Advisor Stephen Osmani Kurt Fredrick Jane Jackman Copyright by Hui-Yi Chu 2012 Abstract In eukaryotic cells tRNAs are transcribed in the nucleus and exported to the cytoplasm for their essential role in protein synthesis. This export event was thought to be unidirectional. Surprisingly, several lines of evidence showed that mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm and their distribution is nutrient-dependent. This newly discovered tRNA retrograde process is conserved from yeast to vertebrates. Although how exactly the tRNA nuclear-cytoplasmic trafficking is regulated is still under investigation, previous studies identified several transporters involved in tRNA subcellular dynamics. At least three members of the β-importin family function in tRNA nuclear-cytoplasmic intracellular movement: (1) Los1 functions in both the tRNA primary export and re-export processes; (2) Mtr10, directly or indirectly, is responsible for the constitutive retrograde import of cytoplasmic tRNA to the nucleus; (3) Msn5 functions solely in the re-export process. In this thesis I focus on the physiological role(s) of the tRNA nuclear retrograde pathway. One possibility is that nuclear accumulation of cytoplasmic tRNA serves to modulate translation of particular transcripts. To test this hypothesis, I compared expression profiles from non-translating mRNAs and polyribosome-bound translating mRNAs collected from msn5Δ and mtr10Δ mutants and wild-type cells, in fed or acute amino acid starvation conditions.
    [Show full text]
  • The Eukaryotic Translation Initiation Factor 2, a Hero Turned Villain in Β Cells
    The eukaryotic translation initiation factor 2, a hero turned villain in β cells By Baroj Abdulkarim Université libre de Bruxelles Faculty of Medicine ULB Center for Diabetes Research Academic year 2016-2017 Jury Members: Dr. Ingrid Langer (President) Dr. Miriam Cnop (Promoter and secretary) Dr. Mariana Igoillo Esteve (Co-Promoter) Dr. Daniel Christophe Dr. Christophe Erneux Dr. Claudine Heinrichs Dr. Amar Abderrahmani Dr. Patrick Gilon Dedicated to my daughter Elîn 2 Contents Papers constituting this thesis .................................................................................... 4 Abbreviations .............................................................................................................. 5 Abstract ...................................................................................................................... 8 Résumé ...................................................................................................................... 9 Introduction ............................................................................................................... 10 Diabetes mellitus ................................................................................................... 10 How β cells work ................................................................................................ 11 Type 2 and monogenic diabetes ........................................................................ 12 Free fatty acids and diabetes ...............................................................................
    [Show full text]
  • An Infb-Homolog in Sulfolobus Acidocaldarius
    System. Appl. Microbiol. 19,312-321 (1996) © Gustav Fischer Verlag· Stuttgart· lena . New York An infB-Homolog in Sulfolobus acidocaldarius 2 PATRICK J. KEELING!, SANDRA L. BALDAUF!, W. FORD DOOLITTLE!, WOLFRAM ZILLIG , and HANS-PETER KLENK2 1 Dalhousie University, Department of Biochemistry, Halifax, Nova Scotia, Canada B3H 4H7 2 Max-Planck-Institut fur Biochemie, 82152 Martinsried, Germany Received February 13, 1996 Summary We have identified an archaeal homologue of the bacterial translation initiation factor 2 (IF-2 or infB) in a partial open reading frame situated upstream of the gene cluster coding for the large subunits of the DNA­ dependent RNA polymerase (RNAP) in Sulfolobus acidocaldarius. Based on this similarity, a larger genomic clone of this region was isolated and sequenced. Although the putative Sulfolobus translation factor gene is highly similar to infB, it shares an even higher degree of similarity with the recently described FUN12 gene from Saccharomyces cerevisiae. Phylogenetic trees inferred from sequences of homologous translation initiation, elongation and termination factors confirm that both the new Sulfolobus gene and yeast FUN12 are members of the IF-2 family and that the root of the IF-2 subtree determined within a 3­ fold rooted universal treee of IF-2, EF-1a!Tu and EF-2/G strongly supports a close phylogenetic relation­ ship between the archaea and the eukaryotes. The genomic context of the Sulfolobus infB also reveals links between two highly conserved bacterial gene clusters, the RNAP operon and the nusA-infB operon. In bacteria these operons are not linked, but the location of the Sulfolobus infB- and nusA-homologues immediately upstream and downstream of the RNAP gene cluster, respectively, links the two conserved bacterial operons and may indicate an ancient genome reorganization.
    [Show full text]
  • Universally Conserved Translation Initiation Factors
    Proc. Natl. Acad. Sci. USA Vol. 95, pp. 224–228, January 1998 Evolution Universally conserved translation initiation factors NIKOS C. KYRPIDES* AND CARL R. WOESE Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemistry and Life Sciences, MC 110, 407 South Goodwin, Urbana, IL 61801 Contributed by Carl R. Woese, November 14, 1997 ABSTRACT The process by which translation is initiated mRNAs are polycistronic, uncapped, lack long poly(A) tails, has long been considered similar in Bacteria and Eukarya but and have Shine–Dalgarno sequences suggested (erroneously) accomplished by a different unrelated set of factors in the two that the archaeal process resembled the bacterial one. Yet, the cases. This not only implies separate evolutionary histories for M. jannaschii genome showed that archaeal translation initi- the two but also implies that at the universal ancestor stage, ation is remarkably similar to that seen in eukaryotes (10). a translation initiation mechanism either did not exist or was Homologs of eukaryotic factors eIF-1A, eIF-2 (all three of a different nature than the extant processes. We demon- subunits), two of the five eIF-2B subunits (a and d), eIF-4A, strate herein that (i) the ‘‘analogous’’ translation initiation and eIF-5A were reported (10), a list that covers most eu- factors IF-1 and eIF-1A are actually related in sequence, (ii) karyotic factors (except for those involved with mRNA cap the ‘‘eukaryotic’’ translation factor SUI1 is universal in recognition). distribution, and (iii) the eukaryoticyarchaeal translation The three recognized bacterial translation initiation factors factor eIF-5A is homologous to the bacterial translation factor have functional counterparts among the eukaryotic factors— EF-P.
    [Show full text]
  • Codon Recognition in Eukaryotic and Archaeal Translation Initiation: a Common Structural Core
    International Journal of Molecular Sciences Review Start Codon Recognition in Eukaryotic and Archaeal Translation Initiation: A Common Structural Core Emmanuelle Schmitt * , Pierre-Damien Coureux, Auriane Monestier, Etienne Dubiez and Yves Mechulam * Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau CEDEX, France; [email protected] (P.-D.C.); [email protected] (A.M.); [email protected] (E.D.) * Correspondence: [email protected] (E.S.); [email protected] (Y.M.); Tel.: +33-1-69-33-4885 (E.S. & Y.M.) Received: 5 December 2018; Accepted: 13 February 2019; Published: 21 February 2019 Abstract: Understanding molecular mechanisms of ribosomal translation sheds light on the emergence and evolution of protein synthesis in the three domains of life. Universally, ribosomal translation is described in three steps: initiation, elongation and termination. During initiation, a macromolecular complex assembled around the small ribosomal subunit selects the start codon on the mRNA and defines the open reading frame. In this review, we focus on the comparison of start codon selection mechanisms in eukaryotes and archaea. Eukaryotic translation initiation is a very complicated process, involving many initiation factors. The most widespread mechanism for the discovery of the start codon is the scanning of the mRNA by a pre-initiation complex until the first AUG codon in a correct context is found. In archaea, long-range scanning does not occur because of the presence of Shine-Dalgarno (SD) sequences or of short 50 untranslated regions. However, archaeal and eukaryotic translation initiations have three initiation factors in common: e/aIF1, e/aIF1A and e/aIF2 are directly involved in the selection of the start codon.
    [Show full text]
  • Revealing Gene Transcription and Translation Initiation Patterns in Archaea, Using an Interactive Clustering Model
    Extremophiles (2004) 8:291–299 DOI 10.1007/s00792-004-0388-1 ORIGINAL PAPER Xiu-Feng Wan Æ Susan M. Bridges Æ John A. Boyle Revealing gene transcription and translation initiation patterns in archaea, using an interactive clustering model Received: 16 May 2003 / Accepted: 11 March 2004 / Published online: 19 May 2004 Ó Springer-Verlag 2004 Abstract An interactive clustering model based on Keywords Archaea Æ Clustering Æ K-means Æ positional weight matrices is described and results ob- Transcription initiation Æ Translation initiation tained using the model to analyze gene regulation pat- terns in archaea are presented. The 5¢ flanking sequences of ORFs identified in four archaea, Sulfolobus solfa- taricus, Pyrobaculum aerophilum, Halobacterium sp. Introduction NRC-1, and Pyrococcus abyssi, were clustered using the model. Three regular patterns of clusters were identified Archaea constitute one of the three major domains of for most ORFs. One showed genes with only a ribo- life on earth. They are a widespread group of organisms some-binding site; another showed genes with a tran- found in extreme environments such as the deep ocean, scriptional regulatory region located at a constant bogs, salt brines, and hot acid springs, and also in sub- location with respect to the start codon. A third pattern surface marine waters (Delong et al. 1994). Pelagic combined the previous two. Both P. aerophilum and archaea were reported to constitute more than 30% of Halobacterium sp. NRC-1 exhibited clusters of genes the prokaryotic biomass in coastal Antarctic surface that lacked any regular pattern. Halobacterium sp. waters. More than 30 species of archaea have been iso- NRC-1 also presented regular features not seen in the lated from a single pond in Yellowstone National Park other organisms.
    [Show full text]
  • Comparative Genomic Analysis of Translation Initiation Mechanisms For
    3922–3931 Nucleic Acids Research, 2017, Vol. 45, No. 7 Published online 21 February 2017 doi: 10.1093/nar/gkx124 Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine–Dalgarno sequence in prokaryotes So Nakagawa1,2,*, Yoshihito Niimura3 and Takashi Gojobori4 1Department of Molecular Life Science, Tokai University School of Medicine, Isehara 259-1193, Japan, 2Micro/Nano Technology Center, Tokai University, Hiratsuka 259-1292, Japan, 3Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan and 4King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Kingdom of Saudi Arabia Received September 14, 2016; Revised February 08, 2017; Editorial Decision February 09, 2017; Accepted February 11, 2017 ABSTRACT ribosomal subunit and the complementary sequence in the 5 untranslated region (UTR) of an mRNA (1–3). Subse- In prokaryotes, translation initiation is believed to quently, the 50S (large) ribosomal subunit docks to the 30S occur through an interaction between the 3 tail of subunit to form a 70S ribosome, where an initiator tRNA is a 16S rRNA and a corresponding Shine–Dalgarno used for protein synthesis (2,3). The ribosome binding site (SD) sequence in the 5 untranslated region (UTR) of in the mRNA is called the Shine–Dalgarno (SD) sequence an mRNA. However, some genes lack SD sequences (GGAGG) that is located approximately 10 nucleotides (nt) (non-SD genes), and the fraction of non-SD genes upstream of the initiation codon (1–3). Although this inter- in a genome varies depending on the prokaryotic action process is thought to be a major initiator of prokary- species.
    [Show full text]
  • Recent Advances in Archaeal Translation Initiation
    Recent Advances in Archaeal Translation Initiation Emmanuelle Schmitt, Pierre-Damien Coureux, Ramy Kazan, Gabrielle Bourgeois, Christine Lazennec-Schurdevin, Yves Mechulam To cite this version: Emmanuelle Schmitt, Pierre-Damien Coureux, Ramy Kazan, Gabrielle Bourgeois, Christine Lazennec- Schurdevin, et al.. Recent Advances in Archaeal Translation Initiation. Frontiers in Microbiology, Frontiers Media, 2020, 11, 10.3389/fmicb.2020.584152. hal-02981025 HAL Id: hal-02981025 https://hal.archives-ouvertes.fr/hal-02981025 Submitted on 27 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. REVIEW published: 18 September 2020 doi: 10.3389/fmicb.2020.584152 Recent Advances in Archaeal Translation Initiation Emmanuelle Schmitt*, Pierre-Damien Coureux, Ramy Kazan, Gabrielle Bourgeois, Christine Lazennec-Schurdevin and Yves Mechulam Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau, France Translation initiation (TI) allows accurate selection of the initiation codon on a messenger RNA (mRNA) and defines the reading frame. In all domains of life, translation initiation generally occurs within a macromolecular complex made up of the small ribosomal subunit, the mRNA, a specialized methionylated initiator tRNA, and translation initiation factors (IFs). Once the start codon is selected at the P site of the ribosome and the large subunit is associated, the IFs are released and a ribosome competent for elongation is formed.
    [Show full text]