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Abstract
Codon use among the three domains of life is not confined to the universal genetic code. With only 22 tRNA genes in mammalian mitochondria, exceptions from the universal code are necessary for proper translation. A particularly interesting deviation is the decoding of the isoleucine AUA codon as methionine by the one mitochondrial-encoded tRNA(Met). This tRNA decodes AUA and AUG in both the A- and P-sites of the metazoan mitochondrial ribosome. Enrichment of posttranscriptional modifications is a commonly appropriated mechanism for modulating decoding rules, enabling some tRNA functions while restraining others. In this case, a modification of cytidine, 5-formylcytidine (f(5)C), at the wobble position-34 of human mitochondrial tRNA(f5CAU)(Met) (hmtRNA(f5CAU)(Met)) enables expanded decoding of AUA, resulting in a deviation in the genetic code. Visualization of the codon•anticodon interaction by X-ray crystallography revealed that recognition of both A and G at the third position of the codon occurs in the canonical Watson-Crick geometry. A modification-dependent shift in the tautomeric equilibrium toward the rare imino-oxo tautomer of cytidine stabilizes the f(5)C34•A base pair geometry with two hydrogen bonds.
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2
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Barraud P, Schmitt E, Mechulam Y, Dardel F, Tisné C. A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis. Nucleic Acids Res 2008; 36:4894-901. [PMID: 18653533 PMCID: PMC2528185 DOI: 10.1093/nar/gkn462] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In all organisms, translational initiation takes place on the small ribosomal subunit and two classes of methionine tRNA are present. The initiator is used exclusively for initiation of protein synthesis while the elongator is used for inserting methionine internally in the nascent polypeptide chain. The crystal structure of Escherichia coli initiator tRNAfMet has been solved at 3.1 Å resolution. The anticodon region is well-defined and reveals a unique structure, which has not been described in any other tRNA. It encompasses a Cm32•A38 base pair with a peculiar geometry extending the anticodon helix, a base triple between A37 and the G29-C41 pair in the major groove of the anticodon stem and a modified stacking organization of the anticodon loop. This conformation is associated with the three GC basepairs in the anticodon stem, characteristic of initiator tRNAs and suggests a mechanism by which the translation initiation machinery could discriminate the initiator tRNA from all other tRNAs.
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Affiliation(s)
- Pierre Barraud
- Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, CNRS, 4 avenue de l'Observatoire, 75006 Paris, France
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3
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Köhrer C, RajBhandary UL. The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods 2008; 44:129-38. [PMID: 18241794 PMCID: PMC2277081 DOI: 10.1016/j.ymeth.2007.10.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Accepted: 10/25/2007] [Indexed: 10/22/2022] Open
Abstract
Here we describe the many applications of acid urea polyacrylamide gel electrophoresis (acid urea PAGE) followed by Northern blot analysis to studies of tRNAs and aminoacyl-tRNA synthetases. Acid urea PAGE allows the electrophoretic separation of different forms of a tRNA, discriminated by changes in bulk, charge, and/or conformation that are brought about by aminoacylation, formylation, or modification of a tRNA. Among the examples described are (i) analysis of the effect of mutations in the Escherichia coli initiator tRNA on its aminoacylation and formylation; (ii) evidence of orthogonality of suppressor tRNAs in mammalian cells and yeast; (iii) analysis of aminoacylation specificity of an archaeal prolyl-tRNA synthetase that can aminoacylate archaeal tRNA(Pro) with cysteine, but does not aminoacylate archaeal tRNA(Cys) with cysteine; (iv) identification and characterization of the AUA-decoding minor tRNA(Ile) in archaea; and (v) evidence that the archaeal minor tRNA(Ile) contains a modified base in the wobble position different from lysidine found in the corresponding eubacterial tRNA.
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MESH Headings
- Amino Acyl-tRNA Synthetases/analysis
- Animals
- Archaea/metabolism
- Blotting, Northern/methods
- Electrophoresis, Polyacrylamide Gel/methods
- Humans
- Hydrogen-Ion Concentration
- Lysine/analogs & derivatives
- Lysine/biosynthesis
- Protein Engineering/methods
- Pyrimidine Nucleosides/biosynthesis
- RNA, Bacterial/isolation & purification
- RNA, Transfer/analysis
- RNA, Transfer/isolation & purification
- RNA, Transfer, Cys/biosynthesis
- RNA, Transfer, Ile/metabolism
- RNA, Transfer, Met/metabolism
- Urea
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Affiliation(s)
- Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Uttam L. RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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4
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Acker MG, Shin BS, Dever TE, Lorsch JR. Interaction between eukaryotic initiation factors 1A and 5B is required for efficient ribosomal subunit joining. J Biol Chem 2006; 281:8469-75. [PMID: 16461768 DOI: 10.1074/jbc.m600210200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic initiation factor 5B (eIF5B) is a GTPase that facilitates joining of the 60 S ribosomal subunit to the 40 S ribosomal subunit during translation initiation. Formation of the resulting 80 S initiation complex triggers eIF5B to hydrolyze its bound GTP, reducing the affinity of the factor for the complex and allowing it to dissociate. Here we present a kinetic analysis of GTP hydrolysis by eIF5B in the context of the translation initiation pathway. Our data indicate that stimulation of GTP hydrolysis by eIF5B requires the completion of early steps in translation initiation, including the eIF1- and eIF1A-dependent delivery of initiator methionyl-tRNA to the 40 S ribosomal subunit and subsequent GTP hydrolysis by eIF2. Full activation of GTP hydrolysis by eIF5B requires the extreme C terminus of eIF1A, which has previously been shown to interact with the C terminus of eIF5B. Disruption of either isoleucine residue in the eIF1A C-terminal sequence DIDDI reduces the rate constant for GTP hydrolysis by approximately 20-fold, whereas changing the aspartic acid residues has no effect. Changing the isoleucines in the C terminus of eIF1A also disrupts the ability of eIF5B to facilitate subunit joining. These data indicate that the interaction of the C terminus of eIF1A with eIF5B promotes ribosomal subunit joining and possibly provides a checkpoint for correct complex formation, allowing full activation of GTP hydrolysis only upon formation of a properly organized 80 S initiation complex.
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Affiliation(s)
- Michael G Acker
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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5
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Allen GS, Zavialov A, Gursky R, Ehrenberg M, Frank J. The Cryo-EM Structure of a Translation Initiation Complex from Escherichia coli. Cell 2005; 121:703-12. [PMID: 15935757 DOI: 10.1016/j.cell.2005.03.023] [Citation(s) in RCA: 242] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 03/14/2005] [Accepted: 03/22/2005] [Indexed: 11/22/2022]
Abstract
The 70S ribosome and its complement of factors required for initiation of translation in E. coli were purified separately and reassembled in vitro with GDPNP, producing a stable initiation complex (IC) stalled after 70S assembly. We have obtained a cryo-EM reconstruction of the IC showing IF2*GDPNP at the intersubunit cleft of the 70S ribosome. IF2*GDPNP contacts the 30S and 50S subunits as well as fMet-tRNA(fMet). IF2 here adopts a conformation radically different from that seen in the recent crystal structure of IF2. The C-terminal domain of IF2 binds to the single-stranded portion of fMet-tRNA(fMet), thereby forcing the tRNA into a novel orientation at the P site. The GTP binding domain of IF2 binds to the GTPase-associated center of the 50S subunit in a manner similar to EF-G and EF-Tu. Additionally, we present evidence for the localization of IF1, IF3, one C-terminal domain of L7/L12, and the N-terminal domain of IF2 in the initiation complex.
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Affiliation(s)
- Gregory S Allen
- Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Albany, New York 12201, USA
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6
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Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU. Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 2005; 69:101-23. [PMID: 15755955 PMCID: PMC1082788 DOI: 10.1128/mmbr.69.1.101-123.2005] [Citation(s) in RCA: 415] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Valuable information on translation initiation is available from biochemical data and recently solved structures. We present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. The first section describes the ribosomal features relevant to the initiation process. Subsequent sections describe the structure, function, and interactions of the mRNA, the initiator tRNA, and the initiation factors IF1, IF2, and IF3. Finally, we provide an overview of mechanisms of regulation of the translation initiation event. Translation occurs on ribonucleoprotein complexes called ribosomes. The ribosome is composed of a large subunit and a small subunit that hold the activities of peptidyltransfer and decode the triplet code of the mRNA, respectively. Translation initiation is promoted by IF1, IF2, and IF3, which mediate base pairing of the initiator tRNA anticodon to the mRNA initiation codon located in the ribosomal P-site. The mechanism of translation initiation differs for canonical and leaderless mRNAs, since the latter is dependent on the relative level of the initiation factors. Regulation of translation occurs primarily in the initiation phase. Secondary structures at the mRNA ribosomal binding site (RBS) inhibit translation initiation. The accessibility of the RBS is regulated by temperature and binding of small metabolites, proteins, or antisense RNAs. The future challenge is to obtain atomic-resolution structures of complete initiation complexes in order to understand the mechanism of translation initiation in molecular detail.
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Affiliation(s)
- Brian Søgaard Laursen
- Department of Molecular Biology, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus C, Denmark
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7
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Randau L, Schauer S, Ambrogelly A, Salazar JC, Moser J, Sekine SI, Yokoyama S, Söll D, Jahn D. tRNA recognition by glutamyl-tRNA reductase. J Biol Chem 2004; 279:34931-7. [PMID: 15194701 DOI: 10.1074/jbc.m401529200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During the first step of porphyrin biosynthesis in Archaea, most bacteria, and in chloroplasts glutamyl-tRNA reductase (GluTR) catalyzes the NADPH-dependent reduction of glutamyl-tRNA to glutamate-1-semialdehyde. Elements in tRNA(Glu) important for utilization by Escherichia coli GluTR were determined by kinetic analysis of 51 variant transcripts of E. coli Glu-tRNA(Glu). Base U8, the U13*G22**A46 base triple, the tertiary Watson-Crick base pair 19*56, and the lack of residue 47 are required for GluTR recognition. All of these bases contribute to the formation of the unique tertiary core of E. coli tRNA-(Glu). Two tRNA(Glu) molecules lacking the entire anticodon stem/loop but retaining the tertiary core structure remained substrates for GluTR, while further decreasing tRNA size toward a minihelix abolished GluTR activity. RNA footprinting experiments revealed the physical interaction of GluTR with the tertiary core of Glu-tRNA(Glu). E. coli GluTR showed clear selectivity against mischarged Glu-tRNA(Gln). We concluded that the unique tertiary core structure of E. coli tRNA(Glu) was sufficient for E. coli GluTR to distinguish specifically its glutamyl-tRNA substrate.
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Affiliation(s)
- Lennart Randau
- Institut für Mikrobiologie, Technical University Braunschweig, Spielmannstrasse 7, P. O. Box 3329, D-38023 Braunschweig, Germany
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8
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Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A 2004; 101:7287-92. [PMID: 15123812 PMCID: PMC409911 DOI: 10.1073/pnas.0401799101] [Citation(s) in RCA: 1082] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2003] [Indexed: 11/18/2022] Open
Abstract
A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs.
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Affiliation(s)
- David H Mathews
- Center for Human Genetics and Molecular Pediatric Disease, The Aab Institute of Biomedical Sciences, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 703, Rochester, NY 14642, USA
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9
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Marzi S, Knight W, Brandi L, Caserta E, Soboleva N, Hill WE, Gualerzi CO, Lodmell JS. Ribosomal localization of translation initiation factor IF2. RNA (NEW YORK, N.Y.) 2003; 9:958-69. [PMID: 12869707 PMCID: PMC1370462 DOI: 10.1261/rna.2116303] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2002] [Accepted: 05/15/2003] [Indexed: 05/22/2023]
Abstract
Bacterial translation initiation factor IF2 is a GTP-binding protein that catalyzes binding of initiator fMet-tRNA in the ribosomal P site. The topographical localization of IF2 on the ribosomal subunits, a prerequisite for understanding the mechanism of initiation complex formation, has remained elusive. Here, we present a model for the positioning of IF2 in the 70S initiation complex as determined by cleavage of rRNA by the chemical nucleases Cu(II):1,10-orthophenanthroline and Fe(II):EDTA tethered to cysteine residues introduced into IF2. Two specific amino acids in the GII domain of IF2 are in proximity to helices H3, H4, H17, and H18 of 16S rRNA. Furthermore, the junction of the C-1 and C-2 domains is in proximity to H89 and the thiostrepton region of 23S rRNA. The docking is further constrained by the requisite proximity of the C-2 domain with P-site-bound tRNA and by the conserved GI domain of the IF2 with the large subunit's factor-binding center. Comparison of our present findings with previous data further suggests that the IF2 orientation on the 30S subunit changes during the transition from the 30S to 70S initiation complex.
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Affiliation(s)
- Stefano Marzi
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC) Italy
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10
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Metzler DE, Metzler CM, Sauke DJ. The Nucleic Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Abstract
The core of Escherichia coli tRNA(Cys) is important for aminoacylation of the tRNA by cysteine-tRNA synthetase. This core differs from the common tRNA core by having a G15:G48, rather than a G15:C48 base-pair. Substitution of G15:G48 with G15:C48 decreases the catalytic efficiency of aminoacylation by two orders of magnitude. This indicates that the design of the core is not compatible with G15:C48. However, the core of E. coli tRNA(Gln), which contains G15:C48, is functional for cysteine-tRNA synthetase. Here, guided by the core of E. coli tRNA(Gln), we sought to test and identify alternative functional design of the tRNA(Cys) core that contains G15:C48. Although analysis of the crystal structure of tRNA(Cys) and tRNA(Gln) implicated long-range tertiary base-pairs above and below G15:G48 as important for a functional core, we showed that this was not the case. The replacement of tertiary interactions involving 9, 21, and 59 in tRNA(Cys) with those in tRNA(Gln) did not construct a functional core that contained G15:C48. In contrast, substitution of nucleotides in the variable loop adjacent to 48 of the 15:48 base-pair created functional cores. Modeling studies of a functional core suggests that the re-constructed core arose from enhanced stacking interactions that compensated for the disruption caused by the G15:C48 base-pair. The repacked tRNA core displayed features that were distinct from those of the wild-type and provided evidence that stacking interactions are alternative means than long-range tertiary base-pairs to a functional core for aminoacylation.
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MESH Headings
- Acylation
- Amino Acyl-tRNA Synthetases/metabolism
- Anticodon/genetics
- Base Pairing/genetics
- Base Sequence
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Kinetics
- Models, Molecular
- Molecular Sequence Data
- Mutation/genetics
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Cys/chemistry
- RNA, Transfer, Cys/genetics
- RNA, Transfer, Cys/metabolism
- RNA, Transfer, Gln/chemistry
- RNA, Transfer, Gln/genetics
- Substrate Specificity
- Sulfuric Acid Esters/metabolism
- Thermodynamics
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Affiliation(s)
- T Christian
- Department of Biochemistry and Molecular Pharmacology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, BLSB 222, 19107, USA
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12
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Szkaradkiewicz K, Zuleeg T, Limmer S, Sprinzl M. Interaction of fMet-tRNAfMet and fMet-AMP with the C-terminal domain of Thermus thermophilus translation initiation factor 2. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:4290-9. [PMID: 10866834 DOI: 10.1046/j.1432-1033.2000.01480.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two polypeptides resistant against proteolytic digestion were identified in Thermus thermophilus translation initiation factor 2 (IF2): the central part of the protein (domains II/III), and the C-terminal domain (domain IV). The interaction of intact IF2 and the isolated proteolytic fragments with fMet-tRNAfMet was subsequently characterized. The isolated C-terminal domain was as effective in binding of the 3' end of fMet-tRNAf Met as intact IF2. N-Formylation of Met-tRNAfMet was required for its efficient binding to the C-terminal domain. This suggests that the interaction between the C-terminal domain and the 3' end of fMet-tRNAfMet is responsible for the recognition of fMet-tRNAfMet by IF2 during translation initiation. Moreover, it was demonstrated that fMet-AMP is a minimal ligand of IF2. fMet-AMP inhibits fMet-tRNAfMet binding to IF2 as well as the activity of IF2 in the stimulation of ApUpG-dependent ribosomal binding of fMet-tRNAf Met. Specific interaction of fMet-AMP with IF2 was demonstrated by 1H-NMR spectroscopy. These findings indicate that fMet-AMP and the 3' terminal fMet-adenosine of fMet-tRNAfMet use the same binding site on the C-terminal domain of IF2 and imply that the interaction between the C-terminal domain and the 3' end of fMet-tRNAfMet is primarily responsible for the fMet-tRNAfMet binding and recognition by IF2.
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13
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Meinnel T, Sacerdot C, Graffe M, Blanquet S, Springer M. Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules. J Mol Biol 1999; 290:825-37. [PMID: 10398584 DOI: 10.1006/jmbi.1999.2881] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translation initiation factor IF3, one of three factors specifically required for translation initiation in Escherichia coli, inhibits initiation on any codon other than the three canonical initiation codons, AUG, GUG, or UUG. This discrimination against initiation on non-canonical codons could be due to either direct recognition of the two last bases of the codon and their cognate bases on the anticodon or to some ability to "feel" codon-anticodon complementarity. To investigate the importance of codon-anticodon complementarity in the discriminatory role of IF3, we constructed a derivative of tRNALeuthat has all the known characteristics of an initiator tRNA except the CAU anticodon. This tRNA is efficiently formylated by methionyl-tRNAfMettransformylase and charged by leucyl-tRNA synthetase irrespective of the sequence of its anticodon. These initiator tRNALeuderivatives (called tRNALI) allow initiation at all the non-canonical codons tested, provided that the complementarity between the codon and the anticodon of the initiator tRNALeuis respected. More remarkably, the discrimination by IF3, normally observed with non-canonical codons, is neutralised if a tRNALIcarrying a complementary anticodon is used for initiation. This suggests that IF3 somehow recognises codon-anticodon complementarity, at least at the second and third position of the codon, rather than some specific bases in either the codon or the anticodon.
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Affiliation(s)
- T Meinnel
- Laboratoire de Biochimie UMR7654 du CNRS, Ecole Polytechnique, Palaiseau Cedex, 91128, France
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14
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Moreno JM, Drskjøtersen L, Kristensen JE, Mortensen KK, Sperling-Petersen HU. Characterization of the domains of E. coli initiation factor IF2 responsible for recognition of the ribosome. FEBS Lett 1999; 455:130-4. [PMID: 10428486 DOI: 10.1016/s0014-5793(99)00858-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have studied the interactions between the ribosome and the domains of Escherichia coli translation initiation factor 2, using an in vitro ribosomal binding assay with wild-type forms, N- and C-terminal truncated forms of IF2 as well as isolated structural domains. A deletion mutant of the factor consisting of the two N-terminal domains of IF2, binds to both 30S and 50S ribosomal subunits as well as to 70S ribosomes. Furthermore, a truncated form of IF2, lacking the two N-terminal domains, binds to 30S ribosomal subunits in the presence of IF1. In addition, this N-terminal deletion mutant IF2 possess a low but significant affinity for the 70S ribosome which is increased by addition of IF1. The isolated C-terminal domain of IF2 has no intrinsic affinity for the ribosome nor does the deletion of this domain from IF2 affect the ribosomal binding capability of IF2. We conclude that the N-terminus of IF2 is required for optimal interaction of the factor with both 30S and 50S ribosomal subunits. A structural model for the interaction of IF2 with the ribosome is presented.
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Affiliation(s)
- J M Moreno
- Department of Biostructural Chemistry, Institute of Molecular and Structural Biology, Aarhus University, Denmark
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15
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Ramesh V, Mayer C, Dyson MR, Gite S, RajBhandary UL. Induced fit of a peptide loop of methionyl-tRNA formyltransferase triggered by the initiator tRNA substrate. Proc Natl Acad Sci U S A 1999; 96:875-80. [PMID: 9927661 PMCID: PMC15318 DOI: 10.1073/pnas.96.3.875] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A 16-aa insertion loop present in eubacterial methionyl-tRNA formyltransferases (MTF) is critical for specific recognition of the initiator tRNA in Escherichia coli. We have studied the interactions between this region of the E. coli enzyme and initiator methionyl-tRNA (Met-tRNA) by using two complementary protection experiments: protection of MTF against proteolytic cleavage by tRNA and protection of tRNA against nucleolytic cleavage by MTF. The insertion loop in MTF is uniquely sensitive to cleavage by trypsin. We show that the substrate initiator Met-tRNA protects MTF against trypsin cleavage, whereas a formylation-defective mutant initiator Met-tRNA, which binds to MTF with approximately the same affinity, does not. Also, mutants of MTF within the insertion loop (which are defective in formylation) are not protected by the initiator Met-tRNA. Thus, a functional enzyme-substrate complex is necessary for protection of MTF against trypsin cleavage. Along with other data, these results strongly suggest that a segment of the insertion loop, which is exposed and unstructured in MTF, undergoes an induced fit in the functional MTF.Met-tRNA complex but not in the nonfunctional one. Footprinting experiments show that MTF specifically protects the acceptor stem and the 3'-end region of the initiator Met-tRNA against cleavage by double and single strand-specific nucleases. This protection also depends on formation of a functional MTF.Met-tRNA complex. Thus, the insertion loop interacts mostly with the acceptor stem of the initiator Met-tRNA, which contains the critical determinants for formylation.
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Affiliation(s)
- V Ramesh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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16
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Brock S, Szkaradkiewicz K, Sprinzl M. Initiation factors of protein biosynthesis in bacteria and their structural relationship to elongation and termination factors. Mol Microbiol 1998; 29:409-17. [PMID: 9720861 DOI: 10.1046/j.1365-2958.1998.00893.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Initiation of protein biosynthesis in bacteria requires three initiation factors: initiation factor 1, initiation factor 2 and initiation factor 3. The mechanism by which initiation factors form the 70S initiation complex with initiator fMet-tRNA(fMet) interacting with the initiation codon in the ribosomal P site and the second mRNA codon exposed in the A site is not yet understood. Here, we present a model for the function of initiation factors 1 and 2 that is based on the analysis of sequence homologies, biochemical evidence and the present knowledge of the three-dimensional structures of translation factors and ribosomes. The model predicts that initiation factors 1 and 2 interact with the ribosomal A site mimicking the structure of the elongation factor G. We present data that extend the mimicry hypothesis to initiation factors 1 and 2, originally postulated for the aminoacyl-tRNA x elongation factor Tu x GTP ternary complex, elongation factor G and release factors.
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Affiliation(s)
- S Brock
- Laboratorium für Biochemie, Universität Bayreuth, Germany
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17
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Schweisguth DC, Moore PB. On the conformation of the anticodon loops of initiator and elongator methionine tRNAs. J Mol Biol 1997; 267:505-19. [PMID: 9126834 DOI: 10.1006/jmbi.1996.0903] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The solution conformations of analogues of initiator and elongator tRNA anticodon stem-loops have been compared by NMR. The data indicate that both have conformations closely similar to those reported for crystalline elongator tRNAs. The two loops differ in their dynamics, however: that of the elongator analogue is more flexible than its initiator counterpart. The anticodon stem-loops of initiator tRNAs are more likely to be distinguished from those of elongator tRNAs during initiation on the basis of their distinctive stem sequences, than they are by differences in the conformations of their anticodon loops.
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Affiliation(s)
- D C Schweisguth
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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18
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Yusupova G, Reinbolt J, Wakao H, Laalami S, Grunberg-Manago M, Romby P, Ehresmann B, Ehresmann C. Topography of the Escherichia coli initiation factor 2/fMet-tRNA(f)(Met) complex as studied by cross-linking. Biochemistry 1996; 35:2978-84. [PMID: 8608135 DOI: 10.1021/bi9519415] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
trans-Diamminedichloroplatinum(II) was used to induce reversible cross-links between Escherichia coli initiation factor 2 (IF-2) and fMet-tRNA(f)(Met). Two distinct cross-links between IF-2 and the initiator tRNA were produced. Analysis of the cross-linking regions on both RNA and protein moieties reveals that the T arm of the tRNA is in the proximity of a region of the C-terminal domain of IF-2 (residues Asn611-Arg645). This cross-link is well-correlated with the fact that the C-domain of IF-2 contains the fMet-tRNA binding site and that the cross-linked RNA fragment precisely maps in a region which is protected by IF-2 from chemical modification and enzymatic digestion. Rather unexpectedly, a second cross-link was characterized which involves the anticodon arm of fMet-tRNA(f)(Met) and the N-terminal part of IF-2 (residues Trp215-Arg237).
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Affiliation(s)
- G Yusupova
- Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
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19
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Li S, Kumar NV, Varshney U, RajBhandary UL. Important role of the amino acid attached to tRNA in formylation and in initiation of protein synthesis in Escherichia coli. J Biol Chem 1996; 271:1022-8. [PMID: 8557626 DOI: 10.1074/jbc.271.2.1022] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In attempts to convert an elongator tRNA to an initiator tRNA, we previously generated a mutant elongator methionine tRNA carrying an anticodon sequence change from CAU to CUA along with the two features important for activity of Escherichia coli initiator tRNA in initiation. This mutant tRNA (Mi:2 tRNA) was active in initiation in vivo but only when aminoacylated with methionine by overproduction of methionyl-tRNA synthetase. Here we show that the Mi:2 tRNA is normally aminoacylated in vivo with lysine and that the tRNA aminoacylated with lysine is a very poor substrate for formylation compared with the same tRNA aminoacylated with methionine. By introducing further changes at base pairs 4:69 and 5:68 in the acceptor stem of the Mi:2 tRNA to those found in the E. coli initiator tRNA, we show that change of the U4:A69 base pair to G4:C69 and overproduction of lysyl-tRNA synthetase and methionyl-tRNA transformylase results in partial formylation of the mutant tRNA and activity of the formyllysyl-tRNAs in initiation of protein synthesis. Thus, the G4: C69 base pair contributes toward formylation of the tRNA and protein synthesis in E. coli can be initiated with formyllysine. We also discuss the implications of these and other results on recognition of tRNAs by E. coli lysyl-tRNA synthetase and on competition in cells among aminoacyl-tRNA synthetases.
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Affiliation(s)
- S Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, USA
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20
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Laalami S, Grentzmann G, Bremaud L, Cenatiempo Y. Messenger RNA translation in prokaryotes: GTPase centers associated with translational factors. Biochimie 1996; 78:577-89. [PMID: 8955901 DOI: 10.1016/s0300-9084(96)80004-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
During the decoding of messenger RNA, each step of the translational cycle requires the intervention of protein factors and the hydrolysis of one or more GTP molecule(s). Of the prokaryotic translational factors, IF2, EF-Tu, SELB, EF-G and RF3 are GTP-binding proteins. In this review we summarize the latest findings on the structures and the roles of these GTPases in the translational process.
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Affiliation(s)
- S Laalami
- Institut de Biologie Moléculaire et d'Ingénierie Génétique, URA-CNRS 1172, Université de Poitiers, France
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21
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Schmitt E, Guillon JM, Meinnel T, Mechulam Y, Dardel F, Blanquet S. Molecular recognition governing the initiation of translation in Escherichia coli. A review. Biochimie 1996; 78:543-54. [PMID: 8955898 DOI: 10.1016/s0300-9084(96)80001-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Selection of the proper start codon for the synthesis of a polypeptide by the Escherichia coli translation initiation apparatus involves several macromolecular components. These macromolecules interact in a specific and concerted manner to yield the translation initiation complex. This review focuses on recent data concerning the properties of the initiator tRNA and of enzymes and factors involved in the translation initiation process. The three initiation factors, as well as methionyl-tRNA synthetase and methionyl-tRNA(f)Met formyltransferase are described. In addition, the tRNA recognition properties of EF-Tu and peptidyl-tRNA hydrolase are considered. Finally, peptide deformylase and methionine aminopeptidase, which catalyze the amino terminal maturation of nascent polypeptides, can also be associated to the translation initiation process.
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Affiliation(s)
- E Schmitt
- Laboratoire de Biochimie, URA-CNRS no 1970, Ecole Polytechnique, Palaiseau, France
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22
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Mangroo D, Wu XQ, RajBhandary UL. Escherichia coli initiator tRNA: structure-function relationships and interactions with the translational machinery. Biochem Cell Biol 1995; 73:1023-31. [PMID: 8722017 DOI: 10.1139/o95-109] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We showed previously that the sequence and (or) structural elements important for specifying the many distinctive properties of Escherichia coli initiator tRNA are clustered in the acceptor stem and in the anticodon stem and loop. This paper briefly describes this and reviews the results of some recently published studies on the mutant initiator tRNAs generated during this work. First, we have studied the effect of overproduction of methionyl-tRNA transformylase (MTF) and initiation factors IF2 and IF3 on activity of mutant initiator tRNAs that are defective at specific steps in the initiation pathway. Overproduction of MTF rescued specifically the activity of mutant tRNAs defective in formylation but not mutants defective in binding to the P site. Overproduction of IF2 increased the activity of all mutant tRNAs having the CUA anticodon but not of mutant tRNA having the GAC anticodon. Overproduction of IF3 had no effect on the activity of any of the mutant tRNAs tested. Second, for functional studies of mutant initiator tRNA in vivo, we used a CAU --> CUA anticodon sequence mutant that can initiate protein synthesis from UAG instead of AUG. In contrast with the wild-type initiator tRNA, the mutant initiator tRNA has a 2-methylthio-N6-isopentenyl adenosine (ms2i6A) base modification next to the anticodon. Interestingly, this base modification is now important for activity of the mutant tRNA in initiation. In a miaA strain of E. coli deficient in biosynthesis of ms2i6A, the mutant initiator tRNA is much less active in initiation. The defect is specifically in binding to the ribosomal P site.
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Affiliation(s)
- D Mangroo
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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23
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Mangroo D, RajBhandary UL. Mutants of Escherichia coli initiator tRNA defective in initiation. Effects of overproduction of methionyl-tRNA transformylase and the initiation factors IF2 and IF3. J Biol Chem 1995; 270:12203-9. [PMID: 7538134 DOI: 10.1074/jbc.270.20.12203] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We describe the effects of overproduction of methionyl-tRNA transformylase and initiation factors IF2 and IF3 on the activity, in vivo, of initiator tRNA mutants defective at specific steps of the initiation process in protein synthesis. The activity of the U35A36/G72 and U35A36/G72G73 mutants, which are defective in formylation, was increased by overproduction of methionyl-tRNA transformylase. In contrast, the activity of the C30:G40/U35A36 mutant, which is formylated normally but is defective in binding to the ribosomal P site, was not increased. Overproduction of IF2 had a strong stimulatory effect on the activity of virtually all the mutants carrying the U35A36 anticodon sequence change, including the U35A36, U35A36/G72, U35A36/G72G73, and the C30:G40/U35A36 mutants. In cells overproducing IF2, the amount of protein made by translation of a mutant mRNA, which uses the U35A36 mutant initiator tRNA, is severalfold higher than that made by translation of a wild type mRNA. We discuss the possible implications of this result on overproduction of proteins and on the order of assembly of the 30 S ribosome.mRNA.fMet-tRNA initiation complex in Escherichia coli. Over-production of IF3 did not affect the initiator activity of any of the tRNA mutants studied.
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Affiliation(s)
- D Mangroo
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
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24
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Hou YM. Structural elements that contribute to an unusual tertiary interaction in a transfer RNA. Biochemistry 1994; 33:4677-81. [PMID: 8161525 DOI: 10.1021/bi00181a603] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Transfer RNAs (tRNAs) contain a set of defined tertiary hydrogen-bonding interactions that are established between conserved and semiconserved nucleotides. Although the crystal structures of tRNAs describe each of the tertiary interactions in detailed molecular terms, little is known about the underlying structural parameters that stabilize the tertiary interactions. Escherichia coli (E. coli) tRNA(Cys) has an unusual tertiary interaction between G15 in the dihydrouridine (D) loop and G48 in the variable loop that is critical for cysteine aminoacylation. All other tRNAs have a purine 15 and a complementary pyrimidine 48 that establish a tertiary interaction known as the Levitt base pair [Levitt, M. (1969) Nature 224, 759-763; Klug et al. (1974) J. Mol. Biol. 89, 511-516]. In this study, the G15.G48 tertiary interaction in E. coli tRNA(Cys) was used to investigate the structural elements that contribute to its variation from the Levitt base pair. Analysis with chemical probes showed that substitution of U21 with A21 in the D loop and formation of a Watson-Crick base pair between nucleotides 13 and 22 in the D stem switch the hydrogen-pairing of G15.G48 to a Levitt-like G15.G48 base pair. This switch was accompanied by a decrease of the catalytic efficiency of aminoacylation by 2 orders of magnitude. In contrast, insertion of additional nucleotides in the D or variable loops had little effect.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- Y M Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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25
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Affiliation(s)
- U L RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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26
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Vachon G, Raingeaud J, Dérijard B, Julien R, Cenatiempo Y. Domain of E. coli translational initiation factor IF2 homologous to lambda cI repressor and displaying DNA binding activity. FEBS Lett 1993; 321:241-6. [PMID: 8477856 DOI: 10.1016/0014-5793(93)80117-d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The carboxy-terminal region of translational initiation factor IF2 is a common region to the three active forms of the factor (alpha, beta and gamma) but its function is still unknown. We report here that this region of IF2 carries at least one domain which is homologous to the N-terminal and middle part of the cI repressor of lambda phage. The IF2 homologous domain harbors functionally important features of the lambda repressor, e.g. the helix-turn-helix motif and some of the residues essential for the structure of the hydrophobic core of the repressor. This homologous domain of IF2 was fused to the beta-galactosidase protein. The hybrid protein, as well as IF2 itself, shows a consistent DNA binding activity in nitrocellulose filtration assays but does not display the specificity of the cI repressor for the PR operator. The implication of this domain in the transcriptional activity of IF2, reported by others, is discussed.
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Affiliation(s)
- G Vachon
- Institut de Biologie Moléculaire et d'Ingénierie Génétique, URA CNRS 1172, Université de Poitiers, France
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27
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Giegé R, Puglisi JD, Florentz C. tRNA structure and aminoacylation efficiency. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1993; 45:129-206. [PMID: 8341800 DOI: 10.1016/s0079-6603(08)60869-7] [Citation(s) in RCA: 180] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- R Giegé
- Unité Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Strasbourg, France
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28
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Dyson MR, Mandal N, RajBhandary UL. Relationship between the structure and function of Escherichia coli initiator tRNA. Biochimie 1993; 75:1051-60. [PMID: 7515283 DOI: 10.1016/0300-9084(93)90004-c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Through functional studies of mutant tRNAs, we have identified sequence and/or structural features important for specifying the many distinctive properties of E coli initiator tRNA. Many of the mutant tRNAs contain an anticodon sequence change from CAU-->CUA and are now substrates for E coli glutaminyl-tRNA synthetase (GlnRS). We describe here the effect of further mutating the discriminator base 73 and nucleotide 72 at the end of the acceptor stem on: i) recognition of the mutant tRNAs by E coli GlnRS; ii) recognition by E coli methionyl-tRNA transformylase; and iii) activity of the mutant tRNAs in initiation in E coli. For GlnRS recognition, our results are, in general, consistent with interactions found in the crystal structure of the E coli GlnRS-glutamine tRNA complex. The results also support our previous conclusion that formylation of initiator tRNA is important for its function in initiation.
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MESH Headings
- Acyltransferases/chemistry
- Acyltransferases/genetics
- Acyltransferases/metabolism
- Amino Acyl-tRNA Synthetases/chemistry
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Base Sequence
- Binding Sites
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Hydroxymethyl and Formyl Transferases
- Immunoblotting
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Met
- Structure-Activity Relationship
- Substrate Specificity
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Affiliation(s)
- M R Dyson
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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29
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Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54288-5] [Citation(s) in RCA: 305] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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30
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Gualerzi C, Severini M, Spurio R, La Teana A, Pon C. Molecular dissection of translation initiation factor IF2. Evidence for two structural and functional domains. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)55305-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Wakao H, Romby P, Ebel JP, Grunberg-Manago M, Ehresmann C, Ehresmann B. Topography of the Escherichia coli ribosomal 30S subunit-initiation factor 2 complex. Biochimie 1991; 73:991-1000. [PMID: 1720674 DOI: 10.1016/0300-9084(91)90140-v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The specific effect of the binding of initiation factor IF2 on E coli 16S rRNA within the [IF2/30S/GTP] complex has been probed by crosslinking experiment with trans-diamminedichloro platinum (II) and by phosphate alkylation with ethylnitrosourea. Several 16S rRNA fragments crosslinked to IF2 have been identified and are mostly located in the head and the lateral protrusion of the 30S subunit. The study of the effect of IF2 binding to the 30S subunit reveals that the factor does not tightly bind to the 16S rRNA and induces both isolated reductions and enhancements of phosphate reactivity in the 16S rRNA. Several of them are located near the binding site of IF2 and weak effects are observed in distant parts of the subunit. These results are discussed in the light of current knowledge of the topographical localization of IF2 with the 30S subunit and of its relation with function.
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Affiliation(s)
- H Wakao
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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32
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Ganoza MC, Cunningham C, Chung DG, Neilson T. A proposed role for IF-3 and EF-T in maintaining the specificity of prokaryotic initiation complex formation. Mol Biol Rep 1991; 15:33-8. [PMID: 1875917 DOI: 10.1007/bf00369898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Initiation factor-free 30S subunits of E. coli ribosomes bind aminoacyl-tRNAs more efficiently than fMet-tRNA(fMet). Elongator-tRNA binding was unaffected by IF-1 or IF-2 but was inhibited by IF-3. Their combination reduced this binding up to 40% and stimulated that of fMet-tRNA(fMet). Unexpectedly, EF-T also prevented elongator-tRNA binding by complexing both to the 30S and to the aminoacyl-tRNAs. Using AUGU3 as mRNA, elongator-tRNAs competed with fMet-fRNA(fMet) and with tRNA(fMet), fMet-tRNA(fMet) reacted with puromycin after addition of 50S subunits suggesting that it occupied the P site. EF-T directed binding of phe-tRNA to the 30S.AUGU3 complex at the A site only if fMet-tRNA(fMet) or tRNA(fMet) filled the P/E site. We propose that one function of EF-T may be to prevent the entry of aminoacyl-tRNAs into the 30S particle during initiation. The possibility that a special site for fMet-tRNA resides on 16S rRNA is also discussed.
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MESH Headings
- Binding Sites/physiology
- Binding, Competitive
- Escherichia coli
- Peptide Chain Elongation, Translational
- Peptide Chain Initiation, Translational/physiology
- Peptide Elongation Factors/isolation & purification
- Peptide Elongation Factors/pharmacology
- Peptide Elongation Factors/physiology
- Peptide Initiation Factors/physiology
- Prokaryotic Initiation Factor-3
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Leu/metabolism
- RNA, Transfer, Phe/metabolism
- RNA, Transfer, Ser/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
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Affiliation(s)
- M C Ganoza
- Banting and Best Department of Medical Research, University of Toronto, Ontario Canada
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33
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Gross G, Mielke C, Hollatz I, Blöcker H, Frank R. RNA primary sequence or secondary structure in the translational initiation region controls expression of two variant interferon-beta genes in Escherichia coli. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)38210-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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34
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Romby P, Wakao H, Westhof E, Grunberg-Manago M, Ehresmann B, Ehresmann C, Ebel JP. The conformation of the initiator tRNA and of the 16S rRNA from Escherichia coli during the formation of the 30S initiation complex. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1050:84-92. [PMID: 2207173 DOI: 10.1016/0167-4781(90)90146-s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The conformation of the E. coli initiator tRNA and of the 16S rRNA at different steps leading to the 30S.IF2.fMet-ARN(fMet).AUG.GTP complex has been investigated using several structure-specific probes. As compared to elongator tRNA, the initiator tRNA exhibits specific structural features in the anticodon arm, the T and D loops and the acceptor arm. Initiation factor 2 (IF2) interacts with the T-loop and the minor groove of the T stem of the RNA, and induces an increased flexibility in the anticodon arm. In the 30S initiation complex, additional protection is observed in the acceptor stem and in the anticodon arm of the tRNA. Within the 30S subunit, IF2 does not significantly shield defined portions of 16S rRNA, but induces both reduction and enhancement of reactivity scattered in the entire molecule. Most are constrained in a region corresponding to the cleft, the lateral protrusion and the part of the head facing the protrusion. All the reactivity changes induced by the binding of IF2 are still observed in the presence of the initiator tRNA and AUG message. The additional changes induced by the tRNA are mostly centered around the cleft-head-lateral protrusion region, near positions affected by IF2 binding.
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MESH Headings
- Base Sequence
- Escherichia coli/genetics
- Hydrogen Bonding
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Peptide Chain Initiation, Translational
- Peptide Initiation Factors/metabolism
- Prokaryotic Initiation Factor-2
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Met
- Ribosomes/metabolism
- Ribosomes/ultrastructure
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Affiliation(s)
- P Romby
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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