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Roy B, Liu Q, Shoji S, Fredrick K. IF2 and unique features of initiator tRNA fMet help establish the translational reading frame. RNA Biol 2017; 15:604-613. [PMID: 28914580 DOI: 10.1080/15476286.2017.1379636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Translation begins at AUG, GUG, or UUG codons in bacteria. Start codon recognition occurs in the P site, which may help explain this first-position degeneracy. However, the molecular basis of start codon specificity remains unclear. In this study, we measured the codon dependence of 30S•mRNA•tRNAfMet and 30S•mRNA•tRNAMet complex formation. We found that complex stability varies over a large range with initiator tRNAfMet, following the same trend as reported previously for initiation rate in vivo (AUG > GUG, UUG > CUG, AUC, AUA > ACG). With elongator tRNAMet, the codon dependence of binding differs qualitatively, with virtually no discrimination between GUG and CUG. A unique feature of initiator tRNAfMet is a series of three G-C basepairs in the anticodon stem, which are known to be important for efficient initiation in vivo. A mutation targeting the central of these G-C basepairs causes the mRNA binding specificity pattern to change in a way reminiscent of elongator tRNAMet. Unexpectedly, for certain complexes containing fMet-tRNAfMet, we observed mispositioning of mRNA, such that codon 2 is no longer programmed in the A site. This mRNA mispositioning is exacerbated by the anticodon stem mutation and suppressed by IF2. These findings suggest that both IF2 and the unique anticodon stem of fMet-tRNAfMet help constrain mRNA positioning to set the correct reading frame during initiation.
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Affiliation(s)
- Bappaditya Roy
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Qi Liu
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Shinichiro Shoji
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
| | - Kurt Fredrick
- a Department of Microbiology and Center for RNA Biology , Ohio State University , Columbus , Ohio , USA
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2
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Investigating Bacterial Protein Synthesis Using Systems Biology Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:21-40. [PMID: 26621460 DOI: 10.1007/978-3-319-23603-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein synthesis is essential for bacterial growth and survival. Its study in Escherichia coli helped uncover features conserved among bacteria as well as universally. The pattern of discovery and the identification of some of the longest-known components of the protein synthesis machinery, including the ribosome itself, tRNAs, and translation factors proceeded through many stages of successively more refined biochemical purifications, finally culminating in the isolation to homogeneity, identification, and mapping of the smallest unit required for performing the given function. These early studies produced a wealth of information. However, many unknowns remained. Systems biology approaches provide an opportunity to investigate protein synthesis from a global perspective, overcoming the limitations of earlier ad hoc methods to gain unprecedented insights. This chapter reviews innovative systems biology approaches, with an emphasis on those designed specifically for investigating the protein synthesis machinery in E. coli.
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Abstract
Selection of correct start codons on messenger RNAs is a key step required for faithful translation of the genetic message. Such a selection occurs in a complex process, during which a translation-competent ribosome assembles, eventually having in its P site a specialized methionyl-tRNAMet base-paired with the start codon on the mRNA. This chapter summarizes recent advances describing at the molecular level the successive steps involved in the process. Special emphasis is put on the roles of the three initiation factors and of the initiator tRNA, which are crucial for the efficiency and the specificity of the process. In particular, structural analyses concerning complexes containing ribosomal subunits, as well as detailed kinetic studies, have shed new light on the sequence of events leading to faithful initiation of protein synthesis in Bacteria.
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Revel M, Groner Y, Pollack Y, Scheps R, Berissi H. Protein synthesis machinery and the regulation of messenger RNA translation. CIBA FOUNDATION SYMPOSIUM 2008; 7:69-85. [PMID: 4580347 DOI: 10.1002/9780470719909.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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5
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Nagel K, Voigt J. An inhibitor of elongation factor G (EF-G) GTPase present in the ribosome wash of Escherichia coli: a complex of initiation factors IF1 and IF3? BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1129:145-8. [PMID: 1730051 DOI: 10.1016/0167-4781(92)90478-i] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An inhibitor of elongation factor G (EF-G) GTPase isolated from the ribosome wash of Escherichia coli was shown to stimulate the poly(A,U,G)- and initiation factor 2 (IF2)-dependent binding of N-formyl-[35S]Met-tRNAfMet to ribosomes. In the presence of saturating amounts of the EF-G GTPase inhibitor, neither addition of initiation factor 1 (IF1) nor addition of initiation factor 3 (IF3) caused a further stimulation of the formation of N-formyl-[35S]Met-tRNAfMET/poly(A,U,G)/ribosome complexes. Both IF1 and IF3 were shown to inhibit ribosome-dependent EF-G GTPase, especially when both initiation factors were added either in absence or in the presence of initiation factor 2 (IF2), poly(A,U,G) and N-formyl-Met-tRNAfMet. Therefore, we conclude that the EF-G GTPase inhibitor consisting of two polypeptide subunits with apparent molecular masses of 23,000 and 10,000 Da is a complex of initiation factors IF1 and IF3. The inhibition of EF-G GTPAse by IF3, but not the effects of IF1 in the presence or absence of IF3 could be reversed by increasing the Mg(2+)-concentration as already shown for the EF-G GTPase inhibitor. Therefore, IF1 as well as the EF-G GTPase inhibitor do not influence the ribosome-dependent EF-G GTPase by affecting the association of ribosomal subunits.
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Affiliation(s)
- K Nagel
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Germany
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6
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Abstract
Dexamethasone (2.5 mg/day per kg) treatment of young growing rats resulted in reduced food intake and rapidly inhibited whole-body and lung growth. Although the reduction in food intake partially explained the decrease in whole-body growth, it did not influence lung growth. After 24 h of dexamethasone treatment, ribosomal efficiency in the lung was reduced 44%, producing a 38% decrease in the rate of pulmonary protein synthesis. Extending dexamethasone treatment to 5 days resulted in decreases in both ribosomal efficiency (35%) and capacity (28%), explaining the 53% reduction in lung protein synthesis at this time. After both the acute and chronic steroid regimes, the decreased rates of pulmonary protein synthesis were accompanied by a loss of polyribosomes and an elevated ribosomal monomer pool, indicating that dexamethasone blocked translation at the site of peptide-chain initiation.
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7
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Denslow ND, LiCata VJ, Gualerzi C, O'Brien TW. Interaction of bovine mitochondrial ribosomes with Escherichia coli initiation factor 3 (IF3). Biochemistry 1988; 27:3521-7. [PMID: 3291951 DOI: 10.1021/bi00409a059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mammalian mitochondrial ribosomes are distinguished from their bacterial and eukaryotic-cytoplasmic counterparts, as well as from mitochondrial ribosomes of lower eukaryotes, by their physical and chemical properties and their high protein content. However, they do share more functional homologies with bacterial ribosomes than with cytoplasmic ribosomes. To search for possible homologies between mammalian mitochondrial ribosomes and bacterial ribosomes at the level of initiation factor binding sites, we studied the interaction of Escherichia coli initiation factor 3 (IF3) with bovine mitochondrial ribosomes. Bacterial IF3 was found to bind to the small subunit of bovine mitochondrial ribosomes with an affinity of the same order of magnitude as that for bacterial ribosomes, suggesting that most of the functional groups contributing to the IF3 binding site in bacterial ribosomes are conserved in mitochondrial ribosomes. Increasing ionic strength affects binding to both ribosomes similarly and suggests a large electrostatic contribution to the reaction. Furthermore, bacterial IF3 inhibits the Mg2+-dependent association of mitochondrial ribosomal subunits, suggesting that the bacterial IF3 binds to mitochondrial small subunits in a functional way.
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Affiliation(s)
- N D Denslow
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville 32601-0245
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8
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Pon CL, Gualerzi CO. Mechanism of translational initiation in prokaryotes. IF3 is released from ribosomes during and not before 70 S initiation complex formation. FEBS Lett 1986; 195:215-9. [PMID: 3510902 DOI: 10.1016/0014-5793(86)80163-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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9
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Kelly FJ, Jefferson LS. Control of peptide-chain initiation in rat skeletal muscle. Development of methods for preparation of native ribosomal subunits and analysis of the effect of insulin on formation of 40 S initiation complexes. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)88833-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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10
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Schwartz I, Vincent M, Strycharz WA, Kahan L. Photochemical cross-linking of translation initiation factor 3 to Escherichia coli 50S ribosomal subunits. Biochemistry 1983; 22:1483-9. [PMID: 6340738 DOI: 10.1021/bi00275a024] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Translation initiation factor 3 (IF-3) was bound noncovalently to Escherichia coli 50S ribosomal subunits. Irradiation of such complexes with near-ultraviolet light (greater than 285 nm) resulted in covalent attachment of initiation factor 3 to the 50S subunit. Photo-cross-linking attained its maximum level of 40% of that which was noncovalently bound after 90 min of irradiation. Cross-linking was abolished in the presence of either 0.5 M NH4C1 or 0.25 mM aurintricarboxylic acid, indicating that specific binding of initiation factor 3 to the ribosome was a prerequisite for subsequent covalent attachment. Further analysis showed that all the IF-3 was covalently bound to a small number of 50S subunit proteins. The major cross-linked proteins were identified as L2, L7/L12, L11, and L27 by immunochemical techniques. These results are discussed in light of the proposed mechanism for IF-3 function.
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11
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Chaires JB, Hawley DA, Wahba AJ. Chain initiation factor 3 crosslinks to E. coli 30S and 50S ribosomal subunits and alters the UV absorbance spectrum of 70S ribosomes. Nucleic Acids Res 1982; 10:5681-93. [PMID: 6755396 PMCID: PMC320916 DOI: 10.1093/nar/10.18.5681] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We report a direct procedure to determine the proteins near the IF-3 binding site in purified 30S and 50S ribosomal subunits. This procedure introduces only limited numbers of cleavable crosslinks between IF-3 and its nearest neighbors. The cleavable crosslinking reagent, 2-iminothiolane, was used to crosslink IF-3 in place to both 30S and 50S subunits. Ribosomal proteins S9/S11, S12, L2, L5 and L17 were found, by this approach, to be in close proximity to the factor in purified IF-3-subunit complexes. In addition, IF-3 was shown to alter the ultraviolet absorbance spectrum of E. coli 70S ribosomes at 10 mM Mg2+. The magnitude of the observed difference spectrum at a constant IF-3/ribosome ratio of 1.0, is linearly dependent upon ribosome concentration over the range 5 nM - 55 nM. Titration experiments indicated that the observed effect is maximal at an IF-3/ribosome ratio of approximately 1.0. These results are taken to indicate a conformational change in the 70S ribosome induced by IF-3.
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12
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Valenzuela DM, Chaudhuri A, Maitra U. Eukaryotic ribosomal subunit anti-association activity of calf liver is contained in a single polypeptide chain protein of Mr = 25,500 (eukaryotic initiation factor 6). J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34440-5] [Citation(s) in RCA: 20] [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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13
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Weiel J, Hershey JW. Fluorescence polarization studies of the interaction of Escherichia coli protein synthesis initiation factor 3 with 30S ribosomal subunits. Biochemistry 1981; 20:5859-65. [PMID: 7028112 DOI: 10.1021/bi00523a032] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Steady-state fluorescence polarization techniques were used to study the binding of initiation factor 3 (IF3) to 30S ribosomal subunits. Covalent fluorescent derivatives of IF3 were prepared by treating the pure protein with fluorescein isothiocyanate. The fluorescein-labeled IF3 (F-IF3) contained 0.8--1.7 dye molecules per protein. Polyacrylamide gel electrophoretic analysis of the derivatized forms is consistent with the view that the probe is randomly attached, presumably to lysine epsilon-amino groups. The activity of F-IF3 is not impaired in assays for binding to 30S ribosomal subunits or in promoting formylmethionyl-tRNA binding to 70S ribosomes. Fluorescence polarization values were measured at different F-IF3 and 30S ribosomal subunit concentrations, and the association constant and number of binding sites were calculated. In buffer containing 10 mM magnesium acetate and 100 mM ammonium chloride, the association constant is (3.1 +/- 1.4) x 10(7) M-1, and the number of ribosomal binding sites is 1.2 +/- 0.2. The value for the association constant varies inversely with the ammonium chloride and magnesium acetate concentrations by a small amount. Competition studies show that nonderivatized IF3 binds to 30S ribosomal subunits with the same affinity as F-IF3. Therefore, the association constants measured for F-IF3 are valid for IF3 as well.
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14
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Cooperman BS, Expert-Bezançon A, Kahan L, Dondon J, Grunberg-Manago M. IF-3 crosslinking to Escherichia coli ribosomal 30 S subunits by three different light-dependent procedures: identification of 30 S proteins crosslinked to IF-3--utilization of a new two-stage crosslinking reagent, p-nitrobenzylmaleimide. Arch Biochem Biophys 1981; 208:554-62. [PMID: 7020604 DOI: 10.1016/0003-9861(81)90544-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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15
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Goss DJ, Parkhurst LJ, Wahba AJ. Kinetic studies of the rates and mechanism of assembly of the protein synthesis initiation complex. Biophys J 1980; 32:283-93. [PMID: 7018606 PMCID: PMC1327306 DOI: 10.1016/s0006-3495(80)84957-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Rate constants for a number of the assembly reactions involved in forming Escherichia coli ribosome initiation complexes have been measured. These reactions were monitored in a stopped-flow device in which Rayleigh scattering and fluorescence anisotropy were followed as a function of time. Fluorescence was induced by laser excitation modulated at 50 kHz. Aminoacyl-tRNA, initiation factor 3 (IF3), and 70S ribosomes were labeled with fluorescent probes. The light-scattering and fluorescence data show that the antiassociation model for IF3 function cannot be correct. IF3 can be considered to act as an effector in an allosteric model for ribosome function. Fluorescence anisotropy stopped-flow experiments provided rate constants for the binding of IF3 to both 30S subunits and to the intact 70S ribosome. Aminoacyl-tRNA's and nucleotide triplets appear to bind rapidly to 70S ribosomes and then a slow first-order conformational change occurs.
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17
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Pon CL, Gualerzi C. Qualitative and semiquantitative assay of Escherichia coli translational initiation factor IF-3. Methods Enzymol 1979; 60:230-9. [PMID: 379522 DOI: 10.1016/s0076-6879(79)60020-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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18
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Zipori P, Bosch L, van Duin J. Translation of MS2 RNA in vitro in the absence of initiation factor IF-3. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 92:235-41. [PMID: 103712 DOI: 10.1111/j.1432-1033.1978.tb12741.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An Escherichia coli cell-free translational system, deprived of initiation factor IF-3, has been used to study the role of the factor in protein synthesis. In this system, 30-S ribosomal subunits are preincubated together with MS2 phage RNA in a small volume in the presence of 10 mM Mg(Ac)2; the missing components required for protein synthesis are then added and assembly of elongating ribosomes is allowed to occur. This stepwise assembly process permits formation of functional complexes which can carry out protein synthesis in the complete absence of IF-3. The translational products, obtained in the absence of IF-3, have been analysed and shown to be similar to those synthesized in the presence of the factor. The main product observed is the phage coat protein.
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Michalski CJ, Sells BH, Chowdhury RM, Wahba AJ. Molecular morphology of ribosomes. Influence of chain-initiation factor IF-3 and ribosomal protein S1 on ribosome conformation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 89:589-94. [PMID: 361394 DOI: 10.1111/j.1432-1033.1978.tb12563.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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20
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van der Hofstad GA, Buitenhek A, van den Elsen PJ, Voorma HO, Bosch L. Binding of labeled initiation factor IF-1 to ribosomal particles and the relationship to the mode of IF-1 action in ribosome dissociation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 89:221-8. [PMID: 359328 DOI: 10.1111/j.1432-1033.1978.tb20916.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The binding of labeled initiation factor IF-1 to ribosomal particles has been studied in relation to the mode of action of this factor in the dissociation of 70-S ribosomes. It is demonstrated that IF-1 interacts specifically with active 70-S tight couples and free 30-S subunits. The binding of IF-1 to both 70-S and 30-S particles is not influenced by the Mg2+ concentration and the affinity of the factor for both particles is about the same. The interaction of IF-1 with these particles is highest at low Tris-HCl concentrations. Under these conditions IF-1 shows a slight dissociating activity. Using 3H-labeled IF-1 and 14C-labeled IF-3 the formation of a 30-S-subunit.IF-1 . IF-3 complex from 70-S ribosomes is demonstrated. Our studies show that IF-3 enhances the binding of IF-1 to the 30-S subunit. In contrast to IF-1, which binds about equally well to 70-S and 30-S particles in the absence of IF-3, 14C-labeled IF-3 binds predominantly to the 30-S subunit. This finding confirms the view that IF-3 acts as an anti-association factor. On the other hand, IF-1 enhances the supply of 30-S subunits in the presence of IF-3 by acting on the 30-S moiety of the 70-S ribosome.
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van der Hofstad GA, Buitenhek A, Bosch L, Voorma HO. Initiation factor IF-3 and the binary complex between initiation factor IF-2 and formylmethionyl-tRNA are mutually exclusive on the 30-S ribosomal subunit. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 89:213-20. [PMID: 359327 DOI: 10.1111/j.1432-1033.1978.tb20915.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The formation of 30-S initiation complexes depends strongly on initiation factor IF-3; at molar ratios of IF-3 to 30-S ribosomes up to one a stimulation is observed, whereas at ratios higher than one, initiation complex formation declines strongly. The target of the observed inhibition of fMet-tRNA binding at high concentrations of IF-3 is the 30-S initiation complex itself. On the one hand addition of IF-3 to preformed 30-S initiation complexes leads to a release of bound fMet-tRNA which is linear with the amount of factor added, whereas no effect on isolated 70-S initiation complexes is seen. The release of fMet-tRNA from preformed 30-S initiation complexes is accompanied by a release of IF-2 in a one-to-one molar ratio which is in agreement with our previous findings showing that binding of fMet-tRNA takes place via a binary complex: IF-2 . fMet-tRNA (Eur. J. Biochem. 66, 181--192 and 77, 69--75). On the other hand increasing amounts of both IF-2 and fMet-tRNA relieve the IF-3-induced inhibition of 30-S initiation complex formation. From these findings it is concluded that IF-3 and the IF-2 . fMet-tRNA complex are mutually exclusive on the 30-S ribosome. This implies that under our experimental conditions MS2 RNA binding precedes fMet-tRNA binding if one accepts that the presence of IF-3 on the 30-S subunit is obligatory for messenger binding.
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22
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Laughrea M, Dondon J, Grunberg-Manago M. The relationship between the 3'-end of 16 S RNA and the binding of initiation factor IF-3 to the 30 S subunit of E. coli. FEBS Lett 1978; 91:265-8. [PMID: 354964 DOI: 10.1016/0014-5793(78)81188-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Weiel J, Hershey JW. Fluorescence polarization studies of the binding of fluorescein-labeled initiation factor IF3 to 30 S ribosomal subunits from Escherichia coli. FEBS Lett 1978; 87:103-6. [PMID: 344061 DOI: 10.1016/0014-5793(78)80144-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Laughrea M, Moore PB. Physical properties of ribosomal protein S1 and its interaction with the 30 S ribosomal subunit of Escherichia coli. J Mol Biol 1977; 112:399-421. [PMID: 327076 DOI: 10.1016/s0022-2836(77)80189-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Naaktgeboren N, Roobol K, Voorma HO. The effect of initiation factor IF-1 on the dissociation of 70-S ribosomes of Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 72:49-56. [PMID: 319002 DOI: 10.1111/j.1432-1033.1977.tb11223.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
By means of exchange studies, in which 3H-labelled 50-S subunits and unlabelled 70-S ribosomes from Escherichia coli MRE 600 were used, it has been demonstrated that the 30-S subunit is the only target for IF-3 in the dissociation of 70-S ribosomes. The interference of IF-3 with the dynamic equilibrium of 70-S in equilibrium 50-S + 30-S occurs by binding of the factor to the 30-S subunit. The 30-S-IF-3 complex in impaired in the association reaction, which implies that IF-3 is acting as an anti-association factor. The action of IF-1 is two-fold. Firstly IF-1 increases the rate of exhcange of the ribosomal subparticles in the 70-S ribosome without changing the position of the equilibrium. Thus the spontaneous equilibrium is attained more rapidly in the presence of IF-1. This kinetic effect of IF-1 is also demonstrated in the IF-3-mediated dissociation of 70-S ribosomes. Secondly IF-1 is able to increase the IF-3-mediated dissociation. It seems likely that the explanation for the latter phenomenon must be sought in the binding of IF-1 to 70-S ribosomes, resulting in a loosening of the ribosomes structure, as well as to 30-S. IF-3 complex, thaereby slowing down the association reactions of the subunits.
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Richter D, Isono K. The mechanism of protein synthesis-initiation, elongation and termination in translation of genetic messeges. Curr Top Microbiol Immunol 1977; 76:83-125. [PMID: 334484 DOI: 10.1007/978-3-642-66653-7_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Michalski CJ, Sells BH, Wahba AJ. Molecular morphology of ribosomes: effect of chain initiation factor 3 on 30 S subunit conformation. FEBS Lett 1976; 71:347-50. [PMID: 793863 DOI: 10.1016/0014-5793(76)80967-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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Risuleo G, Gualerzi C, Pon C. Specificity and properties of the destabilization, induced by initiation factor IF-3, of ternary complexes of the 30-S ribosomal subunit, aminoacyl-tRNA and polynucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 67:603-13. [PMID: 9282 DOI: 10.1111/j.1432-1033.1976.tb10726.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Initiation factor IF-3 causes the destabilization of preformed ternary complexes of 30-S ribosomal subunit, codons and aminoacyl-tRNAs or peptidyl-tRNA. This destabilization is dilution-dependent and affects all ternary complexes with the exception of those containing the initiator fMet-tRNA, which remain more resistant to IF-3-induced destabilization under the various conditions studied. Several possible reasons for this specificity have been examined. It was found that the basis for the specificity is not: (a) an intrinsic greater stability of the ternary complexes containing fMet-tRNA, (b) the amoung of aminoacyl-tRNA bound to the ribosome, (c) the conditions under which the ternary complex is made or (d) the formylation of the amino group. On the other hand, the nature of the polynucleotide in response to which the ternary complex is formed was found to influence the amount of aminoacyl-tRan bound to the ribosome, and to some extent the amount of aminoacyl-tRNA which can be relased. The ternary complex containing the mischarged initiator tRNA fVal-tRNAfMet displays greater resistance to the IF-3-induced destabilization than the complex containing fVal-tRNAVal. These results indicate that the specificity of the IF-3 activity is due to the special structural feature of the initiator tRNA molecule and to some extent to the nature of the polynucleotide. The IF-3-induced destabilization of ternary complexes was found to be little affected by variations in reaction conditons, so that this IF-3 activity can be used to measure the stoichiometric binding of IF-3 to the ribosome over a broad range of pH and K+ and Mg2+ concentrations. Several antibiotics have been tested for their capacity to interfere with this reaction; only high concentrations of tetracycline blocked this IF-3 activity.
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29
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Heimark RL, Kahan L, Johnston K, Hershey JW, Traut RR. Cross-linking of initiation factor IF3 to proteins of the Escherichia coli 30 S ribosomal subunit. J Mol Biol 1976; 105:219-30. [PMID: 823340 DOI: 10.1016/0022-2836(76)90108-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ochoa S. Initiation of protein synthesis. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 1976; 63:347-55. [PMID: 787809 DOI: 10.1007/bf00607927] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Gottleib M, Davis BD, Thompson RC. Mechanism of dissociation of ribosomes of Escherichia coli by initiation factor IF-3. Proc Natl Acad Sci U S A 1975; 72:4238-42. [PMID: 1105575 PMCID: PMC388695 DOI: 10.1073/pnas.72.11.4238] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Initiation factor IF-3 clearly can cause dissociation of ribosomes by binding to 30S subunits and thus shifting the spontaneous equilibrium, but it theoretically may also do so by binding to 70S ribosomes. Previously reported experiments with differentially labeled ribosomes and subunits seemed to eliminate the latter mechanism, but these experiments neglected a substantial decrease in the specific activity of the added subunits resulting from net dissociation of the ribosomes by IF-3. The present experiments eliminate or correct this effect. The results exclude direct action on 70S ribosomes as a significant mechanism of dissociation by IF-3.
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Gualerzi C, Grandolfo M, Paradies HH, Pon C. Letter to the editor: Circular dichroism analysis of the ribosomal binding of initiation factor IF-3. J Mol Biol 1975; 95:569-73. [PMID: 1097719 DOI: 10.1016/0022-2836(75)90318-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Grunberg-Manago M, Dessen P, Pantaloni D, Godefroy-Colburn T, Wolfe AD, Dondon J. Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes. J Mol Biol 1975; 94:461-78. [PMID: 1100842 DOI: 10.1016/0022-2836(75)90215-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Sun TT, Heimark RL, Traut R R. The protein topography of the E. coli 30S ribosomal subunit: a preliminary model E. coli/30S subunit/ribosome/spatial arrangement of proteins. Mol Cell Biochem 1975; 6:33-41. [PMID: 1091849 DOI: 10.1007/bf01731864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A three dimensional model is presented which shows the apatial arrangement of 20 of the 21 proteins of the 30S ribosomal subunit of Escherichia coli. The model fulfills several purposes: (a) It summarizes currently available structural and functional data on ribosomal proteins; (b) It suggests an interesting correlation between stoichiometry and function. Functional proteins are both clustered and fractional; (c) It can be evaluated in relationships or point out critical experiments by which it can be tested.
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Pon CL, Gualerzi C. Effect of initiation factor 3 binding on the 30S ribosomal subunits of Escherichia coli. Proc Natl Acad Sci U S A 1974; 71:4950-4. [PMID: 4612534 PMCID: PMC434017 DOI: 10.1073/pnas.71.12.4950] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Under certain conditions, initiation factor 3 (IF-3) can cause the release of aminoacyl-tRNA bound to 30S ribosomal subunits of E. coli. It is shown that this IF-3-induced aminoacyl-tRNA release cannot be attributed to either nucleolytic attack or competition between IF-3 and aminoacyl-tRNA for the same ribosomal binding site. It was found that the 30S-aminoacyl-tRNA-codon complexes formed in the absence of IF-3 are intrinsically different from those prepared in the presence of IF-3. In the absence of IF-3, the ribosomal binding of aminoacyl-tRNA is a virtually irreversible process, since the bound aminoacyl-tRNA can neither be spontaneously released upon dilution nor exchanged for unbound aminoacyl-tRNA. In the presence of IF-3, the binding of one molecule of IF-3 per 30S ribosome renders the binding of aminoacyl-tRNA reversible upon dilution and promotes exchange between bound and unbound aminoacyl-tRNA. It is suggested that this difference is due to a conformational transition of the 30S ribosomal subunit induced by the binding of IF-3. The possible implications of this finding in relation to the mechanism of action of IF-3 and its functional role in the cell are discussed.
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Hawley DA, Slobin LI, Wahba AJ. The mechanism of action of initiation factor 3 in protein synthesis. II. Association of the 30S ribosomal protein S12 with IF-3. Biochem Biophys Res Commun 1974; 61:544-50. [PMID: 4616691 DOI: 10.1016/0006-291x(74)90991-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Hawley DA, Miller MJ, Slobin LI, Wahba AJ. The mechanism of action of initiation factor 3 in protein synthesis. I. Studies on ribosomes crosslinked with dimethylsuberimidate. Biochem Biophys Res Commun 1974; 61:329-37. [PMID: 4613353 DOI: 10.1016/0006-291x(74)90570-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Jay G, Abrams WR, Kaempfer R. Resistance of bacterial protein synthesis to double-stranded RNA. Biochem Biophys Res Commun 1974; 60:1357-64. [PMID: 4214381 DOI: 10.1016/0006-291x(74)90347-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Szer W, Leffler S. Interaction of Escherichia coli 30S ribosomal subunits with MS2 phage RNA in the absence of initiation factors. Proc Natl Acad Sci U S A 1974; 71:3611-5. [PMID: 4610580 PMCID: PMC433825 DOI: 10.1073/pnas.71.9.3611] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
MS2 RNA binds at 0 degrees to 30S subunits from E. coli and, to a smaller extent, to those of a Pseudomonas species, as judged by filtration on nitrocellulose membranes; this mRNA does not bind to 30S subunits from Bacillus brevis or Caulobacter crescentus. Binding does not depend on the presence of initiation factors; it is sensitive to aurintricarboxylic acid but insensitive to edeine and is competitive with such synthetic polynucleotides as poly(U) and poly(AUG). Complex formation can also be detected by electrophoresis on polyacrylamide-agarose gels. By this procedure, E. coli 30S subunits are separated into two major components. Only the more slowly moving component, which contains the ribosomal protein S1, interacts with the RNA.
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Paradies HH, Franz A, Pon CL, Gualerzi C. Conformational transition of the 30 S ribosomal subunit induced by initiation factor 3 (IF-3). Biochem Biophys Res Commun 1974; 59:600-7. [PMID: 4604265 DOI: 10.1016/s0006-291x(74)80022-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Schiff N, Miller MJ, Wahba AJ. Purification and Properties of Chain Initiation Factor 3 from T4-infected and Uninfected Escherichia coli MRE 600. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42544-1] [Citation(s) in RCA: 24] [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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Fakunding JL, Traugh JA, Traut RR, Hershey JW. Purification and phosphorylation of initiation factor IF2. Methods Enzymol 1974; 30:24-31. [PMID: 4604996 DOI: 10.1016/0076-6879(74)30005-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Lee-Huang S, Ochoa S. Purification of two messenger-discriminating species of initiation factor 3 (IF3) from Escherichia coli. Methods Enzymol 1974; 30:45-53. [PMID: 4604999 DOI: 10.1016/0076-6879(74)30008-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Ochoa S, Mazumder R. 1. Polypeptide Chain Initiation. ACTA ACUST UNITED AC 1974. [DOI: 10.1016/s1874-6047(08)60133-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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