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Takada H, Morita M, Shiwa Y, Sugimoto R, Suzuki S, Kawamura F, Yoshikawa H. Cell motility and biofilm formation in Bacillus subtilis are affected by the ribosomal proteins, S11 and S21. Biosci Biotechnol Biochem 2014; 78:898-907. [PMID: 25035996 DOI: 10.1080/09168451.2014.915729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Bacillus subtilis differentiates into various cellular states in response to environmental changes. It exists in two states during the exponential growth phase: motile cells and connected chains of sessile cells. Here, we identified new regulators of cell motility and chaining, the ribosomal proteins S21 (rpsU) and S11 (rpsK). Their mutants showed impaired cell motility (observed in a laboratory strain) and robust biofilm formation (observed in an undomesticated strain). The two major operons for biofilm formation, tapA-sipW-tasA and epsA-O, were strongly expressed in the rpsU mutant, whereas the flagellin-encoding hag gene and other SigD-dependent motility regulons were not. Genetic analysis revealed that the mutation of remA, the transcriptional activator of the eps operon, is epistatic to that of rpsU, whereas the mutation of antagonistic regulators of SinR is not. Our studies demonstrate that S11 and S21 participate in the regulation of bistability via the RemA/RemB pathway.
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Affiliation(s)
- Hiraku Takada
- a Department of Bioscience , Tokyo University of Agriculture , Tokyo , Japan
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2
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Connolly K, Culver G. Overexpression of RbfA in the absence of the KsgA checkpoint results in impaired translation initiation. Mol Microbiol 2013; 87:968-81. [PMID: 23387871 DOI: 10.1111/mmi.12145] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2012] [Indexed: 01/05/2023]
Abstract
KsgA, a universally conserved small ribosomal subunit (SSU) rRNA methyltransferase, has recently been shown to facilitate a checkpoint within the ribosome maturation pathway. Under standard growth conditions removal of the KsgA checkpoint has a subtle impact on cell growth; yet, upon overexpresssion of RbfA, a ribosome maturation factor, KsgA becomes essential. Our results demonstrate the requirement of KsgA, in the presence of excess RbfA, both for the incorporation of ribosomal protein S21 to the developing SSU, and for final maturation of SSU rRNA. Also, when SSU biogenesis is perturbed by an imbalance in KsgA and RbfA, a population of 70S-like particles accumulates that is compositionally, functionally and structurally distinct from mature 70S ribosomes. Thus, our work suggests that KsgA and RbfA function together and are required for SSU maturation, and that additional checkpoints likely act to modulate malfunctional 70S particle formation in vivo.
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Affiliation(s)
- Keith Connolly
- Departments of Biology and of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
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Van Duin J, Wijnands R. The function of ribosomal protein S21 in protein synthesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 118:615-9. [PMID: 7028483 DOI: 10.1111/j.1432-1033.1981.tb05563.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The function of ribosomal protein S21 in protein synthesis has been examined by (a) inactivation of S21 in situ with specific antibodies and (b) the use of 30-S subunits reconstituted in the absence of S21. The results from the two approaches are consistent, 30-S subunits treated with anti-S21 or lacking S21 are still active in the translation of poly(U) or poly(A, G, U). They are also functional in fMet-tRNA binding when directed by poly(A, G, U) or the AUG triplet. They are not active in the translation of MS2 RNA or Escherichia coli mRNA. The defect of S21-deficient 30-S ribosomes can be traced back to their inability to bind MS2 RNA at the initiation step of protein synthesis. Addition of S21 to S21-deprived subunits restores the MS2-RNA-dependent initiation complex formation.
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4
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Politz SM, Noller HF, McWhirter PD. Ribonucleic acid-protein cross-linking in Escherichia coli ribosomes: (4-azidophenyl)glyoxal, a novel heterobifunctional reagent. Biochemistry 1981; 20:372-8. [PMID: 7008843 DOI: 10.1021/bi00505a023] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have used the heterobifunctional reagent (4-azidophenyl)glyoxal (APG) to cross-link RNA to protein in Escherichia coli 30S ribosomal subunits. Synthesis and characterization of the reagent are described. Like other dicarbonyl reagents (e.g., kethoxal), APG reacts specifically with guanosine among the four ribonucleosides. The azido group in APG can be photolyzed with UV light (lambda greater than 300 nm), yielding an unstable nitrene which is potentially reactive with many groups in proteins and nucleic acids. Conditions for APG modification of guanylic acid residues in 30S subunits are described; photolysis of bound APG results in cross-linking of approximately 5% of the total 30S proteins to 16S RNA. A specific subset of the 30S proteins is cross-linked to 16S RNA by APG.
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5
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Brauer D, Röming R. The primary structure of protein S3 from the small ribosomal subunit of Escherichia coli. FEBS Lett 1979; 106:352-7. [PMID: 387449 DOI: 10.1016/0014-5793(79)80531-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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6
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Poldermans B, Roza L, Van Knippenberg P. Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86815-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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7
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Suryanarayana T, Subramanian AR. Specific association of two homologous DNA-binding proteins to the native 30-S ribosomal subunits of Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 520:342-57. [PMID: 213117 DOI: 10.1016/0005-2787(78)90232-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The native 30-S ribosomal subunits from Escherichia coli are shown to be associated with two proteins which are different from the known ribosome-associated and ribosomal proteins. Neither protein is foune on native 50-S subunits or on intact ribosomes in the cell extract. The purified proteins re-bind in vitro to free 30-S subunits, but do not bind to either free 50-S subunits or intact ribosomes. The proteins, denoted NS1 and NS2, have been purified and characterized. Both proteins showed the same molecular weight of 9500 by sodium dodecyl sulfate gel electrophoresis but 34 000 by gel filtration. Upon treatment with cross-linking reagents the purified proteins gave higher molecular weight species up to the tetrameric ones showing that they exist in solution as tetramers. The amino acid compositions, tryptic fingerprint patterns and N-terminal sequences of the two proteins have been determined. These data show that NS1 and NS2 possess distinct primary structures but with extensive sequence homology. Antibodies raised against the purified proteins cross-reacted in double immuno-diffusion tests confirming further the homology. Because of the similarity in properties a sample of the DNA-binding protein HD (Berthold, V. and Geider, K. (1976) Eur. J. Biochem. 71, 443--449) was compared to NS1 and NS2. In terms of several criteria, the protein HD is found to be a mixture of two proteins, namely NS1 and NS2. The present report is the first instance of an association of DNA-binding proteins to the ribosome.
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Turchinsky MF, Broude NE, Kussova KS, Abduraschidova GG, Muchamedganova EV, Schatsky IN, Bystrova TF, Budowsky EI. Polynucleotide-protein interactions in the translation system. Detection of contacts between some ribosomal split proteins and 16-S RNA in 30-S subunits of Escherichia coli ribosomes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 90:83-8. [PMID: 361396 DOI: 10.1111/j.1432-1033.1978.tb12577.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Direct contacts between 16-S RNA and split proteins S2, S3, S5, S14 and S21 inside the 30-S subunit of Escherichia coli ribosomes were evidenced by the formation of ultraviolet-induced (lambda = 254 nm) RNA-protein cross-links. 30-S subunits were reassembled from core particles and a mixture of split proteins containing in each case a single 125I-labelled protein. All the proteins tested are cross-linked as a result of a single-hit process; proteins S3 and S21 were cross-linked at the highest rate.
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Subramanian AR, van Duin J. Exchange of individual ribosomal proteins between ribosomes as studied by heavy isotope-transfer experiments. MOLECULAR & GENERAL GENETICS : MGG 1977; 158:1-9. [PMID: 342903 DOI: 10.1007/bf00455113] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Whether the individual ribosomal proteins undergo exchange between robosomes in vivo during cell growth was examined using heavy isotope transfer methodology. E. coli was grown first in a heavy isotope medium in the presence of [3H] leucine and then transferred to normal medium and allowed to grow for one generation in the presence of [14C] leucine. The "heavy" and "light" ribosomes that were present in such cells were separated by sedimentation and the ribosomal proteins resolved by two-dimensional gel electrophoresis. The individual proteins were burnt in O2 and their contents of [3H] and [14C] labels determined. From the analysis of the data we find that the great majority of the ribosomal proteins of E. coli does not undergo exchange during cell growth. Proteins which were found to exchange to varying levels in different transfer experiments were S1, S2, L7/L12, L9, L10 and L33. All of them except L9 exchanged to the same levels in control experiments in which separately grown heavy and light cells were mixed and processed. These proteins therefore undergo exchange during cell breakage and ribosome isolation. Protein L9 consistently showed appreciably greater exchange in transfer experiments as compared to the controls suggesting that it may exchange in vivo.
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Robertson WR, Dowsett SJ, Hardy SJ. Exchange of ribosomal proteins among the ribosomes of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1977; 157:205-14. [PMID: 340925 DOI: 10.1007/bf00267399] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The exchange of ribosomal proteins among ribosomes of E. coli has been measured, using a density label technique. As expected most of the proteins do not exchange appreciably. However a substantial fraction of each of proteins S1, S2, S21, L7/L12, L9, L10, L11, L26 and L33 is found to exchange, but exchange of S1, S2, L7/L12, L10, L11 and L26 is found to occur in vitro after lysis of the cells, and therefore it is not possible to say whether or not these proteins also exchange in vivo. tin contrast S21, l9 and L33 do not exchange after lysis of the cells and we therefore conclude that these proteins exchange in vivo. The maximum level of exchange of S21, L9 and L33 is attained so rapidly that we were unable to show whether or not it was dependent on protein synthesis.
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12
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Grunberg-Manago M, Gros F. Initiation mechanisms of protein syntehesis. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1977; 20:209-84. [PMID: 333512 DOI: 10.1016/s0079-6603(08)60474-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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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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14
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Sommer A, Traut RR. Identification of neighboring protein pairs in the Escherichia coli 30 S ribosomal subunit by crosslinking with methyl-4-mercaptobutyrimidate. J Mol Biol 1976; 106:995-1015. [PMID: 789904 DOI: 10.1016/0022-2836(76)90348-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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Ilan J, Ilan J. Requirement for homologous rabbit reticulocyte initiation factor 3 for initiation of alpha- and beta-globin mRNA translation in a crude protozoal cell-free system. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33116-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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16
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van Dieijen G, van Knippenberg PH, van Duin J. The specific role of ribosomal protein S1 in the recognition of native phage RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 64:511-8. [PMID: 776620 DOI: 10.1111/j.1432-1033.1976.tb10330.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The previously reported requirement of ribosomal protein S1 for translation of phage RNA is now shown to be related to the involvement of the protein in initiation complex formation. The structure of the messenger RNA appears to be uniquely related to S1 function, since translation and initiation and midly unfolded phage RNA (by modification with formaldehyde) are independent of S1. It is proposed that S1 functions in conjunction with initiation factor IF-3 by recognizing and unfolding elements of the tertiary structure of phage RNA. A model is suggested for S1 function in both initiation of protein synthesis and initiation of phage RNA replication.
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17
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Kay AC, Graffe M, Grunberg-Manago M. Purification and properties of two initiation factors from Bacillus stearothermophilus. Biochimie 1976; 58:183-99. [PMID: 782553 DOI: 10.1016/s0300-9084(76)80369-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Two initiation factors have been isolated from the thermophilic bacterium, Bacillus stearothermophilus, and purified to near homogeneity. The two factors possess physical characteristics and activities associated with the E. coli initiation factors IF-2 and IF-3, and are interchangeable with these factors. The two systems present, however, several differences : S-IF-2 is significantly more heat stable than E. coli IF-2, loosing less than 50 per cent of its activity after 20 minutes at 70degreesC. S-IF-2 alone is unable to promote initiation complex formation on B. stearothermophilus or E. coli ribosomes, and S-IF-3 is absolutely necessary for initiation of complex formation on B. stearothermophilus ribosomes. No factor corresponding to IF-1 has been found. S-IF-3 appears to be able to replace at least partially IF-1, since S-IF-3 and E. coli IF-2 are sufficient to promote maximum fMet-tRNA binding to E. coli ribosomes, while E. coli IF-3 and IF-2 also require IF-1. The differences between the two systems are perhaps required because of the elevated temperature at which B. stearothermophilus normally grows.
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18
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Shimizu M, Craven GR. Chemical inactivation of Escherichia coli 30-S ribosomes by iodination. Identification of proteins involved in tRNA binding. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 61:307-15. [PMID: 1107046 DOI: 10.1111/j.1432-1033.1976.tb10023.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
30-S ribosomal subunits are inactivated by iodination for both enzymic fMet-tRNA and non-enzymic Phe-tRNA binding activities. This inactivation is due to modification of the protein moiety of the ribosome. Reconstitutions were performed with 16-S RNA and mixtures of total protein isolated from modified subunits and purified proteins isolated from unmodified subunits. This allowed identification of the individual proteins which restore tRNA binding activity. S3, S14 and S19 were identified as proteins involved in fMet-tRNA binding. S1, S2, S3, S14 and S19 were identified as proteins involved in Phe-tRNA binding. Modified particles shown normal sedimentation constants and complete protein compositions both before and after reconstitution. This suggests that the loss of activity is due to modification of one or more of the actual binding sites located on the 30-S subunit and that restoration of activity is due to structural correction at this site rather than to correction of an assembly defect.
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Brimacombe R, Nierhaus KH, Garrett RA, Wittmann HG. The ribosome of Escherichia coli. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1976; 18:1-44, 323-5. [PMID: 790471 DOI: 10.1016/s0079-6603(08)60585-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Hardy SJ. The stoichiometry of the ribosomal proteins of Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1975; 140:253-74. [PMID: 1107798 DOI: 10.1007/bf00334270] [Citation(s) in RCA: 164] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A ribosome preparation from E. coli made without stringent washing procedures has been shown to contain the same relative amounts of nearly all the ribosomal proteins as ribosomes in intact cells. Stoichiometric measurements on all the proteins of this preparation except for L8, L20, L31 and L34 have been made using an isotope dilution technique. When the scatter of the values obtained, the uncertainty in the molecular weights, and the losses occurring during extraction are taken into account, none of the proteins except L7/L12 is present at a level significantly different from one molecule per ribosome. There are multiple copies of L7/L12. These data suggest that the ribosomes of Escherichia coli are homogeneous in vivo.
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21
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Pichon J, Marvaldi J, Marchis-Mouren G. The in vivo order of protein addition in the course of Escherichia coli 30 S and 50 S subunit biogenesis. J Mol Biol 1975; 96:125-37. [PMID: 1099210 DOI: 10.1016/0022-2836(75)90186-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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22
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Schwartz I, Gordon E, Ofengand J. Photoaffinity labeling of the ribosomal A site with S-(p-azidophenacyl)valyl-tRNA. Biochemistry 1975; 14:2907-14. [PMID: 1098691 DOI: 10.1021/bi00684a018] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
S-(p-Azidophenacyl)valyl-tRNA, an analog of valyl-tRNA which has a photoaffinity label attached to its 4-thiouridine residue, was bound to the ribosomal A site at 10 mM Mg2+. Binding was stimulated 25-fold by the presence of elongation factor EFTu. Photoactivation of the p-azidophenacyl group by irradiation resulted in covalent linking of 6% of the noncovalently bound tRNA to the ribosomes. Covalent linking was dependent on the simultaneous presence of ribosomes, poly(U2,G),EFTu.GTP, required irradiation, and did not occur when S-(phenacyl)valyl-tRNA, a nonphotolyzable analog, replaced S-(p-azidophenacyl)valyl-tRNA. The attached tRNA was distributed approximately equally between both the 30S and 50S subunits. At the 30S subunit, 30% of the tRNA was bound to protein while 70% was linked to 16S RNA. At the 50S subunit, however, negligible binding to the 23S RNA was observed. More than 90% of the tRNA was attached to low molecular weight material according to sodium dodecyl sulfate-sucrose gradient analysis, and more than 87% of this fraction consisted of tRNA-protein complexes as assayed by phenol solubility and electrophoretic mobility before and after protease treatment. These results, in conjunction with our previous report (I. Schwartz and J Ofengand (1974), Proc. Natl. Acad. Sci. U.S.A. 71, 3951) which showed that covalent linking of this same tRNA derivative at the ribosomal P site resulted in attachment solely to the 16S RNA, demonstrate that 16S, but not 23S or 5S rRNA, is an important component of the tRNA binding site in the region of the 4-thiouridine residue and furthermore show that ribosomal A and P sites are topologically distinct.
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23
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Abstract
The calculated in vivo polypeptide chain growth rate for Staphylococcus auteus MF-31 grown in nutritionally rich medium assuming all the ribosomes were functional was found to be approximately 16 amino acids/s/ribosome, but decreased to 10.2 amino acids/s/ribosome for cells grown in poor medium. An in vitro analysis revealed that 70S ribosomes isolated from rich medium cells were more active than similar 70S ribosomes derived from cells grown in poor medium. The 30S subunit was found responsible for the increased activity of the rich monosomes, whereas the 50S subunit appeared to be capable of either high or low activity.
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24
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Van Dieijen G, Van Der Laken CJ, Van Knippenberg PH, Van Duin J. Function of Escherichia coli ribosomal protein S1 in translation of natural and synthetic messenger RNA. J Mol Biol 1975; 93:351-66. [PMID: 1095761 DOI: 10.1016/0022-2836(75)90282-x] [Citation(s) in RCA: 115] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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25
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Brouwer J, Planta RJ. The origin of high molecular weight proteins in ribosomal preparations of Bacillus licheniformis. FEBS Lett 1975; 53:73-5. [PMID: 1140399 DOI: 10.1016/0014-5793(75)80685-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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26
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27
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28
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Schwartz I, Ofengand J. Photo-affinity labeling of tRNA binding sites in macromolecules. I. Linking of the phenacyl-p-azide of 4-thiouridine in (Escherichia coli) valyl-tRNA to 16S RNA at the ribosomal P site. Proc Natl Acad Sci U S A 1974; 71:3951-5. [PMID: 4610566 PMCID: PMC434304 DOI: 10.1073/pnas.71.10.3951] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The phenacyl-p-azide of 4-thiouridine in (E. coli) tRNA(1) (Val) was prepared for use as a photo-affinity probe of tRNA binding sites on ribosomes. The derivatized tRNA was 90-100% as active as control tRNA for aminoacylation, nonenzymatic binding to the ribosomal P site, elongation factor Tu(EFTu)-dependent binding to the A site, EFTu-GTP-aa-tRNA ternary complex formation, and transfer of valine into polypeptide. Irradiation of p-azidophenacyl-[(3)H]valyl-tRNA bound noncovalently to the ribosomal P site resulted in covalent attachment of 15-20% of the noncovalently bound tRNA to the ribosomes. The linking occurred exclusively to the 16S RNA of the 30S ribosomal subunit, thus suggesting that the region of the ribosome within 9 A of the 4-thiouridine of tRNA, when it is bound in the P site, is solely 16S RNA.
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29
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Inouye H, Pollack Y, Petre J. Physical and functional homology between ribosomal protein S1 and interference factor i. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 45:109-17. [PMID: 4213953 DOI: 10.1111/j.1432-1033.1974.tb03535.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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30
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Marvaldi J, Pichon J, Delaage M, Marchis-Mouren G. Individual ribosomal protein pool size and turnover rate in Escherichia coli. J Mol Biol 1974; 84:83-96. [PMID: 4598367 DOI: 10.1016/0022-2836(74)90213-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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31
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van Duin J, van Knippenberg PH. Functional heterogeneity of the 30 S ribosomal subunit of Escherichia coli. 3. Requirement of protein S1 for translation. J Mol Biol 1974; 84:185-95. [PMID: 4598364 DOI: 10.1016/0022-2836(74)90221-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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32
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Spirin AS. Structural transformations of ribosomes (dissociation, unfolding and disassembly). FEBS Lett 1974; 40:suppl:S38-47. [PMID: 4605150 DOI: 10.1016/0014-5793(74)80687-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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33
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34
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Gausing K. Ribosomal protein in E. coli: rate of synthesis and pool size at different growth rates. MOLECULAR & GENERAL GENETICS : MGG 1974; 129:61-75. [PMID: 4600015 DOI: 10.1007/bf00269266] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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35
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Held WA, Nomura M, Hershey JW. Ribosomal protein S21 is required for full activity in the initiation of protein synthesis. MOLECULAR & GENERAL GENETICS : MGG 1974; 128:11-22. [PMID: 4595779 DOI: 10.1007/bf00267291] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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36
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Lelong JC, Gros D, Gros F, Bollen A, Maschler R, Stöffler G. Function of individual 30S subunit proteins of Escherichia coli. Effect of specific immunoglobulin fragments (Fab) on activities of ribosomal decoding sites. Proc Natl Acad Sci U S A 1974; 71:248-52. [PMID: 4592687 PMCID: PMC387978 DOI: 10.1073/pnas.71.2.248] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Specific anti-30S protein immunoglobulin G fragments (Fab) were used to determine the contribution of each of the 30S ribosomal proteins to: (1) polyphenylalanine synthesis, (2) initiation factor-dependent binding of fMet-tRNA, (3) T-factor-dependent binding of phenylalanyl-tRNA, and (4) fixation of radioactive dihydrostreptomycin. Twenty of the 21 possible antibodies (antibody against S17 excepted) were used. In conditions where all the 30S proteins were accessible to Fabs, all of these monovalent antibodies strongly inhibited polyphenylalanine synthesis in vitro. Antibodies against S4, S6, S7, S12, S15, and S16, however, showed a weaker effect.30S proteins can be classified into four categories by their contributions to the function of sites "A" and "P": class I appears nonessential for tRNA positioning at either site (S4, S7, S15, and S16); class II includes proteins whose role in initiation is critical (S2, S5, S6, S12, and S13); class III (S8, S9, S11, and S18) corresponds to proteins whose blockade prevents internal (elongation factor Tudependent) positioning; and class IV includes entities that are essential for activities of both "A" and "P" sites (S1, S3, S10, S14, S19, S20, and S21). Dihydrostreptomycin fixation to the 30S or 70S ribosomes was inhibited by antibodies against S1, S10, S11, S18, S19, S20, and S21, but only weakly by the anti-S12 (Str A protein) Fab. The significance of these results is discussed in relation to 30S protein function, heterogeneity, and topography.
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37
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Lubsen NH, Davis BD. Use of purified polysomes from rabbit reticulocytes in a specific test for initiation factors. Proc Natl Acad Sci U S A 1974; 71:68-72. [PMID: 4521057 PMCID: PMC387933 DOI: 10.1073/pnas.71.1.68] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Initiation factors, extracted from ribosomal particles by high salt, are usually tested for with the extracted ribosomes. However, it is theoretically possible that such tests may respond not only to factors (i.e., proteins that join and leave a ribosome during its cycle), but also to true ribosomal proteins that may have been extracted. We have eliminated this circularity by tests with purified polysomes, which have not been extracted with high salt; the polysomes are deficient in initiation factors because they have been largely separated from the native subunits. Tests with both systems, applied to extracts of different classes of particles, suggest that high salt does extract both initiation factors and essential ribosomal proteins. Extracts of native subunits contain both, and stimulate both systems; while, in the presence of these extracts, the extracts of polysomes further stimulate only the extracted ribosomes.
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38
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Strom AR, Visentin LP. Acidic ribosomal proteins from the extreme halophile, Halobacterium cutirubrum. The simultaneous separation, identification and molecular weight determination. FEBS Lett 1973; 37:274-80. [PMID: 4763334 DOI: 10.1016/0014-5793(73)80477-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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39
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Benne R, Ebes F, Voorma HO. Sequence of events in initiation of protein synthesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 38:265-73. [PMID: 4129820 DOI: 10.1111/j.1432-1033.1973.tb03058.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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40
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41
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Brouwer J, Planta RJ. Structural heterogeneity of 30S and 50S ribosomal subunits in Bacillus licheniformis. Mol Biol Rep 1973; 1:135-42. [DOI: 10.1007/bf00357153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/1973] [Indexed: 11/28/2022]
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42
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Rummel DP, Noller HF. Use of protection of 30S ribosomal proteins by tRNA for functional mapping of the E. coli ribosome. NATURE: NEW BIOLOGY 1973; 245:72-5. [PMID: 4580791 DOI: 10.1038/newbio245072a0] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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43
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van Knippenberg PH, van Duin J, Lentz H. Stoichiometry of initiation factor IF-3 in exponentially growing Escherichia coli MRE600. FEBS Lett 1973; 34:95-8. [PMID: 4581001 DOI: 10.1016/0014-5793(73)80711-2] [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: 01/11/2023]
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44
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45
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Slobin LI. Structural and functional properties of ribosomes crosslinked with dimethylsuberimidate. Proc Natl Acad Sci U S A 1972; 69:3769-73. [PMID: 4566460 PMCID: PMC389868 DOI: 10.1073/pnas.69.12.3769] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
To test whether a 30S ribosomal subunitformylmethionyl-tRNA-mRNA complex is an obligatory intermediate in protein synthesis, 70S ribosomes from Escherichia coli were crosslinked with the bifunctional imidoester, dimethylsuberimidate. Crosslinked ribosomes contained covelently joined 30S and 50S subunits, as judged by their inability to dissociate at low Mg(2+) concentrations. Treatment of 70S ribosomes with high salt (1 M NH(4)Cl), either before or after reaction with the crosslinking reagent, produced two different crosslinked ribosomal particles, one of "60 S" and the other "70 S." Preliminary evidence indicates that both particles can bind N-acetylphenylalanyl-tRNA at low Mg(2+) concentrations and are active for polyphenylalanine syntheses. Crosslinked ribosomes were functional when tested with poly(U) as an mRNA in systems requiring initiation factors and N-acetylphenylalanyl-tRNA for activity. Under optimal crosslinking conditions, they retained 80% of the activity of unmodified ribosomes for polyphenylalanine synthesis. Despite the maintenance of these functional capacities, such ribosomes had a sharply reduced ability to bind fMet-tRNA and were completely inactive in protein synthesis with bacteriophage f2 RNA as a messenger. We conclude that 70S ribosomes must dissociate into subunits to initiate protein synthesis with natural mRNAs.
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46
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Weber HJ. Stoichiometric measurements of 30S and 50S ribosomal proteins from Escherichia coli. MOLECULAR & GENERAL GENETICS : MGG 1972; 119:233-48. [PMID: 4567157 DOI: 10.1007/bf00333861] [Citation(s) in RCA: 130] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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47
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Deusser E. Heterogeneity of ribosomal populations in Escherichia coli cells grown in different media. MOLECULAR & GENERAL GENETICS : MGG 1972; 119:249-58. [PMID: 4567158 DOI: 10.1007/bf00333862] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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48
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Bollen A, Pêtre J, Grosjean H. Direct biochemical approach to the structural heterogeneity of 30 S ribosomes from Escherichia coli. FEBS Lett 1972; 24:327-330. [PMID: 11946699 DOI: 10.1016/0014-5793(72)80383-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- A Bollen
- University of Brussels, Department of Molecular Biology, Rue des Chevaux, 67, B-1640, Rhode Saint Genèse, Belgium
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Deusser E, Wittmann HG. Ribosomal proteins: variation of the protein composition in Escherichia coli ribosomes as function of growth rate. Nature 1972; 238:269-70. [PMID: 4558554 DOI: 10.1038/238269a0] [Citation(s) in RCA: 47] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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