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Rangel-Chavez C, Galan-Vasquez E, Martinez-Antonio A. Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology. MOLECULAR BIOSYSTEMS 2017; 13:665-676. [PMID: 28256660 DOI: 10.1039/c6mb00789a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Genetic information in genomes is ordered, arranged in such a way that it constitutes a code, the so-called cis regulatory code. The regulatory machinery of the cell, termed trans-factors, decodes and expresses this information. In this way, genomes maintain a potential repertoire of genetic programs, parts of which are executed depending on the presence of active regulators in each condition. These genetic programs, executed by the regulatory machinery, have functional units in the genome delimited by punctuation-like marks. In genetic terms, these informational phrases correspond to transcription units, which are the minimal genetic information expressed consistently from initiation to termination marks. Between the start and final punctuation marks, additional marks are present that are read by the transcriptional and translational machineries. In this work, we look at all the experimentally described and predicted genetic elements in the bacterium Escherichia coli K-12 MG1655 and define a comprehensive architectural organization of transcription units to reveal the natural genome-design and to guide the construction of synthetic genetic programs.
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Affiliation(s)
- Cynthia Rangel-Chavez
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
| | - Edgardo Galan-Vasquez
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
| | - Agustino Martinez-Antonio
- Biological Engineering Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav), Campus Irapuato, Km. 9.6 Libramiento Norte Carr, Irapuato-León 36821, Irapuato Gto, Mexico.
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Abstract
My Ph.D. thesis in the laboratory of Severo Ochoa at New York University School of Medicine in 1962 included the determination of the nucleotide compositions of codons specifying amino acids. The experiments were based on the use of random copolyribonucleotides (synthesized by polynucleotide phosphorylase) as messenger RNA in a cell-free protein-synthesizing system. At Yale University, where I joined the faculty, my co-workers and I first studied the mechanisms of protein synthesis. Thereafter, we explored the interferons (IFNs), which were discovered as antiviral defense agents but were revealed to be components of a highly complex multifunctional system. We isolated pure IFNs and characterized IFN-activated genes, the proteins they encode, and their functions. We concentrated on a cluster of IFN-activated genes, the p200 cluster, which arose by repeated gene duplications and which encodes a large family of highly multifunctional proteins. For example, the murine protein p204 can be activated in numerous tissues by distinct transcription factors. It modulates cell proliferation and the differentiation of a variety of tissues by binding to many proteins. p204 also inhibits the activities of wild-type Ras proteins and Ras oncoproteins.
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Affiliation(s)
- Peter Lengyel
- From the Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520
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Abstract
My journey into a research career began in fermentation biochemistry in an applied science department during the difficult post-World War II time in Japan. Subsequently, my desire to do research in basic science developed. I was fortunate to be a postdoctoral fellow in the United States during the early days of molecular biology. From 1957 to 1960, I worked with three pioneers of molecular biology, Sol Spiegelman, James Watson, and Seymour Benzer. These experiences helped me develop into a basic research scientist. My initial research projects at Osaka University, and subsequently at the University of Wisconsin, Madison, were on the mode of action of colicins as well as on mRNA and ribosomes. Following success in the reconstitution of ribosomal subunits, my efforts focused more on ribosomes, initially on the aspects of structure, function, and in vitro assembly, such as the construction of the 30S subunit assembly map. After this, my laboratory studied the regulation of the synthesis of ribosomes and ribosomal components in Escherichia coli. Our achievements included the discovery of translational feedback regulation of ribosomal protein synthesis and the identification of several repressor ribosomal proteins used in this regulation. In 1984, I moved to the University of California, Irvine, and initiated research on rRNA transcription by RNA polymerase I in the yeast Saccharomyces cerevisiae. The use of yeast genetics combined with biochemistry allowed us to identify genes uniquely involved in rRNA synthesis and to elucidate the mechanism of initiation of transcription. This essay is a reflection on my life as a research scientist.
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Affiliation(s)
- Masayasu Nomura
- Department of Biological Chemistry, University of California, Irvine, California 92697-1700
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Raskas HJ, Okubo CK. Transport of viral RNA in kb cells infected with adenovirus type 2. ACTA ACUST UNITED AC 2010; 49:438-49. [PMID: 19866771 PMCID: PMC2108321 DOI: 10.1083/jcb.49.2.438] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Messenger RNA transport was studied in KB cells infected with the nuclear DNA virus adenovirus type 2. Addition of 0.04 µg/ml of actinomycin completes the inhibition of ribosome synthesis normally observed late after infection and apparently does not alter the pattern of viral RNA synthesis: Hybridization-inhibition experiments indicate that similar viral RNA sequences are transcribed in cells treated or untreated with actinomycin. The polysomal RNA synthesized during a 2 hr labeling period in the presence of actinomycin is at least 60% viral specific. Viral messenger RNA transport can occur in the absence of ribosome synthesis. When uridine-3H is added to a late-infected culture pretreated with actinomycin, viral RNA appears in the cytoplasm at 10 min, but the polysomes do not receive viral RNA-3H until 30 min have elapsed. Only 25% of the cytoplasmic viral RNA is in polyribosomes even when infected cells have been labeled for 150 min. The nonpolysomal viral RNA in cytoplasmic extracts sediments as a broad distribution from 10S to 80S and does not include a peak cosedimenting with 45S ribosome subunits. The newly formed messenger RNA that is ribosome associated is not equally distributed among the ribosomes; by comparison to polyribosomes, 74S ribosomes are deficient at least fivefold in receipt of new messenger RNA molecules.
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Affiliation(s)
- H J Raskas
- Institute for Molecular Virology and the Department of Pathology, Saint Louis University School of Medicine, Saint Louis, Missouri 63104
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5
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Kafatos FC. Cytoplasmic particles carrying rapidly labeled RNA in developing insect epidermis. Proc Natl Acad Sci U S A 2010; 59:1251-8. [PMID: 16591632 PMCID: PMC224859 DOI: 10.1073/pnas.59.4.1251] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- F C Kafatos
- THE BIOLOGICAL LABORATORIES, HARVARD UNIVERSITY
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Affiliation(s)
- M Nomura
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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7
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Nomura M. Switching from prokaryotic molecular biology to eukaryotic molecular biology. J Biol Chem 2009; 284:9625-35. [PMID: 19074426 DOI: 10.1074/jbc.x800014200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Masayasu Nomura
- Department of Biological Chemistry, University of California, Irvine, California 92697-1700, USA.
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8
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Kraus BL, Spremulli LL. Chloroplast initiation factor 3 from Euglena gracilis. Identification and initial characterization. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)89172-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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9
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Zipori P, Bosch L, Van Dieijen G, van der Hofstad GA. The 50-S ribosomal subunit inhibits functional interaction between the 30-S subunit and phage RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 92:225-33. [PMID: 365532 DOI: 10.1111/j.1432-1033.1978.tb12740.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Judewicz ND, Algranati ID. Association and dissociation of Neurospora crassa cytoplasmic ribosomes. J Bacteriol 1978; 133:418-21. [PMID: 145436 PMCID: PMC222029 DOI: 10.1128/jb.133.1.418-421.1978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dissociation and association factors of ribosomal particles were detected in extracts from Neurospora crassa at different stages of growth. The dissociation factor was easily released into the S100 supernatant fraction, whereas the association factor remained bound to the ribosomes.
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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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12
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Favaudon V, Pochon F. Magnesium dependence of the association kinetics of Escherichia coli ribosomal subunits. Biochemistry 1976; 15:3903-12. [PMID: 786363 DOI: 10.1021/bi00663a001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The magnesium dependence of the Escherichia coli ribosomal subunits association has been investigated by the stopped-flow technique using isolated 30S and 50S particles depleted of polyamines and any initiation factor. Binding of the fluorescent probe bis(8-anilino-1-naphthalenesulfonate) to the ribosomal proteins occurs through biphasic kinetics. A dark reaction corresponding to a very rapid, reversible complexation of the dye molecule is followed by a slow photochemical reaction that gives rise to irreversible addition of the probe. Only the 30S subparticle exhibits a magnesium-dependent conformational change from the kinetic analysis of the dark reaction. The 70S formation kinetics are limited by a conformational change of the 30S subunit if this particle is depleted of Mg2+ (1 mM Mg2+/50 mM K+), while its activated structure is restored by incubation with 8 mM Mg2+/50 mM K+. No rate-limiting conformation rearrangement of the 50S subunit could ever be evidenced. The Mg2+ dependence of the association kinetics of preactivated ribosomal particles is satisfactorily explained by electrostatic effects and/or formation of salt bridges, in agreement with the results of Wishnia and co-workers (Wishnia, A. Boussert, A., Graffe, M., Dessen, P., and Grunberg-Manago, M. (1975), J. Mol. Biol. 93, 499). Equilibrium studies indicate that the ribosomal preparations we used are of B type, according to Debey et al. (Debey, P., Hui Bon Hoa, G., Douzou, P., Godefroy-Colburn, T., Graffe, M., AND Grunberg-Manago, M. (1975) Biochemistry 14, 1553). The addition of spermidine results in a drastic fall of the need of Mg2+ for association, but it does not allow conversion of B-type particles into A-type ones at 25 degrees C. In addition to that, some 30S-bound spermidine appears to be involved directly in the coupling reaction.
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14
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Otaka T, Kaji A. Micrococcin: acceptor-site-specific inhibitor of protein synthesis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1974; 50:101-6. [PMID: 4615898 DOI: 10.1111/j.1432-1033.1974.tb03876.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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16
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Ghosh K, Ghosh HP, Simsek M, Bhandary ULR. Initiator Methionine Transfer Ribonucleic Acid from Wheat Embryo. J Biol Chem 1974. [DOI: 10.1016/s0021-9258(19)42379-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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17
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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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18
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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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19
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Role of Elongation Factor G and a Protein Factor on the Release of Ribosomes from Messenger Ribonucleic Acid. J Biol Chem 1973. [DOI: 10.1016/s0021-9258(19)43330-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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21
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Fakunding JL, Hershey JW. The Interaction of Radioactive Initiation Factor IF-2 with Ribosomes during Initiation of Protein Synthesis. J Biol Chem 1973. [DOI: 10.1016/s0021-9258(19)43759-9] [Citation(s) in RCA: 33] [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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22
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Harvey RJ. Growth and initiation of protein synthesis in Escherichia coli in the presence of trimethoprim. J Bacteriol 1973; 114:309-22. [PMID: 4572717 PMCID: PMC251769 DOI: 10.1128/jb.114.1.309-322.1973] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Escherichia coli grew exponentially at a reduced rate in the presence of 50 or 100 mug of trimethoprim/ml if the low-molecular-weight products of folate metabolism or their precursors (thymidine, purines, methionine, glycine, and pantothenate) were supplied in the medium. Folate metabolism was inhibited 99.9% by these concentrations of trimethoprim, but a low level of formylation of methionyl transfer ribonucleic acid (met-tRNA(F)) could be detected. However, in a medium containing all major amino acids, nucleosides, and vitamins, formylation of met-tRNA(F) was undetectable in the presence of trimethoprim. No other amino-masked amino acids were detected, and methionine remained a major amino-terminal amino acid of mature proteins. met-tRNA(F) was rapidly labeled with exogenous methionine and was associated with 30s ribosomal subunits and 70s ribosomes. It was concluded that initiation of protein synthesis can occur with unformylated met-tRNA(F) in E. coli. Changes in macromolecular composition were associated with the lack of formylation, in particular a fourfold increase in both met-tRNA(F) and ribosomal subunits. These changes would tend to compensate for the low specific rate of initiation with unformylated met-tRNA(F).
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23
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Favelukes G, Sorgentini D, Bard E, Martone de Borrajo C. Intermediate stages in the ribosomal cycle of reticulocytes. BASIC LIFE SCIENCES 1973; 1:393-409. [PMID: 4589687 DOI: 10.1007/978-1-4684-0877-5_31] [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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Chapter V Methods for Assessing Damage to Bacteria Induced by Chemical and Physical Agents. METHODS IN MICROBIOLOGY 1973. [DOI: 10.1016/s0580-9517(08)70162-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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26
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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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Manzoli FA, Grossi CE, Stefoni S, Bartoli S. Thymus and bursal ribosomes in the developing chicken. Poult Sci 1972; 51:972-5. [PMID: 4646679 DOI: 10.3382/ps.0510972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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28
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Kozak M, Nathans D. Translation of the genome of a ribonucleic acid bacteriophage. BACTERIOLOGICAL REVIEWS 1972; 36:109-34. [PMID: 4555183 PMCID: PMC378432 DOI: 10.1128/br.36.1.109-134.1972] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Abstract
Synthesis of viral ribonucleic acid (RNA) polymerase, maturation protein, and coat protein in Escherichia coli infected with bacteriophage R17 occurs mainly on polysomes containing four or more ribosomes. The 30S ribosomal subunits through trimer-size polysomes, which are associated with all of the R17-specific proteins and are predominant in the infected cell, synthesize only coat protein. These structures may accumulate as products derived from larger polysomes as a result of failure in the release of nascent polypeptides after termination of chain growth. Appreciable amounts of viral coat protein remain attached to ribosomes and polysomes during R17 bacteriophage replication, supporting the hypothesis of the repressor role of this protein. The time course of synthesis of virus-specific proteins obtained from the polysomes of infected cells demonstrated regulated R17 messenger RNA translation consistent with the idea that coat protein is preferentially synthesized whereas the synthesis of noncoat proteins is suppressed.
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Erdmann VA, Fahnestock S, Higo K, Nomura M. Role of 5S RNA in the functions of 50S ribosomal subunits. Proc Natl Acad Sci U S A 1971; 68:2932-6. [PMID: 5289238 PMCID: PMC389563 DOI: 10.1073/pnas.68.12.2932] [Citation(s) in RCA: 87] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
50S ribosomal subunits from Bacillus stearothermophilus can be reconstituted from their dissociated components, namely a 5S RNA-free protein fraction, a 5S RNA-free 23S ribosomal RNA fraction, and purified 5S RNA. The biological activity of reconstituted particles in polypeptide synthesis is dependent on the presence of 5S RNA. In the absence of 5S RNA, particles are produced that have greatly reduced activity in (a) polypeptide synthesis directed by synthetic, as well as natural, messenger RNA, (b) peptidyl transferase assay, (c) [(3)H]UAA binding dependent on peptide chain termination factor R1, (d) G factor-dependent [(3)H]GTP binding, and (e) codon-directed tRNA binding assayed in the presence of 30S subunits. Thus, 5S RNA is an essential 50S ribosomal component.
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32
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BURGESS ANNB, MACH BERNARD. Formation of an Initiation Complex with Purified Mammalian Ribosomal Subunits. ACTA ACUST UNITED AC 1971. [DOI: 10.1038/newbio233209a0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Groner Y, Revel M. A novel form of initiation factors from escherichia coli which binds formyl methionyl tRNA and GTP: "F2-F3 complex". EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 22:144-52. [PMID: 4999814 DOI: 10.1111/j.1432-1033.1971.tb01525.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Voorma HO, Benne R, den Hertog TJ. Binding of aminoacyl-tRNA to ribosomes programmed with bacteriophage MS2-RNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 18:451-62. [PMID: 5545002 DOI: 10.1111/j.1432-1033.1971.tb01263.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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38
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Beljanski M, Bourgarel P, Beljanski M. Drastic alteration of ribosomal RNA and ribosomal proteins in showdomycin-resistant Escherichia coli. Proc Natl Acad Sci U S A 1971; 68:491-5. [PMID: 5277106 PMCID: PMC388967 DOI: 10.1073/pnas.68.2.491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In a mutant of Escherichia coli resistant to showdomycin, both the 50S and 30S ribosomal subunits contain RNA species in which the purine concentration greatly exceeds that of pyrimidines. The same is true for total rapidly-labeled RNA. The modified ribosomal RNA hybridizes poorly with homologous DNA, which is apparently unchanged in base composition. Acrylamide gel electrophoresis of mutant ribosomal proteins shows a highly altered protein pattern for both ribosomal subunits, although the activity of these ribosomes is not decreased.
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39
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App AA, Bulis MG, McCarthy WJ. Dissociation of ribosomes and seed germination. PLANT PHYSIOLOGY 1971; 47:81-6. [PMID: 16657584 PMCID: PMC365816 DOI: 10.1104/pp.47.1.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ribosomes from rice embryos (Oryza sativa) were dissociated into ribosomal subunits in vitro by systematic reduction of the Mg(2+) concentration. Ribosomes from imbibed (28 C) embryos were more easily dissociated than those from nonimbibed embryos. This was not observed with ribosomes from either imbibed, nonviable embryos, or from embryos imbibed at 0 C. Ribosomes from embryos which had been imbided and subsequently dehydrated resembled ribosomes from nonimbibed embryos in their resistance to dissociation. The change in the resistance to dissociation was essentially complete after the first 20 minutes of imbibition at 28 C, and accompanied activation in vivo of protein synthesis as determined by amino acid incorporation in vitro. Ribosomes from either imbibed or nonimbibed embryos could be dissociated into subunits by 0.5 m KCl. These subunits were separated by density gradient centrifugation, and, if recombined, were active for polyphenylalanine synthesis in vitro. The individual subunits prepared from nonimbibed embryos could be replaced by the corresponding subunit fraction from imbibed embryos without loss of capacity to support polyphenylalanine synthesis. The change in the ease of dissociation of ribosomes appears to be a physiological process, and its possible relationship to the initiation of protein synthesis during seed germination is discussed.
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Affiliation(s)
- A A App
- Boyce Thompson Institute for Plant Research, Yonkers, New York 10701
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40
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Abstract
1. The sedimentation pattern of Yoshida hepatoma ribosomes shows mainly a high dimer peak and an intermediate peak between those of monomer and dimer. 2. The treatment of the postmitochondrial supernatant with EDTA or potassium chloride leads to the dissociation of ribosomes into subunits, through a decrease ofthe ribosomal Mg(2+)/phosphorus ratio. Provided that the deprivation of endogenous Mg(2+) is not complete, the subunits reassociate into active polyribosomes after addition of magnesium chloride to the medium. If the Mg(2+)/phosphorus ratio is lowered below 0.01 (mumol/mumol), structural changes occur, that become evident by a loss of protein and by a decreased sedimentation rate, which render the subribosomal particles unable to reassociate. 3. In the re-formation of polyribosomes from subunits, during the progressive increase of the concentration of magnesium chloride in the medium, the formation of monomeric ribosomes seems to be intermediate. 4. A dimerization of monomers and subunits occurs at concentrations of magnesium chloride greater than those required for the re-formation of polyribosomes and a preincubation for 1h at 0 degrees C is necessary for the maximum dimerization, whereas the complete reconstitution of polyribosomes is immediate.
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41
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Georgiev GP, Samarina OP. D-RNA containing ribonucleoprotein particles. ADVANCES IN CELL BIOLOGY 1971; 2:47-110. [PMID: 4949655 DOI: 10.1007/978-1-4615-9588-5_2] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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42
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Sabol S, Sillero MA, Iwasaki K, Ochoa S. Purification and properties of initiation factor F3. Nature 1970; 228:1269-73. [PMID: 4922687 DOI: 10.1038/2281269a0] [Citation(s) in RCA: 140] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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43
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Metlas R, Bećarević A, Popić S, Simić M. Binding of the in vitro synthesized RNA to rat liver 40 S ribosomal subunit. FEBS Lett 1970; 12:1-3. [PMID: 11945526 DOI: 10.1016/0014-5793(70)80579-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- R Metlas
- Laboratory of Biochemistry, Boris Kidrich Institute of Nuclear Sciences, Beograd, Yugoslavia
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44
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Affiliation(s)
- I Suzuka
- Department of Biophysics, National Institute of Animal Health, Kodaira, 187, Tokyo, Japan
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van Duin J, VAN Dieijen G, Dieijen G, van Knippenberg PH, Bosch L. Different species of 70S ribosomes of Escherichia coli and their dissociation into subunits. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 17:433-40. [PMID: 4924194 DOI: 10.1111/j.1432-1033.1970.tb01183.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Kaempfer R. Dissociation of ribosomes on polypeptide chain termination and origin of single ribosomes. Nature 1970; 228:534-7. [PMID: 4919500 DOI: 10.1038/228534a0] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Kan YW, Golini F, Thach RE. A new protein synthesis factor from Escherichia coli. Proc Natl Acad Sci U S A 1970; 67:1137-42. [PMID: 4924442 PMCID: PMC283328 DOI: 10.1073/pnas.67.3.1137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A new factor that effects protein synthesis by Escherichia coli extracts was partially purified from the 1 M NH(4)Cl wash of E. coli ribosomes. This factor stimulates the binding of aminoacyl-tRNA to 30S ribosomes, and it increases the rate of synthesis of polyphenylalanine in the presence of 30S and 50S subunits.
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Remold-O'Donnell E, Thach RE. A New Method for the Purification of Initiation Factor F2 in High Yield, and an Estimation of Stoichiometry in the Binding Reaction. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)62714-0] [Citation(s) in RCA: 33] [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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Bernstein IA, Chakrabarti SG, Kumaroo KK, Sibrack LA. Synthesis of protein in the mammalian epidermis. J Invest Dermatol 1970; 55:291-302. [PMID: 4922903 DOI: 10.1111/1523-1747.ep12260109] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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50
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Leader DP, Wool IG, Castles JJ. A factor for the binding of aminoacyl transfer RNA to mammalian 40S ribosomal subunits. Proc Natl Acad Sci U S A 1970; 67:523-8. [PMID: 5289006 PMCID: PMC283239 DOI: 10.1073/pnas.67.2.523] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A factor present in rat liver supernatant catalyzes binding of Phe-tRNA to 40S ribosomal subunits from rat skeletal muscle. This factor could be distinguished from aminoacyltransferase I by a number of criteria: (1) at lower concentrations of magnesium (5 mM) the 40S binding factor was approximately seven times as effective as T-I in catalyzing binding of Phe-tRNA to 40S subunits; (2) the kinetics of the binding reaction were different when catalyzed by the 40S binding factor, in particular the initial rate was greater than in the presence of T-I-indeed, the kinetics of the T-I catalyzed reaction resembled nonenzymic binding; (3) GTP was required for maximal binding of Phe-tRNA to 40S subunits in the presence of the 40S binding factor, but not for the T-I catalyzed reaction; (4) the 40S binding factor was inactivated by N-ethylmaleimide whereas T-I was not; (5) finally, the 40S binding factor was more susceptible to heat inactivation. Binding of aminoacyl-tRNA to 40S ribosomal subunits may be a paradigm for the initiation of protein synthesis, and the 40S binding factor may play a role in the process.
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