PHAGE f2 RNA-DIRECTED BINDING OF FORMYLMETHIONYL-TRNA TO RIBOSOMES AND THE ROLE OF 30S RIBOSOMAL SUBUNITS IN INITIATION OF PROTEIN SYNTHESIS

Consensus architecture of promoters and transcription units in Escherichia coli: design principles for synthetic biology

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.

Wanderings in biochemistry

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.

Journey of a Molecular Biologist

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.

Transport of viral RNA in kb cells infected with adenovirus type 2

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.

Association and dissociation of Neurospora crassa cytoplasmic ribosomes

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.

Magnesium dependence of the association kinetics of Escherichia coli ribosomal subunits

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.

Growth and initiation of protein synthesis in Escherichia coli in the presence of trimethoprim

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).

Structural and functional properties of ribosomes crosslinked with dimethylsuberimidate

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.

Polysomal localization of R17 bacteriophage-specific protein synthesis

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.

Role of 5S RNA in the functions of 50S ribosomal subunits

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.

Drastic alteration of ribosomal RNA and ribosomal proteins in showdomycin-resistant Escherichia coli

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.

Dissociation of ribosomes and seed germination

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.

The dissociation of Yoshida hepatoma ribosomes into active particles

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.

A new protein synthesis factor from Escherichia coli

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.

A factor for the binding of aminoacyl transfer RNA to mammalian 40S ribosomal subunits

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.