Mapping of ribosomal protein genes by in vitro protein synthesis using DNA fragments of lambdafus3 transducing phage DNA as templates

An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel

The influence of the ribosome on nascent chains is poorly understood, especially in the case of proteins devoid of signal or arrest sequences. Here, we provide explicit evidence for the interaction of specific ribosomal proteins with ribosome-bound nascent chains (RNCs). We target RNCs pertaining to the intrinsically disordered protein PIR and a number of mutants bearing a variable net charge. All the constructs analyzed in this work lack N-terminal signal sequences. By a combination chemical crosslinking and Western-blotting, we find that all RNCs interact with ribosomal protein L23 and that longer nascent chains also weakly interact with L29. The interacting proteins are spatially clustered on a specific region of the large ribosomal subunit, close to the exit tunnel. Based on chain-length-dependence and mutational studies, we find that the interactions with L23 persist despite drastic variations in RNC sequence. Importantly, we also find that the interactions are highly Mg+2-concentration-dependent. This work is significant because it unravels a novel role of the ribosome, which is shown to engage with the nascent protein chain even in the absence of signal or arrest sequences.

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.

Isolation and preliminary characterization of the Streptococcus mutans rpsJ gene

We previously reported that four putative open reading frames were identified in the regions flanking the Streptococcus mutans GS-5 fructosyltransferase gene. For one of these, ORF 4, only a small region had been isolated and the first 30 nucleotides had been sequenced. In order to determine whether this open reading frame is part of an expressed gene, we isolated a DNA fragment containing intact ORF 4 and a portion of the downstream ORF 5 by inverse polymerase chain reaction. A comparison of the deduced amino acid sequences of ORF 4 and ORF 5 with other proteins revealed that the ORF 4 and ORF 5 gene products were highly homologous to ribosomal proteins S10 and L3, respectively, of several bacteria. To identify the precise transcriptional start site for the ORF 4 gene, primer extension analysis was carried out. The results indicated initiation at a G residue with corresponding -10 and -35 regions homologous to the Escherichia coli consensus promoter sequences. These results indicate that the sequences of ORF 4 and ORF 5 are consistent with the structures of ribosomal proteins S10 and L3, respectively, and are present in a ribosomal protein operon.

A technique for targeted mutagenesis of the EF-Tu chromosomal gene by M13-mediated gene replacement

A generally applicable system for targeted mutagenesis of a chromosomal sequence is described. The Escherichia coli tufA gene was mutated using a recombinant M13mp9 phage vector carrying a tuf gene. Integration via crossing over with the chromosomal tufA target gene produced an M13 lysogen. These lysogens were screened for resistance to kirromycin. The M13 phage carrying tufA mutations were efficiently retrieved by a genetic procedure. Genetic mapping was performed with the M13 vectors. The same recombinant M13 phage was used for mutagenesis, lysogen formation, gene replacement, retrieval, mapping and sequencing of kirromycin mutants. Three different mutations yielding resistance to kirromycin were found: two of these have previously been found and characterised, while the third mutation, Gly316-->Asp, is a new mutant. We also report the identification of a fourth kirromycin-resistant mutant, Gln124-->Lys.

Antisuppression by mutations in elongation factor Tu

Two slow-growing kirromycin-resistant Escherichia coli mutants with altered EF-Tu (Ap and Aa) were studied in vivo in strains with an inactive tufB gene. Mutant form Aa was isolated as an antisuppressor of the tyrT(Su3) nonsense suppressor, as described here. Ap, the tufA gene product of strain D2216 (from A. Parmeggiani), has previously been shown to give an increased GTPase activity. The slow cellular growth rates of both EF-Tu mutants are correlated with decreased translational elongation rates. Ap and Aa significantly decrease suppression levels of both nonsense and missense suppressor tRNAs [tyrT(Su3), trpT(Su9), glyT(SuAGA/G)], but have only little or no effect on misreading by wild-type tRNAs. A particular missense suppressor, lysT(SuAAA/G), which acts by virtue of partial mischarging as the result of an alteration in the amino acid stem, is not significantly affected by the EF-Tu mutations. The combination of tufA(Aa) and a rpsD12 ribosomal mutation is lethal at room temperature and the double-mutant strain has an elevated temperature optimum (42 degrees C) for growth rate, translation rate and nonsense suppression. Our data indicate an alterated interaction between Aa and the ribosome, consistent with our in vitro results.

Transcription mapping of the Escherichia coli chromosome by electron microscopy

The distinctive double Christmas tree morphology of rRNA operons as visualized by electron microscopy makes them easy to recognize in chromatin spreads from Escherichia coli. On the basis of the pattern of nascent transcripts on nearby transcription units and the relative distances of the operons from one another and the replication origin, we are now able to specifically identify five of the seven rRNA operons in E. coli. The use of rRNA operons as markers of both position and distance has resulted in the morphological mapping of a significant portion of the E. coli chromosome; over 600 kilobase pairs in the 84- to 90-min and 72-min regions can now be recognized. Since individual rRNA operons could be identified, direct comparisons could be made of their transcriptional activities. As judged by the densities of RNA polymerases along the operons, rrnA, rrnB, rrnC, rrnD, and rrnE were all transcribed at similar levels, with one RNA polymerase every 85 base pairs. The ability to recognize individual operons and specific regions of the chromosome allows direct comparisons of various genetic parameters.

Control of the tRNA-tufB operon in Escherichia coli. 1. rRNA gene dosage effects and growth-rate-dependent regulation

'Ribosome feedback' effects on the expression of the genes specifying tRNA and EF-Tu in E. coli have been studied at increased rrnB doses (rRNA gene doses). We confirm previous observations that the introduction into the cell of a multicopy plasmid carrying the rrnB operon reduces the cellular content of most tRNAs, including those encoded by the tRNA-tufB operon, but leaves the 5S rRNA content unaffected. Increase of the dosage of intact, but not of deleted rRNA genes, causes a slight drop in total EF-Tu that can be fully accounted for by a decrease in EF-TuB level. The drop in EF-TuB content (approx. 25%) is much smaller than that in tRNA content (approx. 80%). The synthesis rate of total EF-Tu is hardly affected, indicating that the turnover of EF-Tu has not changed. The ratio of tRNA over tuf RNA synthesis rates remains the same after elevation of rrnB dosage. Considering the large decrease in tRNA content this means that both RNA synthesis rates decrease to approximately the same extent. The relatively small drop in EF-Tu synthesis must be due, therefore, to an enhancement of the number of EF-Tu molecules synthesized per mRNA molecule. Apparently a post-transcriptional mechanism, regulating EF-Tu synthesis, becomes operative under these conditions. Growth-rate-dependent regulation of the tRNA-tufB operon has been studied using lysogens carrying tRNA':lacZ and tRNA-tufB':lacZ operon fusions and a tufB':lacZ' gene fusion. These experiments show that the cellular contents of tRNA, tufB RNA and EF-TuB vary in direct proportion to the growth rate. This indicates that growth rate control of tRNA-tufB operon transcription resembles that of stable RNA operons and not of r-protein operons, and that the read-through of the terminator at the end of the tRNA gene cluster remains unaltered.

Novel rpoA mutation that interferes with the function of OmpR and EnvZ, positive regulators of the ompF and ompC genes that code for outer-membrane proteins in Escherichia coli K12

The expression of the ompF and ompC genes that code for major outer-membrane proteins of Escherichia coli is positively regulated by the products of the ompR and envZ genes. Recently, we isolated the ompR77 mutation, which suppresses the envZ11 mutation. In this work, a novel mutation that interferes with the suppression of the envZ11 mutation by ompR77 was isolated. The mutation was located in the rpoA gene that codes for the alpha subunit of DNA-dependent RNA polymerase. These results suggest that an interaction between the positive regulators and RNA polymerase is involved in the initiation of transcription of the ompF and ompC genes. In addition, the results suggest that during transcription the RNA polymerase migrates along DNA strands with the alpha subunit facing backward and the beta beta' subunits facing forward.

Organization of the genes for protein synthesis elongation factors Tu and G in the cyanobacterium Anacystis nidulans

The genes for protein synthesis elongation factors Tu and G were cloned from the cyanobacterium Anacystis nidulans. The locations of these genes were mapped within the cloned DNA fragment by hybridization with Escherichia coli probes. The organization of the cloned fragment and the DNA flanking it in the A. nidulans chromosome was also determined. The elongation factor Tu and G genes are adjacent to one another and in the same 5'-to-3' orientation. In contrast to other gram-negative bacteria, A. nidulans contains only one gene for elongation factor Tu.

Suppressors of temperature-sensitive mutations in a ribosomal protein gene, rpsL (S12), of Escherichia coli K12

Temperature-sensitive (ts) mutations were isolated within a ribosomal protein gene (rpsL) of Escherichia coli K12. Mutations were mapped by complementation using various transducing phages and plasmids carrying the rpsL gene, having either a normal or a defective promoter for the rpsL operon. One of these mutations, ts118, resulted in a mutant S12 protein which behaved differently from the wild-type S12 on CM-cellulose column chromatography. Suppressors of these ts mutations were isolated and characterized; one was found to be a mutation of a nonribosomal protein gene which was closely linked to the RNAase III gene on the E. coli chromosome. This suppressor, which was recessive to its wild-type allele, was cloned into a transducing phage and mapped finely. A series of cold-sensitive mutations, affecting the assembly of ribosomes at 20 degrees C, was isolated within the purL to nadB region of the E. coli chromosome and one group, named rbaA, mapped at the same locus as the suppressor mutation, showing close linkage to the RNAase III gene.

Transcription of ribosomal component genes and lac in a relA+/relA pair of Escherichia coli strains

To determine the stringent response, a repression of gene activity during amino acid starvation assumed to be mediated by the effector necleotide guanosine tetraphosphate (ppGpp), of metabolically regulated constitutive genes, we measured the transcription of ribosomal protein genes, the constitutive lac operon, and stable RNA genes in a variety of growth media and after amino acid starvation in a relA+/relA pair of Escherichia coli B/r strains. For rRNA and tRNA (stable RNA) it has previously been shown that the distinction between stringent control and growth rate control is unfounded, as the function describing the stable RNA gene activities at different concentrations of guanosine tetraphosphate is independent of growth conditions (exponential growth or amino acid starvation) and of the relA allele present. Here, the results indicated that the stringent responses of ribosomal protein genes and lac differ from their metabolic control during exponential growth in different media. This can be explained by polarity and RNA polymerase sink effects during amino acid starvation which are irrelevant for stable RNA genes but which are superimposed on mRNA gene activities.

Localization of the target site for translational regulation of the L11 operon and direct evidence for translational coupling in Escherichia coli

The L11 ribosomal protein operon in Escherichia coli consists of the structural genes for proteins L11 and L1. Hybrid deletion plasmids were constructed carrying these two genes with decreasing amounts of the leader mRNA under lac transcriptional control. Measurements of mRNA and protein synthesis directed by these plasmids in vitro and in vivo demonstrate that the regulation of this operon is posttranscriptional and identifies a region of the mRNA, preceding the proximal L11 gene, important for successful feedback inhibition of L11 and L1 synthesis by L1. Additionally, deletions extending to the ribosome binding site of the L11 gene fail to synthesize both L11 and the downstream L1 protein although synthesis of the corresponding mRNA remains unchanged. These results directly demonstrate the presence of translational coupling in this bicistronic operon.

Transcription of the S10 ribosomal protein operon is regulated by an attenuator in the leader

Previous studies have shown that ribosomal protein L4 specifically inhibits the expression of its own operon, the 11-gene S10 operon. To elucidate the mechanism for this regulation, we have examined the effect of protein L4 on transcription of the S10 operon. Hybridization and gel electrophoresis studies indicate that in the presence of excess L4 only RNA molecules about 140 bases long are transcribed from the S10 operon. These short RNA molecules contain the leader, but not structural gene, sequences. Our results suggest that protein L4 stimulates premature termination (attenuation) of transcription about 30 bases upstream from the start of the first structural gene of the S10 operon. The attenuation appears to be independent of the regulation of translation of the operon. We suggest that attenuation of transcription plays a primary role in the autogenous regulation of the S10 operon.

A previously unidentified gene in the spc operon of Escherichia coli K12 specifies a component of the protein export machinery

The gene prlA codes for a factor that appears to function in the export of proteins in Escherichia coli. This conclusion is based on the finding that mutations altering the prlA gene product restore export of envelope proteins with defective signal sequences. Previous results showed that the prlA gene lies in an operon (spc) known to code for ten different ribosomal proteins. Our studies show that the prlA gene lies promoter-distal to the last known ribosomal protein gene in this operon. Evidence from gene fusions constructed in vitro suggests that prlA codes for a protein containing at least 300 amino acids. Thus a heretofore unidentified protein specified by a gene within the spc operon appears to be a component of the cellular protein export machinery.

An amber mutation in the gene encoding the beta' subunit of Escherichia coli RNA polymerase

An Escherichia coli strain carrying an amber mutation (UAG) in rpoC, the gene encoding the beta prime subunit of RNA polymerase, was isolated after mutagenesis with nitrosoguanidine. The mutation was moved into an unmutagenized strain carrying the supD43,74 allele, which encodes a temperature-sensitive su1 amber suppressor, and sue alleles, which enhance the efficiency of the suppressor. In this background, beta prime is not synthesized at high temperature. Suppression of the mutation by the non-temperature-sensitive amber suppressor su1+ yields a protein which is functional at all temperatures examined (30, 37, and 42 degrees C).

Isolation of a recombinant lambda phage carrying nusA and surrounding region of the Escherichia coli K-12 chromosome

A recombinant bacteriophage lambda, lambda argG-6, has been isolated which carries the argG gene and neighbouring loci on an EcoRI-generated 15.5 Kb DNA fragment from the Escherichia coli chromosome. The locations of the argG, nusA and pnp genes on the 15.5 Kb DNA fragment have been determined. In the case of nusA, a Tn5 insertion and sub-cloning of restriction fragments were used to locate the gene. The gene products of nusA and pnp have been identified on one- and two-dimensional polyacrylamide gels. The clockwise gene order was found to be argG-nusA-pnp.

In vitro construction of the tufB-lacZ fusion: analysis of the regulatory mechanism of tufB promoter

To investigate the regulatory mechanism of the tufB operon, we have constructed plasmids in which the lac structural genes have been fused to the regulatory region and the 5'-coding sequence of the tufB gene. The fusion was performed by incorporating the 6.6 kb EcoRI-HpaI fragment of plasmid pTUB1, which carried the tufB gene (Miyajima et al. 1979), into the EcoRI and SmaI sites of pMC1403 lac fusion vector (Casadaban et al. 1980). This gene fusion resulted in the production of a hybrid protein consisting of the N-terminal portion (12 amino acid residues) of EF-TuB and the enzymatically active C-terminal half of beta-galactosidase. Bacteria harboring the recombinant plasmid showed a strong Lac+ phenotype. In such a fusion, the lac gene expression was under the control of the tufB promoter. This was evidenced by the following observations; (i) the tufB-lacZ hybrid protein was synthesized constitutively; (ii) its production augmented in parallel with the increase in growth rate; and (iii) on carbon-source upshift, the hybrid protein was produced at a rate 2.5-fold higher than that of the mass increase. Several derivatives of this recombinant plasmid harboring deletions and/or inversions in the tufB regulatory region have been constructed and their properties are described.

Ribosomal protein S4 acts in trans as a translational repressor to regulate expression of the alpha operon in Escherichia coli

Ribosomal protein (r-protein) S4 is the translational repressor which regulates the synthesis rates of r-proteins whose genes are in the alpha operon: r-proteins S13, S11, S4, and L17. In a strain having a mutation in the gene for r-protein S4 (rpsD), the mutant S4 fails to regulate expression of the alpha operon, resulting in specific and significant overproduction of r-proteins S13, S11, and S4. This confirms and extends similar observations made with rpsD mutants (M. O. Olsson and L. A. Isaksson, Mol. Gen. Genet. 169:271-278, 1979) before post-transcriptional regulation of r-protein synthesis was proposed and is consistent with the established regulatory role of r-protein S4. The rpsD mutant has been used to study the question of whether regulatory r-proteins function in trans or strictly in cis as translational repressors. The mutant strain was lysogenized with one or two specialized transducing phages carrying a wild-type S4 gene to obtain strains which were diploid or triploid with respect to the alpha operon. The wild-type and mutant forms of S4 were separated by two-dimensional polyacrylamide gel electrophoresis, which allowed accurate measurement of the relative contributions of r-proteins from different alpha operons within a single cell. We found that expression of r-proteins from the chromosomal alpha operon containing the rpsD allele was reduced when the wild-type S4 was present, with the effect being greater in the triploid strain than in the diploid strain. We conclude that the wild-type S4 acts in trans as a translational repressor to regulate expression from the chromosomal alpha operon.

Evidence for an internal promoter preceding tufA in the str operon of Escherichia coli

We constructed plasmids carrying tufA from which the major promoter for the rpsL-rpsG-fus-tufA operon (also called the str operon) had been removed. These plasmids continued to express tufA, as judged by the ability to complement mocimycin resistance and by electrophoretic analysis of synthesized proteins. Tn5 transpositions into fus, the gene for elongation factor G, which lies immediately on the 5' side of tufA, failed to obstruct the expression of tufA. The subcloning of a 2,000-base-pair PstI-SmaI DNA fragment (containing the intercistronic region between tufA and fus, the distal portion of fus, and the proximal portion of tufA) next to promoterless tetracycline resistance genes (tet) yielded a plasmid that was capable of bestowing resistance to 12 microgram of tetracycline per ml. The removal of an EcoRI fragment that lies within fus destroyed the ability of the 2,000-base-pair PstI-SmaI fragment to promote the transcription of tet. These data indicate that, in addition to the operon's major promoter rpsLp, there is an internal promoter, tufAp, which can be used for the transcription of tufA, tufAp probably lies within fus, about 50 base pairs upstream from its 3' end and 120 base pairs from the start codon of tufA. The relative activities of tufB and of tufA-from-tufAp were estimated by a comparison of beta-galactosidase activities of almost identical EF-Tu-beta-galactosidase protein fusions; they were approximately equal.

Rates of growth, ribosome synthesis and elongation factor synthesis in a tufA defective strain of E. coli

A tufA defective strain of E. coli was isolated which by a single deletion event acquired a tufA-lacZ fusion gene and lost the normal functional tufA gene (see accompanying paper). A correlation between the growth rate of protein synthesis was decreased to about 50% in the tufA defective strain whereas the number of EF-Tu molecules per ribosome was about 80% compared to a normal strain. The results indicate that tufB gene expression was preferentially stimulated in the tufA defective strain but the increased EF-TuB synthesis was not sufficient to make up for the loss of normal EF-TuA synthesis. Introduction of a plasmid that carries a complete tufA gene and the preceeding fusA gene but not the str-promotor into the tufA defective strain did not alleviate the slow growth or low rate of EF-Tu synthesis showing that the high rate of EF-TuA synthesis compared to the other proteins in the str operon is not augmented by a strong second promotor for the tufA gene. The tufA-lacZ fusion which takes the place of the normal tufA gene was expressed at a high rate and the beta-galactosidase activity increased with the growth rate as expected.

Construction and characterization of a tufA-lacZ fusion coding for an E. coli EF-Tu-beta-galactosidase chimeric protein

A new phage lambda cloning vector was constructed that has a single EcoRI site upstream from weakly expressed lacI-Z gene isolated by Müller-Hill and Kania (1974). An EcoRI fragment containing the complete tufA gene of E. coli was cloned on the vector and the recombinant phage was crossed into the str operon that has tufA as its last gene. Subsequent selection gave rise to a tufA-lacZ fusion that codes for a chimeric peptide. The fused peptide has a molecular weight of 148,000 and contains 40% of the N-terminal of EF-Tu followed by part of the lac repressor-beta-galactosidase fusion. The specific activity of the fused peptide is about half of the activity of normal beta-galactosidase.

Duplication of the tuf gene, which encodes peptide chain elongation factor Tu, is widespread in Gram-negative bacteria

The tuf gene which encodes peptide chain elongation factor Tu was found to be duplicated in nine enteric and four nonenteric gram-negative bacteria, but present only in one copy in two gram-positive genera. In two of the nonenteric gram-negative genera, Pseudomonas and Caulobacter, the duplicate tuf genes were found to be very close together on the chromosome, which contrasts with the situation in Escherichia coli, where they are more than 660 kilobases apart.

The conservation of DNA sequences over very long periods of evolutionary time. Evidence against intergeneric chromosomal transfer as an explanation for the presence of Escherichia coli tuf gene sequences in taxonomically-unrelated prokaryotes

In the present study we tried to determine whether the presence of DNA sequences homologous to the Escherichia coli tuf gene (encodes peptide chain elongation factor Tu) in many taxonomically-unrelated prokaryotes is due to selective pressure for these sequences or due to the transfer of chromosomal material subsequent to the divergence of the genera from their progenitors. We found that the degree of sequence homology to the DNA immediately adjacent to the E. coli tuf A gene is either nonexistent or much less than that found for the tuf gene. Furthermore, the tuf-homologous sequences present in one prokaryote were found to be in large part the same as or a subset of those present in others. That is, various prokaryotes share a common subset of tuf-homologous sequences. These findings suggest that strong selective pressure and not recent intergeneric chromosomal transfer is responsible for the ubiquitous presence of certain tuf-homologous sequences. Because the genetic code is degenerate, DNA sequence need not be conserved to conserve protein sequence. Therefore, if the only function of these sequences is to encode protein, their persistence must mean that in some instances codon sequence is selected for.

Regulation of the S10 ribosomal protein operon in E. coli: nucleotide sequence at the start of the operon

We have determined the DNA sequence of a 1250 base pair segment of the Escherichia coli chromosome that carries the promoter for the S10 ribosomal protein operon, the S10 gene and part of the L3 gene. A DNA fragment carrying the putative S10 promoter was cloned into the plasmid mini-Col E1, which contains a transcription termination signal close to the single Hind II site. Cells harboring the hybrid plasmid produced a relatively stable hybrid mRNA with the expected sequence, demonstrating that the promoter functions in vivo. Comparison of the mRNA sequence around the start of the S10 coding region, the presumed target site for L4 repressor protein, with the known binding site for L4 on 23S rRNA revealed the presence of sequence homologies. This supports the model of the translational feedback regulation of the S10 operon by L4.

Regulation of the synthesis of E. coli elongation factor Tu

Rapidly growing E. coli with two active genes (tufA, tufB) for elongation factor (EF) Tu contains three times as much EF-Tu (tuf) mRNA as EF-G (fus) mRNA on a molar basis, but about seven times as much EF-Tu as EF-G or ribosomes. The concentration and translational efficiency of fus (EF-G) mRNA is about that for ribosomal protein mRNAs. The high molar concentration of EF-Tu relative to EF-G or ribosomes is achieved in part by translating tuf mRNA more efficiently than these other mRNAs. In a tufA+ tufB-: : Mu strain, the tuf:fus mRNA ratio is 1, but the concentration of EF-Tu and tuf mRNA is the same as in the wild-type strain. Thus cells with only an active tufA gene increase the concentration but not the translational efficiency of tuf mRNA. In such cells the concentration of fus mRNA is almost three times that in the wild-type strain. Because the tufA gene is distal to but cotranscribed with the fus gene as part of the four gene str operon, the wild-type concentration of tuf mRNA in these tufB- cells must be produced by increasing the concentration of transcript corresponding to the entire str operon. Thus transcription of the tufA gene can only proceed from the str promoter. Extracts of the tufB- cells contain tuf transcripts that correspond not only in size to the entire 4.5 kb str operon, but also to the size (approximately 1 kb) of a tuf gene. Our evidence suggests that this 1 kb tuf transcript is derived by posttranscriptional modification of the primary str operon transcript and that this modification could in part explain the high translational efficiency of tuf mRNA.

Chemistry and biology of E. coli ribosomal protein L12

E. coli ribosomal protein L12, because of its unique features, has been studied in more detail than perhaps any of the other ribosomal proteins. Unlike the other ribosomal proteins that are generally present in stoichiometric amounts, there are four copies of L12 per ribosome, some of which are acetylated on the N-terminal serine. The acetylated species, referred to as L7, has not been shown, as yet, to possess any different biological activity than L12. A specific enzyme that acetylates L12 to form L7, using acetyl-CoA as the acetyl donor, has been purified from E. coli extracts. L12 is also unique in that it does not contain cysteine, tryptophan, histidine, or tyrosine, is very acidic (pI: 4.85) and has a high content of ordered secondary structure (approximately 50%). The protein is normally found in solution as a dimer and also forms a tight complex with ribosomal protein L10. There are three methionine residues in L12, located in the N-terminal region of the protein, one or more of which are essential for biological activity. Oxidation of the methionines to methionine sulfoxide prevents dimer formation and inactivates the protein. The four copies of L12 are located in the crest region(s) of the 50S ribosomal subunit. There is good evidence that the soluble factors, such as IF-2, EF-Tu, EF-G and RF, interact with L12 on the ribosome during the process of protein synthesis. This interaction is essential for the proper functioning of each of the factors and for GTP hydrolysis associated with the individual partial reactions of protein synthesis. The L12 gene is located on an operon that contains the genes for L10 and beta beta' subunits of RNA polymerase at about 88 min on the bacterial chromosome. DNA-directed in vitro systems have been used to study the unique regulation of the expression of these genes. Autogenous regulation, translational control, and transcription attenuation are regulatory mechanisms that function to control the synthesis of these proteins.

The nucleotide sequence of the cloned tufA gene of Escherichia coli

The 4 kb (8.5 % lambda units) EcoRI fragment harboring the tufA gene of Escherichia coli was cloned using plasmid pTUA1 (Shibuya et al., 1979) and its structure was analyzed. The nucleotide sequence of about 1500 base pairs, covering the C-terminal portion of elongation factor EF-G (fus gene), the intercistronic region between fus and tufA, the entire structural gene for tufA with the GUG initiation and UAA termination codons, and the 3' flanking region of tufA, was determined. Comparison of the tufA nucleotide sequence with the tufB sequence (An and Friesen, 1980) and the known amino acid sequence of EF-Tu (Arai et al., 1980) revealed that the products of genes tufA and tufB are identical except for one amino acid at the C-terminal, i.e., glycine for tufA and serine for tufB. Nucleotide differences between tufA and tufB were found at 13 positions. Among them, one in the initiation codon and the other one in the C-terminal amino acid codon had replacements at the first letter of the codons. The other eleven changes were in the third codon positions, which did not affect the amino acid coding. The pattern of codon usage in tufA and tufB is highly nonrandom, and remarkably similar to that in ribosomal protein genes, with the codons for the most abundant species of isoaccepting tRNAs being preferentially utilized (Post et al., 1979; Post and Nomura, 1980).

E. coli ribosomal protein L4 is a feedback regulatory protein

We studied the synthesis of ribosomal proteins encoded by the S10 operon, an eleven gene operon from the str-spc region of the E. coli chromosome, using a lambda fus3 DNA-directed, in vitro protein synthesizing system. Addition of ribosomal protein L4 (1 microM) to in vitro protein synthesis reactions caused selective inhibition of synthesis of the promoter-proximal proteins of the S10 operon, S10, L3, L4, L23 and possibly L2. Proteins of the S10 operon other than L4 did not cause selective inhibition of protein synthesis. Autoregulatory ribosomal proteins previously identified from other operons, L1, S4 and S8, did not inhibit protein synthesis from the S10 operon; nor did L4 cause significant inhibition of protein synthesis from operons other than the S10 operon. As with L1, S4 and S8, L4 inhibits gene expression at the level of translation.

Deletion mapping and heterogenote analysis of a mutation responsible for osmosis-sensitive growth, spectinomycin resistance, and alteration of cytoplasmic membrane in Escherichia coli

Lambda transducing phages carrying Escherichia coli deoxyribonucleic acid of various lengths from the aroE-rpsL region were lysogenized into the F'3 plasmid and were used for heterogenote analysis of YM101, a sucrose-dependent, spectinomycin-resistant mutant of E. coli. Three characteristics of the mutant strain, resistance to spectinomycin, sucrose dependence of growth, and lack of I-19 protein in the cytoplasmic membrane, were shown to be the result of a mutation in a region designated delta 53-spcl. This region extends over 3.6-kilobase pairs and is located within a cluster of ribosomal genes. The mutation is recessive to the wild-type allele.

Polarity of amber mutations in ribosomal protein genes of Escherichia coli

Two amber mutations have been mapped inside the spcA-strA region (now called rpsE-rpsL) on the bacterial genome. Derivatives of the transducing phage lambda fus3 carrying each mutation were constructed and assayed in ultraviolet-irradiated bacteria to identify the mutated genes and measure the polarity of the mutations. The data indicated that both mutations, 3162(Am) and 3161(Am), affect genes coding for ribosomal proteins: rplC (L3) and rpsN (S14), respectively. It was shown also that each mutation exerts, inside of its respective operon (S10 and spc units), a relatively strong polar effect on genes distal to the mutated locus.

Isolation and characterization of stable hybrid mRNA molecules transcribed from ribosomal protein promoters in E. coli

The promoters from the str and spc operons of ribosomal proteins from E. coli were inserted into the Hind II cleavage site of mini-Col E1 (pVH51) plasmid. For both promoters, strains with the hybrid plasmid accumulated a small RNA species not present in strains carrying the vector. These RNAs were analyzed by RNA sequencing techniques and compared to DNA sequences. In both cases, synthesis of the new RNA species is initiated by the cloned r protein promoter at the site predicted by previous in vitro experiments. The RNAs extend across the Hind II site used for cloning and terminate specifically in the vector sequences. The termination site was localized to six consecutive thymine nucleotides preceded by a sequence with dyad symmetry. We found that the RNA from the str promoter was 205 (+/- 3) nucleotides long and that from the spc promoter was 177 (+/- 3) nucleotides long. These "hybrid mRNAs" are much more stable than ordinary mRNA. The str hybrid mRNA has a half-life of about 8 min, and the spc hybrid mRNA has a half-life of about 18 min at 37 degrees C. These hybrid mRNAs provide an in vivo system with which to examine directly the discrete transcription products from ribosomal protein promoters, and to study promoter function and mRNA metabolism in vivo.

Expression of ribosomal protein genes cloned in a hybrid plasmid in Escherichia coli: gene dosage effects on synthesis of ribosomal proteins and ribosomal protein messenger ribonucleic acid

Using ColE1-TnA hybrid plasmid RSF2124 as the cloning vector, we constructed a hybrid plasmid, pNO1001, which carried seven ribosomal protein (r-protein) genes in the spc operon together with their promoter. The plasmid also carried three r-protein genes which precede the spc operon, but did not carry the bacterial promoter for these genes. Expression of r-protein genes carried by pNO1001 was studied by measuring messenger ribonucleic acid and r-protein synthesis in cells carrying the plasmid. It was found that the messenger ribonucleic acid for all the promoter-distal r-protein genes was synthesized in large excess relative to messenger ribonucleic acid from other chromosomal r-protein genes which are not carried by the plasmid. However, only the two promoter-proximal r-proteins, L14 and L24, were markedly overproduced. The absence of large gene dosage effects on the synthesis of other distal proteins appeared to be due, at least in part, to preferential inactivation and/or degradation of the distal message which codes for these proteins; in addition, some preferential inhibition of translation of the distal message might also have been involved. Overproduced L14 and L24 were found to be degraded in recA+ strains at both 30 and 42 degrees C; in recA strains, the degradation took place at 42 degrees C but was very slow or absent at 30 degrees C. The recA strains carrying pNO1001 failed to form colonies at 30 degrees C, presumably because of overaccumulation of r-proteins. The results suggest that degradation of excess r-proteins is an important physiological process.

Chloramphenicol resistance mutation in Escherichia coli which maps in the major ribosomal protein gene cluster

Localized mutagenesis and selection for streptomycin resistance were utilized to isolate a chloramphenicol resistance mutation in Escherichia coli K-12 linked to the strA (rpsL) locus. Bacteriophage P1 transduction verified the map position of the new resistance mutation at 72 min, placing it within a dense cluster of ribosomal protein genes. The map position differs from that of known cmlA and cmlB mutations, which map at 18 and 21 min, respectively. Ribosomes prepared from chloramphenicol-resistant and -sensitive isogenic transductants were analyzed in vitro for activity in formation of N-formylmethionyl-puromycin, polyphenylalanine, and polylysine in the presence of inhibitory concentrations of chloramphenicol. Comparisons were also made of 14C-chloramphenicol binding to 70S ribosomes and of the two-dimensional polyacrylamide gel electrophoresis pattern of ribosomal proteins from each strain. There was no detectable difference between ribosomes from sensitive and resistant strains as measured by these assays. Enzymatic modification by chloramphenicol acetyltransferase is not responsible for the observed phenotype.

Cloning of an EcoRI fragment carrying E. coli tufA gene

EcoRI fragments of the transducing phage lambda fus3 DNA have been linked to the ColEl derivative plasmid RSF2124 (ColEl-Apr) DNA using bacteriophage T4 ligase. Among the plasmids formed, one designated pTUAl was found to contain the E. coli tufA gene. The proof for the presence of tufA gene in pTUAl is based on the following observations: (1) ability of pTUAl DNA and is EcoRI fragments to direct synthesis of EF-Tu in a cell-free protein synthesizing system; and (2) RNA . DNA hybridization of RNA transcribed from phage lambda rifd18 carrying tufB with DNA from pTUAl.

Organization of genes for transcription and translation in the rif region of the Escherichia coli chromosome

The lambdarifd18 transducing phage is known to carry several genes for components of transcriptional and translational machineries; these genes are clustered in the rif region at 88 min on the Escherichia coli genetic map. They include a set of genes for rRNA's (rrnB), a gene for spacer tRNA, tRNA2Glu (tgtB), one of the two genes for EF-Tu (tufB), genes for four ribosomal proteins (rplK, A, J, and L), genes for the beta and beta' subunits of RNA polymerase (rpoB and rpoC), and genes for three tRNA's (tyrU, gluT, and thrT). An additional tRNA gene (subsequently identified as thrU by Landy and his co-workers) and a gene for a protein (protein U) with unknown functions were found to be carried by lambdarif d18. We analyzed the organization of these genes by using various deletion and hybrid phages derived from lambdarif d18 and lambdarif d12, a phage related to lambdarif d18. The expression of various genes was examined in UV-irradiated cells infected with these transducing phages. Two main conclusions were obtained. First, the four tRNA genes are not cotranscribed with the genes in rrnB, even though these tRNA genes are located close to the distal end of rrnB. Second, the four ribosomal protein genes are organized into two separate transcriptional units; rplK and A are in one unit and rplJ and L are in the second unit. The first group of genes was shown to have a promoter separate from that for tufB or protein U. The second group of genes shares the promoter with rpoB and C, as described in a separate paper (M. Yamamoto and M. Nomura, Proc. Natl. Acad. Sci. U.S.A., 75:3891--3895). These and other results described in this paper show that the genes are organized in the following order: promoter, genes in rrnB; promoter, thrU, tyrU, (promoter?) glyT, thrT; (promoter?) tufB; promoter, a gene for protein U; promoter, rplK, rplA; promoter, rplJ, rplL, rpoB, rpoC.