Identification of a gene for the alpha-subunit of RNA polymerase at the str-spc region of the Escherichia coli chromosome

Mutations in AcrR and RNA Polymerase Confer High-Level Resistance to Psoralen-UVA Irradiation

DNA interstrand cross-links, such as those formed by psoralen-UVA irradiation, are highly toxic lesions in both humans and bacteria, with a single lesion being lethal in Escherichia coli. Despite the lack of effective repair, human cancers and bacteria can develop resistance to cross-linking treatments, although the mechanisms of resistance remain poorly defined. Here, we subjected E. coli to repeated psoralen-UVA exposure to isolate three independently derived strains that were >10,000-fold more resistant to this treatment than the parental strain. Analysis of these strains identified gain-of-function mutations in the transcriptional regulator AcrR and the alpha subunit of RNA polymerase that together could account for the resistance of these strains. Resistance conferred by the AcrR mutation is mediated at least in part through the regulation of the AcrAB-TolC efflux pump. Resistance via mutations in the alpha subunit of RNA polymerase occurs through a still-uncharacterized mechanism that has an additive effect with mutations in AcrR. Both acrR and rpoA mutations reduced cross-link formation in vivo. We discuss potential mechanisms in relation to the ability to repair and survive interstrand DNA cross-links. IMPORTANCE Psoralen DNA interstrand cross-links are highly toxic lesions with antimicrobial and anticancer properties. Despite the lack of effective mechanisms for repair, cells can become resistant to cross-linking agents through mechanisms that remain poorly defined. We derived resistant mutants and identified that two gain-of-function mutations in AcrR and the alpha subunit of RNA polymerase confer high levels of resistance to E. coli treated with psoralen-UVA. Resistance conferred by AcrR mutations occurs through regulation of the AcrAB-TolC efflux pump, has an additive effect with RNA polymerase mutations, acts by reducing the formation of cross-links in vivo, and reveals a novel mechanism by which these environmentally and clinically important agents are processed by the cell.

Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions

Codon-tRNA coevolution to maximize protein production has been, until recently, the dominant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two predictions of this hypothesis are 1) selection is weak; and 2) similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent) sites in the highly expressed Escherichia coli ribosomal protein gene rplQ from the wild type to a less-preferred alternative. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked leucine codons and an AAA to AAG mutation being introduced at two closely linked lysine codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a valine codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the araA gene as a selectively neutral phenotypic marker to distinguish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of |s| > 0.02, which is contradictory to the prediction that selection will be weak. The two leucine mutations had significantly different fitness effects, as did the two lysine mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness values, suggesting that negative synergistic epistasis acts on the combination allele.

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.

A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase

A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min. on the bacterial chromosome. The rate of RNA synthesis in vivo and the accumulation of ribosomal RNA were significantly reduced in the mutant at 44 degrees C. The thermostability at 44 degrees C of the purified holoenzyme from mutant cells was about 20% of that of the normal enzyme. Assays with T7 DNA as a template showed that the fraction of active enzyme competent for transcription was reduced as a function of assay temperature but that initiation and elongation were not significantly affected by the alpha mutation. A major effect on the fidelity of transcription was observed with the mutant enzyme, with misincorporation on two different templates stimulated about 4 fold at 37 degrees C. The role of the alpha dimer in the structure and function of RNA polymerase is discussed.

Insertional mutagenesis of a plasmid-borne Escherichia coli rpoB gene reveals alterations that inhibit beta-subunit assembly into RNA polymerase

A plasmid was constructed that overproduces the Escherichia coli RNA polymerase beta subunit from a lac promoter-rpoB fusion. The overproduced, plasmid-encoded beta subunit assembled into functional RNA polymerase that supplied greater than 90% of the transcriptional capacity of the cells. Excess beta subunit segregated into insoluble inclusion bodies and was not deleterious to cell growth. By insertion of a XhoI linker sequence (CTCGAG) and accompanying deletion of variable amounts of rpoB sequences, 13 structural alterations were isolated in the first and last thirds of the plasmid-borne rpoB gene. Twelve of these alterations appeared to reduce or prevent assembly of plasmid-encoded beta subunit into RNA polymerase. One alteration had no discernible effect on assembly or function of the beta subunit; eight others appeared to inhibit assembly but still produced detectable transcriptional activity. Three of these nine alterations produced beta-subunit polypeptides that inhibited cell growth at 32 degrees C, even though they were present in less than 50% of the cell RNA polymerase. When assembled into RNA polymerase, these three altered beta subunits apparently affected essential RNA polymerase functions. Four of the recovered alterations appeared to inhibit completely or almost completely assembly of the beta subunit into RNA polymerase. The results are consistent with a hypothesis that sequences in the first third of the beta-subunit polypeptide are especially important for proper folding and assembly of the beta subunit.

Role of the 5' upstream sequence and tandem promoters in regulation of the rpsU-dnaG-rpoD macromolecular synthesis operon

Bal31 exonuclease deletion analysis and transposon Tn5 mutagenesis of the 5' regulatory region of the rpsU-dnaG-rpoD macromolecular synthesis operon fused to the chloramphenicol acetyltransferase gene (pGLR301) demonstrated that sequences 5' to the operon promoters were not involved in operon transcriptional regulation and that the three tandem promoters P1, P2, and P3 were functionally independent. P2 was the strongest promoter, and P3 was the weakest. P1, P2, and P3 acting in combination appeared to be stronger than the individual promoters.

Developmental expression of three proteins from the first gene of the RNA polymerase sigma 43 operon of Bacillus subtilis

The first gene of the Bacillus subtilis RNA polymerase sigma 43 operon, P23, has a protein-coding capacity of 23,000 daltons. Sequence analysis revealed three potential translational initiation sites within the same reading frame, which could encode proteins of 23,000 (P23), 19,000 (P19), and 9,000 (P9) daltons, respectively. An internal promoter (P3), which is expressed only during the sporulation stage, is located between the second and the third translational start sites. By protein fusion to the Escherichia coli beta-galactosidase gene, we showed that all three translational initiation sites of the P23 gene are used in vivo in both E. coli and B. subtilis, and regulation for differential expression of the three proteins during the development of B. subtilis is coupled to the transcriptional promoter switching mechanism. The physiological function of these multiple gene products is unknown and is currently under investigation.

The genes encoding chloroplast ribosomal proteins S7 and S12 are located in the inverted repeat of Spirodela oligorhiza chloroplast DNA

We have used a variety of methods to localize the genes for ribosomal proteins S7 and S12 on Spirodela chloroplast DNA. Heterologous hybridization with a rps12 gene specific probe from Euglena has revealed the presence of rps12 homologous sequences within the inverted repeat of Spirodela chloroplast DNA on the fragment BamHI-V. In the partial nucleotide sequence of this fragment, two regions of amino acid sequence homology to Euglena S12 can be identified, separated from each other by a 542 bp intron with conserved boundary sequences. As was found for Nicotiana S12, the Spirodela S12 coding regions are for 85 amino acids homologous (79%) to E. coli S12 (starting from residue 38 to the C-terminus). Likewise, we are unable to identify the 37 5' terminal codons of rps12 in Spirodela. The functionality of the Spirodela rps12 sequence is discussed. The rps7 gene is located adjacent to rps12. Chloroplast ribosomal protein C-S11 (homologous to S7) has been detected by immunoprecipitation with both a polyspecific anti 30S serum and an anti C-S11 serum, among the in vitro translation products of mRNAs selected by Spirodela chloroplast DNA fragments BamHI-V and BamHI-P. Since in a DNA dependent E. coli cell free system, only BamHI-V appears to be capable of synthesis of C-S11, it is concluded that rps7 is located entirely within BamHI-V and is transcribed into a mRNA which extends into BamHI-P. As determined by Northern hybridization experiments, rps7 is cotranscribed with rps12; a stable transcript of approx. 1100 b is detected in total cellular Spirodela RNA with either rps12 and rps7 gene specific probes. The rps12 probe additionally detects an approx. 600 b transcript, which presumably corresponds to the excised rps12 intron RNA. Finally we have examined the expression of both rps7 and rps12 during light induced chloroplast development by Northern blotting and by immunoblotting. It is shown, that the steady-state levels of neither chloroplast ribosomal protein transcripts, nor those of the chloroplast ribosomal proteins itself, change significantly during the greening process.

Chemical and functional characterization of an altered form of ribosomal protein S4 derived from a strain of E. coli defective in auto-regulation of the alpha operon

We have isolated a mutant form of Escherichia coli ribosomal protein S4. This mutant is temperature sensitive and apparently fails to autogenously regulate the gene products of the alpha operon, which consists of the genes for proteins S13, S11, S4, L17, and the alpha subunit of RNA polymerase (1). We have shown that this mutation results in the production of an S4 protein with a molecular weight approximately 4,000 daltons less than the wild-type protein. Our chemical analyses demonstrate that the mutant protein is missing its C-terminal section consisting of residues 170-203. However, our studies to determine the capacity of this mutant protein to bind 16S RNA show that this protein is unimpaired in RNA binding function. This observation suggests that the functional domain of protein S4 responsible for translational regulation of the S4 gene products requires more of the protein than the 16S RNA binding domain.

Growth rate-dependent regulation of RNA polymerase synthesis in Escherichia coli

The rate of synthesis of the beta and beta' subunits of RNA polymerase relative to the rate of synthesis of total protein was found to remain constant with increasing steady state growth rate. This is in contrast to the relative synthesis rates of ribosomal proteins which are known to increase with growth rate. Yet the ratio of the rate of transcription of the ribosomal protein (rplJL) and RNA polymerase (rpoBC) domains of the rplKAJLrpoBC gene cluster was found to be invariant. Fusions to lacZ were used to relate the rate of transcription of the rplKAJL genes to the rate of synthesis of total protein. No change was seen at growth rates above 0.8 doublings per hour. This indicates that the growth rate-dependent expression of these ribosomal proteins is regulated at the post-transcriptional level. However because both the relative rate of transcription of rpoBC and rate of synthesis of beta and beta' were found to remain invariant over this growth range it suggests the expression of these RNA polymerase subunits is regulated at the transcriptional level.

Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli

In Escherichia coli some 19 transcription units encoding the 52 ribosomal proteins are scattered throughout the genome. One of the units, the alpha operon, encodes genes for the ribosomal proteins S13, S11, S4 and L17 as well as the alpha subunit of RNA polymerase. We report here the complete 3.0 kb nucleotide sequence of the alpha operon. In addition, we have determined by S1 nuclease mapping the site of transcription termination in this operon.

Salmonella typhimurium rpoB and rpoC genes cloned on lambda phages

Salmonella typhimurium rpoB and rpoC genes, coding for the RNA polymerase subunits beta and beta', respectively, were isolated on lambda phages. Like their E. coli counterparts the two genes are closely linked and probably share a common promoter. The distribution of the target sites for several restriction enzymes, however, shows considerable divergence from the E. coli pattern.

Evidence for clustering of RNA polymerase and ribosomal protein genes in six species of Enterobacteria

32P-labelled DNA fragments from the E. coli beta operon were used as hybridisation probes for homologous DNA sequences in chromosomal digests of six species of Enterobacteria. In all species the hybridisation pattern suggested clustering of the genes comprising the beta operon.

Relative activities of the transcriptional regulatory sites in the rplKAJLrpoBC gene cluster of Escherichia coli

The pattern of transcription of the rplKAJLrpoBC gene cluster of Escherichia coli appears to be complex. At least four different promoters and a transcriptional attenuator have been identified. To compare the relative effect of each of the putative promoters and the attenuator on transcription of these genes, we fused these regulatory sites to lacZ. These transcriptional fusions were constructed on lambda transducing phages so a single copy of each could be stably integrated into the chromosome. The level of beta-galactosidase in a lysogen of each phage reflects the activity of the transcriptional regulatory site. We find that the promoters preceding rplK (rplKp) and rplJ (rplJp) are indeed the major promoters of this gene cluster. The minor promoter before rplL (rplLp) is much weaker and contributes little to the transcription of the downstream genes. Under these conditions, we find no evidence of a promoter (rpoBp) in the rplL-rpoB intercistronic region. The attenuator (atn) terminates ca. 70% of the transcripts initiated at the promoters preceding it. Although we cannot rule out that some transcripts from rplKp may read through into rplJLrpoBC, we find that rplJp alone is sufficient for high-level expression of these genes.

Isolation and physical mapping of the gene encoding the major sigma factor of Bacillus subtilis RNA polymerase

At least four sigma factors separately bind the Bacillus subtilis RNA polymerase core (beta beta' alpha 2), each conferring a different promoter specificity on the holoenzyme in vitro. Using the Broome-Gilbert immunological screening, we isolated recombinant lambda phages that carry rpoD, the gene for the most abundant sigma factor, sigma 55. These phages encode a 55,000-dalton protein whose size, immunological properties, and peptide map identify it as sigma 55. All the phages have in common two adjacent 3.5-kilobase EcoRI fragments from the B. subtilis chromosome; most carry additional genomic DNA. Deletion analysis localized rpoD to a 1.6-kilobase region, suggested the direction of its transcription, and found two additional genes near rpoD, which code for proteins of 62,000 and 17,000 daltons.

A new gene in E. coli RNA synthesis

A novel spontaneous temperature sensitive mutant of Escherichia coli, which stops synthesizing stable RNA and some proteins immediately upon temperature shift from 30 degrees C to 42 degrees C, is described. Stable RNA species are not preferentially degraded in the mutant at the nonpermissive temperature. The guanine polyphosphate compounds, ppGpp (MS1) and pppGpp (MS2), are not produced at 42 degrees C. The mutant strain does not grow at 42 degrees C in either broth or defined minimal medium supplemented with any of a variety of carbon sources. The temperature sensitive mutation in this strain maps between dap A, E and pts I and defines a new locus affecting RNA synthesis in E. coli.

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).

Effects of pH and repellent tactic stimuli on protein methylation levels in Escherichia coli

Intracellular pH (pH(int)) and extracellular pH (pH(ext)) of Escherichia coli were measured at 12-s time resolution by (31)P-nuclear magnetic resonance: a sudden neutral-to-acid shift in pH(ext) (e.g., from 7.0 to 5.6) caused a transient failure of homeostasis, with pH(int) decreasing by about 0.4 unit in ca. 30 s and then returning to its original value (ca. 7.5) over a period of several minutes. Membrane proton conductance was estimated to be 20 pmol s(-1) cm(-2) pH unit(-1). Addition of the membrane-permeant weak acid benzoate at constant pH(ext) also caused a lowering of pH(int); at high concentrations it generated an inverted transmembrane pH gradient (DeltapH). The buffering capacity of the cells was estimated by such experiments to be ca. 50 mM per pH unit. Effects of pH-related stimuli on the methyl-accepting chemotaxis proteins (MCPs) were examined: the steady-state methylation of MCP I was found to decrease when pH(int) was lowered by weak acid addition or when pH(ext) was lowered. The extent of demethylation in the latter case was too great to be explained by imperfect steady-state homeostasis; a small but reproducible undershoot in methylation level correlated with the observed short-term homeostatic failure. MCP II underwent smaller and more complex changes than MCP I, in response to pH-related stimuli. The methylation level of MCP I could not, by any condition tested, be driven below a limit of ca. 15% of the control level (unstimulated cells at pH(ext) 7.0). The weak-acid concentration needed to reach that limit was dependent on pH(ext), as would be expected on the basis of DeltapH-driven concentrative effects. The potency ranking of weak acids was the same with respect to lowering pH(int), demethylating MCP I, and causing repellent behavioral responses. The data are consistent with a model whereby MCP I and hence tactic behavior are sensitive to both pH(int) and pH(ext). Evidence is presented that pH(int) may also have a direct (non-MCP-related) effect on motor function. Comparison of methyl-(3)H- and (35)S-labeled MCP I revealed that in both unstimulated and repellent-stimulated cells the major species did not carry methyl label, yet it had an electrophoretic mobility that indicated that it was more positively charged than the unmethylated form observed in methyltransferase mutants, and it was susceptible to base hydrolysis. This suggests that a substantial fraction of MCP I molecules is methylated or otherwise modified but neither exchanges methyl label nor undergoes reverse modification by repellent stimuli.

Transcriptional and post-transcriptional control of ribosomal protein and ribonucleic acid polymerase genes

A partial restriction of ribonucleic acid (RNA) polymerase activity has been used to dissociate the coordinate synthesis of ribosomal proteins and subunits of RNA polymerase and to identify transcriptional and post-transcriptional control signals which regulate the expression of these component genes. Within the beta operon [which has the genetic organization: promoter (p beta), rplJ (L10), r;lL (L7/L12), attenuator, rpoB (beta), rpoC (beta'), terminator], the restriction caused a disproportionate increase between proximal and distal gene transcriptions; the transcriptional intensities of the proximal ribosomal protein genes and the distal RNA polymerase genes were elevated about two- and fourfold, respectively. Transcription within the operon containing four ribosomal protein genes and the RNA polymerase alpha gene was also enhanced, whereas transcription within operons containing only ribosomal protein genes was virtually unaffected by the restriction. It was thus concluded that the mechanisms controlling transcription initiation or attenuation or both in operons containing RNA polymerase subunit genes are coupled to the global rate of RNA synthesis. By introducing the composite ColE1 plasmid pJC701 carrying the proximal portion of the L10 operon, including the beta subunit gene, it was possible to achieve a 10- and a 30-fold range in the transcriptional intensities of the genes specifying L10 and L7/L12 and beta, respectively. Under these conditions, the relative synthesis rates of L7/L12 and beta protein varied by less than 2-fold and by about 15-fold, respectively. These observations corroborate the existence of a post-transcriptional mechanism which severely restricts translation of excess L7/L12 and L10 ribosomal protein messenger RNA; this mechanism is probably important in maintaining the balanced synthesis of ribosome components under conditions in which their messenger RNA levels are dissociated. Furthermore, the observed reduction in the translation efficiency of beta subunit messenger RNA may be related to an inhibitory effect caused by accumulation of RNA polymerase assembly intermediates.

The gene for ribosomal protein S21, rpsU, maps close to dnaG at 66.5 min on the Escherichia coli chromosomal linkage map

A series of mutations causing alterations in ribosomal protein S21 was mapped close to dnaG, around 66.5 min on the Escherichia coli chromosomal linkage map. They cotransduced about 95% with this marker. These mutations define gene rpsU, which is very likely the structural gene for protein S21.

Autogenous and post-transcriptional regulation of RNA polymerase synthesis

The regulation of gene expression was studied, for the Escherichia coli rpoBC operon, which includes the genes, rpoB and rpoC, for the beta and beta subunits of RNA polymerase, and rplJ and rplL, for the two proteins, L10 and L7/12, of the 50S ribosome. The gene organization agrees well with the accumulated observations indicating the coordinate synthesis of RNA polymerase and ribosomes under various growth conditions for wild-type E. coli cells. On the other hand, the differential regulation of the two essential components observed under restrictive growth conditions, after addition of various drugs or with certain mutants, in particular those carrying mutations in the RNA polymerase genes, was found to take place through two novel regulation systems: The transcriptional termination at an internal attenuation site and the two autogenous and posttranscriptional controls, being specific for the two ribosomal protein genes and the two RNA polymerase subunit genes, respectively. The majority of the transcription initiated from the promoter rpoP beta terminates at an attenuator site between the promoter-proximal rplJL and the promoter-distal rpoBC genes. The frequency of the attenuation seems to control the relative level of RNA polymerase synthesis to that of ribosomes. The expression of rpoBC genes is subject to an autogenous regulation, in which both RNA polymerase holoenzyme and alpha 2 beta complex function as regulatory molecules with repressor activity. The autogenous regulation was found to operate at post-transcriptional step(s), probably at the level of translation. During the study on the regulation of RNA polymerase synthesis, we noticed that the rpoBC operon contained another autogenous regulation circuit, in which the synthesis of L10 and L7/12 was specifically repressed by the L10-L7/12 complex. Molecular mechanisms and physiological meanings of the novel regulations are discussed.

Isolation and characterization of lambda transducing phages for the E. coli genes ksgA and pdxA

Lambda phages carrying the Escherichia coli genes ksgA and pdxA were isolated from secondary site lysogens in araB. 1) The phage genomes were characterized by genetic complementation tests, restriction endonuclease digestion and electron microscopy. 2) A 6.3 kilobasepair (kb) EcoRI restriction fragment carrying both ksgA and pdxA was cloned in a lambda vector; this fragment has proven useful in further characterization of the ksgA gene (Andrésson and Davies, 1980a, b). The ksgA and pdxA genes are about 14 and 12-13 kb, respectively, counterclockwise of the arabinose operon and 1.5 and 2.5-3.5 kb clockwise of folA.

Regulation of ribonucleic acid polymerase synthesis during restriction of an Escherichia coli mutant temperature sensitive for transcription factor sigma

An Escherichia coli mutant temperature sensitive for the sigma subunit of ribonucleic acid polymerase was shifted to restrictive temperatures. In response to these restrictions the transcription of rpoBC increased markedly, and the synthesis rates of the beta and beta' subunits of ribonucleic acid polymerase increased. The ratio of the beta and beta' synthesis rates (beta/beta') decreased.

Feedback regulation of ribosomal protein gene expression in Escherichia coli

The structural genes for Escherichia coli ribosomal protein (r-protein) genes L1, S4, and S11 were inserted into a plasmid vector containing the lac operator and promoter such that the synthesis of L1, S4, and S11 was controlled by lac regulatory elements. Synthesis of L1, S4, and S11 was stimulated by addition of an inducer of the lac operon (isopropyl thiogalactoside) to exponentially growing cells. Elevated synthesis of L1 caused a specific decrease in L11 synthesis, whereas overproduction of S4 resulted in lowered synthesis of S13 and L17. Stimulation of L1 or S4 synthesis also inhibited cell growth. Overproduction of S11 did not affect synthesis of other r-proteins or alter growth. These results confirm previous in vitro studies [Yates, J. L., Arfsten, A. E. & Nomura, M. (1980) Proc. Natl. Acad. Sci. USA 77, 1837-1841] and support the hypothesis that certain r-proteins have the capacity to selectively inhibit synthesis of r-proteins whose genes are in the same operon as their own.

Structural studies of methyl-accepting chemotaxis proteins of Escherichia coli: evidence for multiple methylation sites

Two-dimensional analysis of tryptic peptides from [35S]methionine-labeled methyl-accepting chemotaxis proteins, MCP I and MCP II, demonstrates a high degree of homology between the two proteins. After the methylation sites were labeled with S-adenosyl-L-methyl-3H]methionine, peptides of three distinct migrations in each protein were found to carry a methyl group. These multiple methylations appear to be responsible in part for the observed multiple banding patterns on sodium dodecyl sulfate/polyacrylamide slab gels.

Gene expression in Escherichia coli after amino acid, purine, or pyrimidine exhaustion

Three strains of Escherichia coli B auxotrophic for leucine, guanine, or uracil were analyzed after exhaustion of the respective required nutrient from the growth medium. The pattern of transcription was analyzed by ribonucleic acid-deoxyribonucleic acid filter hybridization to specific deoxyribonucleic acid probes, and the pattern of translation was analyzed by autoradiography after the resolution of proteins on sodium dodecyl sulfate-polyacrylamide gels. The results obtained suggest the following conclusions. (i) Specific regulation of rpoBC transcription occurs at both the promoter (PL10) and the putative attenuator between rplL and rpoB. (ii) The stringent response of ribosomal protein gene expression to amino acid insufficiency is only partially mimicked by purine or pyrimidine insufficiency. (iii) Transcription initiation at PL10 decreases in response to guanine exhaustion, but in contrast increases significantly in response to uracil exhaustion. (iv) The expression of the induced lac operon is severely depressed during any of these exhaustions. These conclusions argue against simple models for regulation of ribonucleic acid polymerase production or promoter choice by the intracellular levels of its substrate nucleotides.

In vitro expression of Escherichia coli ribosomal protein genes: autogenous inhibition of translation

Escherichia coli ribosomal protein L1 (0.5 micro M) was found to inhibit the synthesis of both proteins of the L11 operon, L11 and L1, but not the synthesis of other proteins directed by lambda rifd 18 DNA. Similarly, S4 (1 micro M) selectively inhibited the synthesis of three proteins of the alpha operon, S13, S11, and S4, directed by lambda spcI DNA or a restriction enzyme fragment obtained from this DNA. S8 (3.6 micro M) also showed preferential inhibitory effects on the synthesis of some proteins encoded in the spc operon, L24 and L5 (and probably S14 and S8), directed by lambda spcl DNA or a restriction enzyme fragment carrying the genes for these proteins. The inhibitory effect of L1 was observed only with L1 and not with other proteins examined, including S4 and S8. Similarly, the effect of S4 was not observed with L1 or S8, and that of S8 was not seen with L1 or S4. Inhibition was shown to take place at the level of translation rather than transcription. Thus, at least some ribosomal proteins (L1 S4, and S8) have the ability to cause selective translational inhibition of the synthesis of certain ribosomal proteins whose genes are in the same operon as their own. These results support the hypothesis that certain free ribosomal proteins not assembled into ribosomes act as "autogenous" feedback inhibitors to regulate the synthesis of ribosomal proteins.

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.

Lambda transducing bacteriophage carrying deletions of the argCBH-rpoBC region of the Escherichia coli chromosome

Deletions in the rpoBC region have been transferred to phage lambda and characterized in detail by genetic, structural, and functional tests. We thus extend and confirm knowledge of the organization of this part of the chromosome. The new phages are useful tools for studying the genes for the bacterial transcription and translation machinery.

Isolation and characterization of transducing phage coding for sigma subunit of Escherichia coli RNA polymerase

A transducing phage has been isolated with codes for the sigma subunit of Escherichia coli RNA polymerase. Transducing phage were selected from E. coli shotgun collections of HindIII or Sac I fragments cloned into Charon 25, a new bacteriophage lambda vector that is capble of forming lyosogens at high temperature. Transduction of an E. coli strain carrying a temperature-sensitive mutation in the sigma gene was used for the selection. The positions of restriction sites for Sac I, HindIII, Xho I, Bgl II, and Kpn I in the cloned bacterial DNA segments were determined. Phage containing the HindIII fragment complement both primase (dnaG) and sigma (rpoD) whereas those containing the Sac I fragment complement only sigma. Results of analyses of the proteins made both in vivo after infection of UV-irradiated cells and in vitro in a coupled transcription/translation system suggest that a Sac I site separates the promoter for sigma from the sigma structural gene. The direction of transcription of sigma was determined to be clockwise with respect to the E. coli genetic map.

Control features within the rplJL-rpoBC transcription unit of Escherichia coli

Gene fusions constructed in vitro have been used to examine transcription regulatory signals from the operon which encodes ribosomal proteins L10 and L7/12 and the RNA polymerase beta and beta' subunits (the rplJL-rpoBC operon). Portions of this operon, which were obtained by in vitro deletions, have been placed between the ara promoter and the lacZ gene in the gene-fusion plasmid pMC81 developed by M. Casadaban and S. Cohen. The effect of the inserted DNA segment on the expression of the lacZ gene (in the presence and absence of arabinose) permits the localization of regulatory signals to discrete regions of the rplJL-rpoBC operon. An element that reduces the level of distal gene expression to one-sixth is located on a fragment which spans the rplL-rpoB intercistronic region. This strongly supports the idea that there is an attenuator in this region. The terminator for the operon is located on a fragment which spans the 3' end of the rpoC gene. The major promoter for the operon precedes the rplJ gene [Yamamoto, M. & Nomura, M. (1978) Proc. Natl. Acad. Sci. USA 75, 3891-3895 and Linn, T. & Scaife, J. (1978) Nature (London) 276, 33-37] and was not examined in this study. However, a weak promoter is observed on the fragment that spans the rplJ-rplL intercistronic region. Other regions of the operon may also contain weak promoters. The contribution of these elements to the regulation of this complex operon is discussed.

Altered chemical properties in three mutants of E. coli RNA polymerase sigma subunit

We have analyzed some chemical properties of the sigma subunit of RNA polymerase from the sigma mutants: rpoD1 (Gross et al., 1978), rpoD2 (formerly known as alt-1) (Silverstone et al., 1972; Travers et al., 1978), and rpoD800 (Gross et al., 1979). Each of the three mutants is located at about 66 min on the E. coli genetic map and exhibits an alteration in the enzymatic properties of its sigma subunit. The tryptic peptides and isoelectric focusing behavior were analyzed for mutant and wild type sigma. A single, but different altered lysine tryptic peptide was observed for each mutant. No altered arginine tryptic peptides were observed. The rpoD800 mutant sigma showed an altered isoelectric point. These studies provide chemical evidence that the sigma polypeptide in all three mutants is altered and strongly support the conclusion that the mutations are in the structural gene for sigma.

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.

Expression of RNA polymerase and ribosome component genes in Escherichia coli mutants having conditionally defective RNA polymerases

The expression of the genes coding for the beta and beta' subunits of RNA polymerase, ribosomal RNA, ribosomal proteins, and beta-galactosidase was investigated in strains carrying conditionally lethal mutations affecting either RNA polymerase core assembly or RNA polymerase enzyme activity. The mutant strain XH56 produces a temperature-sensitive beta' subunit and at 42 degrees C is defective in RNA chain initiation; consequently, little or no transcription occurs at the restrictive temperature. A partial restriction, produced by shifting the strain to 39 degrees C, resulted in a rapid fivefold increase in the transcription of the rpoB and C genes and in the synthesis of the beta- and beta'-subunit proteins for which they code. The RNA polymerase assembly-defective strains A2R7 and TS4 exhibited a 1.5- to 2-fold increase in the transcription of the rpoB and C genes and in the synthesis of beta- and beta-subunit proteins after prolonged restriction. These results demonstrate (i) that regulation of the synthesis of the beta- and beta-RNA polymerase subunits is under these conditions primarily transcriptional rather than translational, and (ii) that a stimulation of rpoB and C gene expression results from a restriction on RNA synthesis caused by either RNA polymerase inactivation or inhibition of its assembly. During restriction of the mutant strains, the transcription of the ribosome component genes exhibited patterns which were similar to transcription of the rpoB and C genes, supporting the evidence that genes coding for RNA polymerase are cotranscribed with ribosomal protein genes; transcription of the lacZ gene was observed to decrease concomitant with the stimulation of the rpoB and C genes.

Identification of a single promoter in E. coli for rplJ, rplL and rpoBC

A set of restriction fragments cloned into phage lambda vectors has allowed us to locate a site necessary for full rpoBC expression. We find that these genes for the two large subunits of RNA polymerase and the genes, rplL and rplJ, for two ribosomal proteins, form a single operon.

Genetic mapping of a putative temperature-sensitive transcription mutation in Escherichia coli K12

A putative temperature-sensitive transcription mutant described earlier (Jabbar and Jayaraman, 1976) has been genetically mapped. The locus maps at 38 min to the left of aroD. The mutation is recessive to the wild type and it affects a gene probably other than the genes coding for the alpha and beta subunits of phenylalanine tRNA synthetase and protein synthesis initiation factor IF-3 which also map in the same region.

A transducing lambda phage carrying grpE, a bacterial gene necessary for lambda DNA replication, and two ribosomal protein genes, rpsP (S16) and rplS (L19)

A grpE mutation of Escherichia coli K12, which blocks DNA replication of the phage lambda (Saito and Uchida, 1977), was mapped at 56 min on the standard genetic map. A transducing lambda phage, lambdagrpE22, carrying the wild type allele of the grpE gene was constructed in vitro. Structures of lambdagrpE22 and its viable deletion derivatives were determined by electron microscopic analyses of appropriate heteroduplexes. Proteins coded by the bacterial DNA incorporated into the transducing phages were detected by two-dimensional gel electrophoresis. The results showed that the product of the grpE gene is a weakly acidic protein of molecular weight 24,000. Structural genes for two ribosomal proteins, rplS (L19) and rpsP (S16) were also shown to be carried by lambdagrpE22.

Gene expression in Escherichia coli B/r during partial rifampicin-mediated restrictions of transcription initiation

The antibiotic rifampicin inhibits transcription initiation, but not the elongation and completion of nascent RNA transcripts. Addition of low concentrations of rifampicin only partially blocks initiation but at the same time specifically alters the general pattern of transcription in the culture. The transcription of genes specifying the beta and beta' subunits of RNA polymerase, and to a lesser extent of the genes specifying the RNA and protein components of the ribosome, was specifically stimulated relative to total transcription. In contrast, the transcription of the lactose operon was selectively reduced. These results are consistent with the ideas that the level of expression of the genes specifying the beta and beta' subunits is sensitive to the general rate of RNA synthesis in the culture, and that the expression of the beta and beta' RNA polymerase genes is related to the expression of ribosome component genes.

Contranscription of genes for RNA polymerase subunits beta and beta' with genes for ribosomal proteins in Escherichia coli

The lambdarifd18 transducing phage carries genes for RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase; EC 2.7.7.6) subunits beta and beta' (rpoB,C) and genes for four ribosomal proteins (rplK for L11, rplA for LI, rplJ for L10, and rplL for L7/L12). DNA segments of various sizes, which cover the rifd allele of the rpoB gene, were cloned into lambda vector phages. The hybrid phages were then analyzed for their ability to express the rpoB gene and neighboring ribosomal protein genes in ultraviolet-irradiated lambda-lysogenic and nonlysogenic bacterial hosts. The results show that the rpoB gene is cotranscribed with two neighboring ribosomal protein genes and that in the rpoB,C transcription unit is: promoter, rp1J, rp1L, rpoB, and rpoC.

Over-synthesis and instability of sigma protein in a merodiploid strain of Escherichia coli

We have used two different methods to study the rates of RNA polymerase subunit synthesis in haploid Escherichia coli K12, and a KLF10 rPOB, C+ merodiploid derivative, when grown in glucose-minimal medium at 37 degrees C. Our results indicate that the haploid strain produces beta, beta', alpha and sigma in the molar ratios 1.01:0.99: less than or equal to 2.90:0.26; and that all these subunits are reasonably stable during subsequent growth. The merodiploid produces alpha at the same rate as the haploid, beta and beta' at a 42% higher rate, and sigma at twice the rate. Some 40% of the newly synthesised beta and beta' is degraded within one hour; the residuum is as stable as in the haploid. Alpha is stable throughout. By contrast, sigma is subject to a marked and continuous turnover in the merodiploid. These results are discussed in terms of gene dosage and regulatory effects.