A ribosomal RNA gene, rrnC, of Escherichia coli, mapped by specialized transducing lambdadilv and lambda drbs phages

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Colocalization of centromeric and replicative functions on autonomously replicating sequences isolated from the yeast Yarrowia lipolytica

Two sequences (ARS18 and ARS68) displaying autonomous replication activity were previously cloned in the yeast Yarrowia lipolytica. The smallest fragment (1-1.3 kb) required for extrachromosomal replication of a plasmid is significantly larger in Y. lipolytica than in Saccharomyces cerevisiae. Neither autonomously replicating sequence (ARS) is homologous with known ARS or centromere (CEN) consensus sequences. They share short regions of sequence similarity with each other. These ARS fragments also contain Y. lipolytica centromeres: (i) integration of marker genes at the ARS loci results in a CEN-linked segregation of the markers, (ii) an ARS on a plasmid largely maintains sister chromatid attachment in meiosis I, and (iii) integration of these sequences at the LEU2 locus leads to chromosome breakage. Deletions performed on ARS18 show that CEN and ARS functions can be physically separated, but both are needed to establish a replicating plasmid.

An unusual correlation between ppGpp pool size and rate of ribosome synthesis during partial pyrimidine starvation of Escherichia coli

Escherichia coli was exposed to partial pyrimidine starvation by feeding a pyrBI strain orotate as the only pyrimidine source. Subsequently, differential rates of synthesis of rRNA and of a few ribosome-associated proteins as well as the pool sizes of nucleoside triphosphates and ppGpp were measured. As the orotate concentration in the medium was reduced, the growth rate decreased and the pools of pyrimidine nucleotides, particularly UTP, declined. We did not observe the normal inverse relation between concentration of ppGpp and growth rate; rather, we observed that the ppGpp pool was low at slow growth rates. Upshifts in growth rate were made by adding uracil to a culture growing slowly on orotate. Downshifts could be provoked by adding aspartate plus glutamate to a culture growing at a high concentration of orotate. Following the upshift, both the rates of synthesis of the ribosomal components and the pool of ppGpp increased rapidly, while they all decreased after the downshift. These results are discussed in relation to the role of ppGpp in the growth rate control and the stringent response.

Overproduction of DnaA protein stimulates initiation of chromosome and minichromosome replication in Escherichia coli

Increased synthesis of DnaA protein, obtained with plasmids carrying the dnaA gene controlled by the heat inducible lambda pL promoter, stimulated initiation of replication from oriC about threefold. The overinitiation was determined both as an increase in copy number of a minichromosome and as an increase in chromosomal gene dosage of oriC proximal DNA. The additional replication forks which were initiated on the chromosome did not lead to an overall increase in DNA content. DNA/DNA hybridization showed an amplification encompassing less than a few hundred kilobases on each side of oriC. Kinetic studies showed that the overinitiation occurred very rapidly after the induction, and that the initiation frequency then decreased to a near normal frequency per oriC. The results indicate that the DnaA protein is one important factor in regulation of initiation of DNA replication from oriC.

Physical analysis of deletion mutations in the ilvGEDA operon of Escherichia coli K-12

DNA-DNA hybridization of cloned segments of the Escherichia coli K-12 ilvGEDA operon to genomic blots was used to determine the physical dimensions of a series of deletion mutations of the ilvGEDA operon. The smallest mutation resulted from the deletion of approximately 200 base pairs from within ilvD, whereas the largest mutation resulted from the deletion of 17 kilobases including the rep gene. The structure of three of these mutants indicates that formation of the deletions was mediated by Tn5 (or Tn5-131) that is retained in the chromosome. This is the first observation of this type of Tn5-mediated event. Our analysis of the total acetohydroxy acid synthase activity of strains containing deletions of ilvG indicates that the truncated ilvG polypeptide of wild-type E. coli K-12 lacks enzyme activity. The small 200-base-pair deletion of ilvD confirms the presence of a strong polar site 5' to ilvA. The detailed structure of these deletions should prove useful for the investigation of other genes in this region. This genomic analysis demonstrates that the ilv restriction site map that was established previously by the analysis of recombinant bacteriophage and plasmids is identical to that on the genome.

A bacterial gene, fip, required for filamentous bacteriophage fl assembly

An Escherichia coli mutant which does not support the growth of filamentous bacteriophage fl allows phage fl DNA synthesis and gene expression in mutant cells, but progeny particles are not assembled. The mutant cells have no other obvious phenotype. On the basis of experiments with phage containing nonlethal gene I mutations and with mutant fl selected for the ability to grow on mutant bacteria, we propose an interaction between the morphogenetic function encoded by gene I of the phage and the bacterial function altered in this mutant. The bacterial mutation defines a new gene, fip (for filamentous phage production), located near 84.2 min on the E coli chromosome.

Conditional change of DNA replication control in an RNA polymerase mutant of Escherichia coli

A temperature-sensitive mutant of Escherichia coli with a temperature-dependent change in the control of initiation of DNA replication was isolated. The phenotype of the mutant was dependent on a mutation in the RNA polymerase gene rpoC. In vitro RNA polymerase activity was temperature sensitive. The mutant grew and synthesized DNA at 30 degrees C as did the wild type. After a shift to 39 degrees C, a temperature still permissive for growth, the mutant increased its origin concentration more than twofold. After a shift from 39 to 30 degrees C, initiation of DNA replication was inhibited until the normal origin concentration was reestablished.

Relative map location of the rep and rho genes of Escherichia coli

The rep gene of Escherichia coli was mapped between ilvC and rho by three-factor P1 transductional crosses and also by complementation with a set of lambda transducing phages that contain known amounts of bacterial DNA linked to ilvC. The physical distance between ilvC and rep and between rep and rho were calculated with an accuracy of +/- 0.4 kilobase to be 0 less than or equal to ilvC-rep less than or equal to 3.4 kilobases and 2.0 less than or equal to rep-rho less than or equal to 6.0 kilobases. It was shown that rho-15 is Gro+ for phage ST-1. An ilv::Tn10 mutation was located in ilvY.

Genetical and structural analysis of a group of lambda ilv and lambda rho transducing phages

Eight lambda ilv C transducing phages generated from E. coli K12 secondary site lysogens have been analysed genetically and physically. Two of them carry, in addition, the rho gene and its promotor region, but not the cya gene. The ilv O 603 mutation has been located between ilv G and ilv E. Electrophoretic analysis of the proteins synthesized by these phages in a system of UV irradiated cells allowed us to assign molecular weights of 55000 and 66000 daltons to the ilv C and the ilv D gene products, respectively, and to show that an ilv G-encoded polypeptide of 60000 daltons is made from an ilv O- but not from an ilv O+ phage. The expression of the ilv G gene is discussed in the light of the recent finding of a promoter-attenuator region lying upstream to ilv G. Finally, we have found that one of the lambda ilv phages does not have the classical structure of a transducing phage.

E coli RNA polymerase-rRNA promoter interaction and the effect of ppGpp

The interaction between RNA polymerase and the E coli r (ibosomal) RNA promoters of the rrnX and rrnE operon was studied with the filter-binding technique. Quantitative differences were observed between the rrnX and rrnE promoters: stable rrnX promoter complexes are formed faster, and are less sensitive towards heparin and salt than stable rrnE promoter complexes. The effect of ppGpp, the specific inhibitor of rRNA synthesis, on rrn promoter complex formation was studied. In the presence of ppGpp complexes are formed which cannot be trapped in a transcription complex by addition of the start nucleotides, and are therefore considered to be non-productive. A tentative mode for the action of ppGpp is proposed.

Synthesis and function of ribonucleic acid polymerase and ribosomes in Escherichia coli B/r after a nutritional shift-up

The syntheses of stable ribosomal ribonucleic acid (RNA) and transfer RNA in bacteria depend on the concentration and activity of RNA polymerase and on the fraction of active RNA polymerase synthesizing stable RNA. These parameters were measured in Escherichia coli B/r after a nutritional shift-up from succinate-minimal to glucose-amino acids medium and were found to change in complex patterns during a 1- to 2-h period after the shift-up before reaching a final steady-state level characteristic for the postshift growth medium. The combined effect of these changes was an immediate, one-step increase in the exponential rate of stable RNA synthesis and thus of ribosome synthesis. This suggests that the distribution of transcribing RNA polymerase over ribosomal and nonribosomal genes and the polymerase activity are continuously adjusted during postshift growth to some growth-limiting reaction whose rate increases exponentially. It is proposed that this reaction is the production of amino-acylated transfer RNA and that is exponentially increasing rate results in part from a gradually increasing concentration of aminoacyl transfer RNA synthetases after a shift-up. This idea was tested and is supported by a computer simulation of a nutritional shift-up.

Deletion of a ribosomal ribonucleic acid operon in Escherichia coli

One (rrnE) of the seven operons which codes for ribosomal ribonucleic acid in Escherichia coli was deleted. No significant change in phenotype was observed even under maximum laboratory growth conditions.

Isolation and characterization of lambda b221poriCasnA, a plaque-forming specialized transducing phage carrying the origin of replication of the Escherichia coli chromosome

A specialized transducing phage lambda b221poriCasnA has been isolated carrying oriC the origin of chromosomal replication of Escherichia coli. All phage genes required for lytic growth are retained, thus the phage is capable of lytic growth. The presence of the oriC locus confers upon infecting phage DNA the ability to replicate as a plasmid using only host DNA replication functions. The presence of both oriC and ansA markers has allowed the development of a plaque assay for origin function which can be used to identify mutants at these loci. Comparison of restriction endonuclease cleavage sites present on lambda b221proiCasnA DNA to those on its parent, lambda b221 rex::Tn10 suggests the steps involved in the formation of the transducing phage.

Functional heterogeneity of Escherichia coli ribonucleic acid polymerase holoenzyme

On zone sedimentation Escherichia coli RNA polymerase holoenzyme exhibits functional heterogeneity with respect to template preference, regulation by ppGpp, and affinity for fMet-tRNA. The template preference of a subpopulation of RNA polymerase molecules correlates with both its sedimentation position and its ability to respond to effectors of polymerase selectivity. Incubation of such functionally distinct populations of enzyme molecules at physiological temperatures results in functional and structural equivalence. We suggest that RNA polymerase normally exists as a mixture of interconvertible forms and that promoter selection can be controlled by varying the number and proportions of forms present.

Synthesis and activity of ribonucleic acid polymerase in Escherichia coli

The amounts of ribonucleic acid (RNA) polymerase (beta' subunits) and ribosomes (RNA), and the fraction of RNA polymerase actively engaged in transcription, were measured in Escherichia coli B/r as a function of growth rate. By an improved method of quantitating protein bands on electrophoresis gels, the systematic error and reproducibility of the RNA polymerase determination were estimated to be less than 15 and 6%, respectively. For a threefold increase in growth rate, the fractional synthesis of polymerase (relative to protein) increased 1.5-fold, whereas the fractional synthesis of ribosomal protein increased 2.2-fold. The decrease in the amount of RNA polymerase per ribosome with increasing growth rate is interpreted as an expression of the control of the transcriptional read-through from the genes for ribosomal protein, rplJ,L, to the adjacent genes for RNA polymerase subunits, rpoB,C. The number of active RNA polymerase molecules was determined from the synthesis rates of stable and messenger RNA and the known RNA chain growth rates. Comparison of active and total RNA polymerase indicates that the fraction of active enzyme increases from 20 to 30% in the range of growth rates between 0.6 and 2.0 doublings per hour. Possible causes for the inactive enzyme are discussed.

DNA sequences of promoter regions for rRNA operons rrnE and rrnA in E. coli

The nucleotide sequences have been determined for the promoter regions of two ribosomal RNA operons, rrnA and rrnE, in E. coli. The sequences cover the two in vitro transcription start sites identified for each operon (Gilbert, der Boer and Nomura, 1979). The first two start sites are 283 and 291 bp preceding the mature 16S rRNA (m16S rNA) coding regions for rrnE and rrnA, respectively; the second start sites are 174 and 174 +/- 1 bp preceding the m16S rRNA coding regions for rrnE and rrnA, respectively. Each of these start sites has an identifiable "Pribnow box" sequence 6-7 bp upstream from the start site. The nucleotide sequences of the two operons have nearly complete homology from the m16S rRNA coding regions to positions 145 bp upstream from those regions, and at the regions surrounding the Pribnow boxes preceding the first start sites. The DNA sequences indicate that the RNAs transcribed from the first start sites of rrnE and rrnA are quite different in their first 150 nucleotides. These heterogeneous regions, however, precede the RNAse III cleavage sites (deduced previously by Young and Steitz, 1978), and the "precursor 16S rRNA" molecules are largely homogeneous. The nucleotide sequences of the promoter regions of the two rRNA operons are also compared with those or rrnD and rrnX, determined by Young and Steitz (1979), and some common features are discussed.

Origin of replication, oriC, of the Escherichia coli chromosome: mapping of genes relative to R.EcoRI cleavage sites in the oriC region

A precise genetic-physical map of the tna-ilv region at 82 min on the genetic map of E. coli is obtained through deletion mapping and analysis by restriction endonuclease EcoRI of plasmids, derived from an F' carrying the genes between aroE and ilv. A locus, designated het, which in its diploid state results in slow growth and heterogeneity of cell size due to distorted cell division, maps between bglB and asn, 30-45 kb counterclockwise of ilv. The pattern of R.EcoRI cleavage sites in the het region is identical with the pattern obtained by Marsh and Worcel (1977) who analyzed DNA labeled preferentially in the region of the DNA replication origin (oriC). We suggest that oriC is identical with the het site and that it can be allocated to a position 32 kb counterclockwise of the ilv operon.