Regulation of the deo operon in Escherichia coli: the double negative control of the deo operon by the cytR and deoR repressors in a DNA directed in vitro system.

Summary The synthesis of the four enzymes of the deo operon in Escherichia coli is known from in vivo experiments to be subject to a double negative control, exerted by the products of the cytR and deoR genes.A DNA-directed in vitro protein synthesizing system makes the deo enzymes (exemplified by thymidine phosphorylase) in agreement with in vivo results. Enzyme synthesis is stimulated by cyclic AMP and repressed by the cytR and deoR gene products. Repression by the cytR repressor is reversed by cytidine or adenosine in the presence of cyclic AMP, while repression by the deoR repressor is reversed by deoxyribose-5-phosphate.Assays for the presence of the cytR and deoR repressors were established by use of S-30 extracts prepared from the regulatory mutants.Dissociation constants for repressor-operator binding as well as for repressor-inducer interactions have been estimated from the results.Abbreviations and Symbols deoA (previously designated tpp) Genes coding for: thymidine, phosphorylase - deoB (previously designated drm) deoxyribomutase - deoC (previously designated dra) deoxyriboaldolase - deoD (previously designated pup) purine nucleoside phosphorylase - udp uridine phosphorylase - cytR regulatory gene for cdd, udp, deoC, deoA, deoB, and deoD - deoR (previously designated nucR) regulatory gene for deoC, deoA, deoB, and deoD Enzymes (EC 2.4.2.1) Purine nucleoside phosphorylase or purine nucleoside: orthophosphate(deoxy)ribosyltansferase - (EC 2.4.2.4) thymidine phosphorylase or thymidine: orthophosphate deoxyribosyltransferase - (EC 2.4.2.3) uridine phosphorylase or uridine: orthophosphate ribosyltransferase - (EC 4.1.2.4) deoxyriboaldolase or 2-deoxy-D-ribose-5-phosphate: acetaldehydelyase - (EC 2.7.5.6) phosphodeoxyribomutase The deo operon is defined as the gene cluster consisting of deoC deoA deoB deoD. The deo enzymes are the four enzymes encoded by the four genes of the deo operon. cAMP: cyclic adenosine 3,5-monophosphate. CRP: cyclic AMP receptor protein. dRib-5P: deoxyribose-5-phosphate. THUR: 3,4,5,6-tetrahydrouridine; EDTA: ethylene-diamine-tetra-acetate.     

Effect of Mutations for the ruvABC Genes on Recombination between Direct DNA Repeats in Escherichia coli Strains Carrying Extended Tandem Duplications

The formation of haploid and diploid segregants was studied in Escherichia coli strains carrying heterozygous tandem duplications deoA deoB::Tn5/deoC deoD in the deoCABD operon region, in the genome of mutants forruvABCgenes. Homologous recombination in duplications of rec ⁺ strains and in recBC sbcB, recQand recF mutants, including those with blocks of both the RecBCD and RecF pathway, was shown in our previous work to be similar to adaptive mutagenesis: in this case, practically each cell forms a recombinant on a selective medium. In this work, mutants for ruv genes were found to differ in this respect, forming segregants at a frequency that was decreased by several orders of magnitude. These data confirm the conclusion that the genetic exchange in duplications proceeds through a special pathway of adaptive (or replicative) recombination connected with DNA replication. Upon selection of recombinants under conditions of thymine starvation, recombination cannot also be induced in ruv mutants. The recombinogenic effect of thymine starvation seems to occur at late stages of recombination, which are controlled by ruvABC genes.     

Study of RecA-Independent Homologous Recombination and a Chromosomal Rearrangement in the Escherichia coli Strain Carrying an Extended Heterozygous Tandem Duplication

A heterozygous tandem duplication in the Escherichia coli deo operon region deoAdeoB::Tn5/ deoCdeoDthr::Tn9 with the total length approximately 150 kb, which was obtained in the conjugational mating in the HfrH strain, was examined. By means of digestion with the NotI enzyme, pulsed-field gel electrophoresis, and the conjugational transfer of the duplication in the F^– strain, the chromosomal rearrangement, which occurred in the duplication region upon its stabilization in the bacterial genome, was studied. In a more stable strain, two new NotI sites were shown to appear in the chromosomal region located close to the duplication, which might have resulted from the transposition of the IS50 sequence from Tn5. The data were also obtained indicating the possibility of secondary transposition of the chromosomal segment between the two new NotI sites (approximately 30 kb) in the region located near the duplication. With the use of rec ⁺ and recA strains, two types of haploid and diploid segregants generated by the duplication were studied: DeoD⁺ (the deoD⁺ allele is not expressed in the original duplication due to the polar effect of the deoB::Tn5 insertion) and DeoC DeoD. The segregation of DeoD⁺ clones was shown to be RecA-dependent, whereas the DeoC DeoD segregants selected on the medium that contained thymine at a low concentration (i.e., under conditions of thymine starvation) appeared at a rather high frequency. However, the relative frequency of haploid clones, which have lost the duplication, strongly decreased in the recA genome among segregants of both types.     

ALT: A new factor involved in the synthesis of RNA by Escherichia coli

Summary We have defined a new gene, alt, which affects RNA synthesis in Escherichia coli. Mutants for alt arise among revertants of strains lacking the CRP-cAMP system necessary for full expression of catabolite-sensitive operons. Studies on a temperature-sensitive alt mutant indicate that the alt gene product is necessary for the synthesis of an important class of messenger RNA molecules.     

Study of Homologous Recombination and Chromosomal Rearrangements inEscherichia coliStrains Carrying a Heterozygous Tandem Duplication

Heterozygous tandem duplications formed in conjugational matings in Escherichia coliprovides a convenient model system for studying the evolution of bacterial chromosome. Heterozygous duplications segregate various classes of haploid and diploid recombinants that appear as a result of unequal crossing over between sister chromosomes. In this work, an extended tandem duplication in the deooperon of E. colicarrying deoA deoB::Tn5/deoC deoD thr::Tn9alleles was examined. Recombination between homologous DNA repeats in the duplication was studied in strains carrying different combinations of recBC, sbcBC, recB::Tn10, recQ::Tn3and recF::Tn3mutations. The frequency of recombination between homologous DNA repeats was very high in all strains and did not decrease when the RecBCD and RecF recombinational pathways were simultaneously damaged in strains with the recB sbcBC recQ(or recF) genotype. It is assumed that unequal crossing over between direct DNA repeats in duplications may proceed through a particular pathway of adaptive recombination.     

Studies on the functions of the RNA polymerase components by means of mutations

Summary It had been shown earlier, that RNA polymerase 13 S particles contain the large components with a molecular weight of about 3–10⁵ and small subunits with a molecular weight of 4·10⁴-1·10⁵. These polymerase components easily dissociate and reassociate with restoration of the enzyme activity.Both temperature-sensitive (tsX) and rifamycin-resistant (rif-r-I) mutations proved to affect the large polymerase component without changing the small subunits. These mutations were mapped at different, though closely linked, loci of metB-thi region of E. coli K12 chromosome. These results as well as certain literature data allow to conclude that the large RNA polymerase component consists of at least two polypeptides, one being altered by ts mutation, and the other—by rif-r mutation.The large polymerase component when separated from the small subunits retain the ability to bind to T2 phage DNA while the separate small subunits lack this property. Rifamycin does not affect RNA polymerase-T2 DNA binding while ts mutation leads to inability of the enzyme to form stable complexes with DNA. Therefore, it is likely that the polypeptide affected by ts mutation is responsible for the attachment of RNA polymerase to specific sites of DNA template. On the other hand, the small subunits as well as polypeptide of the large component, which determines RNA polymerase sensitivity to rifamycin, seem not to participate in the enzyme binding to DNA template. It is suggested, that the catalytic site of RNA polymerase is located in the large component and formed by rifamycin-binding polypeptide. The small subunits are supposed to have regulatory function and activate the large components.     

Synthesis of two DNA-dependent RNA polymerases in yeast

Specific activities of Saccharomyces cerevisiae RNA polymerases I and II were measured in cells growing under different nutrient conditions and throughout the mitotic cell cycle. The specific activity of RNA polymerase I (possibly the ribosomal polymerase) does not vary during the yeast cell cycle. In contrast the specific activity of RNA polymerase II (messenger polymerase) increases during the first third of the cycle and thereafter declines. The independent regulation of synthesis of these two enzymes is further emphasised by observations on the response to different nutrient conditions. Shifting cells from minimal to rich medium led to enhanced RNA polymerase I activity but very little change in activity of RNA polymerase II. Furthermore the activity of RNA polymerase I varies directly with change in growth rate whereas the activity of RNA polymerase II is approximately constant over a range of growth rates. From this data it is suggested: (i) The synthesis of these two enzymes is independently regulated; (ii) RNA polymerase I is synthesised continuously throughout the cycle whereas RNA polymerase II is synthesised periodically early in the cell cycle.     

Polarity suppressors increase expression of the wild-type tryptophan operon of Escherichia coli

Three new polarity suppressors, selected to relieve the polar effect of nonsense mutations in the tryptophan (trp) and lactose (lac) operons of Escherichia coli, increase expression distal to nonsense mutations in both operons to a greater extent than suA. These suppressors relieve the polarity created by amber, ochre and frameshift mutations with equal efficiency.Two of the three polarity suppressors elevate enzyme synthesis in the wildtype trp operon two- and fivefold, respectively. The increase in enzyme levels is in each case correlated with increased levels and rates of synthesis of structural gene trp messenger RNA. Since expression of all genes is elevated, these findings suggest the existence of a site early in the wild-type trp operon that affects the extent of operon expression. We located the site affected by these two polarity suppressors between the operator and the first structural gene, trpE. Although the third polarity suppressor also relieves mutational polarity efficiently, it has no detectable effect on expression of the wild-type trp operon.     

RNA Polymerase III of <Emphasis Type="Italic">Blastocladiella emersonii</Emphasis> is Mitochondrial

MULTIPLE RNA polymerases have been shown to exist in a wide variety of eukaryotic organisms^1–5. Two nuclear polymerases have been found in all the cells studied, each with a specific location and a specific function: the DEAE fraction I enzyme is located in the nucleolus and may be involved in the synthesis of ribosomal RNA^1,2,5,6; the DEAE fraction II enzyme is located in the non-nucleolar nucleoplasm and functions in the synthesis of DNA-like RNA^2–5,7. The DEAE fraction III enzyme was reported to exist in sea urchin¹, the aquatic fungus B. emersonii⁵ and to be present sometimes in rat liver preparations^1,8. Although there have been some reports that polymerase III is nuclear, Horgen and Griffin⁵ showed that the enzyme was sensitive to the prokaryotic RNA polymerase inhibitor rifampicin. They suggested that the fraction III enzyme may be mitochondrial, formed as the result of organelle contamination in their crude nuclear preparations. The results of this study show that the DEAE fraction III enzyme in B. emersonii is a mitochondrial enzyme, most likely functioning in the synthesis of mitochondrial RNA. The rifampicin sensitivity of the enzyme is further evidence of a prokaryotic origin of mitochondria^9,10.     

Interaction of RNA polymerase mutations in haploid and merodiploid cells of Escherichia coli K-12

Summary Combination in the same chromosome of tsX mutation which affects the attachment of RNA polymerase to DNA template with either of two rifampicin resistant mutations (rif-r-1 or rif-r-5) is lethal. However tsX forms viable combination with other rifampicin resistant mutation—rif-r-76. Moreover a partial restoration of rifampicin binding capacity takes place: RNA polymerase from double tsX rif-r-76 mutant binds rifampicin better than the enzyme from tsX ⁺ rif-r-76 cells. No mutual influence of rifampicin resistant and streptolydigin resistant mutations was found.Heterozygous merodiploids (rif-r/rif-s and stl-r/stl-s) demonstrate phenotypic dominance of sensitivity to each of the drugs no matter whether resistant allele is localized in chromosome or in episome. However certain chromosomal mutations which themselves have no apparent effect on RNA polymerase may cause dominance of rif-r allele.About a half of total cellular RNA polymerase in crude extracts of rif-r/rif-s and stl-r/stl-s heterogenotes was found to be drug-resistant, though rif-s allele is dominant phenotypically.The development of T2 phage is completely inhibited by rifampicin in haploid rif-s cells and is only slightly affected in rif-r mutant. A partial resistance of phage development to rifampicin was observed in rif-r/rif-s heterogenotes which confirms that both rif-s and rif-r enzymes are simultaneously present in such cells.Sensitive and resistant RNA polymerase function independently when mixture of the two enzymes was incubated with the excess of DNA template. However a competition between the two enzymes for the DNA was observed if the limiting amount of the template is available. The result of this competition to major extent depends on which of the enzymes was added first. It is supposed that in certain conditions normal RNA polymerase may act as a repressor of the mutant enzyme: drug-sensitive RNA polymerase may bind to the template in the presence of the drug and thus prevent the function of drug-resistant enzyme. This hypothesis explains phenotypic dominance of sensitive alleles to resistant alleles which leads to inability of heterogenote cells to multiply in the presence of corresponding drugs.     

VARIATION IN THE CHLOROPLAST GENES RPOC1 AND RPOC2 OF THE GENUS ASTRAGALUS (FABACEAE): EVIDENCE FROM RESTRICTION SITE MAPPING OF A PCR-AMPLIFIED FRAGMENT

A 4,100-base pair (bp) region of the chloroplast genome, amplified via the polymerase chain reaction, was obtained from 14 species of the genus Astragalus and mapped with 23 restriction enzymes. The amplified region encompassed the chloroplast genes RNA polymerase Cl (rpoCl; 90.8% of the gene) and RNA polymerase C2 (rpoC2; 32.7% of the gene) including the intron in rpoC1 and the intergenic spacer between the two genes. Approximately 144 sites (615 bp) were identified; 37 restriction site mutations and one 10-bp length mutation were detected. Estimated interspecific sequence divergence values ranged from 0.00% to 3.92%. Phylogenetic analysis with Wagner and Dollo parsimony both resulted in a single 41-step tree with a consistency index of 0.951. The relative positions of 115 restriction sites were mapped. The insertion and ten of the restriction site mutations mapped to the intron in rpoC1, 18 site mutations mapped to the rpoC1 exons, three site mutations mapped to rpoC2, three site changes mapped to the intergenic spacer, and four site changes were not mapped. This study demonstrates the utility of restriction site analysis of PCR-amplified chloroplast DNA to the study of plant phylogenetic relationships and molecular evolution.     

Trans-dominant mutation affecting restriction and modification in Escherichia coli K-12

Summary We have analysed the mechanism of action of a ts mutation in E. coli, which has an effect on the expression of the restriction and modification phenotype. The frequencies of recombinants obtained in transduction experiments support the idea that the temperature sensitive mutation is located outside the hsd operon in the gene denoted hsd. X. Complementation experiments demonstrated the trans-dominant nature of the temperature sensitive mutation. The possible role of the hsd.X product in the formation of EcoR.K and EcoM.K complexes and their interaction with the recognition site on the DNA is discussed.