Synthesis of penicillin-binding protein 6 by stationary-phase Escherichia coli.

The level of penicillin-binding protein 6, a D-alanine carboxypeptidase I, was found to be 2- to 10-fold higher in stationary-phase cells than in exponentially growing cells of Escherichia coli. This increase appeared to be due to de novo synthesis rather than to an unmasking of preexisting material. There was no comparable change in the amount of any of the other six penicillin-binding proteins.     

Subunit assembly and metabolic stability of E. coli RNA polymerase

Immunological cross-reaction was employed for identification of proteolytic fragments of E. coli RNA polymerase generated both in vitro and in vivo. Several species of partially denatured but assembled RNA polymerase were isolated, which were composed of fragments of the two large subunits, beta and beta', and the two small and intact subunits, alpha and sigma. Comparison of the rate and pathway of proteolytic cleavage in vitro of unassembled subunits, subassemblies, and intact enzymes indicated that the susceptibility of RNA polymerase subunits to proteolytic degradation was dependent on the assembly state. Using this method, degradation in vivo was found for some, but not all, of the amber fragments of beta subunit in merodiploid cells carrying both wild-type and mutant rpoB genes. Although the RNA polymerase is a metabolically stable component in exponentially growing cells of E. coli, degradation of the full-sized subunits was found in two cases, i.e., several temperature-sensitive E. coli mutants with a defect in the assembly of RNA polymerase and the stationary-phase cells of a wild-type E. coli. The in vivo degradation of RNA polymerase was indicated to be initiated by alteration of the enzyme structure.     

The conformation of ribonucleic acids in Escherichia coli ribosomes: Inferences from the mode of action of ribonuclease II

1. Ribonuclease II of Escherichia coli degrades pulse-labelled RNA associated with ribosomes and polyuridylic acid on ribosomes and in solution to mononucleotides. 2. Ribosomal and pulse-labelled RNA in solution and ribosomal RNA in chloramphenicol particles (protein-deficient ribosomes) are degraded to oligonucleotides. 3. Ribosomal RNA in mature ribosomes is not attacked by the enzyme. 4. From the mode of action of ribonuclease II, which is specific for single-stranded polyribonucleotides and does not attack helical forms, it is inferred that pulse-labelled RNA associated with ribosomes of E. coli exists as a single-stranded structure and that ribosomal RNA in chloramphenicol particles has a pronounced helical character. 5. The different behaviour of ribonuclease II towards newly synthesized RNA, ribosomal RNA and chloramphenicol-particle RNA in E. coli ribosomes is discussed.     

The inhibition of ribosomal ribonuclease by bacterial ribosomes

1. A comparison has been made between the ribonuclease activities of untreated ribosomes from Escherichia coli B and Pseudomonas fluorescens and the activities of ribosomes on to which ribosomal ribonuclease from E. coli B has been adsorbed. 2. The normal ribosomes from both species were stable in 5-10mm-Mg(2+) (I0.16) at pH6. The RNA in ribosomes from Ps. fluorescens was attacked by the adsorbed ribonuclease under these conditions, whereas the ribosomes from E. coli B were able to adsorb and inhibit this enzyme. 3. Inhibition was also observed with ribosomes from Aerobacter aerogenes, Proteus vulgaris and two other strains of E. coli. It was not observed in ribosomes from three species of Pseudomonas. 4. The inhibition depended on the integrity of the ribosomes and was not observed under conditions of low Mg(2+) concentration that cause irreversible degradation into more slowly sedimenting particles.     

Regions of RNase E important for 5'-end-dependent RNA cleavage and autoregulated synthesis

RNase E is an important regulatory enzyme that plays a key role in RNA processing and degradation in Escherichia coli. Internal cleavage by this endonuclease is accelerated by the presence of a monophosphate at the RNA 5' end. Here we show that the preference of E. coli RNase E for 5'-monophosphorylated substrates is an intrinsic property of the catalytically active amino-terminal half of the enzyme and does not require the carboxy-terminal region. This property is shared by the related E. coli ribonuclease CafA (RNase G) and by a cyanobacterial RNase E homolog derived from Synechocystis, indicating that the 5'-end dependence of RNase E is a general characteristic of members of this ribonuclease family, including those from evolutionarily distant species. Although it is dispensable for 5'-end-dependent RNA cleavage, the carboxy-terminal half of RNase E significantly enhances the ability of this ribonuclease to autoregulate its synthesis in E. coli. Despite similarities in amino acid sequence and substrate specificity, CafA is unable to replace RNase E in sustaining E. coli cell growth or in regulating RNase E production, even when overproduced sixfold relative to wild-type RNase E levels.     

The roles of RNA polymerase and RNAase I in stable RNA degradation in Escherichia coli carrying the srnB+ gene

In Escherichia coli cells carrying the srnB+ gene of the F plasmid, rifampin, added at 42 degrees C, induces the extensive rapid degradation of the usually stable cellular RNA (Ohnishi, Y., (1975) Science 187, 257-258; Ohnishi, Y., Iguma, H., Ono, T., Nagaishi, H. and Clark, A.J. (1977) J. Bacteriol. 132, 784-789). We have studied further the necessity for rifampin and for high temperature in this degradation. Streptolydigin, another inhibitor of RNA polymerase, did not induce the RNA degradation. Moreover, the stable RNA of some strains in which RNA polymerase is temperature-sensitive did not degrade at the restrictive temperature in the absence of rifampin. These data suggest that rifampin has an essential role in the RNA degradation, possibly by the modification of RNA polymerase function. A protein (Mr 12 000) newly synthesized at 42 degrees C in the presence of rifampin appeared to be the product of the srnB+ gene that promoted the RNA degradation. In a mutant deficient in RNAase I, the extent of the RNA degradation induced by rifampin was greatly reduced. RNAase activity of cell-free crude extract from the RNA-degraded cells was temperature-dependent. The RNAase was purified as RNAase I in DEAE-cellulose column chromatography and Sephadex G-100 gel filtration. Both in vivo and with purified RNAase I, a shift of the incubation mixture from 42 to 30 degrees C, or the addition of Mg2+ ions, stopped the RNA degradation. Thus, an effect on RNA polymerase seems to initiate the expression of the srnB+ gene and the activation of RNAase I, which is then responsible for the RNA degradation of E. coli cells carrying the srnB+ gene.     

Spontaneous mutagenesis in exponentially growing and stationary-phase, umuDC-proficient and -deficient, Escherichia coli dnaQ49

Spontaneous mutations arise not only in exponentially growing bacteria but also in non-dividing or slowly dividing stationary-phase cells. In the latter case mutations are called adaptive or stationary-phase mutations. High spontaneous mutability has been observed in temperature sensitive Escherichia coli dnaQ49 strain deficient in 3'-->5' proofreading activity assured by the e subunit of the main replicative polymerase, Pol III. The aim of this study was to evaluate the effects of the dnaQ49 mutation and deletion of the umuDC operon encoding polymerase V (Pol V) on spontaneous mutagenesis in growing and stationary-phase E. coli cells. Using the argE3(OC) -->Arg+ reversion system in the AB1157 strain, we found that the level of growth-dependent and stationary-phase Arg+ revertants was significantly increased in the dnaQ49 mutant at the non-permissive temperature of 37 degrees C. At this temperature, in contrast to cultures grown at 28 degrees C, SOS functions were dramatically increased. Deletion of the umuDC operon in the dnaQ49 strain led to a 10-fold decrease in the level of Arg+ revertants in cultures grown at 37 degrees C and only to a 2-fold decrease in cultures grown at 28 degrees C. Furthermore, in stationary-phase cultures Pol V influenced spontaneous mutagenesis to a much lesser extent than in growing cultures. Our results indicate that the level of Pol III desintegration, dependent on the temperature of incubation, is more critical for spontaneous mutagenesis in stationary-phase dnaQ49 cells than the presence or absence of Pol V.     

Liposome-Mediated transfer of bacterial RNA into carrot protoplasts

The uptake of liposome-encapsulated E. coli [³H]RNA by carrot (Daucus carota L.) protoplasts was examined. [³H]RNA extracted from protoplasts that had been incubated with [³H]RNA-containing, large, unilamellar lipid vesicles (liposomes) obtained by ether infusion, and examined by sucrose gradient centrifugation and formamide-polyacrylamide gel electrophoresis, appeared substantially degraded, with a total elimination of 23S RNA and a partial loss of 16S RNA. In contrast, no breakdown of the [³H]RNA was apparent in the liposomes after sequestration, even in the presence of externally added ribonuclease, or in the unfused liposomes remaining after incubation of protoplasts with liposomes. Thus, the degradation of the [³H]RNA extracted from the protoplasts must have occurred within the protoplasts and represents evidence for liposome-mediated RNA uptake. Naked RNA added to the protoplast culture was found to be totally degraded after incubation with the protoplasts. The uptake of liposome-sequestered RNA by protoplasts was demonstrated to be a function both of the lipid composition of the liposomal membrane and of the temperature of incubation of the liposomeprotoplast mixture. Furthermore, the mode of this uptake (fusion versus endocytosis) could be manipulated by adjusting the cholesterol content of the liposomal membrane. The implications of the ability to insert RNA into protoplasts without degradation by extracellular nucleases are discussed.     

The effect of ribonuclease on polysomes and ribosomes of bacteria and animal cells

The mildest treatment with ribonuclease that causes any disaggregation of the polysomes of Escherichia coli or HeLa cells simultaneously attacks the RNA of the constituent ribosomes. It is concluded that the susceptibility to ribonuclease of polysomes does not suggest that they are held together by a strand of messenger RNA. The RNA of the larger sub-unit of bacterial ribosomes has particularly sensitive regions resulting in a non-random degradation. The RNA of the smaller sub-unit of E. coli ribosomes is relatively resistant to ribonuclease attack. The same may be true of the respective sub-units of the intact HeLa-cell ribosome, but both sub-units become very sensitive to ribonuclease on dissociation from each other.     

Effect of ethylenediaminetetraacetic acid-Tris(hydroxymethyl)aminomethane on release of the acid-soluble nucleotide pool and on breakdown of ribosomal ribonucleic acid in Escherichia coli

Brief treatment of Escherichia coli with 2 x 10(-4)m ethylenediaminetetraacetic acid (EDTA)-0.12 m tris(hydroxymethyl)aminomethane (Tris), pH 8.0, or 0.12 m Tris alone resulted in the release of the acid-soluble nucleotide pool at 3 or 23 C. Exposure to EDTA-Tris for up to 90 min at 3 C did not result in the release of increasing amounts of 260-mmu-absorbing material. At 23 and 37 C, EDTA-Tris resulted in a steady increase in acid-soluble 260-mmu-absorbing material. Previous growth environment did not alter the release. There appeared to be degradation of 23S ribonucleic acid (RNA) after 10 min of exposure at 23 C. In addition, there was degradation of nucleotides to nucleosides and bases. This occured either within the cells with altered permeability or in the periplasmic space. This occurred in the presence of EDTA and Tris but was not seen with EDTA-phosphate. The mechanism of this degradation is unclear, since it occurs in ribonuclease I-deficient strains. Exposure to Tris buffer for long periods of time at 23 C resulted in release of the nucleotide pool and in degradation of RNA and nucleotides. These studies point out that the EDTA-Tris effect on E. coli must be divided into two parts, an early (4 to 5 min) change in permeability and a later phase of actual RNA breakdown and nucleotide degradation. Studies utilizing EDTA and Tris as agents altering permeability must thus be viewed with caution. Although the cells are viable, they have lost their acid-soluble nucleotide pool and have undergone degradation of some ribosomal RNA.     

Isolation and properties of a single-strand 5'----3' exoribonuclease from Ehrlich ascites tumor cell nucleoli

A single-strand-specific, nucleolar exoribonuclease from Ehrlich ascites tumor cells has been isolated and purified free from other nucleases. The exonuclease degraded single-stranded RNA processively from either a 5'-hydroxyl or a 5'-phosphorylated end and released 5'-mononucleotides. The enzyme digested single-strand poly(C), poly(U), and poly(A) equally well but did not degrade duplex poly(C).poly(I) or poly(A).poly(U). Less than 0.2% of duplex DNA or 1.5% of heat-denatured DNA was degraded under the conditions which resulted in greater than 26% degradation of RNA. The ribonuclease required Mg2+ (0.2 mM) for optimum activity and was inhibited by ethylenediaminetetraacetic acid but not by human placental RNase inhibitor. The native enzyme had a Stokes radius of 42 A and a sedimentation coefficient (S20,w) of 4.3 S. From these values, an apparent molecular weight of 76 000 was derived by using the Svedberg equation. The localization and unique mode of degradation suggest a role for the 5'----3' exoribonuclease in ribosomal RNA processing.     

Lysosomal Physiology in Tetrahymena. II. Effect of Culture Age and Temperature on the Extracellular Release of 3 Acid Hydrolases*

Tetrahymena cultures were grown from a single inoculum and collected on 3 successive days corresponding to the log, transitional, and early stationary phases of growth. Cells were washed and incubated for 5 hr in a dilute salt solution. Intra- and extracellular activities of acid phosphatase, α-glucosidase, and ribonuclease were assayed, and extracellular activities corrected for proteolytic degradation. A marked increase in the cellular content of acid phosphatase and significant decreases in α-glucosidase and ribonuclease occurred with advancing culture age. The intracellular changes in enzyme activities during incubation were roughly similar for cells of all ages. Protein content did not change appreciably during incubation. Extracellular A₂₅₅ release, monitored as an indication of the loss of RNA breakdown products, was at a minimum during incubation of transition cells. Significant quantities of all 3 acid hydrolases were released from cells of all ages except for ribonuclease from transition cells. The release of acid phosphatase and α-glucosidase was approximately proportional to the initial cellular content of these enzymes for cells of different ages and in log cells the effect of temperature on the rates of release was described by the Arrhenius equation. Release of ribonuclease, however, was not proportional to its intracellular content nor did it vary with temperature according to the Arrhenius equation. The results suggest that acid phosphatase and α-glucosidase are released via a first-order process.     

Localization of Escherichia coli poly(A) polymerase I in cellular membrane

Poly(A) polymerase I (PAP I), the pcnB gene product, is the main enzyme responsible for RNA polyadenylation in Escherichia coli. Polyadenylated RNA molecules are rapidly degraded by a multiprotein complex called RNA degradosome. Here we demonstrate that apart from its presence in cytosol, PAP I is also localized in cellular membrane. Although this observation might appear surprising, it was demonstrated recently by others that E. coli RNA degradosome is also associated with the cytoplasmic membrane. Moreover, we show that development of single-stranded RNA bacteriophages MS2 and Qbeta, but not that of single-stranded DNA bacteriophage M13, is more efficient in the pcnB mutant relative to an otherwise isogenic pcnB(+) host.     

Specific inhibition of cell division by colicin E 2 without degradation of deoxyribonucleic acid in a new colicin sensitivity mutant of Escherichia coli

A new class of colicin sensitivity mutants of Escherichia coli was isolated whose cell division was specifically inhibited by colicin E(2) without detectable degradation of deoxyribonucleic acid (DNA) at 30 C. The mutant could not form colonies in the presence of colicin E(2) but recovered colony-forming ability by trypsin treatment even after prolonged incubation with the colicin. Addition of colicin E(2) to the exponentially growing mutant inhibited cell division completely but did not induce degradation of DNA into cold acid-soluble materials nor any breakage of DNA strands. Synthesis of DNA in the mutant was not inhibited, and long filamentous cells with multiple nuclear bodies were formed by the action of colicin E(2). Degradation of ribosomal ribonucleic acid and development of prophage lambda, both of which were induced by colicin E(2) in the sensitive cells, did not occur in the mutant. At the elevated temperature, however, the mutant was found to undergo colicin-induced degradation of DNA. No differences in ultraviolet light nor drug sensitivities were observed in the mutant compared to the parent E. coli. The data suggested that colicin E(2) had a specific inhibitory effect on cell division of E. coli that was not a consequence of DNA degradation.