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Deletion analysis of Qbeta replicase. Participation of the carboxyl-terminal region of the beta-subunit protein in template recognition.

We have analyzed one of the functional domains of Qbeta replicase, an RNA-dependent RNA polymerase of RNA coliphage Qbeta. Deletion mapping analysis of the carboxyl-terminal region of the beta-subunit protein revealed that the terminal 18 amino acid residues (positions 571-588) are dispensable for the replicase reaction. Subsequent deletions up to the Ala-565 residue reduced the RNA polymerizing activity of the replicase in vivo but increased it in vitro. The mutant replicases with enhanced in vitro RNA polymerizing activity were found to have relaxed template specificity for ribosomal RNAs and cellular RNAs as well as Qbeta RNA. Deletions beyond the Ile-564 residue abolished both the RNA polymerizing activity and the binding ability to midivariant (MDV)-poly(+) RNA, a derivative of a natural template for Qbeta replicase, MDV-1 RNA. These results suggest that the carboxyl-terminal part of the beta-subunit participates in RNA recognition of Qbeta replicase.

Amino Acid Sequence↗

rut Sites in the nascent transcript mediate Rho-dependent transcription termination in vivo.

The in vitro function of the coliphage lambda tR1 Rho-dependent terminator is governed primarily by a tripartite upstream sequence element designated rut. To determine the contribution of the different components of the rut site to terminator function in the normal context of coupled translation of the nascent cro message, tR1 variants lacking different rut site sequences were tested for terminator function in vivo. Intact rutA and rutB sequences were both necessary for efficient termination. However, deletion of the upstream rutA was far more detrimental than deletion of rutB. The intervening boxB, which encodes a short RNA stem and loop, could be deleted without reducing termination or detectably altering Rho's interaction with the corresponding cro transcript. The relative importance of these sequence elements was also the same in a minimal in vitro termination assay system. Rut sequences are therefore essential for terminator function in vivo and rutA contributes substantially more to tR1 function than does rutB. The relative contribution of these elements can be ascribed to differences in Rho's binding affinity for the encoded transcripts. If other cellular factors also bind the rut element RNA, they do not alter the relative contribution of its two regions to Rho-dependent transcription termination in vivo.

Adenosine Triphosphatases↗

Translational repression and specific RNA binding by the coat protein of the Pseudomonas phage PP7.

PP7 is a single-strand RNA bacteriophage of Pseudomonas aeroginosa and a distant relative to coliphages like MS2 and Qbeta. Here we show that PP7 coat protein is a specific RNA-binding protein, capable of repressing the translation of sequences fused to the translation initiation region of PP7 replicase. Its RNA binding activity is specific since it represses the translational operator of PP7, but does not repress the operators of the MS2 or Qbeta phages. Conditions for the purification of coat protein and for the reconstitution of its RNA binding activity from disaggregated virus-like particles were established. Its dissociation constant for PP7 operator RNA in vitro was determined to be about 1 nm. Using a genetic system in which coat protein represses translation of a replicase-beta-galactosidase fusion protein, amino acid residues important for binding of PP7 RNA were identified.

Amino Acid Sequence↗

A new model for the domain structure of heparan sulfate based on the novel specificity of K5 lyase.

Elucidation of the molecular structure of heparan sulfate (HS) is the key to understanding its functional versatility as a co-receptor for growth factors and morphogens. We have identified and exploited the novel substrate specificity of the coliphage K5 lyase in studies of the domain organization of HS. We show that K5 lyase cleaves HS principally within non-sulfated sequences of four or more N-acetylated disaccharides. Uniquely, sections comprising alternating N-acetylated and N-sulfated units are resistant to the enzyme, as are the highly sulfated S domains. Spacing of the K5 lyase cleavage sites ( approximately 7-8 kDa) is similar to that of the S domains. On the basis of these findings, we propose a refined model of the structure of HS in which N-acetylated sequences of four to five disaccharide units (GlcNAc-GlcUA)(4-5) are positioned centrally between the S domains. The latter are embedded within N-acetylated and N-sulfated sequences, forming extended regions of hypervariable sulfation distributed at regular intervals along the polymer chain. K5 lyase provides a means of excision of these composite sulfated regions for structural and functional analyses.

Chromatography, Gel↗

Characterization of polynucleotide kinase/phosphatase enzymes from Mycobacteriophages omega and Cjw1 and vibriophage KVP40.

Coliphage T4 Pnkp is a bifunctional polynucleotide 5'-kinase/3'-phosphatase that catalyzes the end-healing steps of a RNA repair pathway. Here we show that mycobacteriophages Omega and Cjw1 and vibriophage KVP40 also encode bifunctional Pnkp enzymes consisting of a proximal 5'-kinase module with an essential P-loop motif, GXGK(S/T), and a distal 3'-phosphatase module with an essential acyl-phosphatase motif, DX- DGT. Biochemical characterization of the viral Pnkp proteins reveals several shared features, including an alkaline pH optimum for the kinase component, an intrinsic RNA kinase activity, and a homotetrameric or homodimeric quaternary structure, that distinguish them from the monomeric DNA-specific phosphatase/kinase enzymes found in mammals and fission yeast. Whereas the phage 5'-kinases differ from each other in their preferences for phosphorylation of 5' overhangs, blunt ends, or recessed ends, none of them displays the preference for recessed ends reported for mammalian DNA kinase. We hypothesize that Pnkp provides phages that have it with a means to evade an RNA-damaging antiviral host response. Genetic complementation of the essential end-healing steps of yeast tRNA splicing by the Omega and Cjw1 Pnkp enzymes establishes their capacity to perform RNA repair reactions in vivo. A supportive correlation is that Omega and Cjw1, which are distinguished from other mycobacteriophages by their possession of a Pnkp enzyme, are also unique among the mycobacteriophages in their specification of putative RNA ligases.

Adenosine Triphosphate↗

Seasonal variations in the microbial population density present in biological sludge.

Sludge produced during the treatment of wastewater is being used as fertilizer in several Gulf countries. The Water and Sewage Authority of Saudi Arabia has targeted the reuse of the total amount of sludge in the future. However, these sludges should be properly treated before reuse as they contain a large number of pathogens and parasites. Little information is available on the microbial characteristics of sludge produced in wastewater treatment plants operating in this region. Variations in the population densities measured by Standard Plate Count, total coliform, fecal coliform, coliphage, and Clostridium perfringens present in the sludge, were monitored during a one year study at Al-Khobar wastewater treatment plant so that the effect of seasonal variations on the fate of these five indicator microorganisms could be investigated. This paper covers an evaluation of the fate of indicator microorganisms in the drying sludge. Insight gained in this study will be helpful in establishing guidelines for the use of sludge as fertilizer for agriculture purposes.

Clostridium perfringens↗

Micro-organism re-growth in wastewater disinfected by UV radiation and ozone: a micro-biological study.

A series of disinfection experiments using UV radiation and ozone was performed on the secondary effluent from a wastewater treatment plant at a pilot plant scale. The microbial population in the inflowing wastewater and the treated outflow water were quantified for each of the treatment modules (fecal coliforms, fecal streptococci, Salmonella spp. (presence/absence), Clostridium Sulphite-reducers, Pseudomonas aeruginosa, Staphylococcus aureus, coliphages, nematodes, intestinal nematodes and pathogenic fungi). Treated water was stored in opaque tanks at a temperature between 20 and 22 degrees C, after which, a one-month study of the regrowth of the bacterial flora, nematodes and fungi was carried out. Clostridium Sulphite-reducers, pathogenic fungi and nematodes were the micro-organisms showing a greatest degree of resistence to UV- and Ozone-treatment. It was only concerning Clostridium and Pseudomonas abatement that significant elimination results were achieved with both technologies.

Clostridium↗

Protein--protein interactions in the eubacterial replisome.

Replication of genomic DNA is a universal process that proceeds in distinct stages, from initiation to elongation and finally to termination. Each stage involves multiple stable or transient interactions between protein subunits with functions that are more or less conserved in all organisms. In Escherichia coli, initiation of bidirectional replication at the origin (oriC) occurs through the concerted actions of the DnaA replication initiator protein, the hexameric DnaB helicase, the DnaC?helicase loading partner and the DnaG primase, leading to establishment of two replication forks. Elongation of RNA primers at each fork proceeds simultaneously on both strands by actions of the multimeric replicase, DNA polymerase III holoenzyme. The fork that arrives first in the terminus region is halted by its encounter with a correctly-oriented complex of the Tus replication terminator protein bound at one of several Ter sites, where it is trapped until the other fork arrives. We summarize current understanding of interactions among the various proteins that act in the different stages of replication of the chromosome of E. coli, and make some comparisons with the analogous proteins in Bacillus subtilis and the coliphages T4 and T7.

Adenosine Triphosphatases↗

Presence of bacteriophages in animal feed as indicators of fecal contamination.

The objectives of this study were to determine if indigenous male specific and somatic bacteriophages could be detected in animal feeds and if isolated phages contained RNA or DNA. Seven fresh feeds, 2 fresh feed ingredients, 7 stored feeds, 2 stored feed ingredients, and 8 samples of poultry diets suspected to contain Salmonella spp. were enriched and spot plated for indigenous phages using Escherichia coli Famp and CN-13 as hosts. Bacteriophage numbers were below detection without enrichment, but both male specific and somatic coliphages were detected in all animal feeds, feed ingredients, and poultry diets after 16 h of enrichment, even after the samples had been stored for 14 months of storage at -20 C. Five out of 9 fresh feeds and 7 out of 8 stored feeds contained RNA somatic phages.

Animal Feed↗

Mechanism of cell wall penetration by viruses. II. Demonstration of cyclic permeability change accompanying virus infection of Escherichia coli B cells.

The virus-induced leakage of host-cell constituents represents a true increase in cellular permeability rather than an unpeeling of cell surface components, since an intracellular enzyme participates in the leakage. All of the T-system bacteriophages exhibit this leakage. The leakage does not occur with salt concentrations which permit only reversible virus-cell attachment but no penetration. These facts support the idea that the reaction underlying cell leakage is a part of the invasive mechanism. With increasing multiplicity of T2 infection of young, fresh Escherichia coli B cells, progressively larger molecules leak out of the cell. Acid-soluble P(32) appears in large amounts with single infection. Appreciable amounts of galactosidase enzyme and RNA do not leak until multiplicities of 5 to 30 are attained. Cellular DNA is not liberated unless sufficiently high multiplicities are used to cause the extensive cell destruction and clearing of the suspension characteristic of lysis-from-without. This progression is interpreted as an increase with T2 multiplicity in the maximum hole size produced in the cell membrane. Calculation shows that this increase in hole size must result from a spreading change in the character of the cell wall, rather than the coincidental juxtaposition of 2 or more viruses at adjacent attachment sites. T1 virus liberates less macromolecular constituents than T2 from E. coli B. The following experimental results constitute evidence that in the course of normal virus infection, a resealing reaction is rapidly instituted in the cell wall which reverses the effect of the original permeability increase, and renders the cell refractory to a second lytic reaction by a homologous virus: (a) Cell leakage induced by T2 virus in the course of normal infection markedly slows down or stops within a few minutes, even when only a small fraction of the material potentially available for leakage has been released, (b) Superinfection after 8 minutes at 37 degrees C., of a cell previously infected with a homologous virus causes little or no appearance of a second leakage of cell constituents. This experiment also leads to the conclusion that the sealing reaction, like that which causes the leakage, also involves a disturbance which spreads over all or most of the cell wall. (c) If a multiple virus infection is allowed to occur at 0 degrees C. and then the cells are placed in a 37 degrees C. bath after completion of attachment, a much greater cell leakage results than if the entire course had occurred at 37 degrees C., as would be expected if a resealing reaction comes into play at 37 degrees C. within a time less than that required by the completion of attachment. The virus particles attaching secondarily at 37 degrees C. are prevented from exercising their permeability-increasing effect by the sealing reaction of the virus which had penetrated first. Although a second homologous cell infection with T1 or T2 phages after a 37 degrees C. incubation fails to yield a second leakage, a second heterologous infection always causes exacerbation of new leakage, which, especially if T1 has preceded T2, may be much greater than the sum of those produced individually by each virus in separate cell suspensions. This phenomenon may be the action responsible for the "depressor" effect which occurs when 2 unrelated viruses attack the same cell. The properties of the sealing phenomenon are such as to make it appear a logical candidate for the mechanism underlying the exclusion of a superinfecting phage from participating in reproductive processes in a cell previously infected with a homologous virus, since the DNA of the second virus would be unable to penetrate the new barrier. Experiments to test this hypothesis revealed that the DNA from such superinfecting virus is completely extractable from cells by washing in dilute buffer, whereas about 40 to 50 per cent of the attached DNA of virus which has invaded virgin cells remains bound to the cells. Most of the viral DNA which appears in the original supernatant when P(32)-labelled T2 invades E. coli B in a multiplicity less than one, does not represent inert material but rather virus DNA which has been split, or split and hydrolyzed as a result of its interaction with the cells, as judged by the altered susceptibility to hydrolytic enzyme or to TCA precipitation. This suggests that 25 per cent or more of the virus DNA may be expendable, at least after the penetration stage of the infection cycle. Mg(++) which strongly depresses the amount of cell leakage attending T2 infection, does not prevent T2 penetration nor does it block the appearance of the exclusion reaction. Hence, if the initial leakage does mirror the lytic process by which a hole for the DNA injection is provided, the Mg(++) does not function by preventing this hole formation. Its effect would have to lie in prevention of the spreading lysis-potentiating reaction or in augmenting the sealing mechanism. A large number of independent lines of evidence indicate that the phenomenon of lysis-from-without exhibited by the T-even coliphages is the result of failure of the sealing mechanism to keep pace with the lytic reaction. This can result from an excess of infecting phages or inhibition of the cellular energy-liberating reaction required by the sealing mechanism. The complete parallelism between the development of refractoriness to lysis-from-without and development of refractoriness to the production of a new leakage from a homologous superinfection is especially convincing in this connection. It is proposed that the early phase of bacteriophage invasion involves the following steps: reversible electrostatic attachment; splitting of the viral DNA from its protein coat; initiation of a lytic reaction in the cell wall at the site of virus attachment; injection of the DNA through the hole so produced; a spreading disturbance over the cell surface which makes it momentarily more susceptible to the lytic reaction; sealing of the hole and a concommittant spread over the cell wall of a reaction making the cell refractory to initiation of a second lytic reaction. Na(+), K(+), and Mg(++) all behave differently in their effect on the leakage produced in the course of T2 invasion of E. coli.

B-Lymphocytes↗

A new ozone-based method for virus inactivation: preliminary study.

The nebulization technique reported here could be used to inactivate viruses with ozone in large volumes of body fluids, such as plasma, partial blood and perhaps whole blood in a short time. Coliphage MS2 was used as a model because it is safe, easy to handle and more resistant to chemical disinfections than viruses such as HIV. The theoretical curves and experimental points, describing ozone inactivation of MS2, form a semi-sigmoid of congruent data. There was a > 7log10 reduction in MS2 viability and the possibilities of minimizing the ozone concentration required to kill viruses are indicated. The analysis was expanded to account for the interaction of ozone with a virus suspension in the shape of a thin film from the experimental findings of Bolton et al. We again find a semi-sigmoid of congruent data for their case, i.e. describing ozone inactivation of the influenza A virus (WSN strain) and the vesicular stomatitis virus versus time. For the method of nebulization, the exposure time of droplets with ozone is a few seconds, whereas for the thin film method the exposure time is measured in hours.

Antiviral Agents↗

Evidence that rifampicin can stimulate readthrough of transcriptional terminators in Escherichia coli, including the attenuator of the rpoBC operon.

The genes encoding the beta and beta' subunits of RNA polymerase in E.coli, rpoB and rpoC, lie downstream of at least two ribosomal protein genes, rplJ (encoding L10) and rplL (L7/12), in a common operon. All four genes are served by promoter PL10, and an attenuator (partial terminator) of transcription, t1, lies between rplJL and rpoBC. Treatment of E.coli with rifampicin, under conditions producing partial inhibition of general RNA synthesis, can stimulate transcription of rpoBC. We have investigated the locus of this effect by fusing PL10 and t1 separately to galK, in suitable plasmids. Our studies of these fusions, and similar fusions involving transcriptional terminators derived from coliphage T7, indicate that low concentrations of rifampicin cause increased readthrough of several different transcriptional terminators in E.coli in vivo, including rpo t1. We discuss whether or not this unspecific mechanism is solely responsible for the observed stimulatory effects of the drug on rpoBC transcription.

Base Sequence↗

The sequence asymmetry of the Escherichia coli chromosome appears to be independent of strand or function and may be evolutionarily conserved.

I have examined potential determinants of the asymmetric distribution of nucleotide sequences in the genome of Escherichia coli as cataloged in GenBank release 44. I have used the frequency of occurrence of all possible tetranucleotides in a given sequence catalog or derivative as a comparative measure of asymmetry. The GenBank-cataloged strand and its complement show statistically similar (not complementary) distributions. The distribution is statistically similar in comparisons between the protein coding subset and the total genome, the coding subset and selected non-coding genes, the coding subset and the remainder of the DNA, and the coding subset and stable RNA sequences. I have compared the distribution in the genome of E. coli with the distributions found in the cataloged genomes of Salmonella typhimurium, Bacillus subtilis, and of coliphages lambda and T7. The distribution summed in both strands of the cataloged DNA differs statistically only in comparisons with lytic bacteriophage T7 because only the two strands of T7 show statistically dissimilar distributions. Despite similarities in tetranucleotide distribution, the pattern of codon complementarity in B. subtilis is different than that documented for E. coli. Thus, sequence asymmetry does not seem related to specific DNA function or to documented similarities or differences in codon bias. The sequence asymmetry of the E. coli genome may thus reflect a hitherto unsuspected pattern impressed on both strands of DNA which is or can be packaged into bacterial genomes.

Bacillus subtilis↗

Phosphorothioate-containing RNAs show mRNA activity in the prokaryotic translation systems in vitro.

Phosphorothioate-containing RNAs were generated by transcription of coliphage T7 DNA using the Sp diastereomers of ribonucleoside 5'-O-(1-thiotriphosphates) and T7 RNA polymerase. RNAs in which a single nucleotide was substituted by the corresponding nucleoside phosphorothioate functioned as mRNA in the cell-free translation systems prepared from Escherichia coli and from an extreme thermophilic bacterium, Thermus thermophilus. This substitution increased the efficiency of protein synthesis by stabilizing the mRNAs in these systems. As the proportion of substituted nucleotides was increased, their mRNA activity was decreased accordingly. As judged from the analysis by SDS-polyacrylamide gel-electrophoresis, the proteins synthesized using phosphorothioate-containing mRNAs as template were identical to those obtained with unsubstituted mRNAs. However, larger proteins which were barely detectable when unsubstituted mRNA was used were well represented when phosphorothioate-RNA was used instead. The advantages in using the phosphorothioate-mRNAs in the in vitro translation systems are discussed.

Cell-Free System↗

The different binding modes of Hoechst 33258 to DNA studied by electric linear dichroism.

The binding mode of the bisbenzimidazole derivative Hoechst 33258 to a series of DNAs and polynucleotides has been investigated by electric linear dichroism. Positive reduced dichroisms were measured for the poly(dA-dT).poly(dA-dT)- and poly(dA).poly(dT)-Hoechst complexes in agreement with a deep penetration of the drug into the minor groove. Similarly, the drug displays positive reduced dichroism in the presence of the DNAs from calf thymus, Clostridium perfringens and Coliphage T4. Conversely, negative reduced dichroisms were obtained when Hoechst 33258 was bound to poly(dG-dC).poly(dG-dC), poly(dA-dC).poly(dG-dT) and poly(dG).poly(dC) as well as with the GC-rich DNA from Micrococcus lysodeikticus indicating that in this case minor groove binding cannot occur. Substitution of guanosines for inosines induces a reversal of the reduced dichroism from negative to positive. Therefore, as anticipated it is the 2-amino group of guanines protruding in this groove which prevents Hoechst 33258 from getting access to the minor groove of GC sequences. The ELD data obtained with the GC-rich biopolymers are consistent with an intercalative binding. Competition experiments performed with the intercalating drug proflavine lend credence to the involvement of an intercalative binding rather than to an external or major groove binding of Hoechst 33258 at GC sequences.

Animals↗

"Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA.

Recent structural analyses of genomic RNAs from RNA coliphages suggest that both well-determined base paired helices and well-determined structural domains that are identified by "energy dot plot" analysis using the RNA folding package mfold, are likely to be predicted correctly. To test these observations with another group of large RNAs, we have analyzed 15 ribosomal RNAs. Published secondary structure models that were derived by comparative sequence analysis were used to evaluate the predicted structures. Both the optimal predicted fold and the predicted "energy dot plot" of each sequence were examined. Each prediction was obtained from a single computer run on an entire ribosomal RNA sequence. All predicted base pairs in optimal foldings were examined for agreement with proven base pairs in the comparative models. Our analyses show that the overall correspondence between the predicted and comparative models varied for different RNAs and ranges from a low of 27% to high of 70%, with a mean value of 49%. The correspondence improves to a mean value of 81% when the analysis is limited to well-determined helices. In addition to well-determined helices, large well-determined structural domains can be observed in "energy dot plots" of some 16S ribosomal RNAs. The predicted domains correspond closely with structural domains that are found by the comparative method in the same RNAs. Our analyses also show that measuring the agreement between predicted and comparative secondary structure models underestimates the reliability of structural prediction by mfold.

Base Sequence↗

The complete nucleotide sequence of bacteriophage HP1 DNA.

The complete nucleotide sequence of the temperate phage HP1 of Haemophilus influenzae was determined. The phage contains a linear, double-stranded genome of 32 355 nt with cohesive termini. Statistical methods were used to identify 41 probable protein coding segments organized into five plausible transcriptional units. Regions encoding proteins involved in recombination, replication, transcriptional control, host cell lysis and phage production were identified. The sizes of proteins in the mature HP1 particle were determined to assist in identifying genes for structural proteins. Similarities between HP1 coding sequences and those in databases, as well as similar gene organizations and control mechanisms, suggest that HP1 is a member of the P2-like phage family, with strong similarities to coliphages P2 and 186 and some similarity to the retronphage Ec67.

Bacteriophage P2↗

Long-range translational coupling in single-stranded RNA bacteriophages: an evolutionary analysis.

In coliphage MS2 RNA a long-distance interaction (LDI) between an internal segment of the upstream coat gene and the start region of the replicase gene prevents initiation of replicase synthesis in the absence of coat gene translation. Elongating ribosomes break up the repressor LDI and thus activate the hidden initiation site. Expression studies on partial MS2 cDNA clones identified base pairing between 1427-1433 and 1738-1744, the so-called Min Jou (MJ) interaction, as the molecular basis for the long-range coupling mechanism. Here, we examine the biological significance of this interaction for the control of replicase gene translation. The LDI was disrupted by mutations in the 3'-side and the evolutionary adaptation was monitored upon phage passaging. Two categories of pseudorevertants emerged. The first type had restored the MJ interaction but not necessarily the native sequence. The pseudorevertants of the second type acquired a compensatory substitution some 80 nt downstream of the MJ interaction that stabilizes an adjacent LDI. In one examined case we confirmed that the second site mutations had restored coat-replicase translational coupling. Our results show the importance of translational control for fitness of the phage. They also reveal that the structure that buries the replicase start extends to structure elements bordering the MJ interaction.

Base Sequence↗