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PubMed1999

The plasmid prophage N15: a linear DNA with covalently closed ends.

Coliphage N15 is a temperate bacteriophage whose prophage is a linear plasmid molecule with covalently closed ends (telomeres). The N15 prophage provided the first example of such DNA in prokaryotes and, up to now, it is the only known example of a linear plasmid in Escherichia coli. The linear N15 mature phage DNA has single-stranded cohesive ends. The phage and plasmid prophage DNAs are circularly permuted. The nucleotide structure of the telomere-forming site tel RL in phage DNA corresponds to the structures of the terminal hairpin loops. It suggests a unique mechanism for conversion of the circular phage DNA to the linear plasmid form, which is performed by the prokaryotic telomerase (protelomerase). The results of a comparison of the protelomerase with integrases lead us to suggest that these proteins may have evolved from a common ancestor. The mechanism of plasmid N15 replication is unknown. We propose that the protelomerase participates in linear plasmid replication, acting as a resolvase of replicative intermediates that are tail-to-tail linear dimers. The sequence analysis of the N15 DNA showed that it represents an evolutionary 'link' between plasmids F, P1, P4 and lambdoid bacteriophages.

Amino Acid Sequence↗
PubMed2003

Partition operon expression in the linear plasmid prophage N15 is controlled by both Sop proteins and protelomerase.

The temperate coliphage N15, unlike most low copy-number prokaryotic replicons, is maintained as a linear DNA molecule with covalently closed ends. Accurate partitioning of the plasmid prophage is assured by a close homologue of the sop locus of the F plasmid. However, the region upstream of the N15 sopAB genes contains multiple putative promoters, in contrast to F sop whose expression is driven by one negatively autoregulated promoter. In addition, the centromere of N15 is represented by four inverted repeats located at widely separated sites within the region essential for replication and control of lytic functions. We have analysed expression of N15 sop genes. We find that transcription of N15 sop is driven by two major promoters. The first, P1, is similar in sequence and function to the F sop promoter; it is repressed by Sop proteins. The second promoter, P2, is upstream of P1 and is several times stronger. It is insensitive to regulation by Sop proteins but is tightly repressed by protelomerase, the N15 enzyme that completes prophage replication by generating hairpin telomeres. These results establish a regulatory link between the partition system and other processes of N15 maintenance.

Coliphages↗
PubMed1969

The proteins of bacteriophage M13.

Particles of the small filamentous coliphage M13 contain not only the major coat protein, which is the product of phage gene 8, but also a minor coat protein, the A protein, which is the product of gene 3. The A protein has a molecular weight of approximately 70,000 daltons, is present in one copy per virion, and is responsible for phage attachment to host cells. Also associated with purified M13 particles is a minor quantity of very small proteinaceous material, but its origin as a phage-coded product has not been demonstrated. At least five phage-specific proteins, including the two coat proteins, are present in appreciable quantities in M13-infected cells. The principal phage protein synthesized is the product of gene 5, which is responsible for phage single-stranded DNA synthesis. This protein has a molecular weight of about 8,000 daltons. Its precise function in DNA synthesis is not yet known. Phage proteins are synthesized at nearly normal rates in cells in which replication of phage double-stranded DNA is blocked by gene 2 mutations. This result suggests that the initial double-stranded DNA molecule serves as the principal template, perhaps the only template, for phage messenger RNA synthesis.

Coliphages↗
PubMed1970

Transduction by bacteriophage T1.

Amber mutants of the virulent coliphage T1 are able to transduce a wide variety of genetic characteristics from permissive to nonpermissive K strains of Escherichia coli.

Coliphages↗
PubMed1972

DNA modification methylase activity of Escherichia coli restriction endonucleases K and P.

The highly purified restriction endonucleases of E. coli K and coliphage P1 transfer methyl groups from S-adenosylmethionine to adenine residues of unmodified DNA. Incubation of unmodified DNA with endonucleases K or P and S-adenosylmethionine renders the DNA resistant to restriction. The enzymes, therefore, have both restriction endonuclease and modification methylase activities.

Chromatography, DEAE-Cellulose↗
PubMed1972

Enzymatic oligomerization of bacteriophage P22 DNA and of linear Simian virus 40 DNA.

Linear double-stranded molecules of the circularly permuted and terminally redundant DNA of Salmonella bacteriophage P22 have been converted to oligomeric products in the presence of polynucleotide ligase coded for by the coliphage T4. The reaction has been monitored by sucrose density-gradient centrifugation and electron microscopy. It goes slowly and gives yields of 30-40%. The products are mainly dimers and trimers, but higher oligomers are also present.DNA ligase extracted from uninfected Escherichia coli seems unable to perform a similar reaction, which is concluded to involve the fully base-paired termini. Linear double-stranded molecules of simian virus(SV) 40 DNA, produced by the action of the bacterial restriction endonuclease R(1), are oligomerized by either ligase; therefore, this reaction seems to involve single-stranded cohesive ends. No mixed products could be found when P22 DNA and linear SV 40 DNA were exposed together to the T4 ligase.

Carbon Isotopes↗
PubMed1972

DNA nucleotide sequence restricted by the RI endonuclease.

The sequence of DNA base pairs adjacent to the phosphodiester bonds cleaved by the RI restriction endonuclease in unmodified DNA from coliphage lambda has been determined. The 5'-terminal nucleotide labeled with (32)P and oligonucleotides up to the heptamer were analyzed from a pancreatic DNase digest. The following sequence of nucleotides adjacent to the RI break made in lambda DNA was deduced from these data and from the 3'-dinucleotide sequence and nearest-neighbor analysis obtained from repair synthesis with the DNA polymerase of Rous sarcoma virus [Formula: see text] The RI endonuclease cleavage of the phosphodiester bonds (indicated by arrows) generates 5'-phosphoryls and short cohesive termini of four nucleotides, (p)A(p)A(p)T(p)T. The most striking feature of the sequence is its symmetry.

Adenine Nucleotides↗
PubMed1973

Translation of bacteriophage Q RNA by cytoplasmic extracts of mammalian cells.

Cytoplasmic extracts from Krebs II mouse ascites cells and from L cells translate messenger RNA from coliphage Qbeta with fidelity to produce products that migrate on polyacrylamide gels with those products directed by Qbeta RNA in an Escherichia coli cell-free system. The mammalian cell extracts correctly initiate and terminate Qbeta coat protein synthesis, as shown by: (i) [(3)H]lysine-and [(3)H]arginine-labeled tryptic peptides derived from the coat-sized product resemble these from authentic Qbeta coat protein, (ii) Qbeta coat (which contains methionine only at the N-terminal end) can be radioactively labeled with methionine only if the methionine is formylated, and (iii) L cell extracts directed by Qbeta am(-)11 (an amber mutant in the coat protein) RNA make no completed coat-sized material, but do make a peptide the size of the authentic amber coat fragment.

Animals↗
PubMed1973

Messenger selection by bacterial ribosomes.

The counterpart of Escherichia coli initiation factor 3(IF-3) was isolated from Caulobacter crescentus, purified to homogeneity, and used in comparative studies on in vitro translation of RNA from the C. crescentus RNA phage Cb5 and of coliphage MS2 RNA. The two phage RNAs are similar in physical properties and analogous in genetic content. The factor, C-IF-3, substitutes for E. coli IF-3 and promotes correct translation of MS2 RNA by E. coli ribosomes. Conversely, E. coli IF-3 substitutes for C-IF-3 in translation of Cb5 RNA by C. crescentus ribosomes. However, each phage RNA could be translated only by host ribosomes or by mixed ribosomes containing the host 30S subunit. C-IF-3 dissociates C. crescentus and E. coli 70S ribosomes into subunits. It binds phage, ribosomal, and, less efficiently, transfer RNA.

Amino Acids↗
PubMed1974

The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.

With a stepwise degradation and terminal labeling procedure the 3'-terminal sequence of E. coli 16S ribosomal RNA is shown to be Pyd-A-C-C-U-C-C-U-U-A(OH). It is suggested that this region of the RNA is able to interact with mRNA and that the 3'-terminal U-U-A(OH) is involved in the termination of protein synthesis through base-pairing with terminator codons. The sequence A-C-C-U-C-C could recognize a conserved sequence found in the ribosome binding sites of various coliphage mRNAs; it may thus be involved in the formation of the mRNA.30S subunit complex.

Bacterial Proteins↗
PubMed1974

Escherichia coli RNA-polymerase binding sites on DNA are only 14 base pairs long and are located between sequences that are very rich in AplusT.

E. coli DNA-dependent RNA-polymerase binding sites on DNAs of T5, T7, and lambda coliphages have been isolated according to three different methods in order to analyze the binding sites themselves as well as the nearest neighboring regions. It is shown that the binding sites are regions that are rather rich in G+C, are about 14 base pairs long and are located between DNA sequences highly enriched in A+T. The biological implications of this result are discussed.

Adenine Nucleotides↗
PubMed1975

Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase.

Highly purified coliphage Qbeta replicase when incubated without added template synthesizes self-replicating RNA species in an autocatalytic reaction. In this paper we offer strong evidence that this RNA production is directed by templates generated de novo during the lag phase. Contamination of the enzyme by traces of RNA templates was ruled out by the following experimental results: (1) Additional purification steps do not eliminate this RNA production. (2) The lag phase is lengthened to several hours by lowering substrate or enzyme concentration. At a nucleoside triphosphate concentration of 0.15 mM no RNA is produced although the template-directed RNA synthesis works normally. (3) Different enzyme concentrations lead to RNA species of completely different primary structure. (4) Addition of oligonucleotides or preincubation with only three nucleoside triphosphates affects the final RNA sequence. (5) Manipulation of conditions during the lag phase results in the production of RNA structures that are adapted to the particular incubation conditions applied (e.g., RNA resistant to nuclease attack or resistant to inhibitors or even RNAs "addicted to the drug," in the sense that they only replicate in the presence of a drug like acridine orange). RNA species obtained in different experiments under optimal incubation conditions show very similar fingerprint patterns, suggesting the operation of an instruction mechanism. A possible mechanism is discussed.

Acridines↗
PubMed1976

Asymmetric orientation of phage M13 coat protein in Escherichia coli cytoplasmic membranes and in synthetic lipid vesicles.

At each stage of infection, the major coat protein of coliphage M13 binds to the E. coli cytoplasmic membrane with its antigenic site exposed to the cell exterior [Wickner, W. (1975) Proc. Nat. Acad. Sci. USA 72, 4749-4753]. This antigenic site is now shown to be at the amino-terminus of the protein. The amino-terminus of M13 coat protein is also found exclusively on the outside of dilauroyl or dimyristoyl lecithin vesicles, formed with coat protein by the cholate dilution technique [Racker, E., et al. (1975) FEBS Lett. 57, 14-18] near the lipid phase transition temperature. The basic carboxyterminus of the coat protein is exclusively on the inside of these vesicles. Vesicles of M13 coat protein and dimyristoyl lecithin when formed below the lipid phase transition temperature have both ends of the coat protein exposed to the vesicle exterior. The asymmetry of a membrane protein can, therefore, be established in the absence of other proteins and of lipid asymmetry; it depends on the physical state of the lipid phase. The factors which cause asymmetry in this model system may affect the distribution of proteins in biological membranes.

Antibodies, Viral↗
PubMed1976

A gene of bacteriophage T4 whose product prevents true late transcription on cytosine-containing T4 DNA.

T-even coliphages have 5-hydroxymethylcytosine in their DNA instead of cytosine. In some T4 mutants, the replicated DNA contains cytosine, but then no late gene products are made. We show that the inability to make late gene products with cytosine-containing T4 DNA is due to a T4 gene products. This gene product, while probably nonessential under normal conditions, interacts with an essential part of the transcription apparatus. Mutations in this gene allow viable T4 particles to be made whose DNA has been substituted almost 100% with cytosine.

Coliphages↗
PubMed1977

Membrane-associated assembly of M13 phage in extracts of virus-infected Escherichia coli.

Assembly of coliphage M13 is known to occur as the viral DNA crosses the cytoplasmic membrane, shedding its virus-coded DNA unwinding protein and acquiring from the membrane approximately 2400 copies of the major coat protein. Conditions are described in which extracts of M13-infected E. coli and membranes prepared from such extracts will support virus assembly at a rate equivalent to that of intact cells. Extracts prepared from cells infected with temperature-sensitive M13 mutants in genes 1, 3, 4, or 5 are temperature-sensitive in this cell-free assembly reaction. Phage assembly in vitro requires magnesium and as yet an unidentified heat-stable cofactor of low molecular weight. The rate of virus assembly is approximately linear with respect to extract concentration over a 10(4)-fold range, consistent with the observation that the entire M13 assembly activity copurifies with the cell membrane fraction.

Cell Membrane↗
PubMed1977

An Escherichia coli mutant with a temperature-sensitive function affecting bacteriophage Qbeta RNA replication.

We report the isolation of E. coli mutant capable of supporting replication of bacteriophage Qbeta at 33 degrees, but not at 40 degrees. Coliphages f2, R23, fd, and yamma formed plaques on mutant cells at both temperatures. Temperature-shift experiments showed that bacteriophage Q beta replication was blocked in the mutant within the first 20-30 min of infection. The defect did not prevent translation of the Qbeta polymerase gene or assembly of catalytically active Qbeta replicase molecules. In fact, mutant cells infected at 40 degrees hyperinduced replicase active both in vivo and in vitro. However, zone sedimentation of the in vivo RNA product showed it to consist of partially double-stranded material sedimenting at 9 S, with little or no viral 32S RNA. The 9S RNA was also found, along with a predominant peak of 32S RNA in parental cells infected at 40 degrees, but not in cells infected at 33 degrees. It thus appears that the temperature-sensitive component is required for viral RNA replication, but not for other RNA synthesis catalyzed by the replicase. Uninfected mutant cells grew normally at 40 degrees in nutrient broth, but not in glucose- or glycerol-minimal media. Revertants selected for their abillity to grow in minimal medium at 40 degrees also supported bacteriophage Qbeta replication at 40 degrees.

Coliphages↗
PubMed1978

Determination of capsid size by satellite bacteriophage P4.

Satellite bacteriophage P4 requires all morphogenic gene products provided by a helper phage, such as coliphage P2, to assemble its own capsid, which is one-third the volume of the larger helper capsid. We have isolated a satellite phage P4 sid (size determination) mutant that is unable to direct the assembly of the small wild-type-size P4 capsid. Instead, this mutant produces P4 plaque-forming units with large P2-size capsids which contain two or three copies of the P4 sid1 genome. P4 sid1 is evidently mutated in a protein that is specifically responsible for determining the precise size and symmetry of the structure into which the helper P2 gene products will assemble. In addition, we have found that the physical size of the genome does not appear to play an essential role in the proper assembly of the icosahedral capsid, since the majority of the P4 sid1 plaque-forming units do not contain a complete capsidful of DNA.

Coliphages↗
PubMed1978

Discrete length classes of DNA depend on mode of dehydration.

The length of double-stranded coliphage lambda DNA, as determined by electron microscopy using the benzyldimethylalkyl ammonium chloride technique, depends on the mode of dehydration. The freeze-dried DNA form is the longest (16.5 micron), whereas dehydration in methanol (15.9 micron) or in ethanol (three forms: 15.2 micron, 13.9 micron, and 12.4 micron) results in progressively shorter molecules. These measured lengths of the freeze-dried, methanol-dehydrated, and shortest ethanol-dehydrated forms correspond to the axial rise per nucleotide pair in the B, C, and A forms of DNA, respectively. The remaining forms of ethanol-dehydrated DNA seem to represent novel intermediary conformations of DNA. In agreement with the predicted increment, DNA exposed to ethidium bromide and freeze-dried is elongated by 39% (22.9 micron). All size classes show the same relative distribution pattern of bound Escherichia coli RNA polymerase molecules (nucleoside triphosphate:RNA nucleotidyltransferase, EC2.7.7.6), used as intramolecular markers, indicating that the dehydration-caused transitions are uniform.

Benzyl Compounds↗