Characterization of the DNA from bacteriophage P2-186 hybrids and physical mapping of the 186 chromosome

Nonessential region of bacteriophage P4: DNA sequence, transcription, gene products, and functions

We sequenced the leftmost 2,640 base pairs of bacteriophage P4 DNA, thus completing the sequence of the 11,627-base-pair P4 genome. The newly sequenced region encodes three nonessential genes, which are called gop, beta, and cII (in order, from left to right). The gop gene product kills Escherichia coli when the beta protein is absent; the gop and beta genes are transcribed rightward from the same promoter. The cII gene is transcribed leftward to a rho-independent terminator. Mutation of this terminator creates a temperature-sensitive phenotype, presumably owing to a defect in expression of the beta gene.

UV induction of coliphage 186: prophage induction as an SOS function

Our results show that UV induction of the 186 prophage depends upon the phage function Tum, with the mutant phenotype of turbid plaques on mitomycin plates and the expression of which is controlled by the host LexA protein. Tum function, encoded near the right-hand end of the coliphage 186 chromosome, is under the control of promoter p95. This promoter is overlapped by a sequence closely related to the consensus sequence of the LexA-binding site. It is proposed that inactivation of LexA after UV irradiation (or by genetic means) leads to prophage induction by permitting expression of Tum which, by unknown means, induces prophage. This mechanism is basically different from that seen with the UV-inducible lambdoid coliphages, which are not regulated by LexA.

DNA replication studies with coliphage 186. II. Depression of host replication by a 186 gene

Using pre-labelling rather than pulse-labelling studies to determine rates of replication, we have shown that coliphage 186 infection is accompanied by a depression in host DNA replication. We have isolated mutants of the phage gene involved and mapped them in the early region of the phage genome. Sequencing the mutants ultimately led us to the identification of the gene that we have named the dhr gene.

High-resolution separation and accurate size determination in pulsed-field gel electrophoresis of DNA. 1. DNA size standards and the effect of agarose and temperature

Pulsed-field gel electrophoresis (PGF) subjects DNA alternately to two electrical fields to resolve DNA ranging from 10,000 base pairs (10 kb) to 10,000 kb in size. The separations are quite sensitive to a variety of experimental variables. This makes it critical to have a wide range of reliable size standards. A technique is described for preparing mixtures of bacteriophage DNA oligomers that span a size range from monomer to more than 30-mer. The relationship between size and mobility of oligomers of different bacteriophage DNA monomers is generally self-consistent. Thus, these samples can serve as primary length standards for DNAs ranging from 10 kb to more than 1500 kb. They have been used to estimate the size of the chromosomal DNAs from various Saccharomyces cerevisiae strains and to test the effect of gel concentration and temperature on PFG. DNA resolution during PFG is slightly improved in agarose gels with small pore sizes, in contrast to continuous electrophoresis where the opposite is observed. PFG mobility is surprisingly sensitive to changes in the running temperature.

Control of gene expression in the P2-related template coliphages. III. DNA sequence of the major control region of phage 186

The PstI fragment (65.5% to 77.4%) of coliphage 186, known genetically to encode the major control genes, has been sequenced, and an analysis performed to assess coding capacity, transcription-translation signals, and to identify any other significant features. Our analysis indicates that the region encodes: seven genes, including the int and cI genes, which overlap, the late control gene B, and two genes, named CP75 and CP76, encoding potential DNA-binding proteins; a promoter pB and terminator tB for the rightward transcription of the B gene, and we predict the existence of this transcript in a lysogen; a promoter pL and terminator tL for leftward transcription that encodes the int and cI genes, and represents the presumed lysogenic transcript; a promoter pR for rightward transcription to give the presumed (early) lytic transcript that is overlapping and convergent with the lysogenic transcript; and finally, a potential operator site for repressor binding in the region of the pR promoter. Preliminary evidence is presented to support this analysis.

Bacteriophage P4 DNA replication. Location of the P4 origin

An electron microscopic examination of replicating bacteriophage P4 DNA molecules has revealed theta-type structures that replicate bidirectionally from a single origin. Many replicating P4 DNA molecules also contain long (2000 bases) single-strand DNA regions at the growing fork that are deployed in a trans configuration, which supports the concept of continuous leading strand and discontinuous lagging strand syntheses. The position of the P4 origin was localized by the use of a plasmid complementation test for replication in vivo, as well as by labeling of DNA replicating in vitro in the presence of a chain-terminating inhibitor. During this study we discovered a second site on the P4 genome which is essential for replication, and we have named it crr (cis region required for replication). The site is located at least 3300 bases from the origin but appears to be required for the initiation of DNA replication in vivo as well as in vitro.

Genetic studies of coliphage 186. I. Genes associated with phage morphogenesis

In coliphage 186, 22 essential genes were defined by complementation studies with amber mutants. Eighteen genes were associated with phage morphogenesis: 11 with phage tail formation, and 7 with phage head formation. The remaining four genes are discussed in the accompanying paper (S. M. Hocking and J. B. Egan, J. Virol. 44:1068-1071, 1982).

Genetic map of coliphage 186 from a novel use of marker rescue frequencies

A genetic map of phage 186 has been constructed, using the frequency of marker rescue from 186 mutant prophages for genes to the left of att, and int promoted recombination for genes to its right. At the left end of the genome lie 7 genes involved in the formation of the phage head, followed to the right by the lysis gene P, a gene (O) of unknown function, and a group of 11 genes involved in the formation of the phage tail. Gene B, the late control gene, lies to the right of this group but to the left of the phage attachment site. To the right of the att site lie the non-essential genes (cI and cII) involved in lysogen formation and the gene (A) required for 186 DNA synthesis.

In vivo transcription studies of coliphage 186

The temporal apperance of transcripts from the 186 chromosome has been determined by pulse-labeling at different times after prophage induction and hybridization of RNA extracts to cloned restriction fragments of 186. Studies with different mutants and induction in the presence of chloramphenicol suggested a controlled pattern of transcription and led us to propose the existence of a primary control gene analogous to the lambda gene N.

Further physical characterization of deletion and substitution mutants affecting the control of lysogeny in bacteriophage P2

A deletion of phage P2, del6 (L.E. Bertani, 1980), thought to remove the structural gene int, and a deletion/substitution, vir94, thought to remove genes int, C and cox, were mapped by electron microscopy, using the heteroduplex technique. Four independent deletion/substitution mutations, all affecting the regulatory region of P2, were compared in all possible combinations with the same technique: two showed sequence homology in their substitution DNA. The results confirm the model proposed for the origin of these mutants, analogous to that for the origin of transducing variants in phage lambda, but suggest in first approximation that the exchange between the P2 DNA and the chromosome of the host bacterium may occur at several different bacterial sites. A map of the regulatory region of P2, based on all data available from the study of deletions and insertions, is presented.

Restriction cleavage maps of coliphages 186 and P2

The restriction enzymes BamHI, Bg/II, EcoRI, HindIII, PstI, XbaI and XhoI have been used to cleave DNA isolated from the related coliphages P2 and 186 for analysis on 1% agarose gels. Three approaches were used to map the sites of cleavage: a) analysis dependent upon the existence of cohesive termini and availability of viable P2-186 hybrids; b) analysis of double digests and redigests of isolated fragments with a second enzyme and c) analysis of partial digests by transfer to nitrocellulose and hybridization with a single fragment. This last approach and the results obtained from it are detailed in a separate paper (Saint and Egan, 1979). The number of sites of each enzyme are as follows: a) 186, BamHI-7, Bg/II-1, EcoRI-3, HindIII-2, PstI-22, XbaI-0 and Xho-I-1; b) P2, BamHI-3, Bg/II-2, EcoRI-3, HindIII-0, PstI-O, XbaI-1 and XhoI-O. All of these sites have been mapped with the exception of PstI for 186, where only the five sites in the right 35% (the control region) have been mapped.

Restriction endonuclease analysis of ribosomal DNA from Saccharomyces cerevisiae

The size and degree of homogeneity of the repetitive units in purified ribosomal DNA (gamma DNA) from Saccharomyces cerevisiae have been analyzed by restriction endonuclease digestion and heteroduplex mapping. Digestion of the gamma DNA with EcoRI yields seven fragments, digestion with Hind II+III yields five fragments, digestion with Hind III alone yields two fragments, and digestion with Sma I yields one fragment. The sum of the fragment molecular weights after digestion with each of the endonucleases is 5.5-5.6 x 10(6). When the DNA strands of the Sma I fragment are dissociated and reannealed, only homoduplexes are formed. We have concluded from these results that the repeating units in yeast ribosomal DNA are 5.6 x 10(6) datons and are homogeneous in size and composition.

EcoRI restriction endonuclease map of the composite R plasmid NR1

A physical map of the composite R plasmid NR1 has been constructed using specific cleavage of deoxyribonucleic acid (DNA) by the restriction endonuclease EcoR-. Digestion of composite NR1 DNA by EcoRI yields thirteen fragments. The six largest fragments (designated A to F) are from the resistance transfer factor component that harbors the tetracycline resistance genes (RTF-TC). The seven smallest fragments (designated G to M) are from the r-determinants component that harbors the chloramphenicol (CM), streptomycin-spectinomycin (SM/SP), and sulfonamide (SA) resistance genes. The largest fragment of several RTF-TC segregants of NR1 that have deleted the r-determinants component is 0.8 X 10(6) daltons larger than fragment A of composite NR1. Only a part of fragment H of the r-determinants component is amplified in transitioned NR1 DNA in Proteus mirabilis, which consists of multiple, tandem sequences of r-determinants attached to a single copy of the RTF-TC component. Both of these changes can be explained by the locations of the excision sites at the RTF-TC: r-determinants junctions that are involved in the dissociation and reassociation of the RTF-TC and r-determinants components. The thirteen fragments of composite NR1 DNA produced by EcoRI have been ordered using partial digestion techniques. The order of the fragments is: A-D-C-E-F-B-H-I-L-K-G-M-J. The approximate locations of the TC, CM, SM/SP, and SA resistance genes on the EcoRI map were determined by analyzing several deletion mutants of NR1.

Isolation of phage P2-186 intervarietal hybrids and 186 insertion mutants

Intervarietal hybrids formed between coliphages P2 and 186 have been isolated and their preliminary genetic characterization described. Three insertion mutants of 186 have also been isolated.