Cloning of DNA fragments of the right end of phage mu and location of the HindIII, SalI, PstI, and BamHI restriction sites on the genetic map of mu

Functionally distinct RNA polymerase binding sites in the phage Mu mom promoter region

Transcription of the phage Mu com/mom operon is trans-activated by another phage gene product, C, a site-specific DNA binding protein. To gain insight into the mechanism by which C activates transcription, we carried out footprinting analyses of Escherichia coli RNA polymerase (= RNAP) binding to various com-lacZ fusion plasmids. KMnO4-sensitive sites (diagnostic of the melted regions in open-complexes) and DNase I-sensitive sites were located by primer-extension analysis. The results are summarized as follows: (i) in vivo, in the absence of C, RNAP bound in the wild-type (wt) promoter region at a site designated P2; in vitro DNase I-footprinting showed that P2 extends from -74 to -24 with respect to transcription initiation. This overlaps a known strong C-binding site (at -35 to -54). RNAP bound at P2 appeared to be in an open-complex, as evidenced by the presence of KMnO4-hypersensitive sites. (ii) In contrast, when C was present in vivo, RNAP bound in the wt promoter region at a different site, designated P1, located downstream and partially overlapping P2. RNAP bound at P1 also appeared to be in an open-complex, as evidenced by the presence of KMnO4-hypersensitive sites. (iii) Two C-independent mutants, which initiate transcription at the same position as the wt, were also analyzed. In vivo, in the absence of C, RNAP bound mutant tin7 (contains a T to G substitution at -14) predominantly at P1; in vitro DNase I-footprinting showed that P1 extends from -56 to +21. With mutant tin6 (a 63 base-pair deletion removing P2, as well as part of P1 and the C-binding site from -35 to -54), RNAP bound to P1 independent of C. We conclude that P1 is the 'functional' RNAP binding site for mom-transcription initiation, and that C activates transcription by promoting binding at P1, while blocking binding at P2.

The bacteriophage Mu gem gene: a positive regulator of the C operon required for normal levels of late transcription

The gem product of bacteriophage Mu modulates synthesis of various host proteins and alters the host chromosome topology. To elucidate the role of the gem gene in Mu development, we analyzed the behavior of several mutants in this gene. The results, obtained with two Mu gem- phages, show that (1) phage growth is significantly delayed and inhibited, (2) early transcription is normal but late transcription is delayed and reduced, (3) DNA replication appears normal, and (4) the Mu C gene, whose product positively regulates Mu late genes, is one of the gem target sites. Transcription of a C promoter-lacZ fusion, carried by the pPH91 plasmid, is stimulated both after infection with Mu gem+ or Mu gem3 and is strains lysogenic for the same phages in the presence of viral immunity. These data suggest that the primary role of the gem product is modulation of gene expression. This control could be carried out by direct interaction with transcription factors or by changing DNA supercoiling.

Localization and regulation of bacteriophage Mu promoters

Mu promoters active during the lytic cycle were located by isolating RNA at various times after induction of Mu prophages, radiolabeling it by capping in vitro, and hybridizing it to Mu DNA fragments on Southern blots. Signals were detected from four new promoters in addition to the previously characterized Pe (early), PcM (repressor), and Pmom (late) promoters. A major signal upstream of C was first observed at 12 min and intensified thereafter with RNA from cts and C amber but not replication-defective prophages; these characteristics indicate that this signal arises from a middle promoter, which we designate Pm. With 20- and 40-min RNA, four additional major signals originated in the C-lys, F-G-I, N-P, and com-mom regions. These signals were missing with RNA from C amber and replication-defective prophages and therefore reflected the activity of late promoters, one of which we presume was Pmom. Uninduced lysogens showed weak signals from five regions, one from the early regulatory region, three between genes B and lys, and one near the late genes K, L, and M. The first of these probably resulted from PcM activity; the others remain to be identified.

Bacteriophage Mu late promoters: four late transcripts initiate near a conserved sequence

Late transcription of bacteriophage Mu, which results in the expression of phage morphogenetic functions, is dependent on Mu C protein. Earlier experiments indicated that Mu late RNAs originate from four promoters, including the previously characterized mom promoter. S1 nuclease protection experiments were used to map RNA 5' ends in the three new regions. Transcripts were initiated at these points only in the presence of C and were synthesized in a rightward direction on the Mu genome. Amber mutant marker rescue analysis of plasmid clones and limited DNA sequencing demonstrated that these new promoters are located between C and lys, upstream of I, and upstream of P within the N gene. A comparison of the promoter sequences upstream from the four RNA 5' ends yielded two conserved sequences: the first (tA . . cT, where capital and lowercase letters indicate 100 and 75% base conservation, respectively), at approximately -10, shares some similarity with the consensus Escherichia coli sigma 70 -10 region, while the second (ccATAAc CcCPuG/Cac, where Pu indicates a purine), in the -35 region, bears no resemblance to the E. coli -35 consensus. We propose that these conserved Mu late promoter consensus sequences are important for C-dependent promoter activity. Plasmids containing transcription fusions of these late promoters to lacZ exhibited C-dependent beta-galactosidase synthesis in vivo, and C was the only Mu product needed for this transactivation. As expected, the late promoter-lacZ fusions were activated only at late times after induction of a Mu prophage. The C-dependent activation of lacZ fusions containing only a few bases of the 5' end of Mu late RNA and the presence of altered promoter sequences imply that C acts at the level of transcription initiation.

Localization and DNA sequence analysis of the C gene of bacteriophage Mu, the positive regulator of Mu late transcription

The C gene of bacteriophage Mu, required for transcription of the phage late genes, was localized by construction and analysis of a series of deleted derivatives of pKN50, a plasmid containing a 9.4 kb Mu DNA fragment which complements Mu C amber mutant phages for growth. One such deleted derivative, pWM10, containing only 0.5 kb of Mu DNA, complements C amber phages and transactivates the mom gene, one of the Mu late genes dependent on C for activation. The DNA sequence of the 0.5 kb fragment predicts a single long open reading frame coding for a 140 amino acid protein. Sequence analysis of DNA containing a C amber mutation located the base change to the second codon of this reading frame. Generation of a frameshift mutation by filling in a BglII site spanning codon 114 of this reading frame resulted in the loss of C complementation and transactivation activity. These results indicate that this open reading frame encodes the Mu C gene product. Comparison of the predicted amino acid sequence of the C protein with those of other transcriptional regulatory proteins revealed some similarity to a region highly conserved among bacterial sigma factors.

Morphogenetic structures present in lysates of amber mutants of bacteriophage Mu

The Mu phage particle is structurally similar to that of the T-even phages, consisting of an icosahedral head and contractile tail. This study continues an analysis of the morphogenesis of the Mu phage particle by defining the structural defects resulting from mutations in specific Mu genes. Defective lysates produced by induction of 55 amber mutants, representing 24 essential genes, were examined in the electron microscope and categorized into eight classes based on the observed phage-related structures. (1) Mutations in genes lys, F and G, and some H mutations, did not cause a visible alteration in particle structure. (2) Mutants defective in genes A, B, and C produced no detectable phage structures, consistent with their lack of production of late RNA. (3) Extracts defective in genes L, M, Y, N, P, Q, V, W, and R contained only head structures, and these appeared normal. (4) K-defective mutants accumulated free heads as well as free tails which were longer than normal and variable in length. (5) Tails which appeared normal were the only structures found in T- and some I-defective extracts. (6) Free tails and empty heads accumulated in D-, E-, and some I- and H-defective extracts. These heads were as much as 16% smaller than normal heads. The heads found in some I amber lysates had a protruding neck-like structure and unusually thick shells suggestive of a scaffolding-like structure. (7) Defects in gene J resulted in the accumulation of unattached tails and full heads. (8) Previous analysis of lysates produced by inversion-defective gin mutants fixed in the G(+) orientation demonstrated that S and U mutants produced particles lacking tail fibers (F.J. Grundy and M.M. Howe (1984), Virology 134, 296-317). In these experiments with Gin+ phages S and U mutants produced apparently normal phage particles. Presumably the tail fiber defects were masked by the production of S' and U' proteins by G(-) phages in the population.

Multiple factors and processes involved in host cell killing by bacteriophage Mu: characterization and mapping

The regions of bacteriophage Mu involved in host cell killing were determined by infection of a lambda-immune host with 12 lambda pMu-transducing phages carrying different amounts of Mu DNA beginning at the left end. Infecting lambda pMu phages containing 5.0 (+/- 0.2) kb or less of the left end of Mu DNA did not kill the lambda-immune host, whereas lambda pMu containing 5.1 kb did kill, thus locating the right end of the kil gene between approximately 5.0 and 5.1 kb. For the Kil+ phages the extent of killing increased as the multiplicity of infection (m.o.i.) increased. In addition, killing was also affected by the presence of at least two other regions of Mu DNA: one, located between 5.1 and 5.8 kb, decreased the extent of killing; the other, located between 6.3 and 7.9 kb, greatly increased host cell killing. Killing was also assayed after lambda pMu infection of a lambda-immune host carrying a mini-Mu deleted for most of the B gene and the middle region of Mu DNA. Complementation of mini-Mu replication by infecting B+ lambda pMu phages resulted in killing of the lambda-immune, mini-Mu-containing host, regardless of the presence or absence of the Mu kil gene. The extent of host cell killing increased as the m.o.i. of the infecting lambda pMu increased, and was further enhanced by both the presence of the kil gene and the region located between 6.3 and 7.9 kb. These distinct processes of kil-mediated killing in the absence of replication and non-kil-mediated killing in the presence of replication were also observed after induction of replication-deficient and kil mutant prophages, respectively.

Role of the F factor oriV1 region in recA-independent illegitimate recombination. Stable replicon fusions of the F derivative pOX38 and pBR322-related plasmids

We have used a mating protocol to isolate recA-independent recombinants of pOX38 , an F factor derivative, and the non-conjugative plasmid pMBO311 . Plasmid pMBO311 is a derivative of pBR322 carrying a DNA insertion that contains IS121 and shows no extensive sequence homology to pOX38 . Twenty-seven cointegrate molecules formed during independent mobilizations of pMBO311 by pOX38 were examined by restriction and Southern hybridization analysis. In general, there were two classes of recombinants. A minority class appears to have been mediated by IS121 , resulting in the formation of cointegrate molecules containing IS121 at the junctions between the two plasmids. The majority class (23/27) apparently involved reciprocal recombination between sites on pOX38 and pMBO311 . IS121 does not seem to be responsible for the formation of this type of cointegrate molecule, since similar structures were generated at approximately the same frequency during mobilization of control plasmids that do not contain IS121 . We have localized the regions involved in this second class of recombination events and find that most (17/23) occur at or near oriV1 , the primary replication initiation site of pOX38 . Twelve of the cointegrate molecules showed identical restriction and Southern hybridization patterns demonstrating a preferred region on pMBO311 as well. This site was localized just distal to the tet genes, within a 640-base AvaI-PvuII segment in the pBR322 portion of the molecule.

Involvement of the invertible G segment in bacteriophage mu tail fiber biosynthesis

The orientation [G(+) or G(-)] of the invertible G segment of bacteriophage Mu DNA determines the host range specificity of the phage particles. In this study the hypothesis that the G segment genes are involved in synthesis of Mu tail fibers has been tested. Serum blocking power (SBP) assays demonstrated that among Mu late gene mutants only those defective in genes S or U encoded by the G segment were defective in G(+) SBP and that they lacked the same antigens. Electron microscopy of lysates produced by inversion-defective gin mutants (isolated by their inability to complement a hin inversion-defective mutant of the Salmonella phase variation segment) showed that G(+) phages with amber mutations in S or U made tail-fiberless particles with contracted tail sheaths. Inversion of G to the G(-) orientation or suppression of the amber mutations restored the normal phage particle morphology. These experiments demonstrate that genes S and U are required for Mu G(+) tail fiber biosynthesis and/or attachment.

A new insertion sequence, IS121, is found on the Mu dI1 (Ap lac) bacteriophage and the Escherichia coli K-12 chromosome

We have discovered a new insertion sequence, now designated IS121, as a component of the Mu dI1 (Ap lac) phage. This sequence is 1.2 kilobases long and contains single recognition sites for the HincII, Bg1II, and HindIII restriction endonucleases. IS121 is present in at least three copies in the chromosome of several Escherichia coli K-12 strains. When present in the nonconjugative plasmid pBR322, IS121 can mediate cointegrate formation with an F' lac plasmid and transfer of pBR322 sequences to suitable recipients. IS121 is also capable of precise or nearly precise excision. As part of the study of IS121, we have determined the physical structure of the Mu dI1 (Ap lac) phage and established an extensive restriction endonuclease map of this phage. A revised schema for the formation of the Mu dI1 (Ap lac) phage is presented.

AvaII and BglI restriction maps of bacteriophage Mu

The AvaII and BglI restriction maps of bacteriophage Mu were derived by restriction analysis of a series of plasmid clones containing segments of Mu DNA which, in combination, covered the entire Mu genome. The plasmids analyzed included pKN36, pKN54, pKN62, pKN50, pKN35, pKN27, pKN48, pKN82, and pKN56 from the collection of W. Schumann and E. G. Bade, and pCM02, a newly constructed plasmid containing the rightmost internal EcoRI-PstI fragment of Mu DNA. BglI cuts Mu DNA at 23 sites, producing 24 fragments which range in size from 0.05 kb up to the approximately 7-kb fragment derived from the right end. AvaII cuts Mu DNA at 17 sites (including 2 within the G segment), producing fragments which range in size from 0.17 to 8.9 kb. The derived maps were confirmed by results of hybridization of 32P-labeled, nick-translated plasmid DNA to AvaII- and BglI-digested Mu DNAs. Evidence for modification of one of the AvaII sites in E. coli was obtained.

Physical characterization of mini-mu and mini-D108

Several derivatives of phages Mu and D108 have been isolated that carry an internal deletion generated by one of the IS1 components of a Tn9 transposon located in the A, B, or S gene of the prenatal phage. The deletions remove most of the lytic functions of the phage but leave intact either genes A and B or gene A and the left and the right end of the phages. These deleted derivatives, called mini-Mu and mini-D108, were physically characterized by electron microscopy and digestion with restriction enzymes. Mini-Mu and mini-D108, which carry an antibiotic resistance marker, are described and some of their genetic properties are summarized in the paper by Toussaint et al. (1981).

In vitro and in vivo manipulations of bacteriophage Mu DNA: cloning of Mu ends and construction of mini-Mu's carrying selectable markers

Recombinant plasmids carrying one or both ends of the bacteriophage Mu genome were constructed by molecular cloning. Transposable mini-Mu's with selectable markers (ampicillin resistance, kanamycin resistance or the entire lac operon of Escherichia coli) inserted between the Mu ends were also constructed. As a source of lac operon DNA, a pBR322 derivative with a 27 kb insert containing the lac operon was constructed. The plasmids with both ends of Mu (mini-Mu's) conferred full Mu immunity upon the host cells. However, the same mini-Mu's containing kan or lac inserts were defective in immunity. A summary of the construction and physical characterization, including restriction endonuclease cleavage maps and some of the biological properties of the plasmids, is presented.