Transcription of bacteriophage Mu. II. Transcription of the repressor gene

Unusual transcriptional and translational regulation of the bacteriophage Mu mom operon

The bacteriophage Mu mom gene encodes a novel DNA modification that protects the viral genome against a wide variety of restriction endonucleases. Expression of mom is subject to a series of unusual regulatory controls. Transcription requires the action of a phage-encoded protein, C, which binds (probably as a dimer) the mom promoter from -33 to -52 (with respect to the transcription start site) in two adjacent DNA major grooves on one face of the helix. No apparent direct interaction between C and the host RNA polymerase (RNAP) is evident; however, C binding alters mom DNA conformation. In the absence of C, RNAP binds the mom promoter at a site that results in transcription in a direction away from the mom gene. The function of this transcription is unknown. An additional layer of transcriptional regulation complexity is due to the fact that the host Dam DNA-(N6-adenine)methyltransferase is required. Dam methylation of three closely spaced upstream GATC sequences is necessary to prevent binding by the host protein, OxyR, which acts as a repressor. Repression is not mediated by inhibition of C binding, but rather through interference with C-mediated recruitment of RNAP to the correct site. Translation of mom is regulated by the phage Com protein. Com is only 62 amino acids long and contains a zinc finger-like structure (coordinated by four cysteine residues) in the amino terminal domain. Com binds mom mRNA 5' to the mom open reading frame, whose translation start signals are contained in a stem-loop translation-inhibition-structure. Com binding to its target site (5' to and adjacent to the translation-inhibition-structure) results in a stable change in RNA secondary structure that exposes the translation start signals.

Regulatory factors acting at the bacteriophage Mu middle promoter

Lytic development of bacteriophage Mu proceeds through three phases of transcription: early, middle, and late. Initiation of middle transcription from Pm requires the phage-encoded activator, Mor. An examination of the sequences surrounding the promoter revealed possible binding sites for Mu proteins A and c, as well as for Escherichia coli integration host factor. Promoter fragments containing 5' and 3' deletions were fused to the lacZ reporter gene and assayed for activity after induction of a Mu prophage or a plasmid-borne mor gene. Sequences upstream of position -62 and downstream of +10 were dispensable for promoter activity. In DNase I footprinting with both crude extract and purified protein, Mor protected Pm sequences from position -56 to -33. Mutations disrupting the dyad symmetry of the terminator of early transcription overlapping the Mor binding site did not reduce promoter activity, suggesting that the symmetry per se is not required for Mor binding or Pm activation. Purified Mu lysogenic repressor (c) also bound to Pm, overlapping the Mor binding site. Production of large amounts of repressor in vivo reduced Mor-dependent promoter activity nearly 10-fold. Promoters with mutations in the repressor binding site showed a reduction in this repressor-mediated inhibition of Pm activity.

Bacteriophage Mu Mor protein requires sigma 70 to activate the Mu middle promoter

Transcription during the bacteriophage Mu lytic cycle occurs in three phases: early, middle, and late. Middle transcription requires the early gene product Mor for its activation. Mor protein overproduction was accomplished by fusing the mor gene to an efficient phage T7 promoter and translation initiation region. A protein fraction highly enriched for Escherichia coli RNA polymerase (E sigma 70) from the Mor-overproducing strain was able to activate transcription from both the tac promoter (Ptac) and the Mu middle promoter (Pm) in vitro. Transcription initiation from Pm was Mor dependent, and the RNA 5' end was identical to that of in vivo RNA. Addition of anti-sigma 70 antibody to transcription reactions containing Ptac and Pm resulted in inhibition of transcription from both promoters; addition of purified sigma 70 restored transcription. These results indicate that Mor-dependent activation requires sigma 70 and therefore imply that Mor is not an alternate sigma factor. This conclusion was further substantiated by a reconstitution experiment with purified proteins in which all three components, Mor, sigma 70, and core RNA polymerase, were required for Pm-dependent transcription in vitro. The sigma 70 dependence of Mor-specific transcription and the amino acid sequence similarity between Mor and C (an activator for Mu late transcription) both support the hypothesis that Mor functions mechanistically as an activator protein.

Kinetics and regulation of transcription of bacteriophage Mu

Mu transcription was analyzed by hybridization of [3H]uridine pulse-labeled RNA from heat-induced Mu lysogens to Mu DNA restriction fragments on nitrocellulose blots. Based on their time of appearance and dependence on Mu functions, we have defined three classes of transcripts: early, middle, and late. Replication-defective prophages containing A or B amber mutations or a deletion of the beta (right) end produced only early RNA derived from the left-most 8 to 10 kb of the Mu genome. A replication-proficient C amber mutant exhibited similar early transcription but at later times also produced middle transcripts from a region including C, which encodes the activator of late transcription. The C mutant did not produce late transcripts from the right-most 26 kb of the Mu genome encoding genes involved in phage morphogenesis and release. These results indicate that Mu DNA replication is required for efficient expression of middle RNA, which is itself required for expression of late transcripts. Amber mutations in essential genes other than A, B, and C had no significant effect on transcription except for polarity of one E mutation. Uninduced Mu c+ and Mu cts prophages produced very low levels of Mu-specific RNA derived from several regions including the c (immunity) gene and the region between genes B and C.

Minute amounts of RNA are synthesized from several regions of the bacteriophage Mu DNA during the lysogenic state

The transcription of phage Mu DNA during the lysogenic state has been quantitatively analysed. For this purpose pulse-labelled RNA from two lysogens and from their nonlysogenic parental strains were hybridized to non-overlapping Mu DNA restriction fragments covering the whole phage genome. The data revealed that all regions of the prophage are transcribed at low rates and that phage promoters are involved in this transcription. For this study an improved assay for quantitative filter hybridization was employed. The high sensitivity and reproducibility that can be obtained with the assay make it suitable for the quantitative analysis of minute amounts of mRNA.

Purification and characterization of the Ner repressor of bacteriophage Mu

The Ner protein of bacteriophage Mu acts as a lambda cro-like negative regulator of the phage's early (transposase) operon. Using the band retardation assay to monitor ner-operator-specific DNA-binding activity, the 8 kDa Ner protein was purified to homogeneity. DNase I footprinting revealed that the purified protein bound and protected a specific DNA operator that contains two 12 bp sites with the consensus sequence 5'-ANPyTAPuCTAAGT-3', separated by a 6 bp spacer region. Moreover, regions corresponding to a turn of the DNA helix flanking these 12 bp repeats are also protected by Ner. Unlike the functionally similar lambda cro protein, gel filtration experiments show that the native molecular mass of Mu Ner to be approx. 8 kDa. These results, plus the pattern of DNase I protection, suggest that the protein may bind as a monomer to each of its specific DNA substrates.

Lysogenization of Escherichia coli him+, himA, and himD hosts by bacteriophage Mu

The possible outcomes of infection of Escherichia coli by bacteriophage Mu include lytic growth, lysogen formation, nonlysogenic surviving cells, and perhaps simple killing of the host. The influence of various parameters, including host himA and himD mutations, on lysogeny and cell survival is described. Mu does not grow lytically in or kill him bacteria but can lysogenize such hosts. Mu c+ lysogenizes about 8% of him+ bacteria infected at low multiplicity at 37 degrees C. The frequency of lysogens per infected him+ cell diminishes with increasing multiplicity of infection or with increasing temperature over the range from 30 to 42 degrees C. In him bacteria, the Mu lysogenization frequency increases from about 7% at low multiplicity of infection to approach a maximum where most but not all cells are lysogens at high multiplicity of infection. Lysogenization of him hosts by an assay phage marked with antibiotic resistance is enhanced by infection with unmarked auxiliary phage. This helping effect is possible for at least 1 h, suggesting that Mu infection results in formation of a stable intermediate. Mu immunity is not required for lysogenization of him hosts. We argue that in him bacteria, all Mu genomes which integrate into the host chromosome form lysogens.

Isolation of point mutations in bacteriophage Mu attachment regions cloned in a lambda::mini-Mu phage

Twenty-one derivatives of a lambda::mini-Mu phage containing point mutations in the Mu attachment regions were isolated after mutD mutagenesis and selection for relief from Mu-specific replicative interference of lambda growth. DNA sequence analysis revealed that the single left-end mutant had suffered a T----C transition at position 1 of the Mu sequence, while the remaining 20 right-end mutants contained single base-pair insertions or deletions within the terminal 19 base pairs. A genetic assay showed that the right-end mutations revealed by sequencing were necessary for relief of the replicative inhibition of lambda growth. The properties of these mutants suggest that the terminal 2-base-pair and subterminal 8-base-pair inverted repeats are important for Mu-specific replicative transposition.

Role of ner protein in bacteriophage Mu transposition

The Ner protein of bacteriophage Mu negatively regulates transcription initiated at the early promoter and at the major repressor promoter. The construction and isolation of a Ner- mutant of Mu is described. Ner is an essential function for Mu, because the mutant phage only forms plaques when complemented for Ner. Mutations in the repressor protein did not abolish the need for Ner. However, when transcription of the repressor gene c was blocked by deleting the major repressor promoter, Ner was no longer essential for normal Mu development.

The overproduction and characterization of the bacteriophage Mu regulatory DNA-binding protein ner

The bacteriophage Mu ner gene has been cloned under the control of the lacUV5 promoter in the expression vector pOP95-15. The gene products of the recombinant plasmid, pUD88, visualized by in vitro coupled transcription-translation, are the bacteriophage Mu ner protein (8 kDa) and a 23 KDa protein consisting of the amino terminus of gpA (Mu transposase) fused to the carboxy terminus of beta-lactamase. DNA-binding activity was measured by the retardation of migration of a 32P-labeled DNA restriction fragment (containing the presumed ner-binding sites) in polyacrylamide gels. We have demonstrated specific association of ner to its binding sites to occur within 30 sec after the addition of impure extracts of ner overproducing cells. Much of this binding was dissociated within 30 sec by competition with a 20-fold molar excess of specific unlabeled DNA restriction fragment, but was resistant to dissociation when competed with unlabeled heterologous DNA for as long as 45 min at 37 degrees. By adapting a method for DNA-footprinting using impure extracts of ner overproducing cells, we were able to determine that the ner-binding sites are located between nucleotides 1026 and 1058 from the Mu left end. These results support the hypothesis that ner is similar to the cro regulatory protein from bacteriophage lambda and acts to regulate Mu early gene expression and the choice between lytic and lysogenic development.

Preferential binding of bacteriophage Mu repressor to supercoiled Mu DNA

It was shown, using a relatively simple assay, that Mu repressor, cI, binds specifically to a region which spans the leftmost HindIII cleavage site on the phage genome. This extends the observations of Kwoh and Zipser [Nature (London) 277, 489-491 (1979)], who were able to define a binding region to the left of this site. These results provide support for the idea that the eight blocks of repeated DNA sequences, which also span the HindIII cleavage site, are involved in repressor binding. These results also indicate that cI repressor has a marked preference for supercoiled DNA.

Regulation of Mu transposition. II. The escherichia coli HimD protein positively controls two repressor promoters and the early promoter of bacteriophage Mu

Two leftward Pc promoters for the repressor gene of bacteriophage Mu have been localized by fusions of the promoter region to the structural galK gene and by S1 nuclease mapping. Transcription initiated at the left-end-proximal promoter (Pc-1) starts 23 bp ahead of the c gene. The second promoter (Pc-2) is located 200 bp from the translation start codon of gene c. The RNA initiated from Pc-2 overlaps 35 bp with the rightward transcript from the early Mu promoter (Pe). The expression from Pe and both repressor promoters is positively regulated by the Escherichia coli HimD (Hip) protein, probably acting as a subunit of the integration host factor (IHF). Two overlapping sequences matching the consensus for the IHF binding site (ihf) are found between Pe and Pc-1.

Cloning and expression of the phage Mu A gene

We have cloned the phage Mu A gene, with and without the gene ner, under the control of the pL promoter of phage lambda in a multicopy plasmid vector. We demonstrate that plasmid-carrying cells are able to support growth of superinfecting Mu A am phages in a temperature-dependent fashion in a host strain carrying a defective lambda prophage which specifies the cI857-coded lambda repressor. In addition, we show that the presence of the ner gene reduces the efficiency of plating of the superinfecting phage. Analysis of proteins specified by the cloned Mu fragments indicates that two proteins, 70 and 33 kDal, are synthesized. The level of synthesis, compared to that of the vector-encoded beta-lactamase, was found to increase with temperature. This indicates that their transcription is driven by the pL promoter. The Mr of the 70-kDal protein is identical to that previously observed for pA.

The early promoter of bacteriophage Mu: definition of the site of transcript initiation

The early promoter of bacteriophage Mu has been identified and characterized by a nitrocellulose filter binding assay and analysis of RNA products transcribed in vitro and in vivo. A tight, heparin resistant, RNA polymerase-DNA binding site overlaps the left Mu Hind III site. In vitro [gamma 32P] ATP initiated transcription begins approximately 25 nucleotides to the right of the Hind III restriction site. Dinucleotide initiation with ApA and S1 mapping of in vitro and in vivo transcripts shows that transcription is initiated 1028 base pairs from the Mu genetic left end.

Nucleotide sequence of the immunity region of bacteriophage Mu

The leftmost 1590 bp of Mu DNA covering the immunity region have been sequenced. This region encodes the cI repressor, the cII or ner function and the beginning of gene A. An open reading frame extends from position 863 to 342 on the l-strand corresponding to cI protein with a molecular weight of 19212. It is preceded by a sequence resembling a promoter. To the right of the HindIII site an open reading frame extends from position 1099 to 1323 corresponding to cII or ner protein (molecular weight of 8505) followed by the beginning of gene A at position 1328. Between position 863 and 1099 promoters for leftward and rightward transcription and operator-like structures can be recognized in the sequence. The promoter for rightward transcription overlaps with the HindIII site and coincides with a RNA polymerase binding site as demonstrated by electron microscopy.