Properties of the recombinant plasmid pGP1 containing part of the early region of bacteriophage mu

Quantitation of DNA-Binding Affinity Using Tethered Particle Motion

The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered Particle Motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to reliably measure binding constants of proteins binding to DNA, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This makes it possible to measure binding properties. We use the bacterial protein Integration Host Factor (IHF) as an example to show how specific binding to DNA can be measured. Moreover, we show a new intuitive quantitative approach to displaying data obtained via TPM.

Regulation of phage Mu repressor transcription by IHF depends on the level of the early transcription

Integration Host Factor (IHF) of E. coli can stimulate both early and repressor transcription of bacteriophage Mu. We introduced several mutations in the early promoter (Pe) and studied the effect of these mutations on the stimulation of early and repressor transcription by IHF. All mutant promoters are still positive regulated by IHF, but the level of stimulation is dependent on the strength of the promoter. The strength of the early promoter has an even greater impact on the regulation of the repressor promoter by IHF: stimulation is observed in the presence of a relatively weak Pe, whereas with a strong Pe the repressor promoter Pc is inhibited by IHF. This inhibition is most probably due to an interference of the early transcription with the opposing repressor transcription. The implication of this type of regulation for the Mu life cycle is discussed.

Autoregulation of phage mu transposase at the level of translation

The bacteriophage Mu A and B genes, which lie adjacent to each other and are colinear on the phage genome, encode proteins that catalyze efficient transposition of Mu DNA. We show that the molar ratio of A and B proteins is approximately 1:20 in extracts prepared after induction of cells containing a Mu lysogen or a plasmid carrying the Mu fragment that encompasses A and B. In cells harboring the cloned genes, the proteins are synthesized from a single transcript. Pulse-chase experiments demonstrate that the lower amounts of A protein are not from preferential turnover of this protein. This suggests the existence of a post-transcriptional mechanism to down-regulate A protein synthesis. From an analysis of the activity of several beta-galactosidase fusions to A protein, we infer that A protein may repress its own translation. By an agarose gel mobility-shift assay, we demonstrate that purified A protein binds specifically in vitro to its mRNA.

Integration host factor of Escherichia coli regulates early- and repressor transcription of bacteriophage Mu by two different mechanisms

Integration host factor (IHF) of E. coli positively regulates both early and repressor transcription of bacteriophage Mu. In this paper we show that although binding of IHF to the same binding site is responsible for both types of transcription regulation, the mechanisms by which these regulations occur are different: Activation of transcription from the early promoter (Pe) requires a helix-dependent orientation of IHF- and RNA polymerase binding sites on the DNA helix with a limited distance between both sites. Activation of repressor transcription shows no helix dependency between promoter and IHF binding site and the distance between both sites can be enlarged at least by 100 base pairs without affecting the positive control. A possible mechanism for both types of transcription stimulation will be discussed.

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.

Histonelike proteins of bacteria

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DNA sequence of the control region of phage D108: the N-terminal amino acid sequences of repressor and transposase are similar both in phage D108 and in its relative, phage Mu

We have determined the DNA sequence of the control region of phage D108 up to position 1419 at the left end of the phage genome. Open reading frames for the repressor gene, ner gene, and the 5' part of the A gene (which codes for transposase) are found in the sequence. The genetic organization of this region of phage D108 is quite similar to that of phage Mu in spite of considerable divergence, both in the nucleotide sequence and in the amino acid sequences of the regulatory proteins of the two phages. The N-terminal amino acid sequences of the transposases of the two phages also share only limited homology. On the other hand, a significant amino acid sequence homology was found within each phage between the N-terminal parts of the repressor and transposase. We propose that the N-terminal domains of the repressor and transposase of each phage interact functionally in the process of making the decision between the lytic and the lysogenic mode of growth.

Conditionally transposition-defective derivative of Mu d1(Amp Lac)

A Mu d1 derivative is described which is useful for genetic manipulation of Mu-lac fusion insertions. A double mutant of the specialized transducing phage Mu d1(Amp Lac c62ts) was isolated which is conditionally defective in transposition ability. The Mu d1 derivative, designated Mu d1-8(Tpn[Am] Amp Lac c62ts), carries mutations which virtually eliminate transposition in strains lacking an amber suppressor. In such strains, the Mu d1-8 prophage behaves like a standard transposon. It can be moved from one strain of Salmonella typhimurium to another by the general transducing phage P22 with almost 100% inheritance of the donor insertion mutation. When introduced into a recipient carrying supD, supE, or supF, 89 to 94% of the Ampr transductants were transpositions of the donor Mu d1-8, from the transduced fragment into new sites. The stability of Mu d1-8 in a wild-type, suppressor-free background was sufficient to permit use of the fusion to select constitutive mutations without prior isolation of deletions to stabilize the fusion. Fusion strains could be grown at elevated temperature without induction of the Mu d prophage. The transposition defect of Mu d1-8 was corrected by a plasmid carrying the Mu A and B genes.

Mutator bacteriophage D108 and its DNA: an electron microscopic characterization

Three types of phage particles were observed on CsCl step gradients when D108 was purified from lysates prepared by induction of a prophage. These particle types were identified to be the mature phage, tailless DNA-filled heads, and a form of nucleoprotein aggregates. The nucleoprotein aggregates banded at a density (rho) of greater than 1.6. DNA molecules isolated from mature phage particles were (38.305 +/- 1.226) kilobases (kb) in length. Denaturation and renaturation of D108 DNA resulted in the formation of linear double-stranded molecules with variable-length single-stranded tails at one end. About 30% of the annealed molecules also carried an internal nonhomology, which was shown to be the region called the G-loop in Mu and P1 DNAs. Following the notation used for different regions of denatured, annealed Mu DNA, we measured the lengths of the equivalent D108 DNA regions to be as alpha-D108 = (32.178 +/- 1.370) kb; G-D108 = (3.07 +/- 0.382) kb; beta-D108 = (2.291 +/- 0.306) kb; SE-D108 = (0.966 +/- 0.433) kb. Formation of D108; Mu heteroduplexes disclosed the presence of five nonhomologies, two of which were partial. One of the partial heterologies was in the G-loop region. The largest nonhomology, (1.393 +/- 0.185) kb in size, was near the c end (immunity region) and probably spans the c and the ner genes of Mu. beta-D108 was shown to carry a (0.556 +/- 0.097)-kb insertion close to its right end. A short 100-base-pair region appeared to have been conserved at the ends of D108 and Mu. Occasionally, a 50-to 100-base-pair-long unpaired region was also observed at the left end of D108: Mu heteroduplexes. These sequences were presumably of bacterial DNA. Taken together, our results complement and extend our earlier genetic studies which established that D108 was a mutator phage heteroimmune to Mu with a host range different from Mu's.