In vitro construction of bacteriophage lambda and plasmid DNA molecules containing DNA fragments from bacteriophage T4

Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future

The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.

Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis

Endonuclease IV encoded by denB of bacteriophage T4 is implicated in restriction of deoxycytidine (dC)-containing DNA in the host Escherichia coli. The enzyme was synthesized with the use of a wheat germ cell-free protein synthesis system, given a lethal effect of its expression in E.coli cells, and was purified to homogeneity. The purified enzyme showed high activity with single-stranded (ss) DNA and denatured dC-substituted T4 genomic double-stranded (ds) DNA but exhibited no activity with dsDNA, ssRNA or denatured T4 genomic dsDNA containing glucosylated deoxyhydroxymethylcytidine. Characterization of Endo IV activity revealed that the enzyme catalyzed specific endonucleolytic cleavage of the 5' phosphodiester bond of dC in ssDNA with an efficiency markedly dependent on the surrounding nucleotide sequence. The enzyme preferentially targeted 5'-dTdCdA-3' but tolerated various combinations of individual nucleotides flanking this trinucleotide sequence. These results suggest that Endo IV preferentially recognizes short nucleotide sequences containing 5'-dTdCdA-3', which likely accounts for the limited digestion of ssDNA by the enzyme and may be responsible in part for the indispensability of a deficiency in denB for stable synthesis of dC-substituted T4 genomic DNA.

Molecular cloning of gltS and gltP, which encode glutamate carriers of Escherichia coli B

Two genes encoding distinct glutamate carrier proteins of Escherichia coli B were cloned into an E. coli K-12 strain by using a cosmid vector, pHC79. One of them was the gltS gene coding for a glutamate carrier of an Na+-dependent, binding protein-independent, and glutamate-specific transport system. The content of the glutamate carrier was amplified about 25-fold in the cytoplasmic membranes from a gltS-amplified strain. The gltS gene was located in a 3.2-kilobase EcoRI-MluI fragment, and the gene product was identified as a membrane protein with an apparent Mr of 35,000 in a minicell system. A gene designated gltP was also cloned. The transport activity of the gltP system in cytoplasmic membrane vesicles from a gltP-amplified strain was driven by respiratory substrates and was independent of the concentrations of Na+, K+, and Li+. An uncoupler, carbonylcyanide m-chlorophenylhydrazone, completely inhibited the transport activities of both systems, whereas an ionophore, monensin, inhibited only that of the gltS system. The Kt value for glutamate was 11 microM in the gltP system and 3.5 microM in the gltS system. L-Aspartate inhibited the glutamate transport of the gltP system but not that of the gltS system. Aspartate was taken up actively by membrane vesicles from the gltP-amplified strain, although no aspartate uptake activity was detected in membrane vesicles from a wild-type E. coli strain. These results suggest that gltP is a structural gene for a carrier protein of an Na+-independent, binding protein-independent glutamate-aspartate transport system.

Identification of two new bacteriophage T4 genes that may have roles in transcription and DNA replication

We have identified two bacteriophage T4 genes, 45.1 and 45.2, that map in the intergenic space between phage replication genes 46 (which encodes a recombination initiation protein) and 45 (which encodes a bifunctional protein required in replication and transcription). The existence of genes 45.1 and 45.2 had not been previously recognized by mutation analysis of the T4 genome. We cloned the T4 gene 45.1/45.2 segment, determined its nucleotide sequence, and expressed its two reading frames at high levels in bacterial plasmids. The results predicted molecular weights of 11,400 (100 amino acids) for gp45.1 and 7,500 (62 amino acids) for gp45.2. We also determined that in T4-infected Escherichia coli, genes 45.1 and 45.2 are cotranscribed with their distal neighbor, gene 45, by at least one mode of transcription. In an accompanying report (K. P. Williams, G. A. Kassavetis, F. S. Esch, and E. P. Geiduschek, J. Virol. 61:600-603, 1987), it is shown that the product of gene 45.1 is the so-called T4-induced 15K protein, an RNA polymerase-binding protein of unknown role in phage development. Possibly, T4 genes 45.2, 45.1, and 45 constitute an operon for host RNA polymerase-binding phage proteins. Jointly with Williams et al., we propose the term rpb (RNA polymerase-binding) to refer to T4 genes whose products bind to the host RNA polymerase and have adopted the name rpbA for T4 gene 45.1.

Sequence organization and control of transcription in the bacteriophage T4 tRNA region

Bacteriophage T4 contains genes for eight transfer RNAs and two stable RNAs of unknown function. These are found in two clusters at 70 X 10(3) base-pairs on the T4 genetic map. To understand the control of transcription in this region we have completed the sequencing of 5000 base-pairs in this region. The sequence contains a part of gene 3, gene 1, gene 57, internal protein I, the tRNA genes and five open reading frames which most likely code for heretofore unidentified proteins. We have used subclones of the region to investigate the kinetics of transcription in vivo. The results show that transcription in this region consists of overlapping early, middle and late transcripts. Transcription is directed from two early promoters, one or two middle promoters and perhaps two late promoters. This region contains all of the features that are seen in T4 transcription and as such is a good place to study the phenomenon in more detail.

Structural genes for flagellar hook-associated proteins in Salmonella typhimurium

The flaW, flaU, and flaV genes of Salmonella typhimurium LT2 were cloned into pBR322. These genes were mapped on the cloned DNA fragments by restriction endonuclease analysis and construction of the deletion derivatives. Their gene products were identified, by the minicell method, as proteins whose molecular weights were estimated to be 59,000 for the flaW product, 31,000 for the flaU product, and 48,000 for the flaV product. These values are identical to those of three species of hook-associated proteins (HAPs), namely, HAP1, HAP3, and HAP2. Furthermore, antibodies against HAP1, HAP3, and HAP2 specifically reacted with the gene products of flaW, flaU, and flaV, respectively. Therefore, we concluded that they are structural genes for HAPs. The antibodies against HAP1 and HAP3 also specifically reacted with the gene products of flaS and flaT of Escherichia coli, respectively. This indicates that these gene products are HAPs in E. coli. This result is consistent with the demonstration that flaS and flaT of E. coli are functionally homologous with flaW and flaU of S. typhimurium.

New control elements of bacteriophage T4 pre-replicative transcription

Bacteriophage T4 pre-replicative genes are transcribed, by Escherichia coli RNA polymerase, in two alternative modes: an early mode and a middle mode. Middle mode transcription is under the control of at least one viral protein, pmotA. We have identified two additional viral genes, motB and motC, that map in the dispensable region of the T4 genome, between genes 39 and 56. pmotB and pmotC are diffusible factors which provide an alternative to the motA dependent mode of middle transcription of many T4 genes. Deletions of motB and motC are in fact lethal only in combination with a motA mutant. motB controls one of the alternative modes of transcription of the rIIA gene. When motA or motB are missing, transcription of rIIA is quantitatively unaffected; when both are missing the transcription rate drops by about 75%. Control of transcription of the tRNA gene cluster is more complex. Transcription of subcluster 2 is maximally reduced (70%) only by deletions that, besides motB, cut out an adjacent region. We guess that this adjacent region codes for an additional control element, which we call motC. The motB gene is situated in a 750-base region between the left end-points of del(39-56)-1 and -4.

Nucleotide sequence of the lysozyme gene of bacteriophage T4. Analysis of mutations involving repeated sequences

The nucleotide sequence of the lysozyme (e) gene of bacteriophage T4 and approximately 130 additional nucleotides on each side has been determined. The 5'-end of the gene for internal protein III appears to be located about 70 base-pairs from the 3'-end of the lysozyme gene. Nucleotide sequence analysis of mutant e genes confirmed that three identified hotspots of frameshift mutations are runs of five A nucleotides in the wild-type gene. The endpoints of two deletions are direct repeats of eight base-pairs in the wild-type gene. Two frameshift mutations with high reversion frequencies are duplications of five or seven base-pairs. The cloning and nucleotide sequence determination of the lysozyme gene will facilitate further study of the molecular biology of T4 lysozyme.

Genetic specificity of DNA synthesized in the absence of T4 bacteriophage gene 44 protein

Upon infection of Escherichia coli B with T4 phage with DO amber mutation in gene 44, a minimal amount of phage DNA is synthesized. This progeny DNA is, for the most part, covalently attached to the parental DNA. Analysis of the genetic representation of this DNA was performed by hybridization to cloned genetic segments. It was shown that areas preferentially replicated differ from origins observed in "normal" replication: under normal conditions, there is a strong origin in the genetic area of genes 50-5 and lack of initiation within the group of genes 40-43 and 35-52. In contrast, in the absence of the gene 44 protein, the genetic area of 50-5 is underrepresented, genes 35-36, tRNA, and genes 40-41 are the most prominent among progeny DNA, and the area of gene 39 is least represented. Since the area of gene 35 is known from the genetic data or other to be a high-frequency recombination area, and since the area of gene 39 is known to display a low frequency of recombination, we postulate that the observed uptake of label occurs at the site-specific recombinational intersections.

Mechanism of pBR322 transduction mediated by cytosine-substituting T4 bacteriophage

A cytosine-substitution type mutant of bacteriophage T4 (T4dC phage) has been shown to mediate the transfer of plasmid pBR322. The transduction frequency was around 10(-2) per singly infected cell at low multiplicity of infection. The transductants contained either a monomer or multimers of pBR322. The transducing capacity of T4dC phage was resistant to methylmethanesulfonate treatment. The results of Southern blotting experiments have indicated that the pBR322 DNA exists as head-to-tail concatemers in the transducing particles. The mechanism of transfer of pBR322 mediated by T4dC phages is discussed.

In vivo expression of the rII region of bacteriophage T4 present in chimeric plasmids

The expression of the T4 rII genes in uninfected cells has been examined by use of recombinant plasmids. Hybridization analysis of pulse-labelled RNA prepared from cells carrying pTB101, a plasmid that contains the end of T4 gene 60 and the beginning of gene rIIA, shows that about 0.7% of the labelled RNA is rII specific. By contrast, only 0.02% of pulse-labelled RNA prepared from cells carrying plasmid pTB301, which probably contains the middle-mode rIB promoter, may be rII specific. When separated strands of T4 DNA were used for hybridization, we found that the pTB101 transcripts have a strand specificity identical to that of the rIIA transcripts made during phage infection. The same strand specificity was observed irrespective of the orientation of the inserted DNA in the vector. This result argues that the transcripts initiate within the inserted DNA rather than somewhere else on the plasmid. We also found that essentially none of the pulse-labelled pTB101 RNA would hybridize to the DNA of a T4 deletion mutant that lacks the rIIA gene. This suggests that little of the gene 60 DNA of the plasmid is being transcribed. In addition to the rII transcript, a new protein of 56,000 Daltons molecular weight is found in cells carrying pTB101. Fingerprint analysis of the protein shows that it is specified by the rIIA gene of the plasmid. Taken together, these results indicate that transcription of the plasmid rIIA gene initiates at or near the beginning of the gene.

Regulation of expression of cloned bacteriophage T4 late gene 23

The parameters governing the activity of the cloned T4 gene 23, which codes for the major T4 head protein, were analyzed. Suppressor-negative bacteria carrying wild-type T4 gene 23 cloned into plasmid pCR1 or pBR322 were infected with T4 gene 23 amber phage also carrying mutations in the following genes: (i) denA and denB (to prevent breakdown of plasmid DNA after infection) and (ii) denA, denB, and, in addition, 56 (to generate newly replicated DNA containing dCMP) and alc/unf (because mutations in this last gene allow late genes to be expressed in cytosine-containing T4 DNA). Bacteria infected with these phage were labeled with (14)C-amino acids at various times after infection, and the labeled proteins were separated by one-dimensional gel electrophoresis so that the synthesis of plasmid-coded gp23 could be compared with the synthesis of other, chromosome-coded T4 late proteins. We analyzed the effects of additional mutations that inactivate DNA replication proteins (genes 32 and 43), an RNA polymerase-binding protein (gene 55), type II topoisomerase (gene 52), and an exonuclease function involved in recombination (gene 46) on the synthesis of plasmid-coded gp23 in relation to chromosome-coded T4 late proteins. In the denA:denB:56:alc/unf genetic background, the phage chromosome-borne late genes followed the same regulatory rules (with respect to DNA replication and gp55 action) as in the denA:denB genetic background. The plasmid-carried gene 23 was also under gp55 control, but was less sensitive than the chromosomal late genes to perturbations of DNA replication. Synthesis of plasmid-coded gp23 was greatly inhibited when both the type II T4 topoisomerase and the host's DNA gyrase are inactivated. Synthesis of gp23 was also substantially affected by a mutation in gene 46, but less strongly than in the denA:denB genetic background. These observations are interpreted as follows. The plasmid-borne T4 gene 23 is primarily expressed from a late promoter. Expression of gene 23 from this late promoter responds to an activation event which involves some structural alteration of DNA. In these respects, the requirements for expressing the plasmid-borne gene 23 and chromosomal late genes are very similar (although in the denA:denB:56:alc/unf genetic background, there are significant quantitative differences). For the plasmid-borne gene 23, activation involves the T4 gp46, a protein which is required for DNA recombination. However, for the reasons presented in the accompanying paper (Jacobs et al., J. Virol. 39:31-45, 1981), we conclude that the activation of gene 23 does not require a complete breakage-reunion event which transposes that gene to a later promoter on the phage chromosome. Ways in which gp46 may actually be involved in late promoter activation on the plasmid are discussed.

Cloning of restriction fragments of DNA from staphylococcal bacteriophage phi 11

EcoRI fragments of Staphylococcus aureus bacteriophage phi 11 DNA were cloned in vector plasmid pSA2100 in S. aureus. The clones were analyzed in marker rescue experiments with suppressor- and temperature-sensitive mutants of phi 11 to correlate the genetic and physical map. Several mutants could be identified on the physical map, and a clone containing fragment EcoRI-B of phi 11 DNA expressed immunity to phage infection. In addition, it was found that recombinant plasmids containing phi 11 DNA sequences can be transferred by high-frequency transduction after phage phi 11 infection of host cells.

Inversions of specific DNA segments in flagellar phase variation of Salmonella and inversion systems of bacteriophages P1 and Mu

Prophages P1 and Mu produces a trans-acting factor possessing the din+ activity which catalyzes the inversion of the specific DNA segment responsible for flagellar phase variation of Salmonella, din mutants were isolated from PICMclr100 phage by selecting phages that did not suppress the yh2 mutation of Salmonella in prophage state. No inversion loop structure was detected among DNA forms arising after denaturation and rehybridization of DNAs extracted from the din mutants. The DNA fragment containing C region of P1 was cloned on a plasmid vector, pCR1. The resulting hybrid plasmid, pKK2, was shown to possess the din+ activity: the vh2 mutant of Salmonella harboring the plasmid changed the flagellar phase. From analysis of the plasmid by use of BamHI and Bgl II, the din gene specifying the din+ activity was located near or within the C region of P1. It is highly plausible that the din gene of P1 was also involved in the inversion of the C region. Similarly, the DNA fragment containing the G and beta segments of Mu was cloned on pCR1. The resulting hybrid plasmid, pII101, also possessed the din+ activity.

Complementation of T4 phage am mutations by hybrid phages lambda-T4

EcoRI fragments of the T4 cytosine-containing DNA (dC-DNA) were cloned in the lambda XIII vector phage carrying the only restriction site for EcoRI in the repressor gene of lambda. 38 genes of T4 were identified in the cloned fragments by means of marker rescue technique. All cloned early genes and some late genes of T4 were able to complement a corresponding am mutations of T4 phage when nonpermissive cells of E.coli were simultaneously infected with hybrid phages lambda-T4 and am mutants of T4. An average burst size for am mutants from su- cells (when complemented by corresponding hybrid phage) was 20-70 pfu for early genes and 1-3 to 20 pfu for late ones. When the extract of cells infected with hybrid phage lambda-T4-22 containing T4 genes 57, 1, 2, 64 was mixed with the extract of cells infected with T4N51 mutant, the complementation in vitro was observed. So, it was shown that normal product of late gene 2 is synthesized in the cells infected with hybrid phage lambda-T4-22 in the absence of positive regulators of transcription coded by early T4 genes.

A new host-vector system allowing selection for foreign DNA inserts in bacteriophage lambda gtWES

An improved vector (lambda gtWES.T5-622) for EcoRI fragments has been derived from EK2 vector lambda gtWES.lambdaB' by replacing the lambda B fragment with two identical 1.1 Md fragments from the pre-early region of bacteriophage T5. The new vector has two advantages which facilitate elimination of parental-type recombinants in an in vitro recombination experiment. Firstly, the 1.1 Md insert is too small to be re-inserted into lambda gtWES in a single copy. Secondly the 1.1 Md T5 fragment carries T5 gene A3 which prevents growth of phage retaining this fragment when the Excherichia coli host carries plasmid ColIb. Thus, essentially all plaques are due to phage with donor DNA inserts and are free of T5 DNA fragments. The size usually given as the theoretical minimum size for insertion into the lambda gt series of vectors is 0.66 Md. We have shown that this size is an underestimate and that the lower limit is about 1.6 Md. A precise estimate is difficult since there is strong selection, among phage having small inserts, for those which have acquired additional genetic material by duplication of the lambda DNA.

Construction and properties of hybrid plasmids carrying the E. coli gal operon

A family of hybrid plasmids carrying the entire gal operon of E. coli and designated pgal was constructed in vitro. In the case of pgal 1 (mol. wt. 16.4 Md), a fragment cut by Bam HI endonuclease from lambda gal phage DNA (lambda D-J-gal-att-int) was joined to pMB9 and cloned in the gal-strain of E. coli, which was grown on selective media with galactose as a sole source of carbon. Plasmid pgal2 was derived from pgal 1 by elimination of the 1.1 Md fragment located between the two EcoRI sites and carrying the lambda att-int region and part of pMB9. To obtain pgal3, the 10.7 Md fragment of lambda DNA located between the two SmaI sites (lambda D-J and part of pMB9) in pgal2 was cut out and the resulting flush-end fragments were sealed by the T4DNA ligase. The mol. wt. of pgal3 containing one SmaI site amounted to 4.6 Md, while several pgal3 variants that had lost their SmaI site were still smaller. Plasmid pgal1 inhibited the growth of the gal- host cells, which effect could be overcome by the accompanying helper pMB9. The presence of pgal2 and pgal3 supported the growth and multiplication of gal- cells on selective media even without the helper plasmid. The total amount of pgal plasmid DNA per cell was constant and equalled 60--70 Md (4 copies of pgal1 or 15--16 copies of pgal3, ColE1 or pMB9). This might explain why the co-presence of pMB9 helper does alleviate the "harmful" effects of the plasmid pgal1 (which carries att-int genes), by reducing the copy number of the latter from four to one.

Molecular cloning of fragments of bacteriophage T4 DNA

Non-glucosylated T4 DNA was digested with R.EcoRI and the resulting fragments covalently joined to lambda vectors. The genetic content of each lambda-T4 hybrid was determined by marker-rescue tests. The isolation of many recombinants containing partial-digestion products of T4 DNA provided the overlapping sequences necessary to order fragments within the T4 genome. The present analyses include parts of the "early" region between genes 42 and 46, and much of the "late" region between genes 50 and 29. T4 cytosine-DNA digested to completion by R.EcoRI was used to identify the fragments of DNA within the lambda-T4 recombinants. The T4 cytosine-DNA was also sensitive to R.HindIII and R.Xho but not to R.BamH1.

Genetic identification of cloned fragments of bacteriophage T4 DNA and complementation by some clones containing early T4 genes

Bacteriophage T4 DNA containing cytosine has been obtained from cells infected with phage mutant in genes 42, 56, denA and denB. This DNA can be cut by a number of restriction endonucleases. Fragments obtained by digestion of this DNA with EcoRI have been cloned using the vector plasmid pCR1. Clones containing T4 DNA were identified by hybridization with radioactive early and late T4 RNA. A simple marker rescue technique is described for the genetic identification of the cloned T4 fragments. Some of the T4-hybrid plasmids which contain entire T4 genes can complement temperature sensitive and amber mutants of T4.

Cloning of yeast transfer RNA genes in Escherichia coli

Four thousand Escherichia coli clones containing yeast DNA inserted into the plasmid pBR313 have been isolated. Of these, 175 clones were identified as carrying yeast transfer RNA genes. The initial analysis of the inserted transfer RNA genes via the colony hybridization technique with individual radioactive transfer RNA species is reported. The data indicate that yeast transfer RNA genes are not highly clustered, although some clustering exists. In addition, it was observed that the reiteration number of different transfer RNA genes may vary extensively.