Arrangement on the chromosome of the known pre-early genes of bacteriophages T5 and BF23

T5-like phage BF23 evades host-mediated DNA restriction and methylation

Bacteriophage BF23 is a close relative of phage T5, a prototypical Tequintavirus that infects Escherichia coli. BF23 was isolated in the middle of the XXth century and was extensively studied as a model object. Like T5, BF23 carries long ∼9.7 kb terminal repeats, injects its genome into infected cell in a two-stage process, and carries multiple specific nicks in its double-stranded genomic DNA. The two phages rely on different host secondary receptors-FhuA (T5) and BtuB (BF23). Only short fragments of the BF23 genome, including the region encoding receptor interacting proteins, have been determined. Here, we report the full genomic sequence of BF23 and describe the protein content of its virion. T5-like phages represent a unique group that resist restriction by most nuclease-based host immunity systems. We show that BF23, like other Tequintavirus phages, resist Types I/II/III restriction-modification host immunity systems if their recognition sites are located outside the terminal repeats. We also demonstrate that the BF23 avoids host-mediated methylation. We propose that inhibition of methylation is a common feature of Tequintavirus and Epseptimavirus genera phages, that is not, however, associated with their antirestriction activity.

Characterization of preearly genes in the terminal repetition of bacteriophage BF23 DNA by nucleotide sequencing and restriction mapping

A finer restriction map of the terminal repetition of bacteriophage BF23 DNA was determined and used to localize a 3.4-kbp deletion in the terminal repetition and to determine the physical location of preearly gene A2-A3. The nucleotide sequence of gene A2-A3 was determined and shown to code for a protein of 125 amino acids with no indication of a membrane transport sequence. The beginning of an adjacent gene, probably gene A1, was also sequenced.

Identity of genes A2 and A3 of bacteriophage BF23

The polypeptide coded by gene A3 of bacteriophage BF23 has been purified and its N-terminal amino acid sequence determined. This sequence is identical to the N-terminal sequence of the polypeptide coded by gene A2. The two gene products have identical molecular weight. We conclude that these two gene products are identical, and are coded by one and the same gene, namely gene A2-A3, which was previously thought to be two genes, A2 and A3.

Direction of transcription in bacteriophage T5 first-step transfer DNA

The transcription of the T5 first-step transfer genes A2 and A3 has been shown to proceed from right to left (i.e., from A3 to A2) on the T5 DNA molecule.

Cloning of bacteriophage T5 DNA fragments. III. Expression in Escherichia coli mini-cells

Use has been made of the mini-cell system to study polypeptide synthesis from cloned EcoRI, HindIII and PstI fragments of T5 DNA. The correlation of certain gene products with known genes has been established, as well as the physical mapping of genes not yet identified genetically. In some cases, it has been possible to demonstrate the presence of T5 promoters on the cloned DNA fragments. The design of experiments to avoid certain artifacts inherent in the use of the mini-cell system is discussed.

Arrangement of the single-stranded fragments in E. coli bacteriophage BF23 DNA

Bacteriophage BF23st(0) DNA was denatured with alkali and fractionated by agarose gel electrophoresis. Seven single-stranded fragments (designated Fragments I--VII) were identified as the major constituents of the phage DNA. The presence of several minor fragments which represent minor populations of the phage genome was also observed. The largest fragment (Fragment I) represents the intact strand of phage DNA, whereas the other fragments form the complementary strand. Thus, BF23st(0) DNA carries single-strand interruptions in only one strand. The arrangement of the major fragments in the nicked strand was determined by use of gamma-exonuclease and agarose gel electrophoresis. From the mode of action of this nuclease, and from the kinetics of release or disappearance of the fragments, the polarity of the fragments in BF23st(0) DNA was specified. In addition, the presence of two types of major phage populations differing in their composition of the fragments was demonstrated. One type has an additional nick (yielding Fragment IV and Fragment V) in a specific fragment (Fragment II) of other type.

Fluorescence changes of a membrane-bound dye during bacteriophage T5 infection of Escherichia coli

The fluorescence intensity of membrane-bound N-phenyl-1-naphthylamine increases dramatically when T5 bacteriophage infect colicin Ib plasmid-containing hosts. This dramatic increase is not seen during normal infections or in infections wherein either the plasmid or the phage contain mutations which allow productive infection to occur. Two smaller increases in fluorescence intensity are seen, however, in all T5 infections in which the characteristic two-step injection of DNA can proceed.

Cloning of bacteriophage T5 DNA fragments in plasmid pBR322 and bacteriophage lambda gtWES

Bacteriophage T5 was digested with the restriction endonucleases HindIII and EcoRI and the resulting fragments were inserted into the plasmid pBR322 and the bacteriophage lambda gtWES as vectors. Approx. 15% of the phage genome was recovered in recombinant clones. The recombinants were characterized by restriction analysis, DNA/DNA hybridization employing Southern blots, and ability to complement or recombine with amber mutants of T5. The results obtained allow revisions of the physical map of the T5 genome and partial correlation of the physical map with the genetic map.

Amino acid and sugar transport in Escherichia coli (ColIb) during abortive infection by bacteriophage T5

T5 bacteriophage cannot replicate in Escherichia coli containing the colicinogenic factor ColIb. We show that active transport of proline and glutamine begins to decline at about 10 min after infection, the same time at which macromolecular synthesis stops during abortive infection. Uptake of alpha-methylglucoside is stimulated, however, and this change is evident even by 5 min after infection. These changes in membrane function do not occur during infections that are productive because of mutations on the plasmid or phage. The results suggest that the abortive infection is caused by membrane depolarization.

Are class I (pre-early) proteins of bacteriophage T5 sufficient to induce abortive infection of ColIb+ Escherichia coli?

When T5 bacteriophage infect a colicin Ib-containing host, a variety of membrane changes and inhibition of macromolecular synthesis occur. This work shows that all these changes also occur when a mutant of T5 that can only inject 8% of its DNA is used. This indicates that all the information necessary for the abortive infection is present on this 8% (first-step-transfer) DNA.

Restriction insensitivity in bacteriophage T5 I. Genetic characterization of mutants sensitive to EcoRI restriction

Unmodified bacteriophage T5 is able to grow normally on bacterial hosts carrying three different Escherichia coli restriction systems, EcoK, EcoPI, and EcoRI. Under the same conditions, the plating efficiency of bacteriophage gamma is less than 10(-9). At least in the case of EcoRI, this lack of in vivo restriction is not due to lack of restriction sites on the T5 DNA molecule. These observations suggest that bacteriophage T5 specifies one or more restriction protection systems. Mutants (ris) of T5 have been isolated which confer sensitivity to EcoRI restriction but not to EcoK or EcoPI. The mutations are located in the pre-early region of the genetic map but are too far apart to be alleles of a single gene. Complementation studies show that the ris mutants can be helped to grow on the EcoRI-restricting host by coinfection with T5+. This result provides evidence for a restriction protection function but does not necessarily show that the ris mutants are defective in such a system.

Pre-early polypeptides of bacteriophages T5 and BF23

Nine pre-early polypeptides have been detected after infection with bacteriophage T5 and 10 pre-early polypeptides have been detected after infection with bacteriophage BF23. Only about one-half of the coding capacity of the redundant ends of the phage DNA, which code for pre-early proteins, is needed for these 9 to 10 pre-early polypeptides. The direction of transcription of pre-early genes A1 and A2 has been established from the size of N-terminal polypeptide fragments induced by amber mutants and from the known intragenic loci of the amber mutations. Some pre-early functions appear to be nonessential, because a viable deletion mutant of BF23 fails to induce three and possibly four of the detectable pre-early polypeptides.

Membrane protein biosynthesis in bacteriophage BF23-infected Escherichia coli

When Escherichia coli is infected with bacteriophage BF23, two new proteins with molecular weights greater than 10,000, as indicated by polyacrylamide gel electrophoresis, are found associated with the cells' membranes. One of these, found associated with both the inner and outer membrane, has a molecular weight of about 55,000 and is regulated by the A1 gene of this phage, a gene found on the spontaneously injected 8% piece of BF23 DNA, DNA that codes for the synthesis of proteins necessary for the injection of the whole phage genome. The other protein, often undetected in whole membrane preparations, is found exclusively associated with the inner membrane. Evidence indicates that this protein is also regulated by the initially injected 8% piece of the DNA.

Identification of the gene controlling the synthesis of the major bacteriophage T5 membrane protein

After infection of Escherichia coli B by bacteriophage T5, a major new protein species, as indicated by polyacrylamide gel electrophoresis, appears in the cells' membranes. Phage mutants with amber mutations in the first-step-transfer portion of their DNA have been tested for their ability to induce membrane protein synthesis after they infect E. coli B. We have found that phage with mutations in the Al gene of T5 do not induce the synthesis of the T5-specific major membrane protein, whereas phage that are mutant in the A2 gene do induce its synthesis. We conclude that gene Al must function normally for T5-specific membrane protein biosynthesis to occur and that only the first 8% (first-step-transfer piece) of the DNA need be present in the cell for synthesis to occur.

Early events after infection of Escherichia coli by bacteriophage T5. II. Control of the bacteriophage-induced 5'-nucleotidase activity

The control of activity of the bacteriophage T5-induced 5'-nucleotidase is dependent upon the amount of T5 parental DNA injected into the cell and expressed. When only the first-step transfer DNA is injected and expressed the amount of 5'-nucleotidase activity observed is two to three times the maximum amount observed after normal T5 infection, and inactivation of the enzyme does not occur. Enzyme inactivation occurs only after the remaining DNA is injected, but only limited expression of this DNA is required. The control of the nucleotidase inactivation process is similar to that for the repair of the nicks in parental DNA, and is probably mediated by a class IIa protein.

Terminal redundancy heterozygotes involving the first-step-transfer region of the bacteriophage T5 chromosome

Individual progeny of two-factor crosses between A1am and A2am T5 phages give rise to bursts containing more than one type of plaque. The simplest explanation for these mixed bursts is that the A1 and A2 genes are located within the terminally repeated portion of the T5 genome and that the mixed bursts are made by "terminal redundancy heterozygotes". The observation of genetic heterozygosity means that the A1 and A2 genes are repeated intact. This implies that the terminal segments of T5 are genetically interchangeable.

Transfection of Escherichia coli spheroplasts. VI. Transfection of nonpermissive spheroplasts by T5 and BF23 bacteriophage DNA carrying amber mutations in DNA transfer genes

DNA was extracted from T5 and BF23 phage carrying amber mutations in genes A2, A1, or D9 and tested for its ability to transfect su minus spheroplasts. DNA from T5 am231, defective in gene A2, transfects Escherichia coli su minus recB minus spheroplasts with an efficiency of 16% of that of wild-type T5 DNA, whereas DNA from T5 am16d or BF23 am57, both defective in gene A1 or its equivalent, transfects E. coli su minus recB minus spheroplasts with an efficiency of 1.4% of that of wild-type T5 DNA, provided E. coli su+ bacteria is used as the indicator in all cases. More than 95% of the progeny from the am231, am16d, and am57 DNA that transfects su minus recB minus spheroplasts is still amber mutant. From these efficiencies of transfection we conclude that the product of gene A2 functions mainly in the mechanism of transfer of phage DNA to intact host cells, and that this function is not essential for transfection of spheroplasts. We also conclude that gene A1 controls functions in addition to DNA transfer, in agreement with previous studies which show that mutations in gene A1 have a pleiotropic effect. Apparently, the absence of these additional functions controlled by gene A1 leads to a high frequency of abortive infection. DNA from amber mutants defective in either gene A1 or A2 does not appreciably transfect su minus rec+ spheroplasts, indicating that the products of these two genes may both be needed to protect T5 DNA from the very active rec BC nuclease in spheroplasts.