MUTANTS OF BACTERIOPHAGES T2 AND T6 DEFECTIVE IN ALPHA-GLUCOSYL TRANSFERASE

Phage-encoded ten-eleven translocation dioxygenase (TET) is active in C5-cytosine hypermodification in DNA

Chemical tailoring of canonical bases expands the functionality of DNA in the same manner that posttranscriptional and -translational modifications enhance functional diversity in RNA and proteins. We describe the activities of ten-eleven translocation dioxygenase (TET)-like iron(II)- and 2-oxo-glutarate–dependent 5mC dioxygenases that are encoded by several bacteriophages to enable hypermodification of C5-methyl cytosine bases in their DNA. Phage TETs act on methylation marks deposited within GpC sequences by functionally-associated cytosine 5-methyltransferases. The hydroxymethyl groups installed are further elaborated by tailoring enzymes, thereby decorating the phage DNA with diverse, complex modifications. These modifications are predicted to have protective roles against host defenses during viral infection.

TET/JBP (ten-eleven translocation/base J binding protein) enzymes are iron(II)- and 2-oxo-glutarate–dependent dioxygenases that are found in all kingdoms of life and oxidize 5-methylpyrimidines on the polynucleotide level. Despite their prevalence, few examples have been biochemically characterized. Among those studied are the metazoan TET enzymes that oxidize 5-methylcytosine in DNA to hydroxy, formyl, and carboxy forms and the euglenozoa JBP dioxygenases that oxidize thymine in the first step of base J biosynthesis. Both enzymes have roles in epigenetic regulation. It has been hypothesized that all TET/JBPs have their ancestral origins in bacteriophages, but only eukaryotic orthologs have been described. Here we demonstrate the 5mC-dioxygenase activity of several phage TETs encoded within viral metagenomes. The clustering of these TETs in a phylogenetic tree correlates with the sequence specificity of their genomically cooccurring cytosine C5-methyltransferases, which install the methyl groups upon which TETs operate. The phage TETs favor Gp5mC dinucleotides over the 5mCpG sites targeted by the eukaryotic TETs and are found within gene clusters specifying complex cytosine modifications that may be important for DNA packaging and evasion of host restriction.

Highlights of the DNA cutters: a short history of the restriction enzymes

In the early 1950's, 'host-controlled variation in bacterial viruses' was reported as a non-hereditary phenomenon: one cycle of viral growth on certain bacterial hosts affected the ability of progeny virus to grow on other hosts by either restricting or enlarging their host range. Unlike mutation, this change was reversible, and one cycle of growth in the previous host returned the virus to its original form. These simple observations heralded the discovery of the endonuclease and methyltransferase activities of what are now termed Type I, II, III and IV DNA restriction-modification systems. The Type II restriction enzymes (e.g. EcoRI) gave rise to recombinant DNA technology that has transformed molecular biology and medicine. This review traces the discovery of restriction enzymes and their continuing impact on molecular biology and medicine.

McrBC: a multisubunit GTP-dependent restriction endonuclease

McrBC-mediated restriction of modified DNA has been studied extensively by genetic methods, but little is known of its molecular action. We have used overproducing plasmid constructs to facilitate purification of the McrBL and McrC proteins, and report preliminary characterization of the activity of the complex. Both proteins are required for cleavage of appropriately modified DNA in vitro, in a reaction absolutely dependent on GTP. ATP inhibits the reaction. The sequence and modification requirements for cleavage of the substrate reflect those seen in vivo. The position of cleavage was examined at the nucleotide level, revealing that cleavage occurs at multiple positions in a small region. Based upon these observations, and upon cleavage of model oligonucleotide substrates, it is proposed that the recognition site for this enzyme consists of the motif RmC(N40-80)RmC, with cleavage occurring at multiple positions on both strands, between the modified C residues. In subunit composition, cofactor requirement, and relation between cleavage and recognition site, McrBC does not fit into any of the classes (types I to IV) of restriction enzyme so far described.

Organization and function of the mcrBC genes of Escherichia coli K-12

Many natural DNA sequences are restricted in Escherichia coli K-12, not only by the classic Type I restriction system EcoK, but also by one of three modification-specific restriction systems found in K-12. The McrBC system is the best studied of these. We infer from the base composition of the mcrBC genes that they were imported from an evolutionarily distant source. The genes are located in a hypervariable cluster of restriction genes that may play a significant role in generation of species identity in enteric bacteria. Restriction activity requires the products of two genes for activity both in vivo and in vitro. The mcrB gene elaborates two protein products, only one of which is required for activity in vitro, but both of which contain a conserved amino acid sequence motif identified as a possible GTP-binding site. The mcrC gene product contains a leucine heptad repeat that could play a role in protein-protein interactions. McrBC activity in vivo and in vitro depends on the presence of modified cytosine in a specific sequence context; three different modifications are recognized. The in vitro activity of this novel multi-subunit restriction enzyme displays an absolute requirement for GTP as a cofactor.

Purification and N-terminal amino acid sequences of two polypeptides encoded by the mcrB gene from Escherichia coli K-12

This report provides a purification method for the two proteins, 51 kDa and 33 kDa, both encoded by the same mcrB gene of the McrBC restriction system in Escherichia coli K-12. The two proteins were produced in large quantity using a T7 expression system and copurified to near homogeneity by DEAE-Sepharose and Affi-Gel blue column chromatography. The N-terminal amino acid sequences of these purified McrB proteins were the same as those predicted from the mcrB DNA sequence by Ross et al. [J. Bacteriol. 171 (1989b) 1974-1981]. The 33-kDa protein totally overlaps the C-terminal part of the 51-kDa protein.

Cloning and structural characterization of the mcrA locus of Escherichia coli

Escherichia coli has DNA restriction systems which are able to recognize and attack modified cytosine residues in the DNA of incoming bacteriophages and plasmids. The locus for the McrA/RglA system of modified cytosine restriction was located near the pin gene of the defective element, e14. Hence, loss of the e14 element through abortive induction after UV irradiation caused a permanent loss of McrA restriction activity. e14 DNA encoding McrA restriction was cloned and sequenced to reveal a single open reading frame of 831 bp with a predicted gene product of 31 kDa. Clones expressing the complete open reading frame conferred both McrA and RglA phenotypes; however, a deletion derivative was found which complemented RglA restriction against nonglucosylated T6gt phage but did not complement for McrA restriction of methylated plasmid DNA. Possible explanations for this activity and a comparison with the different organization of the McrB/RglB restriction system are discussed.

Isolation of temperature-sensitive McrA and McrB mutations and complementation analysis of the McrBC region of Escherichia coli K-12

We isolated temperature-sensitive mcrA and mcrBC mutants of Escherichia coli. At 42 degrees C, they were unable to restrict the T-even bacteriophages T6gt and T4gt or plasmids encoding cloned DNA methylase genes whose specificities confer sensitivity to the McrA and McrBC nucleases. Complementation analysis of the McrBC region (mcrB251) with the complete cloned McrBC system or a derivative with mcrB alone indicated that the mutation shows an absolute defect for the restriction of DNA containing hydroxymethylcytosine and a thermosensitive defect for the restriction of DNA containing methylcytosine. The properties of the McrA temperature-sensitive mutants suggest that some of these mutations can also influence the restriction of DNA containing hydroxymethylcytosine or methylcytosine residues.

Common evolutionary origin of the phage T4 dam and host Escherichia coli dam DNA-adenine methyltransferase genes

We compared the known DNA nucleotide and encoded amino acid sequences of the Escherichia coli and bacteriophage T4 dam (DNA-adenine methyltransferase) genes. Despite the absence of any DNA sequence homology, there were four regions (11 to 33 residues long) of amino acid sequence homology containing 45 to 64% identity. These results suggest that the genes for these two enzymes have a common evolutionary origin.

Analysis of host range restriction in Escherichia coli treated with toluene

Escherichia coli cells treated with toluene replicate DNA when they are provided with deoxyribonucleoside 5'-triphosphates, ATP, Mg(++), and K(+). However, when deoxycytidine 5'-triphosphate is replaced by hydroxymethyl deoxycytidine 5'-triphosphate, incorporation of nucleotides into acid-precipitable material by toluenetreated strains restrictive to nonglucosylated T-even phage is reduced to less than 5% of that normally observed. Even when dCTP is present in the reaction mixture, a similar effect of the hydroxymethyl analogue on DNA replication is observed. In contrast, toluene-treated E. coli K12r6(-)r2,4(-), a strain permissive to the nonglucosylated T-even phage, incorporates hydroxymethyl deoxycytosine into its DNA, and replication proceeds at only a slightly reduced rate in the presence of the hydroxymethyl deoxycytidine 5'-triphosphate. The presence of the hydroxymethyl deoxycytidine 5'-triphosphate in the reaction mixture does not lead to degradation of preexisting DNA of the restrictive host, but it does lead to an irreversible inhibition of further DNA replication; the inhibition is observed only when the hydroxymethyl deoxycytidine 5'-triphosphate is present during replication. Thus phage-specific enzymes are not necessary for the incorporation of hydroxymethylcytosine into phage DNA, and the restrictive mechanism, present in the host cell before infection, can recognize hydroxymethylcytosine residues in its own DNA, as well as the DNA of the T-even phage.

Host-controlled restriction of T-even bacteriophages: relation of endonuclease I and T-even-induced nucleases to restriction

Restriction of nonglucosylated T2 phage (T(*)2) as a function of bacterial growth state was the same for endonuclease I-containing and endonuclease I-deficient strains of Escherichia coli B. Furthermore, E. coli strains with various levels of restriction for T2 had comparable endonuclease I activities. It was also found that a T4 mutant temperature-sensitive for gene 46 and 47 functions was fully restricted at 42 C. It therefore appears that neither endonuclease I nor the phage-induced nucleases whose activities are blocked by mutations in genes 46 and 47 catalyze the initial event in restriction of nonglucosylated T-even phages.

Chemistry and structure of nucleic acids of bacteriophages. Many forms of nucleic acids of bacteriophages show the ways that information is stored and reproduced

The nucleic acids of bacteriophages are characterized by a surprising multiformity. RNA and DNA may occur, the latter in single- or double-stranded form, circular or linear, with or without breaks or single-strand ends. Terminal redundancy may exist and the populations of linear phages may be uniform or randomly permuted. A double-stranded circular DNA does not occur in extracellular bacteriophage, but is often if not always formed after infection of the bacterial host. Phage DNA may be glucosylated or methylated to a certain extent, and the glucose and methyl residues may influence the stability of the DNA inside the host.