Preparation and specificity of endonuclease IV induced by bacteriophage T4

A hexanucleotide sequence (dC1-dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4

Endonuclease (Endo) IV encoded by denB of bacteriophage T4 is an enzyme that cleaves single-stranded (ss) DNA in a dC-specific manner. Previously we have demonstrated that a dTdCdA is most preferable for Endo IV when an oligonucleotide substrate having a single dC residue is used. Here we demonstrate that Endo IV cleaves ssDNAs exclusively at the 5′-proximal dC where a sequence comprises dC residues both at the 5′ proximal and 3′ proximal positions (a dCs tract-dependent cleavage). The dCs tract-dependent cleavage is efficient and occurs when a dCs tract has at least 6 bases. Some dCs tracts larger than 6 bases behave as that of 6 bases (an extended dCs tract), while some others do not. One decameric dCs tract was shown to be cleavable in a dCs tract-dependent manner, but that with 13 dCs was not. The dCs tract-dependent cleavage is enhanced by the presence of a third dC residue at least for a 6 or 7 dCs tract. In contrast to the dCs tract-dependent cleavage, a dCs tract-independent one is generally inefficient and if two modes are possible for a substrate DNA, a dCs tract-dependent mode prevails. A model for the dCs tract-dependent cleavage is proposed.

The Ser176 of T4 endonuclease IV is crucial for the restricted and polarized dC-specific cleavage of single-stranded DNA implicated in restriction of dC-containing DNA in host Escherichia coli

Endonuclease (Endo) IV encoded by denB of bacteriophage T4 is an enzyme that cleaves single-stranded (ss) DNA in a dC-specific manner. Also the growth of dC-substituted T4 phage and host Escherichia coli cells is inhibited by denB expression presumably because of the inhibitory effect on replication of dC-containing DNA. Recently, we have demonstrated that an efficient cleavage by Endo IV occurs exclusively at the 5′-proximal dC (dC₁) within a hexameric or an extended sequence consisting of dC residues at the 5′-proximal and the 3′-proximal positions (dCs tract), in which a third dC residue within the tract affects the polarized cleavage and cleavage rate. Here we isolate and characterize two denB mutants, denB(W88R) and denB(S176N). Both mutant alleles have lost the detrimental effect on the host cell. Endo IV(W88R) shows no enzymatic activity (<0.4% of that of wild-type Endo IV). On the other hand, Endo IV(S176N) retains cleavage activity (17.5% of that of wild-type Endo IV), but has lost the polarized and restricted cleavage of a dCs tract, indicating that the Ser¹⁷⁶ residue of Endo IV is implicated in the polarized cleavage of a dCs tract which brings about a detrimental effect on the replication of dC-containing DNA.

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.

In vivo cleavage of cytosine-containing bacteriophage T4 DNA to genetically distinct, discretely sized fragments

Mutants of bacteriophage T4D that are defective in genes 42 (dCMP hydroxymethylase), 46 (DNA exonuclease), and 56 (dCTPase) produce limited amounts of phage DNA in Escherichia coli B. In this DNA, glucoylated 5-hydroxymethylcytosine is completely replaced by cytosine. We found that this DNA rapidly becomes fragmented in vivo to at least 16 discrete bands as visualized on agarose gels subjected to electrophoresis. The sizes of the fragments ranged from more than 20 to less than 2 kilobase pairs. When DNAs from two of these bands were radioactively labeled in vitro by nick translation and hybridized to XbaI restriction fragments of cytosine-containing T4 DNA, evidence was obtained that the two bands are genetically distinct, i.e., they contain DNA from different parts of the T4 genome. Mutational inactivation of T4 endonuclease II (gene denA) prevented the fragmentation. Three different mutations in T4 endonuclease IV (gene denB) caused the same minor changes in the pattern of fragments. We conclude that T4 endonuclease II is required, and endonuclease IV is involved to a minor extent, in the in vivo production of these cytosine-containing T4 DNA fragments. We view these DNA fragments as "restriction fragments" since they represent degradation products of DNA "foreign" to T4, they are of discrete size, and they are genetically distinct. Thus, this report may represent the first, direct in vivo demonstration of discretely sized genetically distinct DNA restriction fragments.

Bacteriophage XP-12-induced exonuclease which preferentially hydrolyzes nicked DNA

An exonuclease has been partially purified from XP-12-infected Xanthomonas oryzae which is not found in uninfected X. oryzae. Although both the phage-induced exonuclease and the major host exonucleolytic DNase released 5'-mononucleotides, these enzymes differed in their chromatographic behavior, pH optimum, salt inhibition, and heat sensitivity. These two exonucleases preferred different substrates. Nicked native DNA was the best substrate for the phage-induced enzyme, whereas denatured DNA was the best substrate for the host enzyme. Also, the host enzyme had a significant preference for denatured or nicked, normal cytosine-containing DNA (e.g., X. oryzae or T7 DNA) over similarly denatured or nicked 5-methylcytosine-rich DNA (namely, XP-12DNA), whereas the phage-induced enzyme hydrolyzed both types of DNA equally well.

Sequence studies on mouse L-cell satellite DNA by base-specific degradation with T4 endonuclease IV

The base sequence of mouse L-cell satellite DNA was investigated by degradation of the two separated complementary strands with the base specific enzyme, T4 endonuclease IV. Digestion of the heavy strand DNA released a limited number of oligonucleotides which were separated by ionophoresis/homochromatography, isolated, and sequenced by the 'wandering spot' method. The light strand DNA was resistant to digestion with T4 endonuclease IV and no detectable amounts of oligonucleotides were released. The oligonucleotides obtained from the heavy strand were related in sequence, indicating that mouse satellite DNA derived from a short tandemly repeated sequence. The sequence of part of the original repeat unit is proposed to be C-A-T-T-T-T-T-C. Five major oligonucleotides were identified, all of which differ from the proposed original sequence by single base changes. The five major oligonucleotides occur with about equal frequency and together comprise approximately 50% of the oligonucleotides released by T4 endonuclease IV from the heavy strand DNA. In addition to the five major oligonucleotides, several oligonucleotides were found to occur in lesser amounts. Since these oligonucleotides are related to the major oligonucleotides, it is likely that they have arisen from them by mutation.

The nucleotide sequence of two restriction fragments located in the gene AB region of bacteriophage S13

The nucleotide sequence of a double stranded DNA fragment from the gene AB region of bacteriophage S13 DNA has been determined. The fragment was isolated as two adjacent shorter fragments by cleavage of S13 replicative form (RF) DNA with restriction endonuclease III from Hemophilus aegyptius. The strands of the fragments were separated electrophoretically and hydrolyzed with T4 endonuclease IV to yield short oligonucleotides which were then sequenced by partial exonuclease digestion. The complete nucleotide sequence of the restriction fragments was obtained by ordering the inter- and intrastrand overlapping oligonucleotide sequences. The adjacent fragments were 190 nucleotides in length. The sequences included a HindII site, an AluI site and two sequences which may be possible transcription initiation sequences, one with an adjacent sequence homologous to the canonical promoter site sequence T-A-T-Pu-A-T-Pu. Examination of the three possible reading frames for translation of the sequence revealed only one possible complete translation product. The postulated partial sequence of gene A protein has a highly positively charged arginine-rich area which may have importance in DNA binding.