On the direction of reading of bacteriophage T4 gene 43 (deoxyribonucleic acid polymerase)

Evolution of RNA-binding specificity in T4 DNA polymerase

DNA polymerase of phage T4 (T4 gp43), an essential component of the T4 DNA replicase, is a multifunctional single-chained (898-amino acid) protein that catalyzes the highly accurate synthesis of DNA in phage replication. The enzyme functions both as a DNA-binding replication protein and as a sequence-specific RNA-binding autogenous translational repressor. We have utilized a phylogenetic approach to study the relationships between the two nucleic acid-binding functions of the protein. We found that autogenous translational control of gp43 biosynthesis has been conserved in phage RB69, a distant relative of T4, although we also found that the RB69 system differs from its T4 counterpart in two regards: (a) nucleotide sequence and predicted secondary structure of the RNA target (translational operator), and (b) RNA specificity of the protein. T4 gp43 is specific to the RNA operator sequence of the T4 genome whereas RB69 gp43 can bind and repress operator RNA from both phages equally well. In studies with T4-RB69 gp43 chimeras, we mapped T4 gp43 RNA-binding specificity to a protein segment that also harbors important determinants for DNA binding and the polymerase catalytic function. Our results suggest that RNA functions as a regulator of both the dosage and activity of this DNA replication enzyme.

Modular organization of T4 DNA polymerase. Evidence from phylogenetics

We describe the use of a phylogenetic approach to analyze the modular organization of the single-chained (898 amino acids) and multifunctional DNA polymerase of phage T4. We have identified, cloned in expression vectors, and sequenced the DNA polymerase gene (gene 43) of phage RB69, a distant relative of T4. The deduced primary structure of the RB69 protein (RB69 gp43) differs from that of T4 gp43 in discrete clusters of short sequence that are interspersed with clusters of high similarity between the two proteins. Despite these differences, the two enzymes can substitute for each other in phage DNA replication, although T4 gp43 does exhibit preference to its own genome. A 55-amino acid internal gp43 segment of high sequence divergence between T4 and RB69 could be replaced in RB69 gp43 with the corresponding segment from T4 without loss of replication function. The reciprocal chimera and a deletion mutant of the T4 gp43 segment were both inactive for replication and specifically inhibitory ("dominant lethal") to the T4 wild-type allele. The results show that phylogenetic markers can be used to construct chimeric and truncated froms of gp43 that, although inactive for replication, can still exhibit biological specificity.

Genetic mapping of the amino-terminal domain of bacteriophage T4 DNA polymerase

The DNA polymerase of bacteriophage T4 is a multifunctional enzyme that harbors DNA-binding, DNA-synthesizing and exonucleolytic activities. We have cloned in bacterial plasmids about 99% of the structural gene for this enzyme (T4 gene 43). The gene was cloned in six contiguous 5'-terminal DNA fragments that defined seven intragenic mapping regions. Escherichia coli hosts harboring recombinant plasmids carrying the gene 43 subsegments were used in marker-rescue experiments that assigned a large number of ts and nonsense polymerase mutations to different physical domains of the structural gene. Conspicuously, only one missense mutation in a large collection of mutants mapped in the 5'-terminal 450 base-pair segment of the approximately 2700 base-pair gene. To test if this indicated a DNA polymerase domain that is relatively noncritical for biological activity, we mutagenized a recombinant plasmid carrying this 5'-terminal region and generated new conditional-lethal mutations that mapped therein. We identified five new ts sites, some having mutated at high frequency (nitrosoguanidine hot spots). New ts mutations were also isolated in phage genes 62 and 44, which map upstream of gene 43 on the T4 chromosome. A preliminary examination of physiological consequences of the ts gene 43 mutations showed that they exhibit effects similar to those of ts lesions that map in other gene 43 segments: some were mutators, some derepressed gene 43 protein synthesis and they varied in the severity of their effects on T4-induced DNA synthesis at nonpermissive temperatures. The availability of the gene 43 clones should make it possible to isolate a variety of lesions that affect different activities of the T4 DNA polymerase and help to define the different domains of this multifunctional protein.

Initiation characteristics for the synthesis of five T4 phage-specific messenger RNAs in vitro

The involvement of the nucleoside triphosphates in the initiation of the synthesis of the messenger ribonucleic acid of five T4 specific enzymes has been studied. Only one of these, the messenger RNA for deoxynucleosidemonophosphate kinase, can be initiated in the presence of one nucleoside triphosphate, namely ATP. All of the remaining four require the presence of at least two nucleoside triphosphates during the initiation period. The combination of ATP and UTP was best for the initiation of messenger RNA for dihydrofolate reductase, ATP and CTP for deoxycytidylate hydroxymethyltransferase and beta-glucosyltransferase, and ATP and GTP for alpha-glucosyltransferase. We have concluded that there is a great variation in the nucleotide composition and sequence of the initiation sites in T4 DNA. No correlation in the requirements of nucleoside triphosphates during the initiation period could be observed among the five systems studied according to their classification as one type or another of "early" T4 messenger RNA.

Transcription units in bacteriophage T4

We have investigated the possibility of assigning genes of T4 bacteriophage to their units of transcription (scriptons) by studying gene expression from UV-irradiated DNA templates. Since RNA chains are prematurely terminated on UV-irradiated DNA templates and since the promotor distal part of the RNA chain is deleted, the expression of any gene is inversely proportional to the distance between the promotor and the promotor distal end of the gene. We find that the early genes, 43, 45 and rIIB, are promotor proximal. Since at least genes 43 and rIIB are classified as delayed early genes, these results suggest that their synthesis may require the recognition of new promotors. Additional early genes (44, 62, 42, 46, 47, 55, and rIIA) and some late genes (34, 37, and 38) have also been assigned positions relative to their promotors.

Suppression of amber mutations of bacteriophage T4 gene 43 (DNA polymerase) by translational ambiguity

The growth properties of twelve different amber (am) mutants of bacteriophage T4 gene 43 (DNA polymerase) were examined by using nonpermissive (su(-)) as well as permissive (su(+)) Escherichia coli hosts. It was found that most of these mutants were measurably suppressed in su(-) hosts by translational ambiguity (misreading of codons during protein synthesis). The ability of these mutants to grow in response to this form of weak suppression probably means that the T4 gene 43 DNA polymerase can be effective in supporting productive DNA replication when it is supplied in small amounts. By similar criteria, studies with other phage mutants suggested that the products of T4 genes 62 (uncharacterized), 44 (uncharacterized), 42 (dCMP-hydroxymethylase), and 56 (dCTPase) are also effective in small amounts. Some T4 gene products, such as the product of gene 41 (uncharacterized), seem to be partially dispensable for phage growth since am mutants of such genes do propagate, although weakly, in streptomycin-resistant su(-) hosts which appear to have lost the capacity to suppress am mutations by ambiguity.