Inhibition of T4 growth by an RNA polymerase mutation of Escherichia coli: physiological and genetic analysis of the effects during phage development

Bacteriophage T4 genome

Phage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the "cell-puncturing device," combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages-the most abundant and among the most ancient biological entities on Earth.

An RNA polymerase-binding protein that is required for communication between an enhancer and a promoter

Although bacteriophage T4 late promoters are selectively recognized by Escherichia coli RNA polymerase bearing a single protein encoded by T4 gene 55 (gp55), efficient transcription at these promoters requires enhancement by the three T4 DNA polymerase accessory proteins, bound to distal "mobile enhancer" sites. Two principles are shown to govern this transcriptional enhancement: (i) Promoter recognition and communication between the enhancer and the promoter require separate phage-coded proteins. Only RNA polymerase that has the T4 gene 33 protein (gp33) bound to it is subject to enhancement by the three DNA replication proteins. (ii) Transcriptional enhancement in this prokaryotic system is promoter-specific. Promoter specificity is generated by a direct competition of phage T4 gp33 and gp55 with the E. coli promoter recognition protein, sigma 70, for binding to the E. coli RNA polymerase core. Thus, polymerase that contains sigma 70 is competent to transcribe T4 early and middle genes, but lacks the ability to be enhanced by the DNA replication proteins, while polymerase that contains gp55 and gp33 is capable of enhancement via gp33, but its activity is restricted to T4 late promoters by gp55.

Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus

The expression of the late genes in bacteriophage T4 development is closely connected to viral DNA replication. Three T4-encoded DNA polymerase accessory proteins are shown to stimulate transcription at T4 late promoters in an adenosine triphosphate (ATP) hydrolysis-requiring process. The properties of the activation resemble those found for enhancers of eukaryotic transcription. However, the nature of the enhancer of T4 late transcription is novel in that it is a structure--a break in the nontranscribed DNA stand--to which the three replication proteins bind, rather than a sequence. Since the three DNA polymerase accessory proteins are carried on the moving replication fork as part of the replisome, we postulate that viral DNA replication forks act, in vivo, as the mobile enhancers of T4 late gene transcription. Whereas Escherichia coli RNA polymerase bearing the T4 gene 55 protein can selectively recognize T4 late promoters, it is only capable of responding to the transcription-enhancing activity of the three replication proteins on acquiring an additional T4-specific modification.

Transcriptional regulation of bacteriophage SPO1 protein synthesis in vivo and in vitro

There are six classes of SPO1 transcripts which are, at least partially, regulated independently of each other. Analysis of proteins made in infections by phage mutants defective in DNA synthesis, or in genes which positively control transcription, permitted each protein to be assigned to one transcription class. Most of the late proteins belong to transcription class m2l. There seem to be few, if any, phage proteins in the l class whose mRNA synthesis depends absolutely on phage DNA synthesis, UV irradiation of host cells allowed the detection of many additional early proteins. The early proteins detected in vivo were compared with proteins synthesized in vitro, using bacterial or gp28 phage-modified RNA polymerase in an Escherichia coli cell-free system. Proteins characterized in vivo as belonging to the e transcription class could be made efficiently in vitro only when transcription was performed by bacterial RNA polymerase. em proteins could be elicited through the use of either bacterial or gp28 polymerase, indicating that their genes can be transcribed in either the early or the middle mode.

Two alternative mechanisms for initiation of DNA replication forks in bacteriophage T4: priming by RNA polymerase and by recombination

We show that bacteriophage T4 has two alternative mechanisms to initiate DNA replication; one dependent on Escherichia coli RNA polymerase (RNA nucleotidyltransferase, EC 2.7.7.6), and one dependent on general recombination. Continued DNA synthesis under recombination-defective conditions was sensitive to rifampin, an inhibitor of RNA polymerase. On the other hand, DNA synthesis accelerated in spite of the present of rifampin if recombination occurred.

Altered transcriptional termination in a rifampicin-resistant mutant of Escherichia coli which inhibits the growth of bacteriophage T7

A spontaneous rifampicin-resistant mutant of E. coli K12, RpoB26, which inhibits the growth of bacteriophage T7 has been isolated. The mutation is an RNA polymerase mutation; it also restores the wild-type effect of polar mutations in a rho-deficient strain, probably by restoring transcriptional termination. The efficiency of plating (e.o.p.) of wild-type T7, and of some early region deletion and point mutants of T7 tested, is reduced on RpoB26 by a factor of 10(-4). However, some deletion mutants are inhibited more severely (up to 10(-7) on RpoB26. We argue that these differences may reflect variations in the frequency of transcriptional termination before gene 1, an essential gene which codes for the T7 RNA polymerase (Summers and Siegel 1970; Chamberlin et al. 1970). We also present data which suggest that the product of a late T7 gene plays a role, by some interaction with the product of gene 1, in the inhibition of T7 in RpoB26. We suggest that different levels of expression of gene 1 may lead to different degrees of inhibition of T7 strains in RpoB26.

Shutoff of lambda gene expression by bacteriophage T4: role of the T4 alc gene

Bacteriophage T4 normally contains 5-hydroxymethylcytosine instead of cytosine in its DNA. Multiple mutants of T4 which synthesize DNA with cytosine do not transcribe their late genes due to the action of the T4 alc gene (Snyder et al., Proc. Natl. Acad. Sci. U.S.A. 73:3098--3102, 1976), which is also responsible for unfolding the host nucleoid after T4 infection (Sirotkin et al., Nature [London] 265:28--32, 1977; Tigges et al., J. Virol. 24:775--785, 1977). It seems reasonable that T4 alc function plays a role in shutting off host transcription, and the observation that some of the RNA made after infection with a T4 alc mutant hybridizes to Escherichia coli DNA (Sirotkin et al., Nature [London] 265:28--32, 1977; Tigges et al., J. Virol. 24:775--785, 1977) supports this hypothesis. Although it is likely that the roles of the alc function in the blocking of some types of transcription and in the unfolding of the host nucleoid are related, it is not known how these effects are achieved or, in fact, whether all types of transcription are affected equally by the alc function. In an attempt to answer these questions, we studied the effect of T4 alc function on bacteriophage lambda transcription and on the structure of intracellular lambda DNA. We found that the alc function is responsible for the shutoff of lambda late transcription but probably not for the shutoff of lambda early transcription. We also found that alc does not block lambda transcription by directly removing the supercoils from circular lambda DNA via either a nicking or topoisomerase activity. Furthermore, we conclude that T4 infection also prevents the translation of non-T4 mRNA because late lambda mRNA's were made after superinfection by a T4 alcs mutant and were of normal length but were not translated into lambda late proteins.

Novel replicative properties of a capsid mutant of bacteriophage phi chi 174

A capsid mutant of bacteriophage phi chi 174 demonstrates altered requirements for the conversion of viral single-stranded DNA to double-stranded replicative form DNA. In the presence of puromycin at 42 C, wild-type phi chi 174 is unable to complete this replicative event, whereas phi chi ahb is able to do so. Furthermore, in contrast to wild-type phi chi 174, formation of phi chi ahb parental replicative form DNA is sensitive to rifampin under certain experimental conditions. These data suggest that the mutant capsid proteins of phi chi ahb influence the biosynthesis of phi chi ahb complementary strand DNA.