Late sigma factor of bacteriophage T4. Formation and properties of RNA polymerase-promoter complexes

The secret life of the anthrax agent Bacillus anthracis: bacteriophage-mediated ecological adaptations

Ecological and genetic factors that govern the occurrence and persistence of anthrax reservoirs in the environment are obscure. A central tenet, based on limited and often conflicting studies, has long held that growing or vegetative forms of Bacillus anthracis survive poorly outside the mammalian host and must sporulate to survive in the environment. Here, we present evidence of a more dynamic lifecycle, whereby interactions with bacterial viruses, or bacteriophages, elicit phenotypic alterations in B. anthracis and the emergence of infected derivatives, or lysogens, with dramatically altered survival capabilities. Using both laboratory and environmental B. anthracis strains, we show that lysogeny can block or promote sporulation depending on the phage, induce exopolysaccharide expression and biofilm formation, and enable the long-term colonization of both an artificial soil environment and the intestinal tract of the invertebrate redworm, Eisenia fetida. All of the B. anthracis lysogens existed in a pseudolysogenic-like state in both the soil and worm gut, shedding phages that could in turn infect non-lysogenic B. anthracis recipients and confer survival phenotypes in those environments. Finally, the mechanism behind several phenotypic changes was found to require phage-encoded bacterial sigma factors and the expression of at least one host-encoded protein predicted to be involved in the colonization of invertebrate intestines. The results here demonstrate that during its environmental phase, bacteriophages provide B. anthracis with alternatives to sporulation that involve the activation of soil-survival and endosymbiotic capabilities.

The mechanism of transcriptional activation by the topologically DNA-linked sliding clamp of bacteriophage T4

Three viral proteins participate directly in transcription of bacteriophage T4 late genes: the sigma-family protein gp55 provides promoter recognition, gp33 is the co-activator, and gp45 is the activator of transcription; gp33 also represses transcription in the absence of gp45. Transcriptional activation by gp45, the toroidal sliding clamp of the T4 DNA polymerase holoenzyme, requires assembly at primer-template junctions by its clamp loader. The mechanism of transcriptional activation has been analyzed by examining rates of formation of open promoter complexes. The basal gp55-RNA polymerase holoenzyme is only weakly held in its initially formed closed promoter complex, which subsequently opens very slowly. Activation ( approximately 320-fold in this work) increases affinity in the closed complex and accelerates promoter opening. Promoter opening by gp55 is also thermo-irreversible: the T4 late promoter does not open at 0 degrees C, but once opened at 30 degrees C remains open upon shift to the lower temperature. At a hybrid promoter for sigma(70) and gp55-holoenzymes, only gp55 confers thermo-irreversibility of promoter opening. Interaction of gp45 with a C-terminal epitope of gp33 is essential for the co-activator function of gp33.

Sigma competition: the contest between bacteriophage T4 middle and late transcription

In bacterial transcription, diverse sigma-family promoter recognition proteins compete for a common RNA polymerase core. Bacteriophage T4 infection ultimately reduces this competition to a duel between activated viral middle and enhanced late transcription, involving two sigma proteins, two phage-encoded activator proteins and two phage-specific co-activators. This competition has been analyzed in vitro, and the relative abundances in T4-infected Escherichia coli of the participating proteins have been measured. Activated late transcription holds an advantage over activated middle transcription, especially at higher ionic strength. This advantage is further compounded by ADP-ribosylation of the RNA polymerase alpha subunits, and by the phage-specific, RNA polymerase core-bound RpbA subunit. The largest contribution to the middle-late competition is made by gp55, the late sigma factor, but not enough of gp55 is produced during T4 infection to shut off middle transcription by direct competition with sigma(70). AsiA, the originally identified anti-sigma protein is not a major determinant of middle-late competition.

Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein

The 64 amino acid residue product of bacteriophage T7 gene 2 (gp2) binds the Escherichia coli RNA polymerase and inhibits transcription. We localized the gp2 binding site to within 53 amino acid residues in the functionally dispensable region of the RNA polymerase beta' subunit. We investigated the effect of gp2 on transcription at a -10/-35 promoter and at an "extended -10" promoter. Our results indicate that binding of gp2 to the sigma70holoenzyme (Esigma70) prevents promoter recognition at -10/-35 promoters. Once open promoter complexes are formed, however, Esigma70transcription is resistant to gp2, since gp2 can no longer bind RNA polymerase. Surprisingly, transcription inhibition by gp2 is both sigma and promoter-specific. gp2 has little effect on Esigma70transcription from an extended -10 promoter, which does not depend on sigma70region 4 interactions with the -35 promoter box for its activity. gp55-dependent phage T4 late promoter transcription is also resistant to gp2. From these results, we conclude that the interaction of the sigma70region 4 with the -35 consensus promoter element is the primary target of gp2 inhibition.

The anti-sigma factors

A mechanism for regulating gene expression at the level of transcription utilizes an antagonist of the sigma transcription factor known as the anti-sigma (anti-sigma) factor. The cytoplasmic class of anti-sigma factors has been well characterized. The class includes AsiA form bacteriophage T4, which inhibits Escherichia coli sigma 70; FlgM, present in both gram-positive and gram-negative bacteria, which inhibits the flagella sigma factor sigma 28; SpoIIAB, which inhibits the sporulation-specific sigma factor, sigma F and sigma G, of Bacillus subtilis; RbsW of B. subtilis, which inhibits stress response sigma factor sigma B; and DnaK, a general regulator of the heat shock response, which in bacteria inhibits the heat shock sigma factor sigma 32. In addition to this class of well-characterized cytoplasmic anti-sigma factors, a new class of homologous, inner-membrane-bound anti-sigma factors has recently been discovered in a variety of eubacteria. This new class of anti-sigma factors regulates the expression of so-called extracytoplasmic functions, and hence is known as the ECF subfamily of anti-sigma factors. The range of cell processes regulated by anti-sigma factors is highly varied and includes bacteriophage phage growth, sporulation, stress response, flagellar biosynthesis, pigment production, ion transport, and virulence.

Transcriptional activation by a DNA-tracking protein: structural consequences of enhancement at the T4 late promoter

Transcriptional initiation at bacteriophage T4 late promoters is activated from enhancer-like distal sites by the T4 gene 44, 62, and 45 DNA polymerase accessory proteins (gp44, gp62, and gp45, respectively). Enhancement is ATP hydrolysis-dependent and requires protein tracking along DNA. The structural analysis of the enhanced transcription initiation complex shows gp45 located at the upstream end of this promoter complex in the vicinity of its transcriptional coactivator, the T4 gene 33 protein. The ATP-cleaving gene 44 protein-gene 62 protein complex serves as the assembly factor for gp45, but does not stably associate with the enhanced promoter complex. Transcriptional enhancement quantitatively favors, but does not qualitatively change, DNA strand separation in the transcription bubble. A model of the transcriptional activation that rationalizes its DNA-tracking and activation-polarity properties is presented.

The bacteriophage T4 gene mrh whose product inhibits late T4 gene expression in an Escherichia coli rpoH (sigma 32) mutant

In an Escherichia coli rpoH mutant (affecting sigma 32, heat-shock sigma factor) infected at high temperatures with wild-type T4 phage, late T4 transcription and consequently progeny production are dramatically impaired. This defect is due, in part, to insufficient activity of sigma 70 [Frazier and Mosig, J. Bacteriol. 170 (1988) 1384-1388], which is necessary to initiate early T4 transcription. Unexpectedly, however, we found that, in this rpoH host, late T4 transcription is also impaired when the temperature is raised from 30 to 42 degrees C late after infection, when T4 transcription is directed by the T4-encoded sigma factor, sigma gp55. Here, we show that a T4 gene that we call mrh (modulates rpoH), located at 14 kb on the T4 map, is responsible for the inhibition of late T4 transcription in the rpoH mutant host. T4 deletion mutants that lack the mrh gene can produce progeny in the rpoH host, but the Mrh protein, provided in trans from a plasmid-borne mrh gene, inhibits this growth. We have cloned and sequenced this T4 gene and synthesized the Mrh protein in a T7 RNA polymerase-dependent expression system. The Mr of the Mrh protein deduced from the nucleotide sequence is 13419. Gene mrh is cotranscribed with several other, yet unidentified genes, both from an early promoter downstream from the late soc gene (encoding the small outer capsid protein) and from the late soc promoter further upstream.(ABSTRACT TRUNCATED AT 250 WORDS)