Studies on T3-induced Ribonucleic Acid Polymerase

Transcription termination by bacteriophage T3 and SP6 RNA polymerases at Rho-independent terminators

Transcription termination of T3 and SP6 DNA-dependent RNA polymerases have been studied on the DNA templates containing the threonine (thr) attenuator and its variants. The thr attenuator is from the regulatory region of the thr operon of Escherichia coli. The DNA template, encoding the thr attenuator, contains specific features of the rho-independent terminators. It comprises a dG + dC rich dyad symmetry, encoding a stem-and-loop RNA, which is followed by a poly(U) region at the 3'-end. Thirteen attenuator variants have been analyzed for their ability to terminate transcription and the results indicated that the structure as well as the sequence in the G + C rich region of RNA hairpin affect termination of both RNA polymerases. Also, a single base change in the A residues of the hairpin failed to influence termination, whereas changes in the poly(U) region significantly reduced the termination of both T3 and SP6 RNA polymerases. The requirement of a poly(U) region for termination by T3 and SP6 RNA polymerases was studied with nested deletion mutants in this region. The minimum number of U residues required for termination of SP6 and T3 RNA polymerases was five and three, respectively. However, both RNA polymerases needed at least eight U residues to reach a termination efficiency close to that achieved by wild-type thr attenuator encoding nine U residues. In addition, the orientation of the loop sequences of the RNA hairpin did not affect the transcription termination of either of the bacteriophage RNA polymerases.

A simple method of distinguishing the bacterial viruses T3 and T7, and a critical reevaluation of their heterologous and homologous exclusion

A method is presented allowing a clear distinction between bacterial viruses T3 and T7 by plating on selectively permissive host cells. The indicator strains are Escherichia coli cells containing either cloned pif genes (exclusively permissive for T3) or the EcoRV DNA restriction system (permissive only for T7): The efficiencies of plating of the two phages on these hosts differ by more than 8 orders of magnitude. This method was applied to reinvestigate the controversial question of mutual exclusion between T3 and T7. Under single-burst conditions, about 50% of coinfected cells (permissive for both viruses) produced T3 and T7 progeny while about 25% reproduced only T3 and about 25% only T7. The burst size of co-infected cells was slightly reduced, compared to controls infected with only one virus type. Homologous exclusion among T3 phages was also not seen; rather, there was a gene dosage effect: T3-encoded RNA polymerase activity as well as T3-specific RNA synthesis increased proportionally to the multiplicity of infection (2.5-20 plaque-forming units/cell).

Specific binding of monomeric bacteriophage T3 and T7 RNA polymerases to their respective cognate promoters requires the initiating ribonucleoside triphosphate (GTP)

Bacteriophage T3 and T7 RNA polymerases are monomeric proteins of Mr of about 100,000. Each polymerase has stringent specificity for its own promoters that is present only on the homologous phage DNA template. Neither enzyme recognizes the heterologous phage promoters or Escherichia coli RNA polymerase promoters. In the present study, the interaction of T3 and T7 RNA polymerases with their respective cognate promoters was studied by DNase I footprinting techniques. These studies revealed an absolute requirement for the initiating nucleotide (GTP) for each phage RNA polymerase to bind specifically to and protect its cognate promoter from DNase I digestion. In the absence of the initiating nucleotide, both enzymes randomly bind DNA with lower affinity. No other nucleotide can substitute for GTP; however, the addition of GTP + ATP, which causes the synthesis of a hexamer RNA (pppGpGpGpApGpA), makes the DNA-RNA-protein complex highly stable. Nitrocellulose filter binding studies confirmed these observations. On the basis of these results we propose that the binding of the initiating nucleotide (in this case, GTP) drives the phage RNA polymerase into an "initiation conformation" in which the random DNA-binding property of the enzyme is converted to a promoter-specific recognition, and the polymerase is primed to initiate transcription.

Characterization of phage-Xp10-coded RNA polymerase

A bacteriophage-coded RNA polymerase was isolated from bacteriophage-Xp10-infected Xanthomonas campestris pv. oryzae. The enzyme was purified to homogeneity through precipitation by poly(ethylene glycol) and chromatography on DEAE-cellulose, heparin--Sepharose 4B and blue-dextran--Sepharose 4B. It is composed of a single polypeptide of Mr96,000. The enzyme preferred denatured Xp10 DNA, calf thymus DNA, host bacterium DNA and poly[d(A-T)] as templates. The optimal concentration of MgCl2 is 16 mM. The optimal temperature and pH are 37 degrees C and 8.0, respectively. The Km of ATP is 26 microM. DNA, MgCl2 and four ribonucleotides were required for enzyme activity. If ATP alone was present, half of the Xp10 RNA polymerase activity was retained. The enzyme activity was inhibited by KCl, spermidine, actinomycin D, heparin, blue dextran and ethidium bromide; it was resistant to rifampicin and streptovaricin. N-Ethylmaleimide did not affect the enzyme activity. The transcription site and product of Xp10 RNA polymerase upon Xp10 DNA were analyzed by DNA/RNA hybridization and polyacrylamide-agarose composite gel electrophoresis. The enzyme could specifically transcribe the late region of Xp10 genome and produce two RNA bands.

Nucleotide sequence of a major class-III phage-T3 RNA-polymerase promoter located at 98.0% of phage-T3 genetic map

The entire nucleotide sequence of a 409-bp HincII fragment, located within the MboI-E fragment on bacteriophage T3 DNA and containing a major class-III T3 RNA polymerase promoter positioned at 98% on the standard T3 genetic map, has been determined. Alignment of this class-III promoter with previously determined T3 RNA polymerase promoters, with start points of transcription (+1) in register, indicates high degree of sequence conservation between position -16 to +6 among all T3 RNA polymerase promoters. The conserved portion of the (-) strand sequence is 5'-A-TA-T-AT-A-C-C-C-T-C-A-C-T-A-A-A-G-G-G-A---3'. This fragment also contains an open reading frame (ORF) with a translational start codon located at position +146 which is preceded by a potential ribosome binding site (RBS). There is more than 70% amino acid-sequence homology between the deduced sequences of the -NH2 terminal region of this putative T3 phage protein and the corresponding protein coded by bacteriophage T7 (protein of T7 gene 19.5).

Influence of dimethylsulfoxide on transcription by bacteriophage T3-induced RNA polymerase

Dimethylsulfoxide (DMSO) up to 25% (v/v) does not cause irreversible alterations of T3 DNA at 42.5 degrees C as assayed by transcription with T3-specific RNA polymerase. The optimal temperature for the formation of polyanion-resistant ternary complexes of the enzyme, T3 DNA, and nascent RNA chains is lowered by 12.5 degrees C in the presence of 20% (v/v) DMSO. The same solvent concentration, however, decreased the temperature optimal for T3 RNA chain elongation by only 2.5 degrees C, indicating that DMSO preferably affects the initiation of T3 RNA synthesis. DMSO accelerates the loss of T3-specific RNA polymerase activity at 24.5 degrees C. Nevertheless, the speed with which the binary complexes between the phage RNA polymerase and DNA are inactivated by heat (42.5 degrees C) is not altered in presence of 20% (v/v) DMSO. The binding of T3-induced RNA polymerase to T3 DNA in polyanion-resistant ternary complexes is influenced by DMSO which makes the enzyme accessible to the inhibitory action of polyvinyl sulfate. Elongation of T3 RNA chains is slowed down by 20% (v/v) DMSO.

Effect of temperature on the transcription by bacteriophage T3-induced RNA polymerase

Bacteriophage T3-induced RNA polymerase is rapidly inactivated at 42 degrees C. Addition of T3 DNA delays this process for 30 s and reduces the rate with which the enzyme activity is lost indicating that a labile binary complex between T3 DNA and polymerase must have been formed. The ternary complex between T3-specific RNA polymerase, T3 DNA, and nascent RNA chains obtained when the enzyme is incubated with T3 DNA, GTP, ATP, and UTP is stable to heat (42 degrees C) and only slowly inactivated by polyvinyl sulfate. The optimal temperature for the formation of polyanionresistant ternary complexes is 30 degrees C while the elongation of T3 RNA chains proceeds fastest at 38 degrees C.