Gene for the RNA polymerase sigma subunit mapped in Salmonella typhimurium and Escherichia coli by cloning and deletion

Amber dnaG mutation exerting a polar effect on the synthesis of RNA polymerase sigma factor in Escherichia coli

Three amber mutants of Escherichia coli, dnaG9, dnaG24 and dnaG26, affected in the structural gene (dnaG) for "primase" have been isolated from a parental strain carrying a temperature-sensitive amber suppressor (supF-Ts6). These mutants grow at 30 degrees C but not at 42 degrees C since primase is essential for growth and is synthesized only at low temperatures. Chimeric plasmids carrying dnaG+ but no other chromosomal genes of E. coli complemented the amber mutations, and the plasmid carrying a part of dnaG lost the complementing activity. Beside, plasmids carrying a dnaG amber mutation complemented a temperature-sensitive dnaG mutation only in the presence of amber suppressor. One of the amber mutations, dnaG24 which maps proximal to the NH2-terminus of the dnaG gene, exerted a polar effect on the synthesis of RNA polymerase sigma factor in E. coli.

Isolation and physical mapping of the gene encoding the major sigma factor of Bacillus subtilis RNA polymerase

At least four sigma factors separately bind the Bacillus subtilis RNA polymerase core (beta beta' alpha 2), each conferring a different promoter specificity on the holoenzyme in vitro. Using the Broome-Gilbert immunological screening, we isolated recombinant lambda phages that carry rpoD, the gene for the most abundant sigma factor, sigma 55. These phages encode a 55,000-dalton protein whose size, immunological properties, and peptide map identify it as sigma 55. All the phages have in common two adjacent 3.5-kilobase EcoRI fragments from the B. subtilis chromosome; most carry additional genomic DNA. Deletion analysis localized rpoD to a 1.6-kilobase region, suggested the direction of its transcription, and found two additional genes near rpoD, which code for proteins of 62,000 and 17,000 daltons.

Intragenic localization of amber and temperature-sensitive rpoD mutations affecting RNA polymerase sigma factor of Escherichia coli

A set of multi-copy plasmids carrying part or all of the rpoD gene of Escherichia coli have been used to localize several amber and temperature-sensitive mutations affecting RNA polymerase sigma factor. In contrast to the plasmid carrying a complete rpoD sequence, plasmids carrying part of rpoD could not complement any of the rpoD mutations tested. However, the mutants harboring some of the latter plasmids produced wild-type recombinants at high frequency, provided that they carry the recA+ gene. The results permitted us to localize the rpoD mutations into one of the three intragenic segments. Thus, the rpoD285(ts) mutation (Harris et al. 1978) was located on the 0.8 kilobase segment defined by the Bg/II and BamHI sites in the middle segment, and the amber mutation rpoD40 (Osawa and Yura 1980) in the N-terminal 0.8 kilobase segment. Four additional amber mutations were also identified and classified into one of the segments of rpoD. It was further revealed that plasmids carrying certain amber mutations (rpoD47 or rpoD63) in the C-terminal segment of rpoD render all rpoD mutants tested (including rpoD47 and rpoD63 mutants themselves) able to grow at the restrictive condition. It is suggested that the enhanced synthesis of incomplete sigma polypeptides encoded by rpoD47 or rpoD63 phenotypically suppresses the defects in sigma function at least partially.

Cloning of bacterial DNA replication genes in bacteriophage lambda

Recombinant lambda phages containing the genes for dnaZ protein (the gamma subunit of DNA polymerse III holoenzyme), primase (dnaG protein) and dnaC protein from Escherichia coli and Salmonella typhimurium were isolated. Each gene cloned from S. typhimurium has extensive DNA sequence homology to the corresponding E. coli gene. Clones selected by complementation of a dnaA temperature-sensitive mutant appear similar to other isolated suppressors of dnaA (Projan and Wechsler 1981). Derivatives of each cloned fragment suitable for overproduction of the protein were constructed. Of those tested, only the phage containing the E. coli dnaZ gene resulted in significant overproduction.

Regulation of expression of the Escherichia coli dnaG gene and amplification of the dnaG primase

We have isolated lambda transducing phages carrying the Escherichia coli primase gene (dnaG) and mapped restriction sites in the cloned bacterial DNA segments. Several different DNA fragments containing the dnaG gene were inserted into multicopy plasmids. An analysis of the primase levels in cells harboring such plasmids indicates that sequences far upstream from the dnaG gene are required for optimal primase expression. Using this knowledge, we constructed a plasmid with a thermoinducible copy-number, pRLM61, which was employed to amplify intracellular primase levels approximately 100-fold. The dnaG gene is transcribed clockwise with respect to the E. coli genetic map, and a HindIII site located 180 base pairs upstream from the dnaG gene separates the gene from its primary promoter. An apparent transcription termination signal is positioned 30-70 base pairs in front of the primase gene. Transcription proceeds past this strong terminator only when RNA polymerase has first transcribed the bacterial DNA segment proximal to the HindIII site. We suggest that primase expression in E. coli is positively regulated by a mechanism of transcription antitermination mediated by a bacterial factor. We propose, furthermore, that the neighboring structural genes for primase and for the sigma subunit of RNA polymerase are coordinately regulated as part of an operon. This arrangement may enable the bacterial cell to readily control the level of initiation of DNA and RNA synthesis and thus to respond quickly and efficiently to changing conditions.

The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12

We have determined the nucleotide sequence of the rpoD gene which codes for the sigma subunit of RNA polymerase from E. coli K12. The gene, which we formerly cloned as a HindIII restriction fragment in the transducing phage, charon 25, was recloned into several plasmids. We have determined a 2600 base pair DNA sequence which includes the entire structural gene for sigma. The resulting amino acid sequence agrees with previous information obtained about sigma including the amino acid composition, partial sequence data for the N-terminus, the highly acidic nature of the polypeptide, and the cleavage pattern at cysteines. The molecular weight of 70,263 daltons calculated for the 613 amino acid polypeptides is significantly lower than had been determined previously by SDS polyacrylamide gel analysis.

Amber mutations in the structural gene for RNA polymerase sigma factor of Escherichia coli

Amber mutants of Escherichia coli K-12 affected in the structural gene (rpoD) for the sigma subunit of RNA polymerase have been obtained from a strain harboring a temperature-sensitive amber suppressor (supF-Ts6) which is active only at low temperatures. These mutants grow normally at low temperature (30 degrees C) but do not grow at high temperature (42 degrees C) due to the inability to synthesize sigma factor. In one mutant studied in detail (rpoD40), the rate of sigma-factor synthesis at 30 degrees C is about half that of the wild type and is decreased to 10%-15% within 1 h of incubation at 42 degrees C. The synthesis of core polymerase subunits or bulk protein is virtually unaffected at least for 2 h. The defect of the mutant in sigma synthesis and growth at high temperature can be suppressed by any of the amber suppressors tested (supD. supE or supF). RNA-polymerase holoenzymes prepared from the mutant cells carrying each of the suppressors (grown at 42 degrees C) exhibit different thermostabilities attributable to alterations in the sigma factor. The reduced sigma synthesis in the mutant is accompanied by the synthesis of polypeptide tentatively identified as 'amber fragment'. These results as well as the genetic mapping data indicate that the amber mutation (rpoD40) resides within the structural gene for the sigma factor and directly affects sigma synthesis upon inactivation of the suppressor at high temperature.