Characterization of a ts beta' mutant RNA polymerase of Escherichia coli

Localization of Escherichia coli rpoC mutations that affect RNA polymerase assembly and activity at high temperature

We localized five rpoC (beta') mutations affecting Escherichia coli RNA polymerase assembly. The Ts4, XH56, and R120 mutations changed beta' residues conserved throughout eubacteria; the JE10092 mutation occurred in the hypervariable region; rpoC1 (TsX) changed a universally conserved residue and corresponds to yeast rpb1-1. Thus, distinct, predominantly conserved beta' residues participate in interactions holding RNA polymerase together.

Reverse genetics of Drosophila RNA polymerase II: identification and characterization of RpII140, the genomic locus for the second-largest subunit

We have used a reverse genetics approach to isolate genes encoding two subunits of Drosophila melanogaster RNA polymerase II. RpII18 encodes the 18-kDa subunit and maps cytogenetically to polytene band region 83A. RpII140 encodes the 140-kDa subunit and maps to polytene band region 88A10:B1,2. Focusing on RpII140, we used in situ hybridization to map this gene to a small subinterval defined by the endpoints of a series of deficiencies impinging on the 88A/B region and showed that it does not represent a previously known genetic locus. Two recently defined complementation groups, A5 and Z6, reside in the same subinterval and thus were candidates for the RpII140 locus. Phenotypes of A5 mutants suggested that they affect RNA polymerase II, in that the lethal phase and the interaction with developmental loci such as Ubx resemble those of mutants in the gene for the largest subunit, RpII215. Indeed, we have achieved complete genetic rescue of representative recessive lethal mutations of A5 with a P-element construct containing a 9.1-kb genomic DNA fragment carrying RpII140. Interestingly, the initial construct also rescued lethal alleles in the neighboring complementation group, Z6, revealing that the 9.1-kb insert carries two genes. Deleting coding region sequences of RpII140, however, yielded a transformation vector that failed to rescue A5 alleles but continued to rescue Z6 alleles. These results strongly support the conclusion that the A5 complementation group is equivalent to the genomic RpII140 locus.

Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila

We have characterized RpII215, the gene encoding the largest subunit of RNA polymerase II in Drosophila melanogaster. DNA sequencing and nuclease S1 analyses provided the primary structure of this gene, its 7 kb RNA and 215 kDa protein products. The amino-terminal 80% of the subunit harbors regions with strong homology to the beta' subunit of Escherichia coli RNA polymerase and to the largest subunits of other eukaryotic RNA polymerases. The carboxyl-terminal 20% of the subunit is composed of multiple repeats of a seven amino acid consensus sequence, Tyr-Ser-Pro-Thr-Ser-Pro-Ser. The homology domains, as well as the unique carboxyl-terminal structure, are considered in the light of current knowledge of RNA polymerase II and the properties of its largest subunit. Additionally, germline transformation demonstrated that a 9.4 kb genomic DNA segment containing the alpha-amanitin-resistant allele, RpII215C4, includes all sequences required to produce amanitin-resistant transformants.

Isolation and characterization of temperature-sensitive RNA polymerase II mutants of Saccharomyces cerevisiae

Three independent, recessive, temperature-sensitive (Ts-) conditional lethal mutations in the largest subunit of Saccharomyces cerevisiae RNA polymerase II (RNAP II) have been isolated after replacement of a portion of the wild-type gene (RPO21) by a mutagenized fragment of the cloned gene. Measurements of cell growth, viability, and total RNA and protein synthesis showed that rpo21-1, rpo21-2, and rpo21-3 mutations caused a slow shutoff of RNAP II activity in cells shifted to the nonpermissive temperature (39 degrees C). Each mutant displayed a distinct phenotype, and one of the mutant enzymes (rpo21-1) was completely deficient in RNAP II activity in vitro. RNAP I and RNAP III in vitro activities were not affected. These results were consistent with the notion that the genetic lesions affect RNAP II assembly or holoenzyme stability. DNA sequencing revealed that in each case the mutations involved nonconservative amino acid substitutions, resulting in charge changes. The lesions harbored by all three rpo21 Ts- alleles lie in DNA sequence domains that are highly conserved among genes that encode the largest subunits of RNAP from a variety of eucaryotes; one mutation lies in a possible Zn2+ binding domain.

Isolation and characterization of temperature-sensitive RNA polymerase II mutants of Saccharomyces cerevisiae

Three independent, recessive, temperature-sensitive (Ts-) conditional lethal mutations in the largest subunit of Saccharomyces cerevisiae RNA polymerase II (RNAP II) have been isolated after replacement of a portion of the wild-type gene (RPO21) by a mutagenized fragment of the cloned gene. Measurements of cell growth, viability, and total RNA and protein synthesis showed that rpo21-1, rpo21-2, and rpo21-3 mutations caused a slow shutoff of RNAP II activity in cells shifted to the nonpermissive temperature (39 degrees C). Each mutant displayed a distinct phenotype, and one of the mutant enzymes (rpo21-1) was completely deficient in RNAP II activity in vitro. RNAP I and RNAP III in vitro activities were not affected. These results were consistent with the notion that the genetic lesions affect RNAP II assembly or holoenzyme stability. DNA sequencing revealed that in each case the mutations involved nonconservative amino acid substitutions, resulting in charge changes. The lesions harbored by all three rpo21 Ts- alleles lie in DNA sequence domains that are highly conserved among genes that encode the largest subunits of RNAP from a variety of eucaryotes; one mutation lies in a possible Zn2+ binding domain.

Temperature sensitive pet mutants in yeast Saccharomyces cerevisiae that lose mitochondrial RNA

This is a description of a new class of temperature sensitive pet mutants in Saccharomyces cereviase that lose all or part of their mitochondrial RNA at the restrictive temperature. These mutants fall into 8 different complementation groups, mna1 to mna8, and 2 different classes based on their phenotype. Class I mutations, mna1-1 through mna5-1, cause complete or partial loss of mitochondrial RNA at the restrictive temperature. The mutation, mna1-1, is especially interesting since it causes a loss of both mitochondrial DNA and RNA when the mutant is grown on a fermentable carbon source at the restrictive temperature. However, when this mutant is grown at the permissive temperature on a non-fermentable carbon source then shifted to the restrictive temperature, only the mitochondrial RNA is lost. This indicates that the primary cause for the pet phenotype is due to the loss of mitochondrial RNA and not DNA. Class II mutations, mna6-1 through mna8-1, cause complete loss of the 14S rRNA after growth at the restrictive temperature in a fermentable carbon source. This loss appears to be specific for the 14S rRNA, since all other transcripts probed by Northern analysis are normal.

Homology between RNA polymerases of poxviruses, prokaryotes, and eukaryotes: nucleotide sequence and transcriptional analysis of vaccinia virus genes encoding 147-kDa and 22-kDa subunits

We have determined the nucleotide sequence of a region of the vaccinia virus genome encoding RNA polymerase subunits of 22 and 147 kDa and have mapped the 5' and 3' ends of the two mRNAs. The predicted amino acid sequence of the vaccinia 147-kDa subunit shows extensive homology with the largest subunit of Escherichia coli RNA polymerase, yeast RNA polymerases II and III, and Drosophila RNA polymerase II. The regions of homology between the five RNA polymerases are subdivided into five separate domains that span most of the length of each. A sixth domain shared by the vaccinia and the eukaryotic polymerases is absent from the E. coli sequence. In all specified regions, the vaccinia large subunit has greater homology with eukaryotic RNA polymerases II and III than with the E. coli polymerase. Vaccinia virus and eukaryotic RNA polymerases may therefore have evolved from a common ancestral gene after the latter diverged from prokaryotes.

Temperature-sensitive Saccharomyces cerevisiae mutant defective in lipid biosynthesis

A temperature-sensitive mutant of Saccharomyces cerevisiae (DAM303) is described that exhibits an early defect in lipid biosynthesis at the restrictive growth temperature, 37 degrees C. This strain rapidly lost viability after 1 h of incubation at 37 degrees C, and this was accompanied by a significantly reduced incorporation of 32Pi into cellular lipid and an accumulation of [1-14C]acetate into the free fatty acid fraction. The temperature-sensitive DAM303 mutation failed to complement the sec13 mutation described by Novick et al. (Cell 21:205-215, 1980), and from analysis of invertase secretion in the temperature-sensitive DAM303 strain, it is clear that the loss of invertase secretion in the mutant occurs after the loss of phospholipid synthesis. Although the precise nature of the temperature-sensitive lesion in the DAM303 strain has still to be identified, the results from the study of this mutant indicate that a defect in lipid biosynthesis can be correlated with subsequent alterations in extracellular protein secretion and loss of other macromolecular functions including DNA, RNA, and protein syntheses. From studies of this mutant, two procedures of enriching for other temperature-sensitive mutants with defects in lipid biosynthesis have emerged: inositol overproduction and screening for increased buoyant densities.

A mutation in the RNA polymerase beta' subunit causing depressed ribosomal RNA synthesis in Escherichia coli

Macromolecular synthesis in an Escherichia coli mutant with a temperature-sensitive beta' subunit of RNA polymerase was analysed. At the non-permissive temperature ribosomal RNA synthesis is strongly reduced while messenger RNA synthesis is affected to only a slightly extent. The overall protein synthesis is only slightly affected. We conclude that the beta' subunit is involved in promoter recognition and plays a role in transcriptional selectivity.

Cold-sensitive mutations in beta and beta' subunit gene affecting the interaction of RNA polymerase with promoters

RNA polymerases with a cold-sensitive activity were purified from seven mutants of Escherichia coli. Subunit reconstitution experiments have shown that RNA polymerases from three mutants (Rpob262, RpoB264, and RpoB265) owed their cold sensitivity to alterations in the beta subunit. Three mutants (RpoC3, RpoC263, and RpoC267) were shown to be defective in the beta' subunit and one (RpoBC266) in both beta and beta' subunits. Two mutations (rpoC3 and rpoC263) reduced the level of RNA polymerase reconstitution. RNA polymerases from RpoC3 and RpoBC266 mutants are defective in RNA chain elongation at 6 degree C, while all the other mutants are defective in RNA polymerase-promoter interaction. most mutant RNA polymerases differ from the wild-type enzyme in transcription selectivity. The results obtained in this study indicate that both beta and beta' subunits are involved in RNA chain elongation and promoter binding and selection.

A cold-sensitive beta subunit mutant RNA polymerase from Escherichia coli with defects in promoter opening in vitro

A cold-sensitive mutation in the rpoB gene for the RNA polymerase beta subunit increasing the temperature of promoter opening on T2 phage DNA was obtained in Escherichia coli. The mutation also affects the stages preceding promoter opening by increasing the dissociation rate of RNA polymerase--DNA closed complexes. The affinity of RNA polymerase to T2 and lambda DNA is differentially changed by the mutation. The relative efficiency of transcription of these two templates is also changed. These results suggest a participation of the RNA polymerase beta subunit in the interaction with promoters.

Expression of RNA polymerase and ribosome component genes in Escherichia coli mutants having conditionally defective RNA polymerases

The expression of the genes coding for the beta and beta' subunits of RNA polymerase, ribosomal RNA, ribosomal proteins, and beta-galactosidase was investigated in strains carrying conditionally lethal mutations affecting either RNA polymerase core assembly or RNA polymerase enzyme activity. The mutant strain XH56 produces a temperature-sensitive beta' subunit and at 42 degrees C is defective in RNA chain initiation; consequently, little or no transcription occurs at the restrictive temperature. A partial restriction, produced by shifting the strain to 39 degrees C, resulted in a rapid fivefold increase in the transcription of the rpoB and C genes and in the synthesis of the beta- and beta'-subunit proteins for which they code. The RNA polymerase assembly-defective strains A2R7 and TS4 exhibited a 1.5- to 2-fold increase in the transcription of the rpoB and C genes and in the synthesis of beta- and beta-subunit proteins after prolonged restriction. These results demonstrate (i) that regulation of the synthesis of the beta- and beta-RNA polymerase subunits is under these conditions primarily transcriptional rather than translational, and (ii) that a stimulation of rpoB and C gene expression results from a restriction on RNA synthesis caused by either RNA polymerase inactivation or inhibition of its assembly. During restriction of the mutant strains, the transcription of the ribosome component genes exhibited patterns which were similar to transcription of the rpoB and C genes, supporting the evidence that genes coding for RNA polymerase are cotranscribed with ribosomal protein genes; transcription of the lacZ gene was observed to decrease concomitant with the stimulation of the rpoB and C genes.

A mutation affecting the sigma subunit of RNA polymerase changes transcriptional specificity

The RNA polymerase mutation, alt-1, affects the sigma subunit and alters the in vitro selectivity of RNA polymerase to parallel the in vivo phenotype. We propose that the mutation changes the distribution of functionally distinct polymerase isomers.

Physiological studies on a temperature-sensitive Escherichia coli mutant with an altered RNA polymerase beta'-subunit

Some in vivo properties of an Escherichia coli temperature-sensitive mutant (JE10092) with an altered RNA polymerase beta'-subunit are described. RNA synthesis, unlike many peviously isolated temperature-sensitive mutants, stops immediately after the shift to the nonpermissive temperature (43 degrees C). DNA synthesis, protein synthesis and nucleoside triphosphate formation continue after the shift. RNA synthesis is recovered immediately upon transfer to the permissive temperature (30 degrees C). The function of the beta'-subunit in genetic transcription is discussed.

Multiple effects of an RNA polymerase beta' mutation on in vitro transcription

S. tyrphimurium strain BY324 is temperature sensitive due to a mutation (rpo C32) in the gene for the RNA polymerase beta' subunit. Transcription of T7 DNA by RNA polymerase purified from this strain is temperature sensitive in vitro. The enzyme is slightly defective in template binding and RNA chain initiation, but the major defect is in RNA chain elongation. The rate of RNA chain elongation is reduced 4-5 fold relative to wild-type. RNA chain termination does not appear to be affected by the beta' mutation. While the elongation defect is suppressed by glycerol or dimethylsulfoxide, the initiation defect is not. Possible roles for the beta' subunit in enzyme function are discussed in light of these results.