Effects of anti-alpha monoclonal antibodies on initiation and elongation by the Escherichia coli RNA polymerase

Precise Characterization of the Epitope Recognized by a Monoclonal Antibody AgainstEscherichia coliRNA Polymerase

We have recently isolated a monoclonal antibody directed against Escherichia coli RNA polymerase that does not inhibit transcription. This antibody is a useful tool to immobilize this enzyme for transcription assays or protein-protein interaction studies. The epitope of this monoclonal antibody was precisely located by a combination of protein deletion and synthetic peptide scanning. The amino acids of the epitope were also determined. We conclude that this antibody binds an epitope shared by several bacterial species and therefore can be used to characterize or purify other related enzymes.

Conformational changes of E. coli RNA polymerase during transcription initiation

Escherichia coli RNA polymerase-promoter complex undergoes a multistep process to initiate transcription. We have employed fluorescence spectroscopic approaches to detect the conformational states of the enzyme during this multistep process. A fluorescence assay based on the measurement of fluorescence of free and promoter-bound enzyme as a function of temperature within the range of 4 to 37 degrees C showed that, starting with initial 'closed complex', there are conformationally two distinct intermediate states of the polymerase till it attains the final form required for transcription initiation. The equilibrium from closed complex (RPc) to open complex (RPo) consists of at least the following two intermediate complexes: [formula: see text] Higher order structure of RNAP in each of these complexes was probed by means of measurement of accessibilities of the tryptophan fluorophores to the acrylamide. In the next part of the study, TbGTP, a fluorescent substrate, has been used to probe the state of active site in the enzyme for the complexes RPc, RPi1, RPi2 and RPo, respectively. From the comparison of changes in the parameters such as, fluorescence polarization anisotropy of TbGTP and its accessibility to the neutral quencher, acrylamide, in free and promoter-bound enzyme, we have further substantiated the first part of our results. Together these results suggest that formations of RPc and RPi1 do not involve radical conformational changes in the enzyme, while the enzyme undergoes major change in conformation in the steps RPil-->RPi2 and RPi2-->RPo. The strong tryptophan promoter cloned in plasmid pDR720 was chosen as a model promoter in these studies.

Location, structure, and function of the target of a transcriptional activator protein

We have isolated and characterized single-amino-acid substitution mutants of RNA polymerase alpha subunit defective in CAP-dependent transcription at the lac promoter but not defective in CAP-independent transcription. Our results establish that (1) amino acids 258-265 of alpha constitute an "activation target" essential for CAP-dependent transcription at the lac promoter but not essential for CAP-independent transcription, (2) amino acid 261 is the most critical amino acid of the activation target, (3) amino acid 261 is distinct from the determinants for alpha-DNA interaction, and (4) the activation target may fold as a surface amphipathic alpha-helix. We propose a model for transcriptional activation at the lac promoter that integrates these and other recent results regarding transcriptional activation and RNA polymerase structure and function.

Asymmetric arrangement of two alpha subunits within Escherichia coli RNA polymerase. Involvement of one alpha subunit in contact with cAMP receptor protein

Class I transcription factors of Escherichia coli have been proposed to make contact with contact site I on the alpha subunit, C-terminal region of RNA polymerase with the subunit composition of alpha 2 beta beta ' sigma. Both a reconstituted mutant holoenzyme containing two C-terminally truncated alpha-235 subunits and a hybrid enzyme containing one wild-type alpha (alpha-329) and one C-terminal truncated alpha (alpha-235) subunit were found to be as active in transcription from factor-independent simple promoters as the wild-type holoenzyme. The mutant enzyme was, however, inactive in cAMP receptor protein (CRP)-dependent transcription from lacP1 promoter, but the hybrid enzyme was about 50% as active in lacP1 transcription as the wild-type enzyme. The results indicate that only one specific alpha subunit makes contact with CRP.

The alpha subunit of RNA polymerase specifically inhibits expression of the porin genes ompF and ompC in vivo and in vitro in Escherichia coli

Overproduction of the alpha subunit of RNA polymerase in Escherichia coli resulted in inhibition of transcription of two osmoregulated porin genes, ompF and ompC, but not of constitutively expressed housekeeping genes. Overproduction of the sigma subunit did not have any inhibitory effects. The specific inhibitory effect of the alpha subunit was also found to depend upon the OmpR protein, the transcriptional activator for ompF and ompC. These results are in general agreement with other biochemical and genetic evidence suggesting that the alpha subunit is the subunit of RNA polymerase that directly interacts with certain transcriptional activators to initiate transcription.

Transcription activation at Class I CAP-dependent promoters

Catabolite gene activator protein (CAP)-dependent promoters can be grouped into three classes, based on the requirement for transcription activation and the position of the DNA site for CAP. Class I CAP-dependent promoters require only CAP for transcription activation and have the DNA site for CAP located upstream of the DNA site for RNA polymerase. Amino acids 156 to 162 of the promoter-proximal subunit of CAP are essential for transcription activation at Class I CAP-dependent promoters, but are not essential for DNA binding, and are not essential for DNA bending. In the structure of the CAP-DNA complex, these amino acids are located in a surface loop and form a cluster on the surface of the CAP-DNA complex. Amino acids 261, 265, and 270 of the alpha subunit of RNA polymerase are essential for response to transcription activation by CAP at Class I CAP-dependent promoters. Several lines of evidence indicate that transcription activation at Class I CAP-dependent promoters requires a direct protein-protein contact between amino acids 156 to 162 of the promoter-proximal subunit of CAP and a molecule of RNA polymerase bound adjacent to CAP on the same face of the DNA helix. It is a strong possibility that this direct protein-protein contact involves amino acids 261 and 265 of the alpha subunit of RNA polymerase.

Involvement of the Escherichia coli RNA polymerase alpha subunit in transcriptional activation by the bacteriophage lambda CI and CII proteins

Escherichia coli cells harbouring the rpoA341 mutation produce an RNA polymerase which transcribes inefficiently certain operons subject to positive control. Here, we demonstrate that the rpoA341 allele also prevents lysogenization of the host strain by bacteriophage lambda, a process dependent upon the action of two phage-encoded activators. This phenomenon was shown to arise from an inability to establish an integrated prophage rather than a failure to maintain the lysogenic state. The inability of the rpoA341 host to support lysogenization could be completely reversed by CII-independent expression of int and cI in trans. These results led us to propose that the inhibition of lysogenization arises from a defective interaction between the phage lambda transcriptional activator CII and the mutant RNA polymerase at the phage promoters pI and pE. Finally, we also provide genetic evidence for impaired transcription of the cI gene from the CI-activated promoter, pM in the rpoA341 background.

Role of the RNA polymerase alpha subunit in transcription activation

The N-terminal two-thirds of the alpha subunit of Escherichia coli RNA polymerase plays an essential role in the initiation of subunit assembly, by gathering two large subunits, beta and beta', together into a core-enzyme complex. One group of RNA polymerase mutants deficient in response to transcription activation carries mutations in the C-terminal region of the alpha subunit, indicating that the C-terminal region of the alpha subunit is involved in protein-protein contact in positive control of transcription. A set of activators (class I transcription factors) which make contact with this contact site I region on RNA polymerase alpha subunit bind in most cases to DNA upstream of the promoter -35 signal. Genetic fine mapping indicates that a cluster of subsites exists in the contact site I region, each interacting with a set of the class I factors and each consisting of a structure formed by only 5-10 amino acid residues.

Escherichia coli rpoA mutation which impairs transcription of positively regulated systems

The rpoA341 (phs) mutation of Escherichia coli results in decreased expression of several positively regulated operons and has been mapped to within or very near the rpoA gene encoding the alpha subunit of RNA polymerase. We have shown that plasmid-directed synthesis of the wild-type alpha subunit can complement the defective phenotypes associated with this mutation consistent with its proposed location within rpoA. This mutation was mapped by marker rescue to within a 182bp region near the 3' end of rpoA and was subsequently transferred to a plasmid by recombination in vivo. DNA sequence analysis revealed that the RpoA341 phenotype was the result of the substitution of lysine 271 by glutamate within the alpha polypeptide. We discuss this result in relation to our current understanding of the functional organization of the alpha subunit.

Purification of RNA using an anti-RNA monoclonal antibody

Studies of the synthesis and modification of RNA employ many types of in vitro reactions. Often, the RNA product must be concentrated or purified away from other reaction components such as salts, unincorporated nucleotides, protein, or DNA. Here I describe an immunological approach suitable for the isolation of RNA from in vitro reactions. A variety of RNAs of differing size and nucleotide sequence were immunoprecipitated with a monoclonal antibody specific for RNA. RNA binding took place in seconds with nearly quantitative recoveries. Immunoprecipitation was more efficient than ethanol precipitation in removing unincorporated nucleotides. Proteins which do not bind to RNA remained soluble. The immunoprecipitated RNA sample was solubilized directly with a buffered solution suitable for gel electrophoresis under denaturing conditions. Thus, RNAs can be rapidly concentrated for electrophoresis in a single step. Antibody-RNA binding was reversible under nondenaturing conditions in the presence of excess rRNA. This procedure serves as a novel means of purifying RNA and RNA-binding proteins from in vitro reactions.

Bipartite functional map of the E. coli RNA polymerase alpha subunit: involvement of the C-terminal region in transcription activation by cAMP-CRP

The alpha subunit of Escherichia coli RNA polymerase plays a major role in the subunit assembly. Carboxyterminal deletion derivatives lacking 73 or 94 amino acid residues were assembled in vitro into enzyme molecules. Core enzymes consisting of these C-terminal-truncated alpha subunits were as active in RNA synthesis as native core enzyme. By the addition of sigma 70 subunit, these mutant enzymes initiated transcription from certain promoters. The mutant RNA polymerases, however, did not show cAMP-CRP activated transcription. These results demonstrate that the N-terminal region of the alpha subunit is involved in the formation of active enzyme molecule, while the C-terminal region plays an essential role in response to transcription activation by cAMP-CRP.