Identification of a subunit assembly domain in the alpha subunit of Escherichia coli RNA polymerase

Protein-protein communication within the transcription apparatus

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The C terminus of the alpha subunit of RNA polymerase is not essential for transcriptional activation of sigma 54 holoenzyme

Several activators of sigma 70 holoenzyme whose binding sites lie upstream of the -35 region of promoters require the C-terminal region of the alpha subunit of RNA polymerase to activate transcription. (These are among class I activators, which require the C-terminal region of the alpha subunit for transcription activation.) Because transcription by sigma 54 holoenzyme universally depends upon activators whose binding sites lie well upstream (or downstream) of promoters, we determined whether the C-terminal region of the alpha subunit was also required for transcription from the sigma 54-dependent promoter for the glnA operon. Nitrogen regulatory protein C-dependent activation from the glnA promoter remained good when RNA polymerases containing C-terminal truncations of the alpha subunit were employed. This was also the case for nitrogen fixation protein A-dependent activation if a nitrogen fixation protein A-binding site was appropriately placed upstream of the glnA promoter. These results lead to the working hypothesis (as yet untested) that activators of sigma 54 holoenzyme, which appear to make direct physical contact with the polymerase to catalyze a change in its conformation, activate the sigma 54 holoenzyme by contacting the sigma subunit rather than the alpha subunit of the core enzyme.

Evolutionary analysis of the plastid-encoded gene for the alpha subunit of the DNA-dependent RNA polymerase of Pyrenomonas salina (Cryptophyceae)

The nucleotide sequence of the gene coding for the plastid-encoded alpha subunit of DNA-dependent RNA polymerase from the cryptomonad alga Pyrenomonas salina was determined. The deduced amino-acid sequence, corresponding to a 35.2 kDa polypeptide, was compared to homologues from other organisms. Evolutionary relationships were analyzed in detail by the parsimony method together with bootstrap analysis. The deduced phylogenetic tree shows that the cryptomonad gene is the most ancient type of known plastid-encoded RNA polymerase.

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.

Mapping the cAMP receptor protein contact site on the alpha subunit of Escherichia coli RNA polymerase

The C-terminal region (amino acid residues 236-329) of the Escherichia coli RNA polymerase alpha subunit carries the contact site I for positive transcription factors. For detailed mapping of the contact site for the cAMP receptor protein (CRP), we made a library of mutant rpoA by polymerase chain reaction (PCR) mutagenesis, such that each should carry a single mutation on average and exclusively in the C-terminal half of the rpoA gene, and then screened this library for mutants with decreased expression of the lacZ gene. Reconstituted holoenzyme containing the mutant alpha subunits transcribed galP1 but not lacP1 in vitro in the presence of cAMP-CRP. DNA sequence determination of several 'Lac-' mutant rpoA genes revealed that all had mutations clustered within a short segment near the C-terminus of alpha, between amino acid residues 265 and 270. A cluster of contact sites appear to exist within the contact site I region, each comprising of about five amino acids and responding in molecular communication with a different transcription factor(s).

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.

Functional specialization within the alpha-subunit of Escherichia coli RNA polymerase

The RNA polymerase core enzyme of Escherichia coli has the subunit composition alpha 2 beta beta', and when combined with one of several alternative sigma-subunits (initiation-specificity) produces holoenzyme capable of all the steps of transcription. Dimerization of the alpha-subunit and association with the beta-subunit trigger assembly of the core enzyme. Analyses of a set of deletion derivatives of rpoA (which encodes alpha) have indicated that as many as 94 carboxy-terminal amino acids (but not 153) can be removed without preventing assembly of core-like complexes in vitro. Detailed analyses of these deletion mutants have now been performed in vivo. alpha-Polypeptides truncated from the carboxy terminus to amino acid residues 235, 256 or 296 are assembled not merely into core, but also into holoenzyme-like complexes in vivo, and at least in the first two cases both of the two alpha-subunits can be replaced by the truncated versions. Nevertheless, none can complement rpoAts alleles for growth at 42 degrees C. We conclude that the domain(s) of alpha essential for the assembly of RNA polymerase (at least the major holoenzyme species) are confined to the amino-terminal 235 amino acids, while some other essential function(s) require residues close to the carboxy terminus.

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.