Conformational flexibility in sigma70 region 2 during transcription initiation

Different Modes of Transactivation of Bacteriophage Mu Late Promoters by Transcription Factor C

Transactivator protein C is required for the expression of bacteriophage Mu late genes from lys, I, P and mom promoters during lytic life cycle of the phage. The mechanism of transcription activation of mom gene by C protein is well understood. C activates transcription at Pmom by initial unwinding of the promoter DNA, thereby facilitating RNA polymerase (RNAP) recruitment. Subsequently, C interacts with the ß' subunit of RNAP to enhance promoter clearance. The mechanism by which C activates other late genes of the phage is not known. We carried out promoter-polymerase interaction studies with all the late gene promoters to determine the individual step of C mediated activation. Unlike at Pmom, at the other three promoters, RNAP recruitment and closed complex formation are not C dependent. Instead, the action of C at Plys, PI, and PP is during the isomerization from closed complex to open complex with no apparent effect at other steps of initiation pathway. The mechanism of transcription activation of mom and other late promoters by their common activator is different. This distinction in the mode of activation (promoter recruitment and escape versus isomerization) by the same activator at different promoters appears to be important for optimized expression of each of the late genes.

Effect of a domain-spanning disulfide on aminoacyl-tRNA synthetase activity

Enzymes regulated by allostery undergo conformational rearrangement upon binding effector molecules. For modular proteins, a flexible interface may mediate reorientation of the protein domains and transmit binding events to activate catalysis at a distance. Aminoacyl-tRNA synthetases (aaRSs) that use tRNA anticodons as identity elements can be considered allosteric enzymes in which aminoacylation of the tRNA acceptor stem is enhanced upon anticodon binding. We reasoned that anticodon-triggered conformational change might be restricted upon introduction of a disulfide linkage near the core of an aaRS. Here we show that a double cysteine mutation engineered at the Escherichia coli MetRS domain interface spontaneously generates a disulfide linkage. This disulfide clamp has no effect on methionyl adenylate formation but reduces the level of tRNA(Met) aminoacylation approximately 2-fold. Activity is restored upon chemical reduction of the disulfide, demonstrating that E. coli MetRS requires a flexible interface domain for full catalytic efficiency.

Lineage-specific amino acid substitutions in region 2 of the RNA polymerase sigma subunit affect the temperature of promoter opening

Highly conserved amino acid residues in region 2 of the RNA polymerase sigma subunit are known to participate in promoter recognition and opening. We demonstrated that nonconserved residues in this region collectively determine lineage-specific differences in the temperature of promoter opening.

Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element

Recognition of the -10 promoter consensus element by region 2 of the bacterial RNA polymerase sigma subunit is a key step in transcription initiation. sigma also functions as an elongation factor, inducing transcription pausing by interacting with transcribed DNA non-template strand sequences that are similar to the -10 element sequence. Here, we show that the region 1.2 of Escherichia coli sigma70, whose function was heretofore unknown, is strictly required for efficient recognition of the non-template strand of -10-like pause-inducing DNA sequence by sigma region 2, and for sigma-dependent promoter-proximal pausing. Recognition of the fork-junction promoter DNA by RNA polymerase holoenzyme also requires sigma region 1.2 and thus resembles the pause-inducing sequence recognition. Our results, together with available structural data, support a model where sigma region 1.2 acts as a core RNA polymerase-dependent allosteric switch that modulates non-template DNA strand recognition by sigma region 2 during transcription initiation and elongation.

Disulfide cross-linking indicates that FlgM-bound and free sigma28 adopt similar conformations

The dissociable sigma subunit of bacterial RNA polymerase is required for the promoter-specific initiation of transcription. When bound to RNA polymerase, sigma makes sequence-specific promoter contacts and plays a crucial role in DNA melting. In isolation, however, sigma lacks significant promoter binding activity. In the crystal structure of the flagellar sigma factor, sigma(28), bound to the anti-sigma factor, FlgM, sigma(28) adopts a compact conformation in which the promoter binding surfaces are occluded by interdomain contacts. To test whether sigma(28) adopts this conformation in the absence of FlgM, we engineered a set of double cysteine mutants predicted to form interdomain disulfides in the conformation observed in the FlgM complex. We show that these disulfides form in both the presence and absence of FlgM. For two of the mutants, quantitative measurements of disulfide formation under equilibrium conditions suggest that the major solution conformation favors disulfide formation. The results indicate that the compact conformation of sigma(28) observed in the sigma(28)/FlgM structure is similar to the predominant conformation of free sigma(28) in solution. This finding suggests that autoinhibition of DNA binding in free sigma(28) is accomplished by steric occlusion of the promoter binding surfaces by interdomain interactions within the sigma factor as well as by a suboptimal distance between the promoter -10 and -35 element binding determinants in sigma(2) and sigma(4), respectively.

Dual role for transactivator protein C in activation of mom promoter of bacteriophage Mu

Transactivator C protein of bacteriophage Mu activates the mom gene of the phage by an unusual mechanism. DNA binding by C to its site results in unwinding of the neighboring sequences, realigning the out-of-phase promoter elements to facilitate RNA polymerase (RNAP) binding. High level stimulation of a C-independent constitutive promoter mutant (where RNAP is already bound) by the transactivator suggested an additional mechanism of transcription activation at a step after RNAP recruitment. In this study, we have investigated the various steps of promoter-polymerase interactions during transcription initiation by using both the promoter mutant and a positive control (pc) mutant of C protein. The transactivator does not influence formation of the open complex or its stability after facilitating the RNAP binding. However, at a subsequent step, the protein exerts an important role, enhancing the promoter clearance by increasing the productive RNAP.promoter complex. The pc mutant of the transactivator C is compromised at this step, supporting the additional downstream role for C in mom transcription activation. We suggest that this unusual multistep activation of Pmom has evolved to ensure irreversibility of the switch during the late lytic cycle of the phage.

An epitope tag derived from human transcription factor IIB that reacts with a polyol-responsive monoclonal antibody

Polyol-responsive monoclonal antibodies (PR-mAbs) provide a strategy to purify active, nondenatured proteins by a single-step immunoaffinity chromatography procedure. The high affinity interaction between these antibodies and the antigen can be dissociated in the presence of a nonchaotropic salt and a low molecular weight polyhydroxylated compound (polyol). The epitope for PR-mAb IIB8 is located near the N-terminus of the human transcription factor IIB (TFIIB). The epitope is an eight amino acid sequence, TKDPSRVG, that can be fused to a desired protein for use as a purification tag. This epitope tag (termed hIIB) was fused to the C-terminus of green fluorescent protein (GFP). An additional GFP fusion protein utilized another version of hIIB containing a point mutation at position two. These fusion proteins, expressed in Escherichia coli, allowed successful separation of the desired protein in a single chromatographic step. This strategy extends PR-mAb gentle-release purification to numerous expressed proteins.

Development of an epitope tag for the gentle purification of proteins by immunoaffinity chromatography: application to epitope-tagged green fluorescent protein

Polyol-responsive monoclonal antibodies (mAbs) are useful tools for the gentle purification of proteins and protein complexes. These are high-affinity mAbs that release the antigen in the presence of a nonchaotropic salt and a low-molecular-weight polyhydroxylated compound (polyol). The epitope for the polyol-responsive mAb NT73, which reacts with Escherichia coli RNA polymerase, was located at the C terminus of the beta' subunit. Using recombinant DNA techniques, we have identified the epitope to be within the 13-amino-acid sequence SLAELLNAGLGGS and have developed an epitope tag that can be fused to a protein of interest for use as a purification tag. This epitope tag (designated Softag1) was fused to either the N or the C terminus of the green fluorescent protein. These tagged proteins were expressed in E. coli, and the tagged proteins were purified from the soluble fraction by a single-step immunoaffinity chromatography procedure. This approach extends the powerful technique of gentle-release immunoaffinity chromatography to many expressed proteins.

Mutational and functional analysis of a segment of the sigma family bacteriophage T4 late promoter recognition protein gp55

Bacteriophage T4 late promoters, which consist of a simple 8-base pair TATA box, are recognized by the gene 55 protein (gp55), a small, highly diverged member of the sigma family proteins that replaces sigma(70) during the final phase of the T4 multiplication cycle. A 16-amino acid segment of gp55 that is proposed to be homologous to the sigma(70) region 2.2 has been subjected to alanine scanning and other mutagenesis. The corresponding proteins have been examined in vitro for binding to Escherichia coli RNA polymerase core enzyme and for the ability to generate accurately initiating basal as well as sliding clamp-activated T4 late transcription. Mutations in the amino acid 68-83 segment of gp55 generate a wide range of effects on these functions. The changes are interpreted in terms of the multiple steps of involvement of gp55, like other sigma proteins, in transcription. Effects of mutations on RNA polymerase core binding are consistent with the previously proposed homology of amino acids 68-82 of gp55 with sigma(70) region 2.2 and the recently determined structures of the Thermus thermophilus and Thermus aquaticus sigma(70)-RNA polymerase holoenzymes.