Studying Sigma–Core Interactions in Escherichia coli RNA Polymerase by Electrophoretic Shift Assays and Luminescence Resonance Energy Transfer

Studying the salt dependence of the binding of sigma70 and sigma32 to core RNA polymerase using luminescence resonance energy transfer

The study of protein-protein interactions is becoming increasingly important for understanding the regulation of many cellular processes. The ability to quantify the strength with which two binding partners interact is desirable but the accurate determination of equilibrium binding constants is a difficult process. The use of Luminescence Resonance Energy Transfer (LRET) provides a homogeneous binding assay that can be used for the detection of protein-protein interactions. Previously, we developed an LRET assay to screen for small molecule inhibitors of the interaction of σ70 with theβ' coiled-coil fragment (amino acids 100–309). Here we describe an LRET binding assay used to monitor the interaction of E. coli σ70 and σ32 with core RNA polymerase along with the controls to verify the system. This approach generates fluorescently labeled proteins through the random labeling of lysine residues which enables the use of the LRET assay for proteins for which the creation of single cysteine mutants is not feasible. With the LRET binding assay, we are able to show that the interaction of σ70 with core RNAP is much more sensitive to NaCl than to potassium glutamate (KGlu), whereas the σ32 interaction with core RNAP is insensitive to both salts even at concentrations >500 mM. We also find that the interaction of σ32 with core RNAP is stronger than σ70 with core RNAP, under all conditions tested. This work establishes a consistent set of conditions for the comparison of the binding affinities of the E.coli sigma factors with core RNA polymerase. The examination of the importance of salt conditions in the binding of these proteins could have implications in both in vitro assay conditions and in vivo function.

Identification and characterization of the gene encoding the Acidobacterium capsulatum major sigma factor

Acidobacterium capsulatum is an acid-tolerant, encapsulated, Gram-negative member of the ubiquitous, but poorly understood Acidobacteria phylum. Little is known about the genetics and regulatory mechanisms of A. capsulatum. To begin to address this gap, we identified the gene encoding the A. capsulatum major sigma factor, rpoD, which encodes a 597-amino acid protein with a predicted sequence highly similar to the major sigma factors of Solibacter usitatus Ellin6076 and Geobacter sulfurreducens PCA. Purified hexahistidine-tagged RpoD migrates at approximately 70 kDa under SDS-PAGE conditions, which is consistent with the predicted MW of 69.2 kDa, and the gene product is immunoreactive with monoclonal antibodies specific for either bacterial RpoD proteins or the N-terminal histidine tag. A. capsulatum RpoD restored normal growth to E. coli strain CAG20153 under conditions that prevent expression of the endogenous rpoD. These results indicate we have cloned the gene encoding the A. capsulatum major sigma factor and the gene product is active in E. coli.

The Global Transcriptional Response of Escherichia coli to Induced σ32 Protein Involves σ32 Regulon Activation Followed by Inactivation and Degradation of σ32 in Vivo

sigma(32) is the first alternative sigma factor discovered in Escherichia coli and can direct transcription of many genes in response to heat shock stress. To define the physiological role of sigma(32), we have used transcription profiling experiments to identify, on a genome-wide basis, genes under the control of sigma(32) in E. coli by moderate induction of a plasmid-borne rpoH gene under defined, steady-state growth conditions. Together with a bioinformatics approach, we successfully confirmed genes known previously to be directly under the control of sigma(32) and also assigned many additional genes to the sigma(32) regulon. In addition, to understand better the functional relevance of the increased amount of sigma(32) to changes in the transcriptional level of sigma(32)-dependent genes, we measured the protein level of sigma(32) both before and after induction by a newly developed quantitative Western blot method. At a normal constant growth temperature (37 degrees C), we found that the sigma(32) protein level rapidly increased, plateaued, and then gradually decreased after induction, indicating sigma(32) can be regulated by genes in its regulon and that the mechanisms of sigma(32) synthesis, inactivation, and degradation are not strictly temperature-dependent. The decrease in the transcriptional level of sigma(32)-dependent genes occurs earlier than the decrease in full-length sigma(32) in the wild type strain, and the decrease in the transcriptional level of sigma(32)-dependent genes is greatly diminished in a DeltaDnaK strain, suggesting that DnaK can act as an anti-sigma factor to functionally inactivate sigma(32) and thus reduce sigma(32)-dependent transcription in vivo.