A highly conserved sRNA downregulates multiple genes, including a σ transcriptional activator, in the virulence mode of .

Bacterial sRNAs together with the RNA chaperone Hfq post-transcriptionally regulate gene expression by affecting ribosome binding or mRNA stability. In the human pathogen , the causative agent of whooping cough, hundreds of sRNAs have been identified, but their roles in biology are mostly unknown. Here we characterize a Hfq-dependent sRNA (S17), whose level is dramatically higher in the virulence (Bvg) mode.

Conformational change of the response regulator BvgA accompanies its activation of the virulence gene .

The BvgAS two-component system regulates virulence gene expression in . Although precise three-dimensional structural information is not available for the response regulator BvgA, its sequence conservation with NarL and previous studies have indicated that it is composed of 3 domains: an -terminal domain (NTD) containing the phosphorylation site, a linker, and a DNA-binding C-terminal domain (CTD). Previous work has determined how BvgA dimers interact with the promoter (P ) of , the gene encoding the virulence adhesin filamentous hemagglutinin.

The Vibrio cholerae master regulator for the activation of biofilm biogenesis genes, VpsR, senses both cyclic di-GMP and phosphate.

Vibrio cholerae biofilm formation/maintenance is controlled by myriad factors; chief among these are the regulator VpsR and cyclic di-guanosine monophosphate (c-di-GMP). VpsR has strong sequence similarity to enhancer binding proteins (EBPs) that activate RNA polymerase containing sigma factor σ54. However, we have previously shown that transcription from promoters within the biofilm biogenesis/maintenance pathways uses VpsR, c-di-GMP and RNA polymerase containing the primary sigma factor (σ70).

Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic.

Noncoding small RNAs (sRNAs) are crucial for the posttranscriptional regulation of gene expression in all organisms and are known to be involved in the regulation of bacterial virulence. In the human pathogen Bordetella pertussis, which causes whooping cough, virulence is controlled primarily by the master two-component system BvgA (response regulator)/BvgS (sensor kinase). In this system, BvgA is phosphorylated (Bvg mode) or nonphosphorylated (Bvg mode), with global transcriptional differences between the two.

Combining Gel Retardation and Footprinting to Determine Protein-DNA Interactions of Specific and/or Less Stable Complexes.

DNA footprinting is a classic technique to investigate protein-DNA interactions. However, traditional footprinting protocols can be unsuccessful or difficult to interpret if the binding of the protein to the DNA is weak, the protein has a fast off-rate, or if several different protein-DNA complexes are formed. Our protocol differs from traditional footprinting protocols, because it provides a method to isolate the protein-DNA complex from a native gel after treatment with the footprinting agent, thus removing the bound DNA from the free DNA or other protein-DNA complexes.

The Bacteriophage T4 MotB Protein, a DNA-Binding Protein, Improves Phage Fitness.

The lytic bacteriophage T4 employs multiple phage-encoded early proteins to takeover the host. However, the functions of many of these proteins are not known. In this study, we have characterized the T4 early gene , located in a dispensable region of the T4 genome.

The phage T4 MotA transcription factor contains a novel DNA binding motif that specifically recognizes modified DNA.

During infection, bacteriophage T4 produces the MotA transcription factor that redirects the host RNA polymerase to the expression of T4 middle genes. The C-terminal 'double-wing' domain of MotA binds specifically to the MotA box motif of middle T4 promoters. We report the crystal structure of this complex, which reveals a new mode of protein-DNA interaction.

Determining the Architecture of a Protein-DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program.

Determining the structure of a protein-DNA complex can be difficult, particularly if the protein does not bind tightly to the DNA, if there are no homologous proteins from which the DNA binding can be inferred, and/or if only portions of the protein can be crystallized. If the protein comprises just a part of a large multi-subunit complex, other complications can arise such as the complex being too large for NMR studies, or it is not possible to obtain the amounts of protein and nucleic acids needed for crystallographic analyses. Here, we describe a technique we used to map the position of an activator protein relative to the DNA within a large transcription complex.

Bordetella pertussis fim3 gene regulation by BvgA: phosphorylation controls the formation of inactive vs. active transcription complexes.

Two-component systems [sensor kinase/response regulator (RR)] are major tools used by microorganisms to adapt to environmental conditions. RR phosphorylation is typically required for gene activation, but few studies have addressed how and if phosphorylation affects specific steps during transcription initiation. We characterized transcription complexes made with RNA polymerase and the Bordetella pertussis RR, BvgA, in its nonphosphorylated or phosphorylated (BvgA∼P) state at P(fim3), the promoter for the virulence gene fim3 (fimbrial subunit), using gel retardation, potassium permanganate and DNase I footprinting, cleavage reactions with protein conjugated with iron bromoacetamidobenzyl-EDTA, and in vitro transcription.

Architecture of the bacteriophage T4 activator MotA/promoter DNA interaction during sigma appropriation.

Gene expression can be regulated through factors that direct RNA polymerase to the correct promoter sequence at the correct time. Bacteriophage T4 controls its development in this way using phage proteins that interact with host RNA polymerase. Using a process called σ appropriation, the T4 co-activator AsiA structurally remodels the σ(70) subunit of host RNA polymerase, while a T4 activator, MotA, engages the C terminus of σ(70) and binds to a DNA promoter element, the MotA box.

Bacteriophage T4 MotA activator and the β-flap tip of RNA polymerase target the same set of σ70 carboxyl-terminal residues.

Sigma factors, the specificity subunits of RNA polymerase, are involved in interactions with promoter DNA, the core subunits of RNA polymerase, and transcription factors. The bacteriophage T4-encoded activator, MotA, is one such factor, which engages the C terminus of the Escherichia coli housekeeping sigma factor, σ(70). MotA functions in concert with a phage-encoded co-activator, AsiA, as a molecular switch.

Direct interaction of Bcl-2 proteins with tubulin.

A direct interaction between tubulin and several pro-apoptotic and anti-apoptotic members of the Bcl-2 family has been demonstrated by effects on the assembly of microtubules from pure rat brain tubulin. Bcl-2, Bid, and Bad inhibit assembly sub-stoichiometrically, whereas peptides from Bak and Bax promote tubulin polymerization at near stoichiometric concentrations. These opposite effects on microtubule assembly are mutually antagonistic.

Thiol-disulphide interchange in tubulin: kinetics and the effect on polymerization.

All 20 cysteine residues are accessible to disulphide reagents in the tubulin dimer, whereas only four are accessible in taxol-stabilized microtubules. Reaction rates with disulphide reagents are a function of the reagent, are decreased by G nucleotides, and increased with increase in pH and urea. With transient (stop-flow) kinetics, DTNB [5,5'-dithiobis-(2-nitrobenzoic acid)] and 2,2'-dithiodipyridine progress curves cannot be fitted by the sum of exponential terms based only on classes of cysteines.

Charge variants of tubulin, tubulin S, membrane-bound and palmitoylated tubulin from brain and pheochromocytoma cells.

Isoelectric focusing (IEF) of only approximately 1 microg of rat brain tubulin yields 27-30 distinct charge variants in the pH range of 4.5-5.4 with band separations of 0.

The local electrostatic environment determines cysteine reactivity of tubulin.

Of the 20 cysteines of rat brain tubulin, some react rapidly with sulfhydryl reagents, and some react slowly. The fast reacting cysteines cannot be distinguished with [14C]iodoacetamide, N-[(14)C]ethylmaleimide, or IAEDANS ([5-((((2-iodoacetyl)amino)ethyl)amino) naphthalene-1-sulfonic acid]), since modification to mole ratios 1 cysteine/dimer always leads to labeling of 6-7 cysteine residues. These have been identified as Cys-305alpha, Cys-315alpha, Cys-316alpha, Cys-347alpha, Cys-376alpha, Cys-241beta, and Cys-356beta by mass spectroscopy and sequencing.

Autopalmitoylation of tubulin.

Pure rat brain tubulin is readily palmitoylated in vitro using [3H]palmitoyl CoA but no added enzymes. A maximum of approximately six palmitic acids are added per dimer in 2-3 h at 36-37 degrees C under native conditions. Both alpha and beta tubulin are labeled, and 63-73% of the label was hydroxylamine-labile, presumed thioesters.

Preparation and properties of pure tubulin S.

Limited proteolysis of the tubulin dimer (alphabeta) by subtilisin occurs more rapidly with beta than with alpha tubulin. This leads to the formation of an intermediate hybrid dimer, alphabeta(s), before both C termini are cleaved to form tubulin S(alpha(s)beta(s)). The three forms of tubulin usually coexist in subtilisin-treated preparations and such cross-contamination can be reliably detected only by running SDS-polyacrylamide gels well beyond expulsion of the dye front.

Cation selective promotion of tubulin polymerization by alkali metal chlorides.

A role for charge-based interactions in protein stability at the monomer or dimer level is well known. We show here that such interactions can also be important for the higher-order structures of microtubule assembly. Alkali metal chlorides increase the rate of polymerization of pure tubulin driven by either taxol or dimethyl sulfoxide.

Charge-shielding and the "paradoxical" stimulation of tubulin polymerization by guanidine hydrochloride.

Low concentrations of guanidine hydrochloride (GuHCl) increase the rate (and to a lesser degree, the extent) of tubulin polymerization as assessed by light scattering. Maximum enhancement occurs at 120-160 mM GuHCl followed by decreases at higher GuHCl. The latent period is decreased, and there is a 3-4 fold reduction in the critical concentration of polymerization.

Colchicine binding by the "isolated" beta-monomer of tubulin.

At mole ratios of lactoperoxidase to tubulin monomers of 3-4, bovine lactoperoxidase forms 1:1 adducts with both alpha- and beta-tubulin from rat brain, thereby separating the tubulin heterodimer into its monomers. This mixture binds colchicine normally, and we show here by direct photoaffinity labeling that the bulk of the [3H]colchicine becomes attached to beta-tubulin under these conditions. When the alpha-tubulin has been displaced by lactoperoxidase, the ratio of label in beta-tubulin to alpha-tubulin is increased.

Localization of the colchicine-binding site of tubulin.

We have previously shown that rat brain tubulin, a heterodimer consisting of an alpha and beta monomer, can be covalently labeled with [3H]colchicine by near UV irradiation. Most of the label appears in beta-tubulin. We show here that beta-tubulin can be separated and purified from SDS preparative gels and analyzed by proteolysis.

Antimicrotubule properties of benzophenanthridine alkaloids.

Chelidonine, sanguinarine, and chelerythrine are natural benzophenanthridine alkaloids that inhibit taxol-mediated polymerization of rat brain tubulin in the micromolar range. Chelidonine is a weak, competitive inhibitor of colchicine binding to tubulin but does not inhibit podophyllotoxin binding. On the other hand, sanguinarine inhibits both colchicine and podophyllotoxin binding to tubulin with I50 values of 32 and 46 microM, respectively, and chelerythrine inhibits with I50 values of 55 and 60 microM, respectively.

Intermediate filaments and steroidogenesis in adrenal Y-1 cells: acrylamide stimulation of steroid production.

The possible role of intermediate filaments in steroidogenesis was investigated in Y-1 mouse adrenal tumor cells by treatment with acrylamide, which is thought to disrupt intermediate filaments without directly affecting microtubules or microfilaments. Treatment of cells with 5 mM acrylamide increases steroidogenesis after a lag period of 4-6 h and induces rounding of the cells at approximately the same time. The effect of acrylamide on steroidogenesis is not cAMP mediated and occurs before pregnenolone formation.

Colchicine photosensitizes covalent tubulin dimerization.

Pure rat brain tubulin can be cross-linked by ultraviolet irradiation of tubulin-colchicine complexes at the high-wavelength maximum of colchicine to form covalent dimers greater than trimers greater than tetramers. With colchicine concentrations approximately 3 x 10(-4) M (mole ratio to tubulin 3-12) and irradiation for 5-10 min at 95-109 mW/cm2, the yield of dimers is 11-17% and of trimers is 4-6% of the total tubulin. The oligomers show polydispersity and anomalously high apparent molecular masses that converge toward expected values in low-density gels.