Metal-induced structural organization and stabilization of the metalloregulatory protein MntR

MntR is a metalloregulatory protein that helps to modulate the level of manganese in Bacillus subtilis. MntR shows a metal-response profile distinct from other members of the DtxR family of metalloregulatory proteins, which are generally considered to be iron(II)-activated. As part of an ongoing effort to elucidate the mechanism and metal-selectivity of MntR, several biophysical studies on wild-type MntR and two active site mutants, MntR E99C and MntR D8M, have been performed. Using circular dichroism (CD) spectroscopy, the thermal stability of these proteins has been examined in the presence of various divalent metal ions. Fluorescence intensity measurements of 8-anilino-1-naphthalenesulfonic acid (ANS) were monitored to examine the folding of these proteins in the presence of different metal ions. These experiments indicate that MntR undergoes a significant conformational change upon metal binding that results in stabilization of the protein structure. These studies also show that the MntR D8M active site mutation causes a detrimental effect on the metal-responsiveness of this protein. Fluorescence anisotropy experiments have been performed to quantify the extent of metal-activated DNA binding by these proteins to two different cognate recognition sequences. Binding of MntR and MntR E99C to the mntA cognate sequence closely parallels that of the mntH operator, confirming that the proteins bind both sequences with comparable affinity depending on the activating metal ion. Fluorescence anisotropy experiments on MntR D8M indicate significantly impaired DNA binding, providing additional evidence that MntR D8M is a dysfunctional regulator.     

Purification and properties of the DNA-binding protein HPB12 from Bacillus subtilis nucleoid

We report the purification to homogeneity of a 12 KDa protein (HPB12) present in the nucleoids of Bacillus subtilis. From the purification data the abundance of the protein was estimated to about 20,000 monomers per cell. The HPB12 protein is heat-stable and acid-soluble and binds preferentially to supercoiled and linearized double-stranded DNAs. The binding of the protein to the supercoiled DNA occurs very rapidly and appears to be cooperative. Moreover, the complexes are extremely stable and do not dissociate after 90 min. These properties are consistent with a role of the HPB12 protein in the structure of the B. subtilis chromosome.     

DNA-binding activity of amino-terminal domains of the Bacillus subtilis AbrB protein

Two truncated variants of AbrB, comprising either its first 53 (AbrBN53) or first 55 (AbrBN55) amino acid residues, were constructed and purified. Noncovalently linked homodimers of the truncated variants exhibited very weak DNA-binding activity. Cross-linking AbrBN55 dimers into tetramers and higher-order multimers (via disulfide bonding between penultimate cysteine residues) resulted in proteins having DNA-binding affinity comparable to and DNA-binding specificity identical to those of intact, wild-type AbrB. These results indicate that the DNA recognition and specificity determinants of AbrB binding lie solely within its N-terminal amino acid sequence.     

Ribosomal proteins and DNA-binding protein II from the extreme thermophile Bacillus caldolyticus

Crystallographic studies, presently on ribosomal and DNA-binding proteins from the moderate thermophile Bacillus stearothermophilus, can be expected to benefit from the use of even more stable proteins from extreme thermophiles. Bacillus caldolyticus, which is able to grow in the temperature range of 70-80 degrees C, appears to be a suitable candidate. We have compared the two bacilli using two criteria: the two-dimensional gel patterns of ribosomal proteins and the properties of DNA-binding protein II. The latter protein is ubiquitous in the eubacterial kingdom and can be purified in large quantities. B. caldolyticus can be grown at 75 degrees C in continuous culture with a generation time of 45-60 min. The yield of ribosomes compares favorably with that of B. stearothermophilus. The gel patterns of the ribosomal proteins are very similar but several differences, in particular among the 50S proteins, are observed. The N-terminal amino-acid sequence of the DNA-binding protein differs in 3 positions (out of 39) from B. stearothermophilus and the protein shows an increased resistance to thermal denaturation. Tetragonal and monoclinic crystals of DNA-binding protein II have been obtained which are suitable for X-ray studies and the diffraction patterns of the two crystal forms are shown.     

Calmodulin-like protein from Bacillus subtilis

The first example of a calmodulin-like activity in a Gram-positive bacterium, Bacillus subtilis, is reported. A calcium ion-dependent, 3', 5' cyclic-AMP phosphodiesterase-stimulating activity was found in the soluble fraction of cell-free extracts of cells sporulating in a chemically-defined medium; activation was reversed by trifluoperazine. The activity was heat stable, bound to phenothiazine-agarose in a calcium ion-dependent manner and was eluted therefrom with buffer containing EGTA, and displaced authentic beef brain calmodulin from its antibody in a radioimmunoassay.     

The transition state regulator Hpr of Bacillus subtilis is a DNA-binding protein

The synthesis of a variety of proteins, including the well characterized degradative enzymes, which occurs during the transition state between vegetative growth and the onset of sporulation in Bacillus subtilis is controlled by a class of molecules known as transition state regulators. One of these regulators is the product of the hpr gene, first identified by mutations affecting the synthesis of extracellular proteases. We have purified the Hpr protein and found that it binds specifically to DNA fragments carrying the promoters and the upstream regions of the alkaline (aprE) and neutral (nprE) protease genes of B. subtilis. DNase I protection experiments revealed that the Hpr protein is able to bind at four and two regions of the aprE and nprE promoters, respectively. We have also located two Hpr binding sites in the promoter region of a gene of unknown function which is nevertheless known to be developmentally regulated during the transition state and which occurs in the same operon as the gene encoding another transition state regulator, Sin. The location of one of the Hpr binding sites on the aprE gene occurs adjacent to a region to which the Sin protein binds. However, in mixing competition experiments we have shown that Hpr and Sin binding occurred independently, and no visible alterations of protected regions were detected.     

Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein which bridges DNA

Genetic evidence suggests that the Bacillus subtilis lrpC gene product participates in cell growth and sporulation. The purified LrpC protein, which has a predicted molecular mass of 16.4 kDa, is a tetramer in solution. LrpC binds with higher affinity (K_app ~ 80 nM) to intrinsically curved DNA than to non-curved DNA (K_app ~ 700 nM). DNase I footprinting and the supercoiling of relaxed circular plasmid DNA in the presence of topoisomerase I revealed that LrpC induces DNA bending and constrains DNA supercoils in vitro. The LrpC protein cooperatively increases DNA binding of the bona fide DNA-binding and DNA-bending protein Hbsu. LrpC forms inter- and intramolecular bridges on linear and supercoiled DNA molecules, resulting in a large network and DNA compactation. Collectively, these findings suggest that LrpC is an architectural protein and that its activities could provide a means to modulate DNA transactions.     

Serine-threonine protein phosphatases from Bacillus subtilis

Gram-positive soil bacterium Bacillus subtilis possesses six eukaryotic-like serine-threonine protein phosphatases. These enzymes play an important role in the cell. The response to environmental or nutrional stress conditions are controlled by three Rsb phosphatases: RsbX, RsbU and RsbP. Phosphatases are also involved in endospore formation process (SpoIIE) and sugar transport (kinase/phosphatase Hpr). Moreover in the cell there are phosphatases with still unknown function (PrpC and PrpE). Cellular processes, presented here are regulated by serine/threonine protein phosphatases and very important for bacterial survival in natural environment. Protein phosphatases must act in cooperation with protein kinases and deserve the same attention as kinases.     

Conformational studies of the manganese transport regulator (MntR) from <Emphasis Type="Italic">Bacillus subtilis</Emphasis> using deuterium exchange mass spectrometry

The manganese transport regulator (MntR) of Bacillus subtilis is a metalloregulatory protein responsible for regulation of genes involved in manganese uptake by this organism. MntR belongs to the iron-responsive DtxR family, but is allosterically regulated by manganese and cadmium ions. Having previously characterized the metal binding affinities of this protein as well as the DNA-binding activation profiles for the relevant metal ions, we have focused the current study on investigating the structural changes of MntR in solution upon binding divalent transition metal ions. Deuterium exchange mass spectrometry was utilized to investigate the deuterium exchange dynamics between apo-MntR, Co²⁺-MntR, Cd²⁺-MntR, and Mn²⁺-MntR. Comparing the rates of deuteration of each metal-bound form of MntR reveals that the N-terminal DNA-binding motif is more mobile in solution than the C-terminal dimerization domain. Furthermore, significant protection from deuterium exchange is observed in the helices that contribute metal-chelating amino acids to form the metal binding site of MntR. In contrast, the bulk of the DNA-binding winged helix–turn–helix motif shows no difference in deuterium exchange upon metal binding. Mapping of the deuteration patterns onto the crystal structures of MntR yields insight into how metal binding affects the protein structure and complements earlier studies on the mechanism of MntR. Metal binding acts to rigidify MntR, thereby limiting the mobility of the protein and reducing the entropic cost of DNA binding. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

DNA-binding studies of mixed-ligand (ethylenediamine)ruthenium(II) complexes

A series of mixed-ligand ruthenium(II) complexes of the type [Ru(en)(2)bpy](2+) (bpy=2,2-bipyridine; 1), [Ru(en)(2)phen](2+) (phen=1,10-phenantroline; 2), [Ru(en)(2)IP](2+) (IP=imidazo[4,5-f][1,10]phenanthroline; 3), and [Ru(en)(2)PIP](2+) (PIP=2-phenylimidazo[4,5-f][1,10]phenanthroline; 4) have been isolated and characterized by UV/VIS, IR, and (1)H-NMR spectral methods. The binding of the complexes with calf thymus DNA has been investigated by absorption, emission spectroscopy, viscosity measurements, DNA melting, and DNA photo-cleavage. The spectroscopic studies together with viscosity measurements and DNA melting studies support that complexes 1 and 2 bind to CT DNA (=calf thymus DNA) by groove mode. Complex 2 binds more avidly to CT DNA than complex 1, complexes 3 and 4 bind to CT DNA by intercalation mode, 4 binds more avidly to CT DNA than 3. Noticeably, the four complexes have been found to be efficient photosensitisers for strand scissions in plasmid DNA.     

DNA-binding and cleavage studies of macrocyclic copper(II) complexes

Three hexaaza macrocyclic copper (II) complexes with different functional groups have been synthesized and characterized by elemental analysis and infrared spectra. Absorption and fluorescence spectral, cyclic voltammetric and viscometric studies have been carried out on the interaction of [CuL(1)]Cl(2) (L(1)[double bond]3,10-bis(2-methylpyridine)-1,3,5,8,10,12-hexaazacyclotetradecane), [CuL(2)]Cl(2) (L(2)[double bond]3,10-bis(2-propionitrile)-1,3,5,8,10,12-hexaazacyclotetradecane) and [CuL(3)]Cl(2) (L(3)=3,10-bis(2-hydroxyethyl)-1,3,5,8,10,12-hexaazacyclotetradecane) with calf thymus DNA. The results suggest that three complexes can bind to DNA by different binding modes. The spectroscopic studies together with viscosity experiments and cyclic voltammetry suggest that [CuL(1)](2+) could bind to DNA by partial intercalation via pyridine ring into the base pairs of DNA. [CuL(2)](2+) may bind to DNA by hydrogen bonding and hydrophobic interaction while [CuL(3)](2+) may be by weaker hydrogen bonding. The functional groups on the side chain of macrocycle play a key role in deciding the mode and extent of binding of complexes to DNA. Noticeably, the three complexes have been found to cleave double-strand pUC18 DNA in the presence of 2-mercaptoethanol and H(2)O(2).     

Salt-dependent and protein-concentration-dependent changes in the solution structure of the DNA-binding histone-like protein, HBsu, from Bacillus subtilis.

The solution structure of the histone-like DNA-binding protein, HBsu, from Bacillus subtilis in 2 mM sodium cacodylate, pH 7.5, is sensitive to the ionic strength of the buffer. This was shown by circular dichroism measurements at different concentrations of sodium chloride and potassium fluoride. The stability of HBsu is also influenced; at HBsu concentrations of about 0.1 mg.ml-1, melting temperatures of 32 degrees C and 55 degrees C were found in the absence of potassium fluoride and in the presence of 0.5 M potassium fluoride, respectively, exhibiting drastic ionic-strength-dependent differences in the temperature-induced unfolding of HBsu. Furthermore, at low ionic strength, circular dichroism spectra vary markedly depending on the HBsu concentration in the approximate range 0.2-3 mg.ml-1. Such protein-concentration-dependent differences in the spectra were not observed in the presence of 0.5 M potassium fluoride. Very similar circular dichroism spectra of HBsu and the histone-like DNA-binding protein of Bacillus stearothermophilus (HBst) at high ionic strength, indicate comparable structures of both proteins under these conditions. Estimation of the secondary structure content from the circular dichroism spectra yields data which are in satisfactory agreement with the values obtained from the crystal structure of HBst. Transition temperatures of 45 degrees C and 61 degrees C were found in differential scanning calorimetric measurements performed with HBsu in potassium-fluoride-free buffer and in the presence of 0.5 M potassium fluoride, respectively. The thermodynamic data point to the melting of native HBsu dimers into two denatured monomers.