Bacillus Subtilis Membrane Research Articles

Identification of Bacillus subtilis YidC Substrates Using a MifM-instructed Translation Arrest-based Reporter

YidC is a member of the YidC/Oxa1/Alb3 protein family that is crucial for membrane protein biogenesis in the bacterial plasma membrane. While YidC facilitates the folding and complex assembly of membrane proteins along with the Sec translocon, it also functions as a Sec-independent membrane protein insertase in the YidC-only pathway. However, little is known about how membrane proteins are recognized and sorted by these pathways, especially in Gram-positive bacteria, for which only a small number of YidC substrates have been identified to date. In this study, we aimed to identify Bacillus subtilis membrane proteins whose membrane insertion depends on SpoIIIJ, the primary YidC homolog in B. subtilis. We took advantage of the translation arrest sequence of MifM, which can monitor YidC-dependent membrane insertion. Our systematic screening identified eight membrane proteins as candidate SpoIIIJ substrates. Results of our genetic study also suggest that the conserved arginine in the hydrophilic groove of SpoIIIJ is crucial for the membrane insertion of the substrates identified here. However, in contrast to MifM, a previously identified YidC substrate, the importance of the negatively charged residue on the substrates for membrane insertion varied depending on the substrate. These results suggest that B. subtilis YidC uses substrate-specific interactions to facilitate membrane insertion.

Structural characterization of Bacillus subtilis membrane protein Bmr: an in silico approach.

Efflux pump--a membrane protein belonging to Major Facilitator (MF) family and associated with Multi Drug Resistance (MDR) has been a major factor in drug resistance of bacteria. In the era when no new effective antibiotic had been reported for years, the detailed study of these membrane proteins became imperative in order to improve the efficacy of existing drugs. The Bacillus subtilis membrane protein Bmr belongs to the super family of major facilitator proteins and is one of the first-discovered bacterial multidrug-efflux transporters. Development of Bmr inhibitors (B. subtilis) for least resistance, better drug sustainability and effective cellular activity requires three dimensional structure of this protein which has not yet been determined. In this communication structural characterization of this important efflux pump has been attempted using in silico approaches. The modeled structure of Bmr has been found to have 12 main helical segments interspersed by loops of variable lengths at regular intervals with both N- and C-termini on the same side of membrane. Docking of the known inhibitor reserpine on to the predicted structure of Bmr and its mutants signified the importance of the residues Phe143, Val286 and Phe306 in the interaction with the ligand. Besides this, the role of Arg313 and Phe309 in the H-bond formation and π-π interaction respectively, with reserpine was the new significant finding based on the interaction studies. The structure elucidation of Bmr and the role of these residues in binding to the ligand are expected to have a great impact on the efflux pump inhibition studies around the world and hence in the efficiency of the existing antibiotic drugs.

Mode of Action of the Bacterial Thermosensor Desk Involved in Regulating Membrane Fluidity

The Bacillus subtilis membrane harbors the temperature sensing and signaling protein DesK. At low temperatures it triggers expression of a desaturase, which introduces double bonds into pre-existing phospholipids, thereby regulating membrane fluidity. Recently it was discovered [1] that both sensing and transmission of DesK, which has five transmembrane segments, can be captured into one single chimerical transmembrane segment, the so-called ‘minimal sensor' (DesK-MS). This protein can be functionally reconstituted in lipid bilayers, thus providing an excellent model system to study the molecular details of a biologically important signaling mechanism. Here we used synthetic peptides corresponding to functional and non-functional mutants of the minimal sensor in artificial membranes of phosphatidylcholines as convenient model systems. We studied the conformational properties, tilt, and exposure at the lipid/water interface at different bilayer thickness and upon varying temperature by using circular dichroism and fluorescence studies. Based on these results and on mutational studies, we propose a model for the mode of action of DesK-MS, in which an N-terminal “sunken buoy” motif and a C-terminal hydrophilic motif are crucial for DesK-MS functioning. Finally, we explored the possibility of isolating and characterizing DesK-MS in its native membrane in the form of “native nanodiscs” by using copolymers of styrene and maleic acid (SMA). Results of these studies will be presented. [1] Cybulski LE, Martin M, Mansilla MC, Fernandez A, de Mendoza D. Membrane thickness cue for cold sensing in a bacterium. Curr Biol. 2010 20(17):1539-44

DnaK and GroEL chaperones are recruited to the Bacillus subtilis membrane after short-term ethanol stress

To find out membrane tolerance strategy to ethanol in Bacillus subtilis that possesses a powerful system of protection against environmental stresses. Cytoplasmic membranes of B. subtilis were severely affected by even short-term exposure to 3% (v/v) ethanol: the growth rate and membrane protein synthesis were markedly reduced, and no adaptive alterations in phospholipids were detected. Simultaneously, steady-state DPH fluorescence anisotropy (r(ss)) showed that the membrane rigidity increased substantially. Analysis of the membrane phosphoproteome using in vitro labelling with [γ-(32) P]ATP revealed the association of DnaK and GroEL chaperones with membrane, indicating a stress induction process. Upon a long-term 3% (v/v) ethanol stress, the cell growth accelerated slightly and the composition of polar head groups and fatty acids of membrane phospholipids underwent an extensive reconstruction. Correspondingly, membrane fluidity turned back to the original r(ss) values of the control cells. In B. subtilis, the adaptive response to short-term ethanol stress comprises the recruitment of molecular chaperones on the impaired membrane structure; consequently, the phospholipid synthesis is restored and membrane fluidity adapts properly to the continuing ethanol stress. These findings underline the role of membrane lipids in establishing tolerance towards ethanol and also suggest the contribution of molecular chaperones to the membrane and cell recovery.

A Systematic Approach Towards Elucidation of the Mode of Action of a Bacterial Thermosensor

The Bacillus subtilis membrane harbors the temperature sensing and signaling protein DesK. At low temperatures it triggers expression of a desaturase, which introduces double bonds into pre-existing phospholipids, thereby regulating membrane fluidity. Recently it was discovered [1] that both sensing and transmission of DesK, which has five transmembrane segments, can be captured into one single chimerical transmembrane segment, the so-called ‘minimal sensor’. This simple system offers excellent perspectives to study the molecular detail of a biologically very important mechanism. As a first step we analyzed membranes of Bacillus subtilis grown at different temperatures with several biophysical techniques including 31P-NMR and Differential Scanning Calorimetry. We analyzed the membrane lipid headgroup and acyl chain composition and we identified transition temperature fluctuations related to the growth temperature. We found significant differences in membrane lipid composition and phase behavior for Bacillus subtilis membranes depending on growth temperatures. Furthermore the transmembrane segment of the minimal sensor was synthesized and incorporated in the Bacillus membranes. These vesicles were analyzed with Tryptophan Fluorescence Spectroscopy to measure the position of the minimal sensor with respect to the membrane, which shows the switch behavior between high and low temperature of the minimal sensor.[1] Cybulski LE, Martin M, Mansilla MC, Fernandez A, de Mendoza D. Membrane thickness cue for cold sensing in a bacterium. Curr. Biol. 2010

A Systematic Approach Towards Elucidation of the Mode of Action of a Bacterial Thermosensor

The Bacillus subtilis membrane harbors the temperature sensing and signaling protein DesK. At low temperatures it triggers expression of a desaturase, which introduces double bonds into pre-existing phospholipids, thereby regulating membrane fluidity. Recently it was discovered [1] that both sensing and transmission of DesK, which has five transmembrane segments, can be captured into one single chimerical transmembrane segment, the so-called ‘minimal sensor’. This simple system offers excellent perspectives to study the molecular detail of a biologically very important mechanism. As a first step here we analyzed membranes of Bacillus subtilis grown at different temperatures with several biophysical techniques including 31P-NMR and Differential Scanning Calorimetry. We analyzed the membrane lipid headgroup and acyl chain composition and we identified transition temperature fluctuations related to the growth temperature. We found significant differences in membrane lipid composition and phase behavior for Bacillus subtilis membranes depending on growth temperatures. The next step is to synthesize the transmembrane segment of the minimal sensor and incorporate it in these membranes exploiting their properties to elucidate the molecular mechanism of thermosensing in Bacillus subtilis. [1] Cybulski LE, Martin M, Mansilla MC, Fernandez A, de Mendoza D. Membrane thickness cue for cold sensing in a bacterium. Curr Biol. 2010 20(17):1539-44

Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins of Bacillus subtilis membrane based on a proteomic approach.

We analyzed ABC transporter solute-binding proteins (SBPs) of the Bacillus subtilis membrane using a proteomic approach. We prepared a washed cell membrane fraction that was insoluble in 134 mM nondetergent sulfobetaine and then extracted proteins using mixtures of detergents in a stepwise manner. The membrane proteins were resolved by three two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) or two one-dimensional (1-D) PAGE procedures, electroblotted, and digested in the presence of 5% or 80% acetonitrile. Thereafter, matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF MS) identified 637 proteins corresponding to 15.9% of the total cellular proteins. We predicted that among these, 256 were membrane proteins, 101 were lipoproteins or secretory proteins and 280 were soluble proteins containing peripheral proteins that function in both the cytoplasm and the cell membrane such as SecA and FtsY. Among the 637 proteins, we identified 30 SBPs among 38 importers predicted by a bioinformatic search of the genome. We confirmed expression of the genes for the 30 SBPs using DNA microarray analysis. We compared the 2-D gel separation profiles of submembrane fractions solubilized by 1% n-dodecyl-beta-D-maltoside from cells cultured on Luria Bertani (LB), S7, and S7 medium without glutamate as well as DNA microarray data on LB and S7. The results suggested that YcdH, YtmK and YurO are binding proteins for Mn(++), glutamate and glucose, respectively, and that YqiX and YxeM are binding proteins for amino acids (tryptophan in S7 medium).

The effect of osmotic stress on the biophysical behavior of the Bacillus subtilis membrane studied by dynamic and steady-state fluorescence anisotropy

The thermotropic behavior of intact bacterial membranes and vesicles prepared from total and polar lipids isolated from Bacillus subtilis cultures grown at 37 °C in normal (LB) and hyperosmotic (LBN) conditions was studied using 1,6-diphenyl-1,3,5-hexatriene (DPH), 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene p-toluenesulfonate (TMA-DPH), and 2-diethylamino-6-lauroyl-naphthalene (Laurdan) as fluorescent probes. No phase transition of bulk lipids was observed in these preparations at the range of temperature studied. The anisotropy values ( r s) for DPH and TMA-DPH in purified membranes showed significant differences between the LB and LBN conditions, suggesting that there was an increase in membrane packing during the adaptation to osmotic stress. Furthermore, generalized polarization (GP) parameters for Laurdan indicated small but significant changes in water relaxation at the membrane hydrophobic/hydrophilic interface. Membrane preparations showed r s higher values than those of lipid vesicles and a higher temperature dependence of the Laurdan GP parameter. This fact indicates that membrane proteins increase the lipid packing and keep the membrane more sensitive to temperature changes.

DNA Translocation Across Planar Bilayers Containing Bacillus subtilis Ion Channels

The mechanisms by which genetic material crosses prokaryotic membranes are incompletely understood. We have developed a new methodology to study the translocation of genetic material via pores in a reconstituted system, using techniques from electrophysiology and molecular biology. We report here that planar bilayer membranes become permeable to double-stranded DNA (kilobase range) if Bacillus subtilis membrane vesicles containing high conductance channels have been fused into them. The translocation is an electrophoretic process, since it does not occur if a transmembrane electrical field opposing the movement of DNA, a polyanion, is applied. It is not an aspecific permeation through the phospholipid bilayer, since it does not take place if no proteins have been incorporated into the membrane. The transport is also not due simply to the presence of polypeptides in the membrane, since it does not occur if the latter contains gramicidin A or a eukaryotic, multi-protein vesicle fraction exhibiting 30-picosiemens anion-selective channel activity. The presence of DNA alters the behavior of the bacterial channels, indicating that it interacts with the pores and may travel through their lumen. These results support the idea that DNA translocation may take place through proteic pores and suggest that some of the high conductance bacterial channels observed in electrophysiological experiments may be constituents of the DNA translocating machinery in these organisms.

Mutation of the putative nucleotide binding site of the Bacillus subtilis membrane protein ComFA abolishes the uptake of DNA during transformation

ComFA is a membrane protein required for the uptake of transforming DNA following its binding to the Bacillus subtilis competent-cell surface. ComFA, which resembles members of the DEAD family of ATP-driven helicases, contains sequences similar to those found in many ATP-binding proteins and thought to represent the ATP-binding sites of these proteins. We have suggested that ComFA may function as a DNA translocase and/or helicase, using the energy of ATP hydrolysis to mediate the uptake of DNA. As a partial test of this hypothesis, we have introduced mutations into highly conserved glycyl and lysyl residues of the putative ATP-binding site, located, respectively, at positions 151 and 152, and determined the effects of these alterations on in vivo function. A substitution of the conserved lysyl by a glutamyl residue (K152E) and a double G151R-K152N mutation each resulted in a nearly 1,000-fold decrease in transformability, equivalent to that observed in a ComFA null mutant. A K152N mutation caused a partial loss-of-function phenotype. These effects were manifested at the level of DNA uptake; no marked effects on the final levels of DNA binding were noted. When either the K152E mutant allele or the G151R-K152N double mutant allele was combined in single copy with wild-type comFA, a dominant negative phenotype expressed on the level of DNA uptake was observed, suggesting that ComFA acts in a complex with other proteins, with additional molecules of ComFA, or with both.

DNA interpolyelectrolyte complexes as a tool for efficient cell transformation

A tool was developed for enhancement of plasmid penetration into an intact cell, based on increasing DNA hydrophobicity via inclusion into a soluble interpolyelectrolyte complex (IPC) with polycations. The characteristics of formation of DNA IPC with synthetic polycations [poly(N-ethyl-4-vinylpyridinium)bromide (PVP) and PVP modified with 3% of N-cetyl-4-vinylpyridinium units (PVP-C)] were studied using ultracentrifugation and polyacrylamide gel electrophoresis methods. The conditions were established under which the mixing of DNA and polycation aqueous solutions results in the self-assembly of soluble IPC species. Incorporation of DNA into IPC results in the enhancement of DNA binding with isolated Bacillus subtilis membranes. A considerable increase in the efficiency of transformation of B. subtilis cells with pBC16 plasmid resulted from incorporation of the plasmid into the IPC with PVP and CVP.

Site-specific in vitro binding of plasmid pUB110 to Bacillus subtilis membrane fraction.

The in vitro membrane binding of pSL103, a composite plasmid consisting of Staphylococcus aureus plasmid pUB110 and a Bacillus pumilus trpC+ DNA fragment, to the Bacillus subtilis membrane fraction was studied with a total lysate of B. subtilis cells. The binding reaction required a heat treatment at 45 degrees C and had an optimum KCl concentration of 60 mM. Nonradioactive pSL103, but not Escherichia coli plasmid pACYC184, competed with 3H-labeled pSL103 for binding to the membrane. By the use of 32P-labeled restriction fragments of pSL103 and pUB110, it has been found that only the pUB110 portion of pSL103 binds to the membrane and that there are four specific regions in pUB110 which bind to the membrane. Two of the four binding regions flank the replication origin. This in vitro binding was high-salt sensitive and apparently independent of the configurations of the plasmid. We have previously shown that the functional product of the initiation gene dna-1 is required in vivo both for replication initiation and the binding of a DNA region near the replication origin to the membrane. Unlike in vivo binding, which is high-salt resistant and dependent on the product of dna-1 gene (type-I binding), the in vitro binding reported in this paper was high-salt sensitive and independent of the dna-1 gene product (type-II binding).

High-molecular-weight penicillin-binding proteins from membranes of bacilli.

Mixtures of high-molecular-weight, cephalosporin-sensitive penicillin-binding proteins (PBPs) can be purified from Bacillus subtilis membranes by cephalosporin affinity chromatography (G. Kleppe and J. L. Strominger, J. Biol. Chem. 254:4856-4862, 1979). By appropriate modification of this technique, B. subtilis PBP 1 was purified to homogeneity, and a mixture of Bacillus stearothermophilus PBPs 1, 2, and 4 was isolated. [14C]penicillin-PBP complexes of high-molecular-weight PBPs purified from membranes of these two bacilli, after denaturation, were found to have chemical reactivities typical of the penicilloyl-serine derivative formed by D-alanine carboxypeptidase from B. stearothermophilus. Although enzymatic activity catalyzed by these and several other high-molecular-weight PBPs from gram-positive organisms has not been detected with cell wall-related substrates, a slow, enzymatic acylation of B. subtilis PBPs 1, 2ab, and 4 by [14C]-diacetyl-L-lysyl-D-alanyl-D-lactate was demonstrated. Further study is necessary to clarify the physiological relevance of the slow acylation by this analog of a natural cell wall biosynthetic intermediate.

Studies of the high molecular weight penicillin-binding proteins of Bacillus subtilis.

Seven or eight penicillin-binding proteins (PBPs) were detected in Bacillus subtilis membranes. By introducing covalent affinity chromatography employing cephalosporins as ligands, milligram amounts of three high molecular weight PBPs (PBP 1 ab, Mr = 120,000; PBP 2b, Mr = 94,000; and PBP 4, Mr = 78,000) were obtained without any contamination of the major PBP 5, the D-alanine carboxypeptidase. Small amounts of pure PBP 2b could be isolated by manipulation of the affinity chromatography conditions. Structural and physical properties of these proteins as well as the generation of one major penicilloyl peptide from each PBP by digestion with pepsin suggest that each PBP is the product of a separate gene. No enzymatic activity could be found in mixtures of these high molecular weight PBPs employing substrates used for the transpeptidase and D-alanine carboxypeptidase assays in particulate membrane fractions.

DNA replication of bacteriophage θ29 Effect of two viral genes on the association of phage chromosomes with the host cell membrane

The kinetics of DNA arrest and the maintenance of the association of viral chromosomes with the cell membrane were examined by temperature-shift experiments using temperature-sensitive mutants in two early bacteriophage φ29 genes required for phage DNA replication. φ29 ts2(35), a mutant in cistron 2 whose product (protein P2) is continuously required for associating phage DNA with the Bacillus subtilis membrane, does not stop phage DNA synthesis immediately after a shift to the nonpermissive temperature. In contrast, bacteria infected with φ29 ts3(28), a mutant in cistron 3 (which codes for protein P3), stop synthesizing phage DNA immediately after transfer to the nonpermissive temperature. Parental phage DNA in φ29 ts2(35) infections rapidly dissociates from the cell membrane after a shift to 45°, whereas φ29 ts3(28) DNA remains associated with the membrane after the shift to the nonpermissive temperature and then slowly dissociates. Thus the rapid dissociation of parental phage φ29 chromosomes from the membrane is dependent on a functional protein P3. These findings are discussed in terms of possible modes of action of these two proteins and suggest that protein P2 operates as a linker of phage chromosomes to the membrane, whereas protein P3 participates directly in the initiation or in the polymerization of viral DNA molecules.

Tunicamycin, an inhibitor of [formula omitted] peptidoglycan synthesis: A new site of inhibition

Bacillus subtilis membranes can transfer either N-acetylmuramyl-pentapeptide phosphate or N-acetylglucosaminyl phosphate from UMP directly onto undecaprenyl phosphate. Tunicamycin blocks only the latter transfer and inhibits peptidoglycan synthesis by toluenized cells of Bacillus megaterium utilizing added nucleotide sugar precursors or cell wall synthesis by intact cells of B. subtilis . Tunicamycin prevents formation of the cell wall disaccharide lipid intermediate by blocking transfer of N-acetylglucosamine onto undecaprenyl muramyl pentapeptidyl pyrophosphate.

Five Penicillin-binding Components Occur in Bacillus subtilis Membranes

Abstract Membranes of Bacillus subtilis to which [14C]penicillin G had been bound were fractionated by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. Five labeled components were separated. These five components differed from each other in the rates at which they bound penicillins and cephalosporins by up to four orders of magnitude. The major penicillin-binding component, V, was identified as the d-alanine carboxypeptidase, whose activity is not vital for the cell. Three of the other components, in contrast, bound penicillins and cephalosporins at rates comparable to that of the penicillin killing site in this organism.