Visual proteomics.

Visual proteomics attempts to generate molecular atlases by providing the position and angular orientation of protein complexes inside of cells. This is accomplished by template matching (pattern recognition), a cross-correlation-based process that matches the structure of a specific protein complex to the densities of the whole volume or subvolume of a cell, that is typically acquired by cryoelectron tomography. Thereby, a search is performed that scans the entire volume for structural templates contained in a database. In this chapter, we primarily describe the practical experiences gained with visual proteomics during the Leptospira interrogans proteome project [Beck et al. (2009). Visual proteomics of the human pathogen Leptospira interrogans. Nat. Methods 6, 817.]. We give a practical guide how to implement the method and review critical experimental and computational aspects in detail. Based on a survey that has been undertaken for protein complexes from Desulfovibrio vulgaris, we review the difficulty of generating reference structures in detail. Finally, we discuss the high yield targets for technical improvements.

Biofilm formation in Desulfovibrio vulgaris Hildenborough is dependent upon protein filaments.

Desulfovibrio vulgaris Hildenborough is a Gram-negative sulfate-reducing bacterium (SRB), and the physiology of SRBs can impact many anaerobic environments including radionuclide waste sites, oil reservoirs and metal pipelines. In an attempt to understand D. vulgaris as a population that can adhere to surfaces, D. vulgaris cultures were grown in a defined medium and analysed for carbohydrate production, motility and biofilm formation. Desulfovibrio vulgaris wild-type cells had increasing amounts of carbohydrate into stationary phase and approximately half of the carbohydrate remained internal. In comparison, a mutant that lacked the 200 kb megaplasmid, strain DeltaMP, produced less carbohydrate and the majority of carbohydrate remained internal of the cell proper. To assess the possibility of carbohydrate re-allocation, biofilm formation was investigated. Wild-type cells produced approximately threefold more biofilm on glass slides compared with DeltaMP; however, wild-type biofilm did not contain significant levels of exopolysaccharide. In addition, stains specific for extracellular carbohydrate did not reveal polysaccharide material within the biofilm. Desulfovibrio vulgaris wild-type biofilms contained long filaments as observed with scanning electron microscopy (SEM), and the biofilm-deficient DeltaMP strain was also deficient in motility. Biofilms grown directly on silica oxide transmission electron microscopy (TEM) grids did not contain significant levels of an exopolysaccharide matrix when viewed with TEM and SEM, and samples stained with ammonium molybdate also showed long filaments that resembled flagella. Biofilms subjected to protease treatments were degraded, and different proteases that were added at the time of inoculation inhibited biofilm formation. The data indicated that D. vulgaris did not produce an extensive exopolysaccharide matrix, used protein filaments to form biofilm between cells and silica oxide surfaces, and the filaments appeared to be flagella. It is likely that D. vulgaris used flagella for more than a means of locomotion to a surface, but also used flagella, or modified flagella, to establish and/or maintain biofilm structure.

Cr(VI) detoxification by Desulfovibrio vulgaris strain Hildenborough: microbe-metal interactions studies.

Toxic heavy metals constitute a worldwide environmental pollution problem. Bioremediation technologies represent efficient alternatives to the classic cleaning-up of contaminated soil and ground water. Most toxic heavy metals such as chromium are less soluble and toxic when reduced than when oxidized. Sulfate-reducing bacteria (SRB) are able to reduce heavy metals by a chemical reduction via the production of H2S and by a direct enzymatic process involving hydrogenases and c3 cytochromes. We have previously reported the effects of chromate [Cr(VI)] on SRB bioenergetic metabolism and the molecular mechanism of the metal reduction by polyhemic cytochromes. In the current work, we pinpoint the bacteria-metal interactions using Desulfovibrio vulgaris strain Hildenborough as a model. The bacteria were grown in the presence of high Cr(VI) concentration, where they accumulated precipitates of a reduced form of chromium, trivalent chromium [Cr(III)], on their cell surfaces. Moreover, the inner and outer membranes exhibited precipitates that shared the spectroscopic signature of trivalent chromium. This subcellular localization is consistent with enzymatic metal reduction by cytochromes and hydrogenases. Regarding environmental significance, our findings point out the Cr(VI) immobilization mechanisms of SRB; suggesting that SRB are highly important in metal biogeochemistry.

AFM study of the effect of metronidazole on surface structures of sulfate-reducing bacteria.

The effect of metronidazole (ME) on sulfate-reducing bacteria (SRB) was studied by atomic force microscopy (AFM) in this paper. Topography images of SRB cell show that after exposure to ME individual cell shape is sharply modified. Topography and phase images of SRB cell wall show that after exposure to ME not only the roughness of the cell wall increases but also the physical performance of SRB surface is changed to be uniform. AFM frictional loops show that after exposure to ME, SRB surface friction is increased remarkably.

Chromate reduction by immobilized palladized sulfate-reducing bacteria.

Resting cells of Desulfovibrio vulgaris NCIMB 8303 and Desulfovibrio desulfuricans NCIMB 8307 were used for the hydrogenase-mediated reduction of Pd(II) to Pd(0). The resulting hybrid palladium bionanocatalyst (Bio-Pd(0)) was used in the reduction of Cr(VI) to the less environmentally problematic Cr(III) species. The reduction of Cr(VI) by free and agar-immobilized Bio-Pd(0) was evaluated. Investigations using catalyst suspensions showed that Cr(VI) reduction was similar ( approximately 170 nmol Cr(VI)/h/mg Bio-Pd(0)) when Bio-Pd(0) was produced using D. vulgaris or D. desulfuricans. Continuous-flow studies using D. vulgaris Bio-Pd(0) with agar as the immobilization matrix investigated the effect of Bio-Pd(0) loading, inlet Cr(VI) concentration, and flow rate on the efficiency of Cr(VI) reduction. Reduction of Cr(VI) was highest at a D. vulgaris Bio-Pd(0) loading of 7.5 mg Bio-Pd(0)/mL agar (3:1 dry cell wt: Pd(0)), an input [Cr(VI)] of 100 microM, and a flow rate of 1.75 mL/h (approx. 3.5 column volumes/h). A mathematical interpretation predicted the activity of the immobilized Bio-Pd(0) for a given set of conditions within 5% of the value found by experiment. Considering the system as an 'artificial enzyme' analog and application of applied enzyme kinetics gave an apparent K(m) value (K(m app)) of 430 microM Cr(VI) and a determined value of flow-through reactor activity which differed by 11% from that predicted mathematically.

Geophysical imaging of stimulated microbial biomineralization.

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to observe microbial dynamics in real time and with high spatial resolution. Here, we investigate the use of noninvasive geophysical methods to monitor biomineralization at the laboratory scale during stimulated sulfate reduction under dynamic flow conditions. Alterations in sediment characteristics resulting from microbe-mediated sulfide mineral precipitation were concomitant with changes in complex resistivity and acoustic wave propagation signatures. The sequestration of zinc and iron in insoluble sulfides led to alterations in the ability of the pore fluid to conduct electrical charge and of the saturated sediments to dissipate acoustic energy. These changes resulted directly from the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. Scanning and transmission electron microscopy (SEM and TEM) confirmed the sulfides to be associated with cell surfaces, with precipitates ranging from aggregates of individual 3-5 nm nanocrystals to larger assemblages of up to 10-20 microm in diameter. Anomalies in the geophysical data reflected the distribution of mineral precipitates and biomass over space and time, with temporal variations in the signals corresponding to changes in the aggregation state of the nanocrystalline sulfides. These results suggest the potential for using geophysical techniques to image certain subsurface biogeochemical processes, such as those accompanying the bioremediation of metal-contaminated aquifers.

Environmental scanning electron microscope (ESEM) evaluation of crystal and plaque formation associated with biocorrosion.

The biofilm attributed to Desulfovibrio vulgaris growing in the presence of ferrous metals was examined with an environmental scanning electron microscope. This novel microscope produced images of iron sulfide colloids and other iron containing structures that had not been reported previously. A plaque composed of iron sulfide enveloped the surface of the corroding metal while crystals containing magnesium, iron, sulfur, and phosphorus were present in the culture where corrosion was in progress. A structure resembling the tubercule found in aerobic corrosion was observed on stainless steel undergoing biocorrosion and the elements present in this structure included sulfur, iron, chloride, calcium, potassium, and chromium.