Publication Search Results

2009

Bose S, MF Hochella, YA Gorby, DW Kennedy, DE Mccready, AS Madden, and BH Lower. 2009. "Bioreduction of hematite nanoparticles by the dissimilatory iron reducing bacterium Shewanella oneidensis MR-1." Geochimica et Cosmochimica Acta 73(4):962-976. Abstract The surface area normalized reduction rates of hematite (α-Fe2O3) nanoparticles, ranging in size from 11 to 99 nm, by S. oneidensis MR-1 with lactate as the sole electron donor were measured. The reduction kinetics of metal-oxide nanoparticles were examined to determine how S. oneidensis utilizes these environmentally-relevant solid-phase electron acceptors. Nanoparticles involved in geochemical reactions show different properties relative to larger particles of the same phase, and their reactivity is predicted to change as a function of size. As evident from whole cell TEM mounts, the mode of nanoparticle adhesion to cells is different between the more aggregated, pseudo-hexagonal to irregular shaped 11, 12, and 99 nm nanoparticles and the less aggregated 30 and 43 nm rhombohedral particles. Due to the aggregation differences, the 11, 12 and 99 nm particles show less cell contact and coverage than the 30 and 43 nm particles, but the former still show significant rates of reduction. This leads to the provisional speculation that S. oneidensis MR-1 employs a pathway of indirect electron transfer in conjunction with the direct-contact pathway, and the relative importance of the bioreduction mechanism employed may depend upon aggregation level, shape of the particles, and/or crystal faces exposed. In accord with the proposed increase in electronic band-gap for hematite nanoparticles with reduction in size, the smallest particles (11 nm) exhibit a one order of magnitude decrease in reduction rate (surface area normalized) when compared with larger (99 nm) nanoparticles, and the 12 nm rate falls in between these two. This effect may also be due to the passivation of the mineral and cell surfaces by Fe(II), or decreasing solubility due to decrease in size.
Marshall MJ, A Dohnalkova, DW Kennedy, AE Plymale, SH Thomas, FE Loffler, R Sanford, JM Zachara, JK Fredrickson, and AS Beliaev. 2009. "Electron donor-dependent radionuclide reduction and nanoparticle formation by Anaeromyxobacter dehalogenans strain 2CP-C." Environmental Microbiology 11(2):534-543. Abstract Anaeromyxobacter dehalogenans strain 2CP-C can rapidly reduce U(VI) or Tc(VII) to U(IV)O2(s) or Tc(IV)O2(S) using either acetate or H2 as an electron donor source. Kinetic studies reveal that the H2-driven reduction of either U(VI) or Tc(VII) is faster than the acetate-driven reduction. The sub-cellular localization of reduced UO2 is extracellular while TcO2 nanoparticles are both periplasmic and extracellular. While electron donor-specific differences in UO2 nanoparticle aggregate size were observed, the association of UO2 nanoparticles with an exopolymeric substance (EPS) was observed and found to be independent of electron donor source. Electron donor-specific localization differences were not observed in cells incubated with Tc(VII). These finding have direct implications on immobilization strategies for highly soluble radionuclide contaminants in subsurface waters and the development of microbially assisted biostimulation efforts.
Oliveira OV, LC Freitas, TP Straatsma, and RD Lins. 2009. "Interaction between the CBM of Cel9A from Thermobifida fusca and Cellulose Fibers." Journal of Molecular Recognition 22(1):38-45. Abstract Molecular docking and molecular dynamics simulations were used to investigate the binding of a cellodextrin chain in a crystal-like conformation to the carbohydrate-binding module (CBM) of Cel9A from Thermobifida fusca. The fiber was found to bind to the CBM in a single and well-defined configuration in-line with the catalytic cleft, supporting the hypothesis that this CBM plays a role in the catalysis by feeding the catalytic domain with a polyssacharide chain. The results also expand the current known list of residues involved in the binding. The polysaccharide-protein attachment is shown to be mediated by five amine/amide-containing residues. E478 and E559 were found not to interact directly with the sugar chain; instead they seem to be responsible to stabilize the binding motif via hydrogen bonds.
Lower BH, R Yongsunthon, L Shi, L Wildling, HJ Gruber, NS Wigginton, CL Reardon, GE Pinchuk, T Droubay, JF Boily, and S Lower. 2009. "Antibody recognition force microscopy shows that outer membrane cytochromes OmcA and MtrC are expressed on the exterior surface of Shewanella oneidensis MR-1." Applied and Environmental Microbiology 75(9):2931-2935. Abstract Antibody-recognition force microscopy showed that OmcA and MtrC are expressed on the exterior surface of living Shewanella oneidensis MR-1 cells during anaerobic growth, when Fe(III) served as the terminal electron acceptor. OmcA was localized to the interface with hematite, while MtrC was more uniformly displayed on the bacterium’s exterior cell surface. Both cytochromes were also found associated with extracellular material.
Boily JF, and RD Lins. 2009. "Electrostatic Cooperativity of Hydroxyl Groups at Metal Oxide Surfaces." Journal of Physical Chemistry C 113(38):16568-16570. doi:10.1021/jp906124a Abstract The O-H bond distribution of hydroxyl groups at the {110} goethite (R-FeOOH) surface was investigated by molecular dynamics. This distribution was strongly affected by electrostatic interactions with neighboring oxo and hydroxo groups. The effects of proton surface loading, simulated by emplacing two protons at different distances of separation, were diverse and generated several sets of O-H bond distributions. DFT calculations of a representative molecular cluster were also carried out to demonstrate the impact of these effects on the orientation of oxygen lone pairs in neighboring oxo groups. These effects should have strong repercussions on O-H stretching vibrations of metal oxide surfaces.h

2008

Lower BH, RD Lins, ZW Oestreicher, TP Straatsma, MF Hochella Jr., L Shi, and S Lower. 2008. "In Vitro Evolution of a Peptide with a Hematite Binding Motif That May Constitute a Natural Metal-Oxide Binding Archetype." Environmental Science & Technology 42(10):3821-3827. doi:10.1021/es702688c Abstract Phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (Fe2O3) from a library of approximately 3 billion different polypeptides. The sequences of these peptides contained the highly conserved amino acid motif, Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr. To better understand the nature of the peptide−metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for Ser-Pro-Ser at a hematite surface. These simulations show that hydrogen bonding occurs between the two serine amino acids and the hydroxylated hematite surface and that the presence of proline between the hydroxide residues restricts the peptide flexibility, thereby inducing a structural-binding motif. A search of published sequence data revealed that the binding motif (Ser/Thr-Pro-Ser/Thr) is adjacent to the terminal heme-binding domain of both OmcA and MtrC, which are outer membrane cytochromes from the metal-reducing bacterium Shewanella oneidensis MR-1. The entire five amino acid consensus sequence (Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr) was also found as multiple copies in the primary sequences of metal-oxide binding proteins Sil1 and Sil2 from Thalassiosira pseudonana. We suggest that this motif constitutes a natural metal-oxide binding archetype that could be exploited in enzyme-based biofuel cell design and approaches to synthesize tailored metal-oxide nanostructures.
Lins RD, ER Vorpagel, M Guglielmi, and TP Straatsma. 2008. "Computer Simulation of Uranyl Uptake by the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa." Biomacromolecules 9(1):29-35. doi:10.1021/bm700609r Abstract Heavy metal environmental contaminants cannot be destroyed but require containment, preferably in concentrated form, in a solid or immobile form for recycling or final disposal. Microorganisms are able to take up and deposit high levels of contaminant metals, including radioactive metals such as uranium and plutonium, into their cell wall. Consequently, these microbial systems are of great interest as the basis for potential environmental bioremediation technologies. The outer membranes of Gram-negative microbes are highly non-symmetric and exhibit a significant electrostatic potential gradient across the membrane. This gradient has a significant effect on the uptake and transport of charged and dipolar compounds. However, the effectiveness of microbial systems for environmental remediation will depend strongly on specific properties that determine the uptake of targeted contaminants by a particular cell wall. To aid in the design of microbial remediation technologies, knowledge of the factors that determine the affinity of a particular bacterial outer membrane for the most common ionic species found in contaminated soils and groundwater is of great importance. Using our previously developed model for the lipopolisaccharide (LPS) membrane of Pseudomonas aeruginosa, this work presents the potentials of mean force as the estimate of the free energy profile for uptake of sodium, calcium, chloride, uranyl ions and a water molecule by the bacterial LPS membrane. A compatible classical parameter set for uranyl has been developed and validated. Results show that the uptake of uranyl is energetically a favorable process relative to the other ions studied. At neutral pH, this nuclide is shown to be retained on the surface of the LPS membrane through chelation with the carboxyl and hydroxyl groups located in the outer-core.
Shi L, S Deng, MJ Marshall, Z Wang, DW Kennedy, A Dohnalkova, HM Mottaz, EA Hill, YA Gorby, AS Beliaev, DJ Richardson, JM Zachara, and JK Fredrickson. 2008. " Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella Oneidensis Outer Membrane Cytochromes MtrC and OmcA." Journal of Bacteriology 190(15):5512-5516. doi:10.1128/JB.00514-08 Abstract Outer membrane decaheme c-type cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 are extracellular lipoproteins important for dissimilatory reduction of solid metal (hydr)oxides during anaerobic respiration. To investigate the roles of type II secretion system (T2S) in translocation of MtrC and OmcA across outer membrane, we measured the effects of deleting two T2S genes, gspD and gspG, on the secretion of MtrC and OmcA when cells were grown under anaerobic conditions. Deletion of gspD or gspG resulted in slightly yellowish supernatants, different from the pink supernatant of wild type (wt). Comparative proteomic analyses revealed that, although MtrC, OmcA and NrfA, a periplasmic nitrite reductase, were present the supernatants of wt and ΔgspD mutant, their peptides counts were much lower in ΔgspD than in wt. Subsequent analyses with heme-staining and Western blot not only confirmed that deletion of gspD or gspG reduced the abundances of MtrC and OmcA in the supernatants, but also revealed that the deletions consequently increased their abundances inside the cells. Complementation of ΔgspG mutant with functional GspG could reverse the effects of deleting gspG on the colors of the supernatants and the abundances of MtrC and OmcA. In contrast, Western results showed that the abundance of NrfA was reduced in the supernatant and the cells of ΔgspD mutant, suggesting that reduced NrfA in the periplasm, where MtrC and OmcA were accumulated, contributed to its reduction in the supernatant. Thus, our results demonstrate at the first time that T2S facilitates translocation of MtrC and OmcA across outer membrane.
Eggleston CM, J Voros, L Shi, BH Lower, T Droubay, and PJ Colberg. 2008. "Binding and Direct Electrochemistry of OmcA, an Outer-Membrane Cytochrome from an Iron Reducing Bacterium, with Oxide Electrodes: A Candidate Biofuel Cell System." Inorganica Chimica Acta 361(3):769-777. doi:10.1016/j.ica.2007.07.015 Abstract Dissimilatory iron-reducing bacteria transfer electrons to solid ferric respiratory electron acceptors. Outer-membrane cytochromes expressed by these organisms are of interest in both microbial fuel cells and biofuel cells. We use optical waveguide lightmode spectroscopy (OWLS) to show that OmcA, an 85 kDa decaheme outer-membrane c-type cytochrome from Shewanella oneidensis MR-1, adsorbs to isostructural Al2O3 and Fe2O3 in similar amounts. Adsorption is ionic-strength and pH dependent (peak adsorption at pH 6.5–7.0). The thickness of the OmcA layer on Al2O3 at pH 7.0 [5.8 ± 1.1 (2r) nm] from OWLS is similar, within error, to that observed using atomic force microscopy (4.8 ± 2 nm). The highest adsorption density observed was 334 ng cm 2 (2.4 · 1012 molecules cm 2), corresponding to a monolayer or 9.9 nm diameter spheres or submonolayer coverage by smaller molecules. Direct electrochemistry of OmcA on Fe2O3 electrodes was observed using cyclic voltammetry, with cathodic peak potentials of 380 to 320 mV versus Ag/AgCl. Variations in the cathodic peak positions are speculatively attributed to redox-linked conformation change or changes in molecular orientation. OmcA can exchange electrons with ITO electrodes at higher current densities than with Fe2O3. Overall, OmcA can bind to and exchange electrons with several oxides, and thus its utility in fuel cells is not restricted to Fe2O3.
Soares TA, TP Straatsma, and RD Lins. 2008. "Influence of the B-band O-antigen chain in the Structure and Electrostatics of the Lipopolysaccharide Membrane of Pseudomonas aeruginosa." Journal of the Brazilian Chemical Society 19(2):312-320. Abstract Classical molecular dynamics simulations of A-B+ LPS membrane model of Pseudomonas aeruginosa were carried out for 12+ ns. The B-band presents a remarkable flexibility remaining fully solvated and does not interact with the sugar units from the LPS core surface residues, in agreement atomic force microscopy experiments. Comparison with previous simulations of the rough LPS membrane suggests that the presence of the B-band promotes membrane expansion. In addition, this O-antigen chain dramatically alters the electrostatic potential and surface charge of the LPS membrane. This is illustrated by the resulting electrostatic surface potential. Comparison with the same property in rough LPS aids to explain the increased ability of B-band expressing microorganisms to adhere to cell surfaces and the necessity of these organisms to loose the O side chain for the development of acute infections.

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