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.
Lower BH, R Yongsunthon, L Shi, L Wildling, HJ Gruber, NS Wigginton, CL Reardon, GE Pinchuk, T Droubay, JF Boily, and SK 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.

2008

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.
Fredrickson JK, and JM Zachara. 2008. "Electron Transfer at the Microbe-Mineral Interface: A Grand Challenge in Biogeochemistry." Geobiology 6(3):245-253. Abstract The interplay between microorganisms and minerals is a complex and dynamic process that has sculpted the geosphere for nearly the entire history of the Earth. The work of Dr. Terry Beveridge and colleagues provided some of the first insights into metal-microbe and mineral-microbe interactions and established a foundation for subsequent detailed investigations of interactions between microorganisms and minerals. Beveridge also envisioned that interdisciplinary approaches and teams would be required to explain how individual microbial cells interact with their immediate environment at nano- or sub-molecular scales and that through such approaches and using emerging technologies that the details of such interactions would be revealed at the molecular level. With this vision as incentive and inspiration, a multidisciplinary, collaborative team-based investigation was initiated to probe the process of electron transfer at the microbe-mineral interface. This grand challenge to this team was to address the hypothesis that multi-heme c-type cytochromes of dissimilatory metal reducing bacteria localized to the cell exterior function as the terminal reductases in electron transfer to Fe(III) and Mn(IV) oxides. This question has been the subject of extensive investigation for years yet the answer has remained elusive. The team involves an integrated group of experimental and computational capabilities at DOE’s Environmental Molecular Sciences Laboratory, a national scientific user facility, as the collaborative focal point. The approach involves a combination of in vitro and in vivo biologic and biogeochemical experiments and computational analyses that, when integrated, provide a conceptual model of the electron transfer process. The resulting conceptual model will be evaluated by integrating and comparing various experimental, i.e., in vitro and in vivo ET kinetics, and theoretical results. Collectively the grand challenge will provide a detailed view of how organisms engage with mineral surfaces to exchange energy and electron density as required for life function.

2007

Droubay T, KM Rosso, SM Heald, DE Mccready, CM Wang, and SA Chambers. 2007. "Structure, Magnetism and Conductivity in Epitaxial Ti-doped -Fe2O3 Hematite: Experiment and density functional theory calculations." Physical Review. B, Condensed Matter and Materials Physics 75(10):, doi:10.1103/PhysRevB.75.104412 Abstract We explore the feasibility of growing epitaxial Ti-doped -Fe2O3 in which Ti(IV) substitutes for Fe(III) preferentially in one magnetic sublattice, but not the other. Such a structure has been predicted by first-principles theory to be energetically likely, and is expected to yield interesting and useful magnetic and electronic properties. However, we find that a majority of Ti dopants disperse and occupy random cation sites in both magnetic sublattices. Density functional theory predicts that the magnetically ordered and magnetically random structures are nearly isoenergetic.
Lower BH, L Shi, R Yongsunthon, T Droubay, DE Mccready, and SK Lower. 2007. "Specific Bonds between an Iron Oxide Surface and Outer Membrane Cytochromes MtrC and OmcA from Shewanella oneidensis MR-1." Journal of Bacteriology 189(13):4944-4952. doi:10.1128/JB.01518-06 Abstract Shewanella oneidensis MR-1 is purported to express outer membrane cytochromes (e.g., MtrC and OmcA) that transfer electrons directly to Fe(III) in a mineral during anaerobic respiration. A prerequisite for this type of reaction would be the formation of a stable bond between a cytochrome and an iron oxide surface. Atomic force microscopy (AFM) was used to detect whether a specific bond forms between a hematite (Fe2O3) thin film, created with oxygen plasma assisted molecular beam epitaxy (MBE), and recombinant MtrC or OmcA molecules coupled to gold substrates. Force spectra displayed a unique force signature indicative of a specific bond between each cytochrome and the hematite surface. The strength of the OmcA-hematite bond was approximately twice as strong as the MtrC-hematite bond, but direct binding to hematite was twice as favorable for MtrC. Reversible folding/unfolding reactions were observed for mechanically denatured MtrC molecules bound to hematite. The force measurements for the hematite-cytochrome pairs were compared to spectra collected between an iron oxide and S. oneidensis under anaerobic conditions. There is a strong correlation between the whole cell and pure protein force spectra suggesting that the unique binding attributes of each cytochrome complement one another and allow both MtrC and OmcA to play a prominent role in the transfer of electrons to Fe(III) in minerals. Finally, by comparing the magnitude of binding force for the whole cell vs. pure protein data, we were able to estimate that a single bacterium of S. oneidensis (2 x 0.5 μm) expresses ~104 cytochromes on its outer surface.
Wigginton NS, KM Rosso, and MF Hochella. 2007. "Mechanisms of Electron Transfer in Two Decaheme Cytochromes from a Metal-Reducing Bacterium." Journal of Physical Chemistry B 111(44):12857-12864. doi:10.1021/jp0718698 Abstract Single-molecule current-voltage (I–V) spectra were collected using a scanning tunneling microscope for two decaheme c-type cytochromes, OmcA and MtrC, which are outer-membrane proteins from the dissimilatory metal-reducing bacterium Shewanella oneidensis. Although the two cytochromes are similar in heme count, charge-carrying amino-acid content, and molecular mass, their I–V spectra are significantly different. The I–V spectra for OmcA show smoothly varying symmetric exponential behavior. These spectra are well fit by a coherent tunneling model that is based on a simple square barrier description of the tunneling junction. In contrast, the I–V spectra for MtrC have pronounced breaks in slope in the positive tip bias range. Two large peaks in the normalized differential conductance spectra of MtrC were fit to a tunneling model that accounts for the possibility of transient population of empty states stabilized by vibrational relaxation. Reorganization energies deduced for the two features are similar to those normally assigned to metal centers in other metalloproteins. Work function measurements of the cytochrome films were used to convert the energies of these two spectral features to the normal hydrogen electrode scale for comparison with the midpoint potential measured using protein film voltammetry, which showed good correspondence. We conclude that MtrC mediates tunneling current by heme orbital participation. The difference in tunneling behavior between OmcA and MtrC suggests distinct physiological functions for the two cytochromes; in contrast to OmcA, MtrC appears to be tuned to a specific operating potential.
Kerisit SN, KM Rosso, M Dupuis, and M Valiev. 2007. "Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces." Journal of Physical Chemistry C 111(30):11363-11375. Abstract The interface between electron transfer proteins such as cytochromes and solid phase mineral oxides is central to the activity of dissimilatory-metal reducing bacteria. A combination of potential-based molecular dynamics simulations and ab initio electronic structure calculations are used in the framework of Marcus’ electron transfer theory to compute elementary electron transfer rates from a well-defined cytochrome model, namely the small tetraheme cytochrome (STC) from Shewanella oneidensis, to surfaces of the iron oxide mineral hematite (α-Fe2O3). Room temperature molecular dynamics simulations show that an isolated STC molecule favors surface attachment via direct contact of hemes I and IV at the poles of the elongated axis, with electron transfer distances as small as 9 Å. The cytochrome remains attached to the mineral surface in the presence of water and shows limited surface diffusion at the interface. Ab initio electronic coupling matrix element (VAB) calculations of configurations excised from the molecular dynamics simulations reveal VAB values ranging from 1 to 20 cm-1, consistent with nonadiabaticity. Using these results, together with experimental data on the redox potential of hematite and hemes in relevant cytochromes and calculations of the reorganization energy from cluster models, we estimate the rate of electron transfer across this model interface to range from 1 to 1000 s-1 for the most exothermic driving force considered in this work, and from 0.01 to 20 s-1 for the most endothermic. This fairly large range of electron transfer rates highlights the sensitivity of the rate upon the electronic coupling matrix element, which is in turn dependent on the fluctuations of the heme configuration at the interface. We characterize this dependence using an idealized bis-imidazole heme to compute from first principles the VAB variation due to porphyrin ring orientation, electron transfer distance, and mineral surface termination. The electronic matrix element and consequently the rate of electron transfer are found to be sensitive to all parameters considered. This work indicates that biomolecularly similar solvent-exposed bis-histidine hemes in outer-membrane cytochromes such as MtrC or OmcA are likely to have an affinity for the oxide surface in water governing the approach and interfacial conformation and, if allowed sufficient conformational freedom, will achieve distances and configurations required for direct interfacial electron transfer.

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