Browsing by Author "Lower, Brian H."

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    Bioreduction of Hematite Nanoparticles by Shewanella oneidensis MR-1
    Bose, Saumyaditya (Virginia Tech, 2006-12-08)
    A dissertation is presented on the bioreduction of hematite (α-Fe2O3) nanoparticles. The study shows that an alternative extracellular electron transfer mechanism other than the classical 'direct-contact' mechanism may be simultaneously employed by Shewanella oneidensis MR-1 during solid-phase metal reduction. This conclusion is supported by analysis of the bioreduction kinetics of hematite nanoparticles coupled with microscopic investigations of cell-mineral interactions. 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. To demonstrate these size-dependent effects, the surface area normalized reduction rates of hematite nanoparticles by S. oneidensis MR-1 with lactate as the sole electron donor were measured. As evident from whole cell TEM analysis, the mode of nanoparticle adhesion to cells is different between the more aggregated, pseudo-hexagonal to irregular shaped 11 nm, 12 nm, 99 nm and the less aggregated 30 nm and 43 nm rhombohedral particles. The 11 nm, 12 nm and 99 nm particles show less cell contact and coverage than the 30 nm and 43 nm particles but 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 mechanism employed depends upon aggregation level and the shape of the particles or crystal faces exposed. In accord with the proposed increase in electronic band-gap for hematite nanoparticles, the smallest particles (11 nm) exhibit one order of magnitude decrease in reduction when compared with larger (99 nm) particles, and the 12 nm rates fall 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.
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    Interfacial and long-range electron transfer at the mineral-microbe interface
    Wigginton, Nicholas Scott (Virginia Tech, 2008-04-21)
    The electron transfer mechanisms of multiheme cytochromes were examined with scanning tunneling microscopy (STM). To simulate bacterial metal reduction mediated by proteins in direct contact with mineral surfaces, monolayers of purified decaheme cytochromes from the metal-reducing bacterium Shewanella oneidensis were prepared on Au(111) surfaces. Recombinant tetracysteine sequences were added to two outermembrane decaheme cytochromes (OmcA and MtrC) from S. oneidensis MR-1 to ensure chemical immobilization on Au(111). STM images of the cytochrome monolayers showed good coverage and their shapes/sizes matched that predicted by their respective molecular masses. Current-voltage (I-V) tunneling spectroscopy revealed that OmcA and MtrC exhibit characteristic tunneling spectra. Theoretical modeling of the single-molecule tunneling spectra revealed a distinct tunneling mechanism for each cytochrome: OmcA mediates tunneling current coherently whereas MtrC temporarily traps electrons via orbital-mediated tunneling. These mechanisms suggest a superexchange electron transfer mechanism for OmcA and a redox-specific (i.e. heme-mediated) electron transfer mechanism for MtrC at mineral surfaces during bacterial metal reduction. Additionally, a novel electrochemical STM configuration was designed to measure tunneling current from multiheme cytochromes to hematite (001) surfaces in various electrolyte solutions. Current-distance (I-s) profiles on hematite (001) reveal predictable electric double layer structure that changes with ionic strength. The addition of the small tetraheme cytochrome c (STC) from S. oneidensis on insulated Au tips resulted in modified tunneling profiles that suggest STC significantly modulates the double layer. This observation is relevant to understanding metal reduction in cases where terminal metal-reducing enzymes are unable to come in direct contact with reducible mineral surfaces. Electronic coupling to the mineral surface might therefore be mediated by a localized ion swarm specific to the mineral surface.
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    Protein O-Kinases in the Archaeon Sulfolobus solfataricus
    Lower, Brian H. (Virginia Tech, 2001-07-23)
    For many years, it has been understood that protein phosphorylation-dephosphorylation constitutes one of the most ubiquitous mechanisms for controlling the functional properties of proteins. Although originally believed to be a eukaryotic phenomenon, protein phosphorylation is now known to occur in all three domains of life Eukarya, Bacteria, and Archaea. Very little is known, however, concerning the origins and evolution of protein phosphorylation-dephosphorylation. Knowledge of the structure and properties of the protein kinases resident in the members of the Archaea represents a key piece of this puzzle. The extreme acidothermophilic archaeon, Sulfolobus solfataricus, exhibits a membrane-associated protein kinase activity. Solubilization of the kinase activity requires the presence of detergent such as Triton X-100 or octyl glucoside, indicating its activity reside in an integral membrane protein. This protein kinase utilizes purine nucleotides as phosphoryl donors in vitro with a requirement for a divalent metal ion cofactor, favoring Mn⁺². A preference for NTPs over NDPs and for adenyl nucleotides over the analogous guanyl nucleotides was observed. The enzyme appears to be a glycoprotein that displays catalytic activity on SDS-PAGE corresponding to a molecular mass of ≈67 kDa, as well as an apparent molecular mass of –125 kDa on a gel filtration column. Challenged with several exogenous substrates revealed the protein kinase to be relatively selective. Only casein, reduced carboxyamidomethylated and maleylated lysozyme (RCM lysozyme), histone H4 proved, and a peptide modeled after myosin light chains (KKRAARATSNVFA) were phosphorylated to appreciable levels in vitro. All of the aforementioned substrates were phosphorylated on threonine, while histone H4 was phosphorylated on serine as well. When the phosphoacceptor threonine in the MLC peptide was substituted with serine an appreciable decrease in phosphorylation was noted. The protein kinase underwent autophosphorylation on threonine and was relatively insensitive to several known "eukaryotic" protein kinase inhibitors. Primary sequence motifs based on known conserved subdomains of eukaryotic protein kinases were used to search the genome of S. solfataricus for eukaryotic-like protein kinase sequences. Six hypothetical proteins were identified from S. solfataricus whose primary sequence exhibited noticeable similarities to eukaryotic protein kinases. The hypothetical protein encoded by ORF sso0197 contained 7 putative subdomains, ORFs sso0433, sso2291, sso2387, and sso3207 contained 8 putative subdomains, and ORF sso3182, contained 9 putative subdomains of the 12 characteristically conserved subdomains found within eukaryotic protein kinases. ORF sso2387 was cloned and expressed in Escherichia coli. The expressed protein, SsPK2, was solubilized from inclusion bodies using 5 M urea. SsPK2 was able to phosphorylate casein, BSA, RCM lysozyme, and mixed histones in vitro. Phosphoamino acid analysis of casein, BSA, and mixed histones revealed that they were all phosphorylated on serine. SsPK2 underwent autophosphorylation on serine at elevated temperature using both purine nucleotide triphosphates as phosphoryl donors in vitro, but exhibited a noticeable preference for ATP. Autophosphorylate of SsPK2 also occurred at elevated temperature using a variety of divalent metals cofactors in order of Mn⁺² > Mg⁺² >> Ca²⁺ ≈ Zn⁺². Polycations such as polyLys stimulated the phosphorylation of exogenous substrates while polyanions such as poly(Glu:Tyr) were shown to inhibit the phosphorylation of exogenous substrates. Of the "eukaryotic" protein kinases inhibitors tested, only tamoxifen had any noticeable effect of the catalytic activity of SsPK2 towards itself and exogenous substrates. A truncated form of SsPK2 containing the perceived catalytic domain also exhibited protein kinase activity towards itself and exogenous substrates. The observed protein kinase activity for SsPK2trunk was similar to that observed for SsPK2. Proteins from the membrane fraction of S. solfataricus subject to phosphorylation in vitro on serine or threonine residues were identified using MALDI-MS / peptide fingerprinting techniques. Nine phosphoproteins were assigned a tentative identification using the ProFound protein search engine from Rockefeller University. The identity of two of nine phosphoproteins, a translational endoplasmic reticulum ATPase and an ≈ 42 kDa hypothetical protein, were determined with a relatively high degree of confidence. Collectively the results suggested MALDI-MS peptide mapping coupled with [³²P] labeling in vivo will have a tremendous potential for mapping out a major portion of the phosphoproteome of S. solfataricus.
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    Shewanella oneidensis MR-1 cell-to-cell signaling and its influences on biogeochemical processes
    Learman, Deric Ronald (Virginia Tech, 2008-05-29)
    The goal of this project is to decipher the quorum sensing (cell-to-cell signaling) abilities of Shewanella oneidensis MR-1, a Gram-negative bacterium well known for its ability to use geologic substrates, such as Fe and Mn oxides, for respiratory purposes. Overall our results show that S. oneidensis cannot utilize either an acyl-homoserine lactone (AHL) or AI-2 quorum sensing signal, despite previous work that indicated that it produced an AHL that would enhance it ability to growth in certain anaerobic environments. Using a variety of quorum sensing signal sensors, no evidence could be found that S. oneidensis has a typical AHL signal. An in silco analysis of the genome also produced little evidence that S. oneidensis has the genes to accept or relay an AHL signal. S. oneidensis can produce a luminescence response in the AI-2 reporter strain, Vibrio harveyi MM32. This luminescence response is abolished upon deletion of luxS, the gene responsible for catalyzing AI-2. Deletion of luxS also affected biofilm formation. Within 16 hours of growth in a biofilm flow-through reactor, the luxS mutant had an inhibited ability to initiate biofilm formation. After 48 hours of growth, the mutant's biofilm had developed similarly to wild-type. The addition of synthetic AI-2 did not restore the mutant's ability to initiation biofilm formation, which led to the conclusion that AI-2 is not likely used as a quorum sensing signal in S. oneidensis for this phenotype. Because of the involvement of LuxS in the activated methyl cycle (AMC) in other organisms, growth on various sulfur sources was examined. A mutation in luxS produced a reduced ability to growth with methionine as the sole sulfur source. Methionine is a key metabolite used in the AMC to produce a methyl source in the cell and homocysteine. This data suggests that LuxS is important in metabolizing methionine and the AMC in S. oneidensis.