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  • 1
    Language: English
    In: Biophysical Journal, 27 January 2015, Vol.108(2), pp.368a-368a
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.bpj.2014.11.2016 Byline: Sahand Pirbadian, Sarah E. Barchinger, Kar Man Leung, Hye Suk Byun, Yamini Jangir, Rachida A. Bouhenni, Samantha B. Reed, Margaret F. Romine, Daad A. Saffarini, Liang Shi, Yuri A. Gorby, John H. Golbeck, Mohamed Y. El-Naggar Author Affiliation: (1) Physics and Astronomy, University of Southern California, Los Angeles, CA, USA (2) Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA (3) Biological Sciences, University of Wisconsin, Milwaukee, WI, USA (4) Pacific Northwest National Laboratory, Richland, WA, USA (5) Civil and Environmental Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA (6) Chemistry, Pennsylvania State University, University Park, PA, USA (7) Molecular and Computational Biology Section, Biological Sciences, University of Southern California, Los Angeles, CA, USA Article Note: (miscellaneous) 1845-Plat
    Keywords: Electron Transport;
    ISSN: 0006-3495
    E-ISSN: 15420086
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  • 2
    Language: English
    In: BMC Genomics, 2011, Vol.12(1)
    Description: Genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. While a variety of computational tools have been developed for this purpose, errors in the gene models and use of protein sorting signals that are not recognized by the more commonly accepted tools can diminish the accuracy of their output. As part of an effort to manually curate the annotations of 19 strains of Shewanella, numerous insights were gained regarding the use of computational tools and proteomics data to predict protein localization. Identification of the suite of secretion systems present in each strain at the start of the process made it possible to tailor-fit the subsequent localization prediction strategies to each strain for improved accuracy. Comparisons of the computational predictions among orthologous proteins revealed inconsistencies in the computational outputs, which could often be resolved by adjusting the gene models or ortholog group memberships. While proteomic data was useful for verifying start site predictions and post-translational proteolytic cleavage, care was needed to distinguish cellular versus sample processing-mediated cleavage events. Searches for lipoprotein signal peptides revealed that neither TatP nor LipoP are designed for identification of lipoprotein substrates of the twin arginine translocation system and that the +2 rule for lipoprotein sorting does not apply to this Genus. Analysis of the relationships between domain occurrence and protein localization prediction enabled identification of numerous location-informative domains which could then be used to refine or increase confidence in location predictions. This collective knowledge was used to develop a general strategy for predicting protein localization that could be adapted to other organisms. Journal Article.
    Keywords: Basic Biological Sciences Applied Life Sciencesaccuracy ; Arginine ; Bacteria ; Cleavage ; Forecasting ; Genes ; Lipoproteins ; Peptides ; Proteins ; Secretion ; Sorting ; Strains ; Substrates ; Translocation
    ISSN: 14712164
    E-ISSN: 14712164
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  • 3
    Language: English
    In: Applied and Environmental Microbiology, 82:255-267, 2016
    Description: To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (est. 〉85% of gene complement) genome sequences for 17 of the 20 detected member species and revealed two Halomonas spp. and two Rhodobacteraceae sp. variants indistinguishable by amplicon analysis. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggest different mechanisms may result in expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9x – 2700x). Journal Article.
    Keywords: Microdiversity ; Metagenomic Sequencing ; Parallel Consortia ; Microdiversity ; Metagenomic Sequencing ; Parallel Consortia
    Source: SciTech Connect (U.S. Dept. of Energy, Office of Scientific and Technical Information)
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  • 4
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 107:326-331, 2010, Vol.107(1)
    Description: Shewanella species are widespread in nature, enjoying a cosmopolitan distribution in marine,freshwater, sedimentary and soil environments (1), and have attracted considerable attention in recent years because of their ability to reduce an extensive number of different electron 3 acceptors, including the solid (oxy)hydroxides of iron and manganese, such as Fe(OH)3 and MnO2, using one or more proposed mechanisms of extracellular electron transport (EET) (2, 3). The EET ability of Shewanella species is consistent with their ability to generate electric current in microbial fuel cells in the absence of exogenous electron shuttles (4). Various strategies of extracellular electron transfer have been proposed in metal-reducing microbes, including naturally-occurring (2) or biogenic (5-7) soluble mediators that ‘shuttle’ electrons from cells to acceptors, as well as direct transfer using multiheme cytochromes located on the cell exterior (8) and transfer via conductive nanowires (9-11). S. oneidensis MR-1 features several proteins that are involved with the transport of electrons to the exterior of the cell where they play an important role with regard to the reduction of solid electron acceptors such as metal oxides. These include two outer-membrane decaheme c-type cytochromes (MtrC and OmcA), a membrane spanning protein (MtrB), and two periplasmic multi-heme c-type cytochromes (MtrA and CymA). Deletion of the genes encoding any of these proteins leads to phenotypes that are greatly inhibited with regard to metal-oxide reduction and current production in microbial fuel cells (MFCs) (12, 13). The mutation of genes that code for proteins involved in the movement of cytochromes to the outer membrane also results in loss of metal-reducing phenotypes (13). The shewanellae are highly motile, by virtue of a single polar flagellum, and individual S. oneidensis MR-1 cells have been tracked swimming at speeds of up to, and sometimes over, 100 μm/sec, although the average swimming speed of cells in a population is considerably lower (14). Research has also shown that S. oneidensis MR-1 also displays chemotactic responses to several soluble electron acceptors, including Fe(III) citrate (15, 16) and that the CheA-3 histidine protein kinase is required for this chemotactic behavior to be observed (14). Strain MR-1 has 4 also been shown to be very sensitive to the presence of electron acceptors. For example, strain MR-1 ceases motility after a short time in the absence of an electron acceptor; however motility can be restored upon the re-addition of an electron acceptor. Here we present data that suggest that the shewanellae exhibit a motility response not previously reported: we call it electrokinesis. This response occurs intermittently with the cells in proximity to a solid electron acceptor, such as a manganese oxide particle or the working electrode of an electrochemical cell, and motility is observed to increase after contact. In addition to increased swimming velocities, cells occasionally pause on the solid acceptor surface, then after brief contact (up to 1 second) the cells typically swim away in the opposite direction from which they approached. Electrokinesis is not a uniform response that can be observed in all cells, although if an electron shuttle is added, all cells rapidly become motile. Journal Article.
    Keywords: Direct Energy Conversionbinding Energy ; Citrates ; Cytochromes ; Electric Currents ; Electrochemical Cells ; Electrodes ; Electron Transfer ; Electrons ; Fuel Cells ; Genes ; Histidine ; Iron ; Manganese ; Manganese Oxides ; Membranes ; Mutations ; Oxides ; Phosphotransferases ; Proteins ; Soils ; Strains ; Transport ; Valence
    ISSN: 0027-8424
    E-ISSN: 10916490
    Source: SciTech Connect (U.S. Dept. of Energy, Office of Scientific and Technical Information)
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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 02 September 2014, Vol.111(35), pp.12883-8
    Description: Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic-abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution.
    Keywords: Bioelectronics ; Extracellular Electron Transfer ; Membrane Cytochromes ; Respiration ; Bacterial Outer Membrane Proteins -- Physiology ; Nanowires -- Ultrastructure ; Periplasm -- Physiology ; Shewanella -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 2017, Vol.114(7)
    Description: Only a small fraction of vitamin B12-requiring organisms are able to synthesize B12 de novo, making it a common commodity in microbial communities. Initially recognized as an enzyme cofactor of a few enzymes, recent studies have revealed additional B12-binding enzymes and regulatory roles for B12. Here we report the development and use of a B12-based chemical probe to identify B12-binding proteins in a nonphototrophic B12-producing bacterium. Two unexpected discoveries resulted from this study. First, we identified a new light-sensing B12-binding transcriptional regulator and demonstrated that it controls folate and ubiquinone biosynthesis. Second, our probe captured proteins involved in folate, methionine, and ubiquinone metabolism suggesting that it may play a role as an allosteric effector of these processes. These metabolic processes produce precursors for synthesis of DNA, RNA, and protein. Thereby, B12 modulates growth, and by limiting its availability to auxotrophs, B12-producing organisms may facilitate coordination of community metabolism. Journal Article.
    Keywords: DNA Biosynthesis ; Auxotrophs ; DNA Probes ; Enzymes ; Transcription ; Methionine ; Cofactors ; Vitamin B12 ; RNA ; Ubiquinone ; Allosteric Properties ; DNA ; Folic Acid ; Metabolism ; Ecosystem and Ecology Studies;
    ISSN: 0027-8424
    E-ISSN: 10916490
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  • 7
    Language: English
    In: Applied and environmental microbiology, 01 January 2016, Vol.82(1), pp.255-67
    Description: To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated 〉85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.
    Keywords: Genetic Variation ; Metagenome ; Metagenomics -- Methods ; Microbial Consortia -- Genetics
    ISSN: 00992240
    E-ISSN: 1098-5336
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  • 8
    Language: English
    In: Journal of Biological Chemistry, 2011, Vol.286(46)
    Description: The pyridine nucleotide cycle (PNC) is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial PNC was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds bacterial species suggested that NMN deamidase reaction is the only possible way of nicotinamide salvage in the marine bacterium Shewanella oneidensis. This prediction was verified via purification of native NMN deamidase from S. oneidensis followed by the identification of the respective gene, termed pncC. Enzymatic characterization of the PncC protein, as well as phenotype analysis of deletion mutants, confirmed its proposed biochemical and physiological function in S. oneidensis. Of the three PncC homologs present in E. coli, NMN deamidase activity was confirmed only for the recombinant purified product of the ygaD gene. A comparative analysis at the level of sequence and three dimensional structure, which is available for one of the PncC family member, shows no homology with any previously described amidohydrolases. Multiple alignment analysis of functional and non functional PncC homologs, together with NMN docking experiments, allowed us to tentatively identify the active site area and conserved residues therein. An observed broad phylogenomic distribution of predicted functional PncCs in bacterial kingdom is consistent with a possible role in detoxification of NMN, resulting from NAD utilization by DNA ligase. Journal Article.
    Keywords: Basic Biological Sciences Applied Life Sciencesalignment ; Detoxification ; Distribution ; Dna ; Enzymes ; Forecasting ; Functionals ; Genes ; Homeostasis ; Metabolism ; Mutants ; Nicotinamide ; Nucleotides ; Phenotype ; Purification ; Pyridine ; Recycling ; Residues
    ISSN: 0021-9258
    ISSN: 1083351X
    E-ISSN: 1083351X
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  • 9
    Language: English
    In: Journal of Biological Chemistry, 2011, Vol.286(41)
    Description: Bacteria exploit multiple mechanisms for controlling central carbon metabolism (CCM). Thus, a bioinformatic analysis together with some experimental data implicated HexR transcriptional factor as a global CCM regulator in some lineages of Gammaproteobacteria operating as a functional replacement of Cra regulator characteristic of Enterobacteriales. In this study we combined a large-scale comparative genomic reconstruction of HexRcontrolled regulons in 87 species of Proteobacteria with the detailed experimental analysis of HexR regulatory network in Shewanella oneidensis model system. Although nearly all of the HexR-controlled genes are associated with CCM, remarkable variations were revealed in the scale (from 1-2 target operons in Enterobacteriales up to 20 operons in Aeromonadales) and gene content of HexR regulons between 11 compared lineages. A predicted 17-bp pseudo-palindrome with a consensus tTGTAATwwwATTACa, was confirmed as HexR-binding motif for 15 target operons (comprising 30 genes) by in vitro binding assays. The negative effect of the key CCM intermediate, 2-keto-3-deoxy-6- phosphogluconate, on the DNA-regulator complex formation was verified. A dual mode of HexR action on various target promoters, repression of genes involved in catabolic pathways and activation of gluconeogenic genes, was for the first time predicted by the bioinformatc analysis and experimentally verified by changed gene expression pattern in S. oneidensis AhexR mutant. Phenotypic profiling revealed the inability of this mutant to grow on lactate or pyruvate as a single carbon source. A comparative metabolic flux analysis of wild-type and mutant strains of S. oneidensis using 13Clactate labeling and GC-MS analysis confirmed the hypothesized HexR role as a master regulator of gluconeogenic flux from pyruvate via the transcriptional activation of phosphoenolpyruvate synthase (PpsA). Journal Article.
    Keywords: Basic Biological Sciences Applied Life Sciencesbacteria ; Carbon ; Carbon Sources ; Functionals ; Genes ; In Vitro ; Lactates ; Metabolism ; Mutants ; Phosphoenolpyruvate ; Promoters ; Strains ; Targets ; Proteobacterial ; Carbon Metabolism ; Hexr ; Transcriptional Regulator ; Shewanella Oneidensis ; Comparative Genomics Approach ; Escherichia-Coli ; Pseudomonas-Putida ; Utilization Pathways ; Gene-Expression ; High-Throughput ; Binding Domain ; Protein ; Bacteria ; Catabolism
    ISSN: 0021-9258
    E-ISSN: 1083351X
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  • 10
    In: Applied and Environmental Microbiology, July, 1996, Vol.62(7), p.2647(4)
    Description: Subsurface bacterial strains expressing a plasmid, containing either toluene dioxygenase gene (tod) or toluene-4-monooxygenase (tmo) gene, and either an Escherichia coli tac (Ptac) or a Pseudomonas putida meta (Pm) promotor degrade both toluene and trichloroethylene (TCE). The plasmids are introduced into the bacteria by electroporation. Toluene degradation is higher in strains expressing Ptac while TCE degradation is similar in the presence of both Ptac and Pm. The tod gene is more efficient for toluene degradation while tmo is better for TCE degradation.
    Keywords: Microbial Genetic Engineering -- Research ; Gene Expression -- Physiological Aspects ; Toluene -- Observations ; Trichloroethylene -- Analysis ; Biodegradation -- Research
    ISSN: 0099-2240
    E-ISSN: 10985336
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