DOCSLIB.ORG

Physiological Models of Geobacter Sulfurreducens and Desulfobacter Postgatei to Understand Uranium Remediation in Subsurface Systems

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Physiological Models of Geobacter Sulfurreducens and Desulfobacter Postgatei to Understand Uranium Remediation in Subsurface Systems University of Massachusetts Amherst ScholarWorks@UMass Amherst Doctoral Dissertations Dissertations and Theses November 2014 PHYSIOLOGICAL MODELS OF GEOBACTER SULFURREDUCENS AND DESULFOBACTER POSTGATEI TO UNDERSTAND URANIUM REMEDIATION IN SUBSURFACE SYSTEMS Roberto Orellana University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/dissertations_2 Part of the Environmental Microbiology and Microbial Ecology Commons, and the Microbial Physiology Commons Recommended Citation Orellana, Roberto, "PHYSIOLOGICAL MODELS OF GEOBACTER SULFURREDUCENS AND DESULFOBACTER POSTGATEI TO UNDERSTAND URANIUM REMEDIATION IN SUBSURFACE SYSTEMS" (2014). Doctoral Dissertations. 278. https://doi.org/10.7275/5822237.0 https://scholarworks.umass.edu/dissertations_2/278 This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. PHYSIOLOGICAL MODELS OF GEOBACTER SULFURREDUCENS AND DESULFOBACTER POSTGATEI TO UNDERSTAND URANIUM REMEDIATION IN SUBSURFACE SYSTEMS A Dissertation Presented by ROBERTO ORELLANA ROMAN Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY September 2014 Microbiology Department © Copyright by Roberto Orellana Roman 2014 All Rights Reserved PHYSIOLOGICAL MODELS OF GEOBACTER SULFURREDUCENS AND DESULFOBACTER POSTGATEI TO UNDERSTAND URANIUM REMEDIATION IN SUBSURFACE SYSTEMS A Dissertation Presented by ROBERTO ORELLANA ROMAN Approved as to style and content by: _______________________________________ Derek R. Lovley, Chair _______________________________________ Kristen M. De Angelis, Member _______________________________________ James F. Holden, Member _______________________________________ Jason M. Tor, Member ____________________________________ John Lopes, Department Head Microbiology DEDICATION Para Loreto, Leonor e Ignacio. Essentially, all models are wrong, but some are useful. George E. P. Box v ACKNOWLEDGMENTS I would like to thank Derek Lovley for being a constant source of guidance, critical thinking and support. I arrived to his lab not having idea of anaerobic bacteria and I have learned a lot throughout these years. I would also like to give thanks to my other committee members; Kristen DeAngelis, Jim Holden, and Jason Tor. They have spent many hours discussing the results and have very valuable insights. Also I thank to several mentors in the lab Carla Risso, Marzia Miletto, and Melissa Barlett that give me support, advice, and motivation. I thank current and past lab members: Arianna Gray, Sean Murphy, Pier Luc Tremblay, Shabir Dar, Dawn Holmes, Ching Leang, Pravin Shrestha, Toshiyuki Ueki, Jo Philips, Nikhil Malvankar, Tunde Mester, Joy Ward, Manju Sharma and Areen Banerjee for valuable help at all stages of this dissertation. Also, I want to thanks to the researchers from other universities that collaborate along this research. Thanks speacially to Luis Comolli (LBNL), Janet Leavitt (UNM), Kim Hixson, and Mary Lipton (PNNL). I am highly indebted to my friends Burcu Unal, Jennifer Lin and Jesus Alvelo for help in many things and endless support especially when things got tough. I also have special thanks to the administrative people in the department: Maryanne Wells, Sue Laford, Ruthie Allies and Lorell Perreault for the countless times they save me from administrative issues during grad school. Also, I want to thanks to the department head John Lopes for his interesting conversations about science and soccer. I am grateful for all other students in the department that made my time here easier and enjoyable, especially George Hamaoui, Jennifer Hayashi, Joanne Lau, and Sarah Hensley. Above all, I owe gratitude especially to my wife, my parents and sister. Without their encouragement, patience and love I would not have been capable of finishing this story with a happy end. vi ABSTRACT PHYSIOLOGICAL MODELS OF GEOBACTER SULFURREDUCENS AND DESULFOBACTER POSTGATEI TO UNDERSTAND URANIUM REMEDIATION IN SUBSURFACE SYSTEMS SEPTEMBER 2014 ROBERTO ANDRES ORELLANA ROMAN B.A., UNIVERSITY OF CHILE Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Derek R. Lovley Geobacter species are often the predominant Fe(III)-reducing microorganisms in many sedimentary environments due to their capacity for extracellular electron transfer. This exceptional physiological capability allows them to couple acetate oxidation to uranium (U(VI)) reduction, that is one of the most significant interactions between radionuclides and microorganisms that naturally takes place in uranium-contaminated environments. Although this process has been proposed as a promising strategy for the in situ bioremediation of uranium-contaminated groundwater, little is known about the molecular mechanisms involved in U(VI) reduction and the interaction between Geobacter and other microbial species. In the first two research chapters, this dissertation aim to study the interaction between Geobacter sulfurreducens, a primary model organism to elucidate the physiological capabilities of Geobacter species, and U(VI). Our findings presented here suggest that G. sulfurreducens requires outer-surface c-type cytochromes, but not pili, for vii the reduction of uranium, and U(IV), the product of U(VI) reduction was precipitated at the outer cell surface. Our results also suggest that there is not one specific U(VI)- detoxification specific mechanism for uranium detoxification in G. sulfurreducens. Rather, resistance to U(VI) appears to be accomplished with multiple stress response systems, that includes detoxification and oxidative stress response, and regulatory networks that facilitate fast adaptation to rapidly changing conditions. The third research chapter of this dissertation examines the physiology of Desulfobacter postgatei, a competitor for acetate during in situ bioremediation of subsurface systems at a uranium-contaminated site in Rifle, CO. Our findings suggest that novel enzymatic complexes, such as the energy-converting hydrogenase related complex, Ehr, the proton-translocating ferredoxin:NADP+ oxidoreductase, Rnf, and also the NADH-dependent reduced ferredoxin:NADP+ oxidoreductase, Nfn, are involved in energy conservation, making D. postgatei a major competitor for acetate in several environments. viii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ................................................................................................. vi ABSTRACT ............................................................................................................. vii LIST OF TABLES ........................................................................................................... xiii LIST OF FIGURES ......................................................................................................... xiv CHAPTER 1. INTRODUCTION ...........................................................................................................1 1.1 Central objective and goals ................................................................................1 1.2 Bioremediation of uranium contamination ........................................................2 1.3 In situ bioremediation of uranium by microbial reduction ................................3 1.4 Geobacter species ..............................................................................................4 1.5 Insights of Uranium reduction by Geobacter sulfurreducens............................5 1.6 Physiological response of G. sulfurreducens to environmental relevant levels of Uranium .........................................................................................7 1.7 In situ stimulation of Geobacter towards uranium reduction ............................7 1.8 Subsurface microbial ecology during in situ bioremediation of uranium-contaminated groundwater ............................................................8 2. U(VI) REDUCTION BY A DIVERSITY OF OUTER SURFACE C-TYPE CYTOCHROMES OF GEOBACTER SULFURREDUCENS .............................12 2.1 Introduction ......................................................................................................12 2.2 Material and methods .......................................................................................14 2.2.1 Bacterial strains, culture conditions, cell suspension ..............................14 2.2.2 Transmission electron microscopy .........................................................15 2.2.3 X-Ray Energy Dispersive Spectroscopy .................................................16 2.2.4 Software ..................................................................................................16 2.2.5 X-Ray Absorption Near Edge Structure (XANES) ................................17 2.2.6 qRT-PCR.................................................................................................17 2.3 Results and discussion .....................................................................................18 2.3.1 U(VI) Reduction with Genetically Modified Strains ..............................18 2.3.2 Speciation and Localization of Uranium ................................................19 2.4 Implications......................................................................................................19
Load more

Recommended publications
  • Multiple Lateral Transfers of Dissimilatory Sulfite Reductase
    JOURNAL OF BACTERIOLOGY, Oct. 2001, p. 6028–6035 Vol. 183, No. 20 0021-9193/01/$04.00ϩ0 DOI: 10.1128/JB.183.20.6028–6035.2001 Copyright © 2001, American Society for Microbiology. All Rights Reserved. Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes MICHAEL KLEIN,1 MICHAEL FRIEDRICH,2 ANDREW J. ROGER,3 PHILIP HUGENHOLTZ,4 SUSAN FISHBAIN,5 1 4 6 1 HEIKE ABICHT, LINDA L. BLACKALL, DAVID A. STAHL, AND MICHAEL WAGNER * 1 Lehrstuhl fu¨r Mikrobiologie, Technische Universita¨t Mu¨nchen, D-85350 Freising, and Department of Biogeochemistry, Max Planck Downloaded from Institute for Terrestrial Microbiology, D-35043-Marburg,2 Germany; Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada3; Advanced Wastewater Management Centre, Department of Microbiology and Parasitology, The University of Queensland, Brisbane 4072, Queensland, Australia4; Department of Civil Engineering, Northwestern University, Evanston, Illinois 60208-31095; and Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington 98195-27006 Received 26 February 2001/Accepted 3 July 2001 http://jb.asm.org/ A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. In addition, the sequence of the dsrAB gene homologs of the sulfite reducer Desulfitobacterium dehalogenans was determined. In contrast to previous reports, comparative analysis of all available DsrAB sequences produced a tree topology partially inconsistent with the corresponding 16S rRNA phylogeny. For example, the DsrAB sequences of -several Desulfotomaculum species (low G؉C gram-positive division) and two members of the genus Thermode sulfobacterium (a separate bacterial division) were monophyletic with ␦-proteobacterial DsrAB sequences.
    [Show full text]
  • Design, Analysis and Application of Synthetic Microbial Consortia Xiaoqiang Jia, Chang Liu, Hao Song, Mingzhu Ding, Jin Du, Qian Ma, Yingjin Yuan *
    ARTICLE IN PRESS Synthetic and Systems Biotechnology ■■ (2016) ■■–■■ Contents lists available at ScienceDirect Synthetic and Systems Biotechnology journal homepage: keaipublishing.com/synbio Design, analysis and application of synthetic microbial consortia Xiaoqiang Jia, Chang Liu, Hao Song, Mingzhu Ding, Jin Du, Qian Ma, Yingjin Yuan * Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China ARTICLE INFO ABSTRACT Article history: The rapid development of synthetic biology has conferred almost perfect modification on single cells, Received 17 May 2015 and provided methodological support for synthesizing microbial consortia, which have a much wider Received in revised form 28 January 2016 application potential than synthetic single cells. Co-cultivating multiple cell populations with rational Accepted 12 February 2016 strategies based on interacting relationships within natural microbial consortia provides theoretical as Available online well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding Keywords: of natural microbial consortia. According to their composition complexity, synthetic microbial consor- Synthetic microbial consortium Single/two/multiple species tia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc. © 2016 Authors. Production and hosting by Elsevier B.V. on behalf of KeAi Communications Co., Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by- nc-nd/4.0/).
    [Show full text]
  • Control Engineering Perspective on Genome-Scale Metabolic Modeling
    Control Engineering Perspective on Genome-Scale Metabolic Modeling by Andrew Louis Damiani A dissertation submitted to the Graduate Faculty of Auburn University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Auburn, Alabama December 12, 2015 Key words: Scheffersomyces stipitis, Flux Balance Analysis, Genome-scale metabolic models, System Identification Framework, Model Validation, Phenotype Phase Plane Analysis Copyright 2015 by Andrew Damiani Approved by Jin Wang, Chair, Associate Professor of Chemical Engineering Q. Peter He, Associate Professor of Chemical Engineering, Tuskegee University Thomas W. Jeffries, Professor of Bacteriology, Emeritus; University of Wisconsin-Madison Allan E. David, Assistant Professor of Chemical Engineering Yoon Y. Lee, Professor of Chemical Engineering Abstract Fossil fuels impart major problems on the global economy and have detrimental effects to the environment, which has caused a world-wide initiative of producing renewable fuels. Lignocellulosic bioethanol for renewable energy has recently gained attention, because it can overcome the limitations that first generation biofuels impose. Nonetheless, in order to have this process commercialized, the biological conversion of pentose sugars, mainly xylose, needs to be improved. Scheffersomyces stipitis has a physiology that makes it a valuable candidate for lignocellulosic bioethanol production, and lately has provided genes for designing recombinant Saccharomyces cerevisiae. In this study, a system biology approach was taken to understand the relationship of the genotype to phenotype, whereby genome-scale metabolic models (GSMMs) are used in conjunction with constraint-based modeling. The major restriction of GSMMs is having an accurate methodology for validation and evaluation. This is due to the size and complexity of the models.
    [Show full text]
  • Helical Domain That Prevents Access to the Substrate-Binding Cleft
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE Researchprovided Article by Elsevier1193 - Publisher Connector The prosequence of procaricain forms an a-helical domain that prevents access to the substrate-binding cleft Matthew R Groves, Mark AJ Taylor, Mandy Scott, Nicola J Cummings Richard W Pickersgill* and John A Jenkins* Background: Cysteine proteases are involved in a variety of cellular processes Address: Department of Food Macromolecular including cartilage degradation in arthritis, the progression of Alzheimer’s Science, Institute of Food Research, Earley Gate, disease and cancer invasion: these enzymes are therefore of immense biological Whiteknights Road, Reading, RG6 6BZ, UK. importance. Caricain is the most basic of the cysteine proteases found in the *Corresponding authors. latex of Carica papaya. It is a member of the papain superfamily and is E-mail: [email protected] homologous to other plant and animal cysteine proteases. Caricain is naturally [email protected] expressed as an inactive zymogen called procaricain. The inactive form of the Key words: caricain, cysteine protease, density protease contains an inhibitory proregion which consists of an additional 106 modification, X-ray structure, zymogen N-terminal amino acids; the proregion is removed upon activation. Received: 25 June 1996 Results: The crystal structure of procaricain has been refined to 3.2 Å Revisions requested: 23 July 1996 Revisions received: 12 August 1996 resolution; the final model consists of three non-crystallographically related Accepted: 28 August 1996 molecules. The proregion of caricain forms a separate globular domain which binds to the C-terminal domain of mature caricain.
    [Show full text]
  • Enhanced Phosphorylation of High-Mobility-Group Proteins In
    Proc. Nati. Acad. Sci. USA Vol. 78, No. 4, pp. 2189-2193, April 1981 Biochemistry Enhanced phosphorylation of high-mobility-group proteins in nuclease-sensitive mononucleosomes from butyrate-treated HeLa cells (hyperphosphorylation/transcriptionally active chromatin/sodium butyrate) BEATRIZ LEVY-WILSON Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92717 Communicated by James F. Bonner, December 29, 1980 ABSTRACT The protein composition of nucleosome fractions MATERIALS AND METHODS differing in their sensitivity to micrococcal nuclease and derived from butyrate-treated or untreated HeLa cells has been com- Cell Cultures. HeLa cells, line S3, were grown in monolay- pared. Most of the high-mobility-group-14 (HMG-14) and HMG- ers, either in T-150 culture flasks or in roller bottles, at 370C 17 content of HeLa cell chromatin is associated with those nu- in minimal essential medium (Flow Laboratories, Rockville, cleosomes that are preferentially sensitive to micrococcal nu- MD) supplemented with 7% bovine calfserum (KC Biologicals) clease. Furthermore, electrophoresis of these two HMG proteins and penicillin (100 units/ml) and streptomycin (100 Ag/ml) from the transcriptionally active chromatin fraction MN, of bu- (Sigma). In experiments involving sodium butyrate, this com- tyrate-treated cells resolves them into a series ofbands. The mul- pound was added to the cultures at a final concentration of5 mM tiple band pattern of HMG-14 and -17 from butyrate-treated cells about 20 hr prior to harvesting of the cells. results from hyperphosphorylation rather than hyperacetylation. Preparation of Nuclei. HeLa cell nuclei were prepared as Phosphorylation of these two small nonhistone proteins may play described by Milcarek et al.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Like Domains Identified in the Genome Sequences of Leptospira Interrogans
    RESEARCH ARTICLE Features of Two New Proteins with OmpA- Like Domains Identified in the Genome Sequences of Leptospira interrogans Aline F. Teixeira1,2, Zenaide M. de Morais3, Karin Kirchgatter4, Eliete C. Romero5, Silvio A. Vasconcellos3, Ana Lucia T. O. Nascimento1,2* 1 Centro de Biotecnologia, Instituto Butantan, Sao Paulo, SP, Brazil, 2 Programa de Pós-Graduação Interunidades em Biotecnologia,Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil, 3 Laboratório de Zoonoses Bacterianas, Faculdade de Medicina Veterinária e Zootecnia, Universidade de Sao Paulo, Sao Paulo, SP, Brazil, 4 Nucleo de Estudos em Malária, Superintendência de Controle de Endemias - Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, SP, Brazil, 5 Centro de Bacteriologia, Instituto Adolfo Lutz, Sao Paulo, Brazil * [email protected] Abstract OPEN ACCESS Citation: Teixeira AF, de Morais ZM, Kirchgatter K, Leptospirosis is an acute febrile disease caused by pathogenic spirochetes of the genus Romero EC, Vasconcellos SA, Nascimento ALTO Leptospira. It is considered an important re-emerging infectious disease that affects humans (2015) Features of Two New Proteins with OmpA- worldwide. The knowledge about the mechanisms by which pathogenic leptospires invade Like Domains Identified in the Genome Sequences of Leptospira interrogans. PLoS ONE 10(4): e0122762. and colonize the host remains limited since very few virulence factors contributing to the doi:10.1371/journal.pone.0122762 pathogenesis of the disease have been identified. Here, we report the identification and char- Academic Editor: Odir A Dellagostin, Federal acterization of two new leptospiral proteins with OmpA-like domains. The recombinant pro- University of Pelotas, BRAZIL teins, which exhibit extracellular matrix-binding properties, are called Lsa46 - LIC13479 and Received: October 17, 2014 Lsa77 - LIC10050 (Leptospiral surface adhesins of 46 and 77 kDa, respectively).
    [Show full text]
  • Genomic Analyses of Unique Carbohydrate and Phytohormone Metabolism in the Macroalga Gracilariopsis Lemaneiformis (Rhodophyta)
    Sun et al. BMC Plant Biology (2018) 18:94 https://doi.org/10.1186/s12870-018-1309-2 RESEARCH ARTICLE Open Access Genomic analyses of unique carbohydrate and phytohormone metabolism in the macroalga Gracilariopsis lemaneiformis (Rhodophyta) Xue Sun1, Jun Wu2, Guangce Wang3, Yani Kang1,2, Hong Sain Ooi4, Tingting Shen2, Fangjun Wang1, Rui Yang1, Nianjun Xu1* and Xiaodong Zhao2* Abstract Background: Red algae are economically valuable for food and in industry. However, their genomic information is limited, and the genomic data of only a few species of red algae have been sequenced and deposited recently. In this study, we annotated a draft genome of the macroalga Gracilariopsis lemaneiformis (Gracilariales, Rhodophyta). Results: The entire 88.98 Mb genome of Gp. lemaneiformis 981 was generated from 13,825 scaffolds (≥500 bp) with an N50 length of 30,590 bp, accounting for approximately 91% of this algal genome. A total of 38.73 Mb of scaffold sequences were repetitive, and 9281 protein-coding genes were predicted. A phylogenomic analysis of 20 genomes revealed the relationship among the Chromalveolata, Rhodophyta, Chlorophyta and higher plants. Homology analysis indicated phylogenetic proximity between Gp. lemaneiformis and Chondrus crispus. The number of enzymes related to the metabolism of carbohydrates, including agar, glycoside hydrolases, glycosyltransferases, was abundant. In addition, signaling pathways associated with phytohormones such as auxin, salicylic acid and jasmonates are reported for the first time for this alga. Conclusion: We sequenced and analyzed a draft genome of the red alga Gp. lemaneiformis, and revealed its carbohydrate metabolism and phytohormone signaling characteristics. This work will be helpful in research on the functional and comparative genomics of the order Gracilariales and will enrich the genomic information on marine algae.
    [Show full text]
  • Biofilm Engineering Approaches for Improving the Performance Of
    REVIEW published: 05 July 2018 doi: 10.3389/fenrg.2018.00063 Biofilm Engineering Approaches for Improving the Performance of Microbial Fuel Cells and Bioelectrochemical Systems Maria Joseph Angelaalincy 1, Rathinam Navanietha Krishnaraj 2, Ganeshan Shakambari 1, Balasubramaniem Ashokkumar 3, Shanmugam Kathiresan 4 and Perumal Varalakshmi 1* 1 Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, India, 2 Department of Chemical and Biological Engineering, Composite and Nanocomposite Advanced Manufacturing – Biomaterials Center, Rapid City, SD, United States, 3 Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India, 4 Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India Microbial fuel cells (MFCs) are emerging as a promising future technology for a wide range Edited by: Abudukeremu Kadier, of applications in addition to sustainable electricity generation. Electroactive (EA) biofilms National University of Malaysia, produced by microorganisms are the key players in the bioelectrochemical systems Malaysia involving microorganism mediated electrocatalytic reactions. Therefore, genetically Reviewed by: modifying the organism for increased production of EA biofilms and improving the extra G. Velvizhi, Indian Institute of Chemical electron transfer (EET) mechanisms may attribute to increase in current density of a MFC Technology (CSIR), India and an increased COD removal in wastewater treatment plant coupled MFC systems. Özlem Onay, Anadolu University, Turkey Extracellular polysaccharides (EPS) produced by the organisms attribute to both biofilm *Correspondence: formation and electron transfer. Although cell surface modification, media optimization Perumal Varalakshmi and operation parameters validation are established as enhancement strategies for a fuel [email protected] cell performance, engineering the vital genes involved in electroactive biofilm formation Specialty section: is the future hope.
    [Show full text]
  • Crystal Structure of Cathepsin X: a Flip–Flop of the Ring of His23
    st8308.qxd 03/22/2000 11:36 Page 305 Research Article 305 Crystal structure of cathepsin X: a flip–flop of the ring of His23 allows carboxy-monopeptidase and carboxy-dipeptidase activity of the protease Gregor Guncar1, Ivica Klemencic1, Boris Turk1, Vito Turk1, Adriana Karaoglanovic-Carmona2, Luiz Juliano2 and Dušan Turk1* Background: Cathepsin X is a widespread, abundantly expressed papain-like Addresses: 1Department of Biochemistry and v mammalian lysosomal cysteine protease. It exhibits carboxy-monopeptidase as Molecular Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia and 2Departamento de well as carboxy-dipeptidase activity and shares a similar activity profile with Biofisica, Escola Paulista de Medicina, Rua Tres de cathepsin B. The latter has been implicated in normal physiological events as Maio 100, 04044-020 Sao Paulo, Brazil. well as in various pathological states such as rheumatoid arthritis, Alzheimer’s disease and cancer progression. Thus the question is raised as to which of the *Corresponding author. E-mail: [email protected] two enzyme activities has actually been monitored. Key words: Alzheimer’s disease, carboxypeptidase, Results: The crystal structure of human cathepsin X has been determined at cathepsin B, cathepsin X, papain-like cysteine 2.67 Å resolution. The structure shares the common features of a papain-like protease enzyme fold, but with a unique active site. The most pronounced feature of the Received: 1 November 1999 cathepsin X structure is the mini-loop that includes a short three-residue Revisions requested: 8 December 1999 insertion protruding into the active site of the protease. The residue Tyr27 on Revisions received: 6 January 2000 one side of the loop forms the surface of the S1 substrate-binding site, and Accepted: 7 January 2000 His23 on the other side modulates both carboxy-monopeptidase as well as Published: 29 February 2000 carboxy-dipeptidase activity of the enzyme by binding the C-terminal carboxyl group of a substrate in two different sidechain conformations.
    [Show full text]
  • In Silico Prediction and Threading Based Epitope Mapping of Ompa-Like Outer Membrane Leptospiral Lipoprotein Loa22
    International Journal Of Scientific & Engineering Research, Volume 6, Issue 3, March-2015 477 ISSN 2229-5518 In silico prediction and threading based epitope mapping of OmpA-like outer membrane Leptospiral Lipoprotein Loa22 Angela Asir Ramasamy Victor1$, Sunil Abraham1$, Jebasingh Tennyson1, Nityananda Pradhan2* $ Authors equally contributed to this paper Abstract — Loa22 is OmpA-like outer membrane protein from Leptospira interrogans characterized in the C-terminus domain which play an important role in the infection and immunological responses of leptospirosis. [1,2]. Phylogenetic tree was constructed for Loa22 by comparing it with Lipoproteins (LipL 71, 45, 41, 31, 32, 21 and 48) and with outer membrane proteins (OmpL 1, 47, 54, 36, 37). The comprising lineages of Loa 22 have largely varying rates of evolution. In the present study the physicochemical properties of Loa22 were assessed. The structure of Loa22 was predicted by threading method in RaptorX server and the structure was energy minimized and validated by using SAVES server. The stereochemical quality and the protein backbone conformations were done by Ramachandran Plot analysis. Four sequential and conformational B cell epitopes of Loa22 were found in Ellipro server and mapped to find the sequential epitopes. The same B cell linear epitopes was also predicted by ABC Pred, BepiPred 1.0 server. All these epitopes were found to be in higher values. The results of the present study will help to elucidate the function of Loa22 and epitope-based vaccine development for Leptospirosis. Key words: Leptospira, Lipoprotein, OmpA, outer membrane protein, Loa22, Phylogenetic analysis, B-cell epitope, List of abbreviations: SAVES: Structural Analysis and Verification Server; MEGA: Molecular Evolutionary Genetic Analysis; PI: Protrusion Index; LBP: Local Bootstrap values; ACC: Auto Cross Covariance NEFF: Number of Effective sequence homologs.
    [Show full text]
  • Open Matthew R Moreau Ph.D. Dissertation Finalfinal.Pdf
    The Pennsylvania State University The Graduate School Department of Veterinary and Biomedical Sciences Pathobiology Program PATHOGENOMICS AND SOURCE DYNAMICS OF SALMONELLA ENTERICA SEROVAR ENTERITIDIS A Dissertation in Pathobiology by Matthew Raymond Moreau 2015 Matthew R. Moreau Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The Dissertation of Matthew R. Moreau was reviewed and approved* by the following: Subhashinie Kariyawasam Associate Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Bhushan M. Jayarao Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Mary J. Kennett Professor, Veterinary and Biomedical Sciences Vijay Kumar Assistant Professor, Department of Nutritional Sciences Anthony Schmitt Associate Professor, Veterinary and Biomedical Sciences Head of the Pathobiology Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Salmonella enterica serovar Enteritidis (SE) is one of the most frequent common causes of morbidity and mortality in humans due to consumption of contaminated eggs and egg products. The association between egg contamination and foodborne outbreaks of SE suggests egg derived SE might be more adept to cause human illness than SE from other sources. Therefore, there is a need to understand the molecular mechanisms underlying the ability of egg- derived SE to colonize the chicken intestinal and reproductive tracts and cause disease in the human host. To this end, the present study was carried out in three objectives. The first objective was to sequence two egg-derived SE isolates belonging to the PFGE type JEGX01.0004 to identify the genes that might be involved in SE colonization and/or pathogenesis.
    [Show full text]