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Investigation of Chemotaxis Genes and Their Functions in Geobacter Species

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Investigation of Chemotaxis Genes and Their Functions in Geobacter Species University of Massachusetts Amherst ScholarWorks@UMass Amherst Open Access Dissertations 9-2009 Investigation of Chemotaxis Genes and Their Functions in Geobacter Species Hoa T. Tran University of Massachusetts Amherst, [email protected] Follow this and additional works at: https://scholarworks.umass.edu/open_access_dissertations Part of the Microbiology Commons Recommended Citation Tran, Hoa T., "Investigation of Chemotaxis Genes and Their Functions in Geobacter Species" (2009). Open Access Dissertations. 129. https://scholarworks.umass.edu/open_access_dissertations/129 This Open Access Dissertation is brought to you for free and open access by ScholarWorks@UMass Amherst. It has been accepted for inclusion in Open Access Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. INVESTIGATION OF CHEMOTAXIS GENES AND THEIR FUNCTIONS IN GEOBACTER SPECIES A Dissertation Presented by HOA T. TRAN 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 2009 Department of Chemistry © Copyright by Hoa T. Tran 2009 All Rights Reserved INVESTIGATION OF CHEMOTAXIS GENES AND THEIR FUNCTIONS IN GEOBACTER SPECIES A Dissertation Presented by HOA T. TRAN Approved as to style and content by: _______________________________________ Robert M. Weis, Chair _______________________________________ Derek R. Lovley, Co-chair _______________________________________ Michael J. Knapp, Member _______________________________________ Michael J. Maroney, Member ____________________________________ Bret Jackson, Department Head Department of Chemistry DEDICATION To my loving husband, my family, and my brother Ngoc Tran ACKNOWLEDGMENTS The success of this research is due to contributions from many people and I would like to express my gratitude to them. I would like to thank my advisors Dr. Robert M. Weis and Dr. Derek R. Lovley for great support, guidance, and patience, and for giving me freedom to develop and conduct my research. I would like to extend my thanks to Dr. Michael J. Knapp and Dr. Michael J. Maroney for their time serving as committee members during my doctoral studies. I would like to thanks all my current and former labmates in the Lovley and Weis labs for keeping me in good spirits while I am in the lab, and for their willingness to offer help when I needed it. Special thanks to Frances M. Antommattei and Richard Glaven for their patient mentorship and helpful advice, to Zara Summers for help with microarray analysis, and to Ned Young for help with phylogenetic trees. I would like to express my thanks to Tünde Mester and Xinlei Qian for their advice on protein work. Special gratitude to Lubna Al-Challah, Muktak Aklujkar, and Tatiana Y. Besschetnova for their endless support and great friendship. I would like to thank my collaborator Julia Krushkal for her help in analyzing the regulation of chemotaxis genes and for making my manuscript readable. I am grateful to John Leszyk and Mary Lipton for performing mass spectrometry analysis. My special thanks to Dale Callaham for helps and advises on microscopic works. My special thanks to Betsy Blunt and Joy Ward for keeping the lab and my work running smoothly. I also would like to thank the personnel and faculty of the Department of Chemistry and Department of Microbiology of the University of Massachusetts Amherst. v ABSTRACT INVESTIGATION OF CHEMOTAXIS GENES AND THEIR FUNCTIONS IN GEOBACTER SPECIES SEPTEMBER 2009 HOA T. TRAN, B.Sc., HANOI UNIVERSITY OF EDUCATION M.Ed., VICTORIA UNIVERSITY M. Sc., UNIVERSITY OF LEEDS Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Robert M. Weis and Derek R. Lovley Geobacter species are δ-Proteobacteria and are often predominant in the Fe(III) reduction zone of sedimentary environments. Their abilities to remediate contaminated environments and to produce electricity have inspired extensive studies. Cell motility, biofilm formation, and type IV pili, which have been shown to be regulated by chemotaxis genes in other bacteria, all appear important for the growth of Geobacter species in changing environments and for electricity production. The genomes of Geobacter species show the presence of a significant number of chemotaxis gene homologs, suggesting important roles for them in the physiology of Geobacter species, although gene functions are not yet identified. In this study, we focus on identifying chemotaxis components and studying their functions in Geobacter species. We identified a large number of homologs of chemotaxis genes, which are arranged in six or more major clusters in the genomes of Geobacter sulfurreducens, Geobacter metallireducens, and Geobacter uraniireducens. Based on homology to known pathways, functions of some chemotaxis clusters were assigned; others appear to vi be unique to Geobacter species. We discuss the diversity of chemoreceptors and other signaling proteins as well the regulation of chemotaxis genes in Geobacter species. The functions of chemotaxis genes were studied in G. sulfurreducens, whose genome contains ~ 70 chemotaxis gene homologs, arranged in 6 major clusters. These chemotaxis clusters are also found in other Geobacter species with similar gene order and high level of gene identity, suggesting that our study in G. sulfurreducens could be extrapolated to other Geobacter species. We identified the function of the che5 cluster of G. sulfureducens as regulation of the biosynthesis of extracellular materials. We showed that G. sulfurreducens KN400 is chemotactic, and that this behavior is flagellum- dependent. Our preliminary data indicated that G. sulfurreducens may use the che1 cluster, which is found exclusively in Geobacteraceae, to regulate chemotaxis. Our studies demonstrated important roles of chemotaxis genes in Geobacter physiology and their presence in large numbers could be one of the reasons why Geobacter species outcompete other species in bioremediation sites. Further studies are warranted for better understanding of the mechanisms of Che-like pathways and their potential use in optimization of conditions for applications of Geobacter species in bioremediation and electricity generation. vii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ...................................................................................................v ABSTRACT ....................................................................................................................... vi LIST OF TABLES ...............................................................................................................x LIST OF FIGURES ........................................................................................................... xi CHAPTER 1. INTRODUCTION ...................................................................................................1 The chemotaxis system in Escherichia coli ...............................................................1 Chemotaxis-like sytems in other species ......................................................................4 Physiological characteristics and potential applications of Geobacter species .................6 2. INDENTIFICATION OF CHEMOTAXIS COMPONENTS IN THE GENOMES OF GEOBACTER SPECIES .................................................................................10 Introduction ............................................................................................................10 Methods..................................................................................................................12 Results and discussion ...........................................................................................15 Conclusion .............................................................................................................45 3. A CHE CLUSTER OF GEOBACTER SULFURREDUCENS REGULATES GENE EXPRESSION ............................................................................................47 Introduction ............................................................................................................47 Methods..................................................................................................................49 Results ....................................................................................................................57 Discussion ..............................................................................................................77 4. PRELIMINARY DATA FROM CHEMOTAXIS STUDY OF A MOTILE GEOBACTER SULFURREDUCENS STRAIN ...................................................86 Introduction ............................................................................................................86 Methods..................................................................................................................89 Results and discussions ..........................................................................................94 Conclusion ...........................................................................................................103 5. FUTURE STUDIES.............................................................................................105 Examination of the formation of MCP class-specific clusters .............................105 viii Examination of whether a CheR group is MCP class-specific and MCP- tether specific .................................................................................................108
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