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Dissimilatory Iron-Reducing and Endosporulating Bacteria

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Dissimilatory Iron-Reducing and Endosporulating Bacteria DISSIMILATORY IRON-REDUCING AND ENDOSPORULATING BACTERIA by ROB UCHE ONYENWOKE (Under the Direction of Juergen Wiegel) ABSTRACT This dissertation represents a diversified study of the biochemical, physiological, and genetic traits of members of the low G+C subdivision of the Gram-type positive bacteria, also known as the ‘Firmicutes’. The phylum ‘Firmicutes’ contains a diverse array of taxa that are not easily separated into coherent phylogenetic groups by any one physiological trait, such as endospore-formation or dissimilatory iron reduction. This dissertation considers numerous contemporary, and highly convergent in providing breadth and scope of the subject matter, methods of study. The principle aim was to examine the lineage ‘Firmicutes’ by a) a genomic study of the occurrence or absence of endosporulation genes in numerous members of the lineage, b) classic biochemical studies of the enzymes responsible for biotic iron reduction, and c) culture-dependent studies and isolations of various ‘Firmicutes’ to both identify new iron- reducers and better resolve the taxonomy of the lineage. The work with endosporulation genes has shown there might not be a distinct set of “endosporulation-specific” genes. This raises several new questions about this exceptionally complex process. The work described here on “ferric reductases” suggests there are enzymes capable of iron reduction that also have additional activities. The isolation of novel bacteria presented here have added to the diversity of the ‘Firmicutes’ but have also added to the phylogenetic and taxonomic complexity of this group. Traditional boundaries for families and genera have been weakened or shown to be in need of further studies. INDEX WORDS: Gram-type positive bacteria, Firmicutes, Thermophiles, Endospores, Dissimilatory iron reduction, Quinones, Oxidative stress, The University of Georgia THE PHYSIOLOGY OF THE FIRMICUTES: NOVEL DISSIMILATORY IRON-REDUCING BACTERIA, OXIDOREDUCTASE ENZYMES, AND THE ENDOSPORULATING BACTERIA by ROB UCHE ONYENWOKE B.S., The University of Georgia, 2000 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS, GEORGIA 2006 © 2006 Rob Uche Onyenwoke All Rights Reserved THE PHYSIOLOGY OF THE FIRMICUTES: NOVEL DISSIMILATORY IRON-REDUCING BACTERIA, OXIDOREDUCTASE ENZYMES, AND THE ENDOSPORULATING BACTERIA by ROB UCHE ONYENWOKE Major Professor: Dr. Juergen Wiegel Committee: Dr. Michael W. W. Adams Dr. Harry A. Dailey Dr. Robert J. Maier Dr. William B. Whitman Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia December 2006 iv ACKNOWLEDGEMENTS First of all, I would like to express my gratitude to all of my family, friends, and members of the University of Georgia/Athens community who have made my matriculation such a rich and fulfilling period of my life. I thank my parents for their continued support of me as I have progressed forward in my life. I thank Juergen Wiegel, my advisor and friend, for his guidance and support, and my committee members for all of their thoughtful suggestions and willingness to foster my academic development. Finally, I would like to say that I have been privileged to have had the opportunity to work with so many wonderful people in the Department of Microbiology. v TABLE OF CONTENTS Page ACKNOWLEDGEMENTS........................................................................................................... iv LIST OF TABLES......................................................................................................................... ix LIST OF FIGURES ....................................................................................................................... xi CHAPTER 1 INTRODUCTION AND LITERATURE REVIEW .....................................................1 Thermophiles.............................................................................................................1 The ‘Firmicutes’........................................................................................................2 Isolation and characterization of ‘Firmicutes’ ..........................................................8 Biotic metal reduction .............................................................................................10 Iron transport, binding, and acquisition...................................................................12 Dissimilatory Fe(III) reduction ...............................................................................14 Possible mechanisms for Fe(III) reduction .............................................................17 Iron reductases.........................................................................................................21 Cellular localization of iron reductases...................................................................22 Cytochromes............................................................................................................25 Other possible mechanisms for Fe(III) reductases..................................................27 2 THE GENUS THERMOANAEROBACTERIUM.........................................................45 Abstract ...................................................................................................................46 vi 3 THE GENUS THERMOANAEROBACTER ................................................................71 Abstract ...................................................................................................................72 4 RECLASSIFICATION OF THERMOANAEROBIUM ACETIGENUM AS CALDICELLULOSIRUPTOR ACETIGENUS COMB. NOV. AND EMENDATION OF THE GENUS DESCRIPTION ...........................................119 Abstract .................................................................................................................120 Results and discussion...........................................................................................120 5 SPORULATION GENES IN MEMBERS OF THE LOW G+C GRAM-TYPE POSITIVE BRANCH (FIRMICUTES).................................................................132 Abstract .................................................................................................................133 Introduction ...........................................................................................................133 Materials and methods...........................................................................................136 Results and discussion...........................................................................................139 Acknowledgments .................................................................................................145 6 CHARACTERIZATION OF A SOLUBLE OXIDOREDUCTASE WITH AN FE(III) REDUCTION ACTIVITY FROM CARBOXYDOTHERMUS FERRIREDUCENS.........163 Abstract .................................................................................................................164 Introduction ...........................................................................................................164 Materials and methods...........................................................................................166 Results ...................................................................................................................172 Discussion .............................................................................................................177 Acknowledgements ...............................................................................................180 vii 7 IRON (III) REDUCTION: A NOVEL ACTIVITY OF THE HUMAN NAD(P)H OXIDOREDUCTASE...........................................................................................208 Abstract .................................................................................................................209 Introduction ...........................................................................................................209 Experimental procedures.......................................................................................211 Results ...................................................................................................................213 Discussion .............................................................................................................215 Acknowledgements ...............................................................................................218 9 CONCLUSION .........................................................................................................242 REFERENCES ............................................................................................................................244 APPENDICES .............................................................................................................................300 A NOVEL CHEMOLITHOTROPHIC, THERMOPHILIC, ANAEROBIC BACTERIA THERMOLITHOBACTER FERRIREDUCENS GEN. NOV., SP. NOV. AND THERMOLITHOBACTER CARBOXYDIVORANS SP. NOV...............................300 Abstract .................................................................................................................301 Introduction ...........................................................................................................302 Materials and methods...........................................................................................304 Results ...................................................................................................................312
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