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The Physiology and Evolution of Selenite Respiration in Bacteria Duquesne University Duquesne Scholarship Collection Electronic Theses and Dissertations Spring 5-8-2020 The Physiology and Evolution of Selenite Respiration in Bacteria Michael Wells Follow this and additional works at: https://dsc.duq.edu/etd Part of the Biochemistry Commons, Environmental Microbiology and Microbial Ecology Commons, Evolution Commons, and the Microbial Physiology Commons Recommended Citation Wells, M. (2020). The Physiology and Evolution of Selenite Respiration in Bacteria (Doctoral dissertation, Duquesne University). Retrieved from https://dsc.duq.edu/etd/1871 This One-year Embargo is brought to you for free and open access by Duquesne Scholarship Collection. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Duquesne Scholarship Collection. THE PHYSIOLOGY AND EVOLUTION OF SELENITE RESPIRATION IN BACTERIA A Dissertation Submitted to the Bayer School of Natural and Environmental Sciences Duquesne University In partial fulfillment of the requirements for the degree of Doctor of Philosophy By Michael Wells May 2020 Copyright by Michael Wells 2020 THE PHYSIOLOGY AND EVOLUTION OF SELENITE RESPIRATION IN BACTERIA By Michael Wells Approved January 28, 2020 _________________________________ ______________________________ Dr. John F. Stolz Dr. Partha Basu Professor of Environmental Microbiology Chair, Department of Chemistry and (Committee Chair) Chemical Biology Professor of Chemistry (Committee Member) _________________________________ ______________________________ Dr. Jan Janecka Dr. Nancy Trun Assistant Professor of Biology Associate Professor of Biology (Committee Member) (Committee Member) _________________________________ ______________________________ Dr. Philip Reeder Dr. Joseph McCormick Dean, Bayer School of Natural and Chair, Department of Biological Environmental Sciences Sciences Professor Professor of Biology iii ABSTRACT THE PHYSIOLOGY AND EVOLUTION OF SELENITE RESPIRATION IN BACTERIA By Michael Wells May 2020 Dissertation supervised by Dr. John F. Stolz The selenium oxyanions selenate (Se(VI)) and selenite (Se(IV)) can be utilized by some bacteria and archaea as terminal electron acceptors in anaerobic respiration. Se(VI) and Se(IV) respiration is mediated by a phylogenetically and ecologically diverse array of organisms, suggesting that selenium respiration is ubiquitous in natural environments. Several respiratory Se(VI) reductases have been characterized in bacteria, revealing that Se(VI) respiration has evolved independently several times in this domain. Se(IV) respiration, in contrast, has yet to be characterized. I have purified and characterized the first respiratory Se(IV) reductase from Bacillus selenitireducens MLS10. The Se(IV) reductase appeared to purify as a single 80 kDa enzyme and contained both iron and molybdenum. The enzyme was highly specific for Se(IV). The genome of MLS10 demonstrated that this enzyme was part of an operon encoding a putative respiratory Se(IV) reductase (Srr) complex. Srr was electrophoretically purified from MLS10 iv periplasm using non-denaturing gels, and identified using in-gel enzyme assays for Se(IV) reducing activity. Multiple subunits from Srr were identified using liquid chromatography tandem mass spectrometry, confirming the operon codes for a Srr complex. The enzyme was designated SrrA. Phylogenetic analysis determined that SrrA was a member of the polysulfide reductase catalytic subunit (PsrA) and thiosulfate reductase catalytic subunit (PhsA) lineage of molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)- containing molybdoenzymes. Analysis of the operons associated with each catalytic subunit in the phylogeny revealed that putative PsrA, PhsA, and SrrA homologs did not form monophyletic clades with respect to one another. Furthermore, while putative Srr operons were not observed in archaea, Srr was present throughout the PsrA/PhsA lineage in bacteria. To determine if Srr is a reliable marker for Se(IV) respiration, I attempted to ascertain if two organisms, Bacillus beveridgei MLTeJB and Desulfitobacterium hafniense PCP-1, expressed Srr when cultivated in the presence of Se(IV). MLTeJB was shown to express SrrA when grown on both Se(VI) and Se(IV). Definitive identification of the Se(IV) reductase expressed by PCP-1 when grown on Se(VI) was not possible due to the low expression levels of the enzyme. This work represents the first physiological and evolutionary studies of Se(IV) respiration. v DEDICATION To my sister Annie, a continual source of support and guidance as I have transitioned from one life to another. I am perpetually in awe of her selflessness, compassion, and wisdom, and am so grateful every day for the privilege of being her brother. To İstanbul, to Türkiye, I remain forever indebted to a city and a culture that showed me how to be the man I aspire to be. So many people, too many to innumerate, let me into their culture, their homes, and their lives. I have been forever changed because of it. vi TABLE OF CONTENTS Page Abstract ................................................................................................................................................ iv Dedication ............................................................................................................................................ vi Acknowledgement .............................................................................................................................. vii List of tables ......................................................................................................................................... ix List of figures ........................................................................................................................................ x Chapter 1: Introduction, hypothesis, and specific aims...................................................................... 1 Chapter 2: A review of the selenium biogeochemical cycle and of selenium metabolism............ 19 Chapter 3: Materials and methods ................................................................................................... 103 Chapter 4: The respiratory selenite reductase of Bacillus selenitireducens strain MLS10.......... 119 Chapter 5: Selenite metabolism in Thermus scotoductus SA-01, Desulfitobacterium hafniense PCP-1, and Bacillus beveridgei MLTeJB ....................................................................................... 143 Chapter 6: Phylogenetic analysis of SrrA and other Dimethyl Sulfoxide Reductase (DMSOR) family member catalytic subunits .................................................................................................... 163 Appendix 1: MLS10 and MLTeJB media and trace elements solution ........................................ 204 Appendix 2: PCP-1 medium and trace elements and vitamins solutions ...................................... 206 Appendix 3: SA-01 media and trace elements and vitamins solutions ......................................... 208 References ......................................................................................................................................... 211 vii LIST OF TABLES Page Table 4.1. ........................................................................................................................................... 127 Table 5.1 ............................................................................................................................................ 151 Table 5.2 ............................................................................................................................................ 158 Table 6.1 ............................................................................................................................................ 172 Table 6.2 ............................................................................................................................................ 189 viii LIST OF FIGURES Page Figure 4.1 .......................................................................................................................................... 126 Figure 4.2 .......................................................................................................................................... 128 Figure 4.3 .......................................................................................................................................... 129 Figure 4.4 .......................................................................................................................................... 131 Figure 4.5 .......................................................................................................................................... 133 Figure S4.1 ........................................................................................................................................ 140 Figure 5.1 .......................................................................................................................................... 150 Figure 5.2 .......................................................................................................................................... 154 Figure 5.3 .......................................................................................................................................... 156 Figure 5.4 .........................................................................................................................................
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