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Rhodococcus Equi ATCC 13557

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Rhodococcus Equi ATCC 13557 The genomic evaluation of estrogen degradation by Rhodococcus equi ATCC 13557 Sarah Louisa Flint A thesis submitted to Newcastle University in partial fulfilment of the requirements for the Degree of Doctor of Philosophy in the faculty of Science, Agriculture and Engineering. School of Civil Engineering and Geosciences Newcastle University Newcastle upon Tyne NE1 7RU February 2019 Abstract Estrogens estrone (E1), 17β-Estradiol (E2), and estriol (E3) are steroidal hormones produced naturally, and the synthetic estrogen 17α-Ethinylestradiol (EE2) is contained in the contraceptive pill. In 2012, the European Commission proposed international environmental limits in freshwater bodies on EE2 and E2, with Environmental Quality Standard (EQS) values of 0.035 and 0.4 ng/L, respectively. Despite their low concentrations (ng/L) in the environment, several studies demonstrated their harmful effect to aquatic organisms. Some bacteria have been identified to biodegrade estrogen with varied efficiency. Biodegradation is a low cost and sustainable method that could help in the removal of estrogens. This study aims to provide the framework with which to elucidate, identify and characterise those genes involved in estrogen degradation by a genomic evaluation of steroid degrading bacteria. Firstly, a putative estrogen biodegradation pathway was postulated, and a database of the major genes potentially involved in it was compiled, by combining existing information on the degradation of estrogen, and its better characterised analogue – testosterone, for which there is a complete degradation pathway. The genome of Rhodococcus equi ATCC13557, a known estrogen degrading bacterium, was sequenced, assembled and mapped. Genome analysis revealed a gene cluster potentially coding for enzymes involved in estrogen degradation; 3- carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy- phenyl)propionate hydroxylase, 3-oxosteroid 1-dehydrogenase and transcriptional regulator IcIR family. Specific primer sets were developed to target these genes, and using quantitative reverse transcription PCR (RT-qPCR), gene expression when exposed to E2 and EE2, was quantified relative to the control, without estrogen, and normalised to the reference genes, malate dehydrogenase and arginine deiminase. Gene expression of putative cytochrome P450 monooxygenase was upregulated initially in the presence of estrogen, therefore may be involved in one of the first steps in estrogen degradation. The RT-qPCR experiment was complemented by biodegradation studies, however, metabolites analysis is required to confirm the postulated estrogen biodegradation pathway. P a g e | ii Author’s declaration I hereby certify that all work presented is my own, except where otherwise acknowledged. Sarah Louisa Flint P a g e | iii Table of Contents The genomic evaluation of estrogen degradation by Rhodococcus equi ATCC 13557 ...................................................................................................................... i Abstract ................................................................................................................... ii Author’s declaration................................................................................................ iii Table of Contents ................................................................................................... iv Table of figures .................................................................................................... viii Table of tables ....................................................................................................... xii Table of equations ................................................................................................ xiv Abbreviations ........................................................................................................ xv Acknowledgements ............................................................................................ xviii Chapter 1: General Introduction ........................................................................ 1 1.1 What is estrogen? .............................................................................................................. 1 1.2 Pharmaceutical usage of estrogen ..................................................................................... 3 1.3 The concentration of estrogen detected in the aquatic environment .............................. 4 1.4 The sources of estrogen in the environment ..................................................................... 7 1.5 The environmental fate of estrogens in the environment and their effects ..................... 9 1.6 Legislation ........................................................................................................................ 13 1.7 Chemical and physical removal methods of estrogen ..................................................... 14 Sewage treatment plants ......................................................................................... 14 Biodegradation of estrogen ..................................................................................... 16 1.8 Known estrogen degrading bacteria ................................................................................ 16 1.9 The genomic potential of bacteria to degrade estrogen ................................................. 25 1.10 Aims.................................................................................................................................. 26 Chapter 2: Creating a hypothetical estrogen degradation pathway ................. 28 2.1 Introduction ..................................................................................................................... 28 2.2 Materials and methods .................................................................................................... 32 P a g e | iv 2.3 Results and Discussion ..................................................................................................... 33 Chapter 3: Genome assembly and evaluation ................................................ 40 3.1 Introduction ..................................................................................................................... 40 3.2 Materials and methods .................................................................................................... 48 Genome sequencing ................................................................................................. 48 Genome assembly .................................................................................................... 50 Annotation ............................................................................................................... 52 Creating a graphical map of the genome ................................................................. 52 Genomic analysis ...................................................................................................... 53 3.3 Results and Discussion ..................................................................................................... 54 Quality assessment................................................................................................... 54 CLC assembly ............................................................................................................ 55 SPAdes assembly ...................................................................................................... 59 Comparison of the SPAdes and CLC assemblies of R. equi ATCC13557 ................... 63 Genome comparison ................................................................................................ 64 Genome evaluation for genes coding for enzymes potentially involved in estrogen degradation .............................................................................................................................. 66 Chapter 4: Developing a sample preparation method for the quantification of estrogens in degradation experiments ................................................................. 80 4.1 Introduction ..................................................................................................................... 80 4.2 Materials and methods .................................................................................................... 84 Comparison of different methods to separate bacterial biomass from the aqueous phase 84 Comparison of methods for dissolving estrogen into aqueous growth media ........ 87 Statistical analysis and graphing software ............................................................... 89 4.3 Results .............................................................................................................................. 89 Comparison of different methods to separate bacterial biomass from the aqueous phase. 89 P a g e | v Comparison of methods for dissolving estrogen into aqueous growth media ....... 90 4.4 Discussion ......................................................................................................................... 95 Chapter 5: Degradation experiments .............................................................. 98 5.1 Introduction ..................................................................................................................... 98 5.2 Materials and methods .................................................................................................... 99 Bacterial
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