New insight into the catabolic pathway redundancies of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1

OF THE DISSERTATION ii ACKNOWLEDGEMENTS iv TABLE OF CONTENTS vi LIST OF FIGURES ix LIST OF TABLES x CHAPTER 1: LITERATURE REVIEW 1 1.1. THE GENUS SPHINGOMONAS 1 1.2. POLYCYCLIC AROMATIC HYDROCARBONS 4 1.3. DIOXIN AND DIOXIN-LIKE COMPOUNDS: 7 1.4. BIOREMEDIATION 9 CHAPTER 2: MATERIALS AND METHODS 12 2.1 BACTERIAL STRAINS, PLASMIDS, AND CULTURE CONDITIONS 12 2.2. CHEMICALS AND REAGENTS 12 2.3. PLASMID DNA EXTRACTION AND MOLECULAR GENETICS METHODS 13 2.4. PRIMER DESIGN 13 2.5. PCR CONDITIONS 14 2.6. OVERLAP EXTENSION PCR 14 2.7. TRIPARENTAL CONJUGATION 14 2.8. GENE KNOCKOUT 15 2.8.1. DxnA1A2 gene knockout 15 2.8.1.1. Construction of plasmid and ΔdxnA1A2::Km mutant 15 2.8.1.2. Complementation 18