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Characterization of Insertion Sequence IS605 in Halanaerobium Hydrogeniformans

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Characterization of Insertion Sequence IS605 in Halanaerobium Hydrogeniformans Scholars' Mine Masters Theses Student Theses and Dissertations Summer 2016 Characterization of insertion sequence IS605 in halanaerobium hydrogeniformans Michael C. Sadler Follow this and additional works at: https://scholarsmine.mst.edu/masters_theses Part of the Genetics Commons, and the Microbiology Commons Department: Recommended Citation Sadler, Michael C., "Characterization of insertion sequence IS605 in halanaerobium hydrogeniformans" (2016). Masters Theses. 7568. https://scholarsmine.mst.edu/masters_theses/7568 This thesis is brought to you by Scholars' Mine, a service of the Missouri S&T Library and Learning Resources. This work is protected by U. S. Copyright Law. Unauthorized use including reproduction for redistribution requires the permission of the copyright holder. For more information, please contact [email protected]. CHARACTERIZATION OF INSERTION SEQUENCE IS605 IN HALANAEROBIUM HYDROGENIFORMANS by MICHAEL SADLER A THESIS Presented to the Faculty of the Graduate School of the MISSOURI UNIVERSITY OF SCIENCE AND TECHNOLOGY In Partial Fulfilment of the Requirements for the Degree MASTERS OF SCIENCE IN APPLIED AND ENVIRONMENTAL BIOLOGY 2016 Approved by Ronald Frank, Advisor Melanie Mormile Dave Westenberg iii ABSTRACT Insertion sequences are the smallest prokaryotic transposable elements. These genes play a significant evolutionary role by promoting genome plasticity. Insertion sequences are highly diverse elements that have largely been uncharacterized. As such, the ability to accurately identify, annotate, and infer genomic impact of insertion sequences is lacking. The study of new insertion sequences contributes knowledge to their annotation and evolution. Halanaerobium hydrogeniformans is a unique organism with an abnormally high number of insertion sequences. A family of insertion sequences, IS200/605, showed several interesting distinctions from other elements in the genome, including severe open reading frame degradation, and was characterized in detail. This research uses bioinformatics tools to present an in depth characterization of a single insertion sequence family in H. hydrogeniformans. From these results insertion sequence activity can be inferred, including transposition capability, element interaction, and insertion sequence evolution. iv ACKNOWLEDGMENTS I would like to extend my greatest appreciation to Dr. Ronald Frank for his mentorship. He accepted me as his student when I had no background or experience in the tools or methodologies used in his lab. He spent a substantial amount of his time in guiding me through the research, the graduate program, and providing career advice. I could not have asked for a better advisor. I would like to thank Dr. Melanie Mormile for serving on my committee and allowing me to spend time in her lab. I would also like to thank Dr. David Westenberg for serving on my committee and providing essential early feedback on research. v TABLE OF CONTENTS Page ABSTRACT ........................................................................................................... iii ACKNOWLEDGMENTS ....................................................................................... iv LIST OF ILLUSTRATIONS ................................................................................... ix LIST OF TABLES ................................................................................................. xi SECTION 1. INTRODUCTION ........................................................................................... 1 1.1. TRANSPOSABLE ELEMENTS ............................................................... 1 1.2. INSERTION SEQUENCES ..................................................................... 2 1.2.1. Organization. .................................................................................... 2 1.2.2. Terminal Inverted Repeats. .............................................................. 3 1.2.3. Target Site Duplications. .................................................................. 3 1.2.4. Target Sequence. ............................................................................. 4 1.3. CATALYTIC CHEMISTRIES ................................................................... 4 1.3.1. DDE. ................................................................................................. 5 1.3.2. Serine. .............................................................................................. 5 1.3.3. Y1. .................................................................................................... 6 1.3.4. Y2. .................................................................................................... 7 1.4. IS200/605 ................................................................................................ 7 1.4.1. TnpA. ................................................................................................ 9 1.4.2. TnpB. .............................................................................................. 10 1.5. MINIATURE INVERTED REPEAT TRANSPOSABLE ELEMENTS ..... 12 vi 1.6. INSERTION SEQUENCE ANNOTATION ............................................. 12 1.7. GENOMIC IMPACT OF TRANSPOSABLE ELEMENTS ...................... 14 1.7.1. Genomic Streamlining. ................................................................... 14 1.7.2. Insertional Mutation. ....................................................................... 15 1.7.3. Gene Expression. ........................................................................... 15 1.7.4. Genomic Rearrangement. .............................................................. 15 1.8. INVASION – EXPANSION – EXTINCTION CYCLES ........................... 16 1.9. HALANAEROBIUM HYDROGENIFORMANS ...................................... 17 1.10. DATABASES AND BIOINFORMATIC TOOLS ................................... 18 1.10.1. NCBI. ............................................................................................ 18 1.10.2. EBI. ............................................................................................... 18 1.10.3. PFAM. ........................................................................................... 19 1.10.4. Phylogeny.fr. ................................................................................. 19 1.10.5. ISfinder. ........................................................................................ 19 1.10.6. ISsaga. ......................................................................................... 19 1.10.7. ExPASy. ....................................................................................... 20 1.10.8. Sequence Alignment. ................................................................... 20 1.10.9. Mfolds. .......................................................................................... 20 1.10.10. Argo. ........................................................................................... 21 1.11. SUMMARY .......................................................................................... 21 2. MATERIALS AND METHODS ..................................................................... 22 2.1. INSERTION SEQUENCE IDENTIFICATION ........................................ 22 2.1.1. Element Ends. ................................................................................ 23 vii 2.1.2. MITES. ............................................................................................ 23 2.2. GENOME BROWSER ........................................................................... 23 2.3. BLAST ................................................................................................... 24 2.4. ALIGNMENTS ....................................................................................... 24 2.5. OPEN READING FRAME DISRUPTION .............................................. 26 2.6. PHYLOGENETIC ANALYSIS ............................................................... 27 2.7. SECONDARY STRUCTURE IDENTIFICATION ................................... 28 3. RESULTS .................................................................................................... 29 3.1. INSERTION SEQUENCE IDENTIFICATION ........................................ 29 3.2. TnpA ...................................................................................................... 30 3.2.1. IS200 tnpA. ..................................................................................... 32 3.2.2. IS605 tnpA. ..................................................................................... 33 3.3. IS605 tnpB ............................................................................................ 34 3.4. IS605 tnpA/tnpB INTER-ORF SPACE .................................................. 37 3.5. ORF tnpB INSERTS .............................................................................. 38 3.6. ORF tnpB PHYLOGENY ....................................................................... 39 3.7. ELEMENT ENDS .................................................................................. 40 3.8. HAIRPIN STRUCTURES ...................................................................... 41 3.8.1. Left End Structure. .......................................................................... 41 3.8.2. Right End Structures. ..................................................................... 42 3.8.3. ORF tnpB Insert Structure. ............................................................. 47 3.9. MINIATURE INVERTED REPEAT TRANSPOSABLE ELEMENTS ..... 47 4. DISCUSSION..............................................................................................
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