UNLV Retrospective Theses & Dissertations 1-1-2000 Bioinformatic analysis: Retroposon sequences containing multiple putative endonucleases Seanna Kathleen Corro University of Nevada, Las Vegas Follow this and additional works at: https://digitalscholarship.unlv.edu/rtds Repository Citation Corro, Seanna Kathleen, "Bioinformatic analysis: Retroposon sequences containing multiple putative endonucleases" (2000). UNLV Retrospective Theses & Dissertations. 1182. http://dx.doi.org/10.25669/ecs3-l18o This Thesis is protected by copyright and/or related rights. It has been brought to you by Digital Scholarship@UNLV with permission from the rights-holder(s). You are free to use this Thesis in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/ or on the work itself. 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BIOINFORMATIC ANALYSIS; RETROPOSON SEQUENCES CONTAINING MULTIPLE PUTATIVE ENDONUCLEASES by Seanna Kathleen Corro Bachelor of Science University of Nevada, Las Vegas 1997 A thesis submitted in partial fulfillment of the requirements for the Master of Science Degree Department of Biological Sciences College of Science and Mattiematics Graduate College University of Nevada, Las Vegas August 2000 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. UMI Number 1401778 UMI UMI Microform 1401778 Copyright 2001 by Bell & Howell Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. Bell & Howell Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, Ml 48106-1346 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. Thesis Approval UNIV The Graduate College University of Nevada, Las Vegas June 19 .2 0 00 The Thesis prepared by ______Seanna Corro Entitled Bloinformatlc Analysis; Retroposon Sequences Containing Multiple Putative Endonucleases_______________________________________ is approved in partial fulfillment of the requirements for the degree of Master of Science ______ ____ _________________________ _ Examination Committee Chair Dean of the Graduate College Examination ( (Research/Thesis Advisor) Examination Committee hnember Graduate College Faculty Representative P R /1017.5 3 /1 .» ' u Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ABSTRACT Bioinformatic Analysis: Retroposon Sequences Containing Multiple Putative Endonucleases By Seanna Kathleen Corro Or. Steven deBelle, Examination Committee Chair Assistant Professor of Biology University of Nevada, Las Vegas Dr. Marcella McClure, Research and Thesis Advisor Associate Professor of Microbiology Montana State University. Bozeman Among the retroposons, the source of the endonuclease activity is known to be variable. We investigated whether any retroposon genomes encode potential multiple endonuclease functions. Amino add alignments were generated to reveal the presence of the characterized ordered-series-of-motifs (OSM) that define four different endonudease functions. These endonuclease functions indude a retroviral-like integrase (IN), an apurinic-apyrimidinic endonuclease (APE), the FDD endonudease recently identified in the R2BM retroposon and an HNH endonudease signature conserved by the group II intron sequences. The results indicate that the spliced leader assodated conserved sequences (SLACS) of T. brucei, cruzi-associated retrotransposon (CZAR) of Trypanosoma cruzi, two crithidia retrotransposable elements (CRE); CRE1 and CRE2 of Crithidia fasciculata and certain INGI retroposon sequences of Trypanosoma brucei contain multiple putative endonuclease functions. Ill Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. TABLE OF CONTENTS ABSTRACT.............................................................................................................................................. iii LIST OF FIGURES .................................................................................................................................. v ACKNOWLEDGEMENTS...................................................................................................................... vi CHAPTER 1 INTRODUCTION ......................................................................................................... 1 CHAPTER 2 RETROPOSON SEQUENCES CONTAINING MULTIPLE ENDONUCLEASE OSMS ...........................................................................................................................13 CHAPTER 3 THE ENDOGENOUS RETROVIRUSES ............................................................... 38 CHAPTER 4 CONCLUDING REMARKS ..................................................................................... 44 BIBLIOGRAPHY ................................................................................................................................... 48 APPENDIX I GLOSSARY OF TERMS AND ACRONYMS ............................................................ 58 VITA ........................................................................................................................................................ 63 IV Reproduced with permission of the copyright owner. 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LIST OF FIGURES Figure 1 Schematic of the Relative Positions of Endonuclease OSMs Previously Observed in Various Retroposons...........................................................................................................5 Figure 2 Schematic of the Relative Positions of Putative Endonuclease Functions Observed in Various Retroposons.......................................................................................................... 6 Figure 3 Integrase Alignment............................................................................................... in pocket Figure 4 HNH Alignment.................................................................................................................. 21 Figure 5 Apurinic Apyrimidinic Endonuclease Alignment Alignment .......................................... 23 Figure 6 Ribonuclease H Alignment .................................................................................... in pocket Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ACKNOWLEDGMENTS Dr. Marcella McClure for teaching me to trust my instincts. Dr. Steven deBelle for acting as advocate and Committee Chair, providing guidance and a supportive environment in which to work. I also extend my gratitude to Dr. Stephen Carper and Dr. George Plopper for enduring the tortures of my committee meetings. Dr. Angela Bakto, Dr. I. King Jordan, Julianna Hudak, John Kowalski, Micah Potter and Ben Sutter for invaluable discussion and assistance. I need to thank Burke Caley, Evalou Caley, Ron Caley, Milo Corro, Paul Corro, Jessica Emery, Pam Kowalski, Florence Oldfield, Ragnhikf Oterholm, George Thome and Lori Thome for encouragement and emotional support. Finally, I thank God that it is over. VI Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. CHAPTER 1 INTRODUCTION The development of highly efficient sequencing techniques has led to an explosion of data. In 1982, there were 602 sequences in GenBank. Today, there are more than six million sequences available in GenBank (http://Www.ncbi.nlm.nih.gov/Genbank/genbankstats.html). GenBank continues to grow at an incredible rate (httpV/www.ncbi.nlm.nih.gov/Web/Newsltr/