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A Bioinformatic Analysis of the Mononegavirales

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A Bioinformatic Analysis of the Mononegavirales A BIOINFORMATIC ANALYSIS OF THE MONONEGAVIRALES TRANSCRIPTION/REPLICATION COMPLEX THROUGH THE DEVELOPMENT OF THE DISSIC PIPELINE by Sean Bruce Cleveland A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology MONTANA STATE UNIVERSITY Bozeman, Montana April, 2013 ©COPYRIGHT by Sean Bruce Cleveland 2013 All Rights Reserved ii APPROVAL of a dissertation submitted by Sean Bruce Cleveland This dissertation has been read by each member of the dissertation committee and has been found to be satisfactory regarding content, English usage, format, citation, bibliographic style, and consistency and is ready for submission to The Graduate School. Marcella A. McClure Approved for the Department of Microbiology Mark Jutila Approved for The Graduate School Dr. Ronald W. Larsen iii STATEMENT OF PERMISSION TO USE In presenting this dissertation in partial fulfillment of the requirements for a doctoral degree at Montana State University, I agree that the Library shall make it available to borrowers under rules of the Library. I further agree that copying of this dissertation is allowable only for scholarly purposes, consistent with “fair use” as prescribed in the U.S. Copyright Law. Requests for extensive copying or reproduction of this dissertation should be referred to ProQuest Information and Learning, 300 North Zeeb Road, Ann Arbor, Michigan 48106, to whom I have granted “the exclusive right to reproduce and distribute my dissertation in and from microform along with the non- exclusive right to reproduce and distribute my abstract in any format in whole or in part.” Sean Bruce Cleveland April 2013 iv DEDICATION I dedicate this dissertation to my fiancé Jessica and my mother Shelby for their undying support and understanding all these years. v ACKNOWLEDGEMENTS I would like to thank the faculty, staff and other students at Montana State University with whom I have worked for over a decade. Every one of them has had a hand in shaping me into the professional and scientist I am today and this would not have been possible without them. I would also like to personally thank Dr. Marcella A. McClure, who has mentored me in Bioinformatics, Virology and Evolution. Without her support, knowledge and gift for teaching I would not have been inspired to come so far. vi TABLE OF CONTENTS 1. INTRODUCTION .......................................................................................................... 1 Summary ........................................................................................................................ 2 Background and Significance ......................................................................................... 2 The Four Families ....................................................................................................... 3 Bornaviridae ......................................................................................................... 3 Paramyxoviridae ................................................................................................... 5 Filoviridae ............................................................................................................ 6 Rhabdoviridae ...................................................................................................... 6 Vesicular Stomatitis Virus (VSV) - The Prototype of the Order ............................... 7 Pathology and Epidemiology ..................................................................................... 7 Vesicular Stomatitis Virus Particle ............................................................................ 9 RdRp Complex .......................................................................................................... 9 Nucleoprotein (N) .................................................................................................... 10 Phosphoprotein (P)................................................................................................... 12 Large Subunit Polymerase (L) ................................................................................. 13 Methods......................................................................................................................... 14 Multiple Sequence Alignments ................................................................................ 14 Phylogenetic Trees ................................................................................................... 15 Disorder and Consensus Prediction ......................................................................... 16 IUPRED ................................................................................................................... 17 Regional Order Neural Network (RONN) ............................................................... 17 DisEMBL ................................................................................................................. 18 PONDR .................................................................................................................... 19 PONDR Fit .............................................................................................................. 19 CORNET.................................................................................................................. 19 ConSEQ ................................................................................................................... 20 Xdet .......................................................................................................................... 20 Co-evolution Analysis using Protein Sequences (CAPS) ........................................ 21 Identification of Co-evolution/Intra-Residue Contact Predictions (CICPs) ................................................................................................. 22 2. A BIOINFORMATICS APPROACH TO THE STRUCTURE, FUNCTION, AND EVOLUTION OF THE NUCLEOPROTEIN OF THE ORDER MONONEGAVIRALES ................................................................. 23 Contribution of Authors and Co-Authors ..................................................................... 23 Manuscript Information Page ....................................................................................... 24 Abstract ......................................................................................................................... 25 Introduction ................................................................................................................... 26 Results ........................................................................................................................... 30 vii TABLE OF CONTENTS - CONTINUED Phylogenetic Analysis ............................................................................................. 30 Disorder Prediction .................................................................................................. 33 Co-evolution and Intra-residue Contact .................................................................. 36 Structural Analysis .................................................................................................. 41 Discussion ..................................................................................................................... 43 Phylogenetic Reconstruction ................................................................................... 43 Disorder ................................................................................................................... 45 Co-evolution and Intra-residue Contact .................................................................. 48 Structural Analysis .................................................................................................. 51 Materials and Methods .................................................................................................. 54 Phylogenetic Reconstruction ................................................................................... 54 Disorder ................................................................................................................... 57 Correlated Mutations and Intra-Residue Contact Prediction .................................. 57 Structural Analysis .................................................................................................. 58 Hydrophobic Residues and MSA Conservation: .................................................... 58 Acknowledgements: ...................................................................................................... 59 References: .................................................................................................................... 60 3. DISORDER, INTRA-RESIDUE CONTACT AND COEVOLUTION PREDICTION OF THE LARGE SUBUNIT POLYMERASE AND PHOSPHOPROTEIN FOR THE ORDER MONONEGAVIRALES USING THE DISICC PIPELINE ................................................................................. 66 Contribution of Authors and Co-Authors ..................................................................... 66 Manuscript Information Page ....................................................................................... 67 Abstract ......................................................................................................................... 68 Introduction ................................................................................................................... 68 Results ..........................................................................................................................
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