American University in Cairo AUC Knowledge Fountain Theses and Dissertations 6-1-2019 Predictions and Computational Analysis of Novel Chromosomal Type II Toxin Antitoxin Systems in the Human Oral Microbiome Ashraf Abd-el-Raouf Bazan Follow this and additional works at: https://fount.aucegypt.edu/etds Recommended Citation APA Citation Bazan, A. (2019).Predictions and Computational Analysis of Novel Chromosomal Type II Toxin Antitoxin Systems in the Human Oral Microbiome [Master’s thesis, the American University in Cairo]. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/770 MLA Citation Bazan, Ashraf Abd-el-Raouf. Predictions and Computational Analysis of Novel Chromosomal Type II Toxin Antitoxin Systems in the Human Oral Microbiome. 2019. American University in Cairo, Master's thesis. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/770 This Thesis is brought to you for free and open access by AUC Knowledge Fountain. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of AUC Knowledge Fountain. For more information, please contact [email protected]. School of Science and Engineering PREDICTION AND COMPUTATIONAL ANALYSIS OF NOVEL CHROMOSOMAL TYPE II TOXIN ANTITOXIN SYSTEMS IN THE HUMAN ORAL MICROBIOME A Thesis Submitted to The Biotechnology Master’s Program In partial fulfillment of the requirements for the degree of Master of Science in Biotechnology By Ashraf A. Bazan BSc in Pharmaceutical Sciences and Drug Design Faculty of Pharmacy, Ain Shams University Under the supervision of Dr. Ahmed Abdellatif, MD, PhD Assistant Professor Biology Department American University in Cairo Dr. Tamer Salem, PhD Dr. Heba Abostate, MD, PhD Professor of Molecular and Cell Biology Assistant Professor of Microbiology Biomedical Science Program, Microbiology and Immunology Department University of Science and Technology at Faculty of Pharmacy Zewail City Egyptian Russian University May/2019 THESIS DEFENSE Student Full Name: ___ Ashraf A. Bazan Student ID: _________________________________________ Thesis Title: _________________________________________ This thesis has been successfully defended. Thesis Supervisor: Name: _________________________________________ Title: _________________________________________ Department: _________________________________________ Institution: _________________________________________ Signature: _______________________Date: _____________ First reader: Name: _________________________________________ Title: _________________________________________ Department: _________________________________________ Institution: _________________________________________ Signature: ________________________Date: ____________ Second reader: Name: _________________________________________ Title: _________________________________________ Department: _________________________________________ Institution: _________________________________________ Signature: _________________________Date: ___________ Department Chair: Name: _________________________________________ Title: _________________________________________ Signature: _________________________Date: ___________ ii DEDICATION I dedicate this work to Allah, my parents Mervat Bazan and Abdel-Raouf Bazan and to patients whom this project could affect their lives by any means. iii ACKNOWLEDGEMENTS Praise be to Allah I would like to acknowledge the helpful guidance and scientific assistance of my supervisors throughout the project. They have been more than a family believing in me and supporting me at the scientific and professional level as well as at the personal level. I recognize the financial support of the American University in Cairo, in terms of the conference travel support, the research grant and the fellowships, which endorsed me for conducting such a project. I acknowledge the grant from the International Center for Genetic Engineering and Biotechnology (ICGEB). supporting this project. I appreciate the assistance of Zymo Research company that conducted much of the practical part of this project. I would like to thank my mentors: Dr. Hamza El-Dorri, Dr. Asma Amleh, Dr. Ahmed Moustafa, Dr. Walid Fouad, Dr. Hassan El-Fawal, Dr. Hassan Azazy and Dr. Anwar Abdel- Nasser. I would like to thank Mr. Osama Said Ali and Mr. Ahmed El-Hossainy. I am principally grateful to Dr. Adham Ramadan. I would like to recognize Mrs. Aya Morsi, Mrs. Manar Zaki and Mr. John Sedky for their supportive provision during the study period at AUC. I would like to express my gratitude to Dr. Asma’s research group for their support and help throughout my journey. Special thanks to Amal Aboul-Fotouh, Mohamed Youssef and Diana George for their help in several occasions. My sincerest gratitude for Laila Ziko and Sara Sonbol who were role models in showing me how to truly work in dedication and good manners. The GSA community at AUC had a great impact on me during this journey, particularly, Chimson Chukwuemeka. I am considerably grateful for the Microbiology and Immunology department at the Egyptian Russian University. My utmost appreciation goes to Dr. Fatma El-Zahraa, Dr. Ahmed Farouk and Dr. Tharwat El-Khamiessy along with the rest of the department for their plentiful support. The support I had from Dr. Mohamed Ehab Aboul-Fotouh, the dean of the pharmacy school, is unparalleled. Finally, I am deeply thankful for Mahmoud A. Shatta, Mohamed Al- Shehaby, Ahmed Safwat, Hussein Ghoneim and Sh. Saeed Abd-El-Mohsen. iv ABSTRACT The American University in Cairo Prediction and Computational Analysis of Novel Chromosomal Type II Toxin Antitoxin Systems in the Human Oral Microbiome By: Ashraf A. Bazan Under supervision of: Dr. Ahmed Abdellatif, Dr. Tamer Salem and Dr. Heba Abostate The importance of the human oral microbiome is progressively receiving considerable attention in recent research, serving as a model niche for studying microevolution. The impact of horizontal gene transfer by mobile genetic elements in such environment is the driving force for the mosaic nature of the oral microbiome. However, there is a missing link between the molecular systems interactions responsible for the plasticity of the genomes and the adaptations of the oral microbiome to physiological and pathological changes. The mobile chromosomal type II Toxin Antitoxin Systems (TASs). are known for their effective role in dynamic environment adaptation and stress response. In this study, we predicted and analyzed the genetic diversity and evolution of type II TAS in the oral microbiome of an Egyptian, presumably healthy, individual. 16S rRNA sequencing (submitted to GenBank). showed taxonomic analysis and microbial diversity and species abundance in three samples of supragingival plaque, subgingival plaque and buccal mucosa. Two hundred and seventy-eight type II TAS were identified from sequenced chromosomal genomes of the oral microbiome by means of exhaustive sequence and 3D structure homology, Hidden Markov Modelling and manual domain analysis. Gene family assignment were proposed since majority of the genes were previously annotated as hypothetical proteins. TAS network of the oral microbiome showed highly interconnected centralities which entails the extensive cross talk and intra-regulatory nature. Molecular ecology analysis of the type II TAS using diversity indexes confirms both diversity and relative abundance of these systems in the oral microbiome. Molecular evolutionary phylogenetic maximum likelihood analysis of the type II TAS, using modified Whelan And Goldman (WAG) as best fit evolution model, was performed for the predicted toxin antitoxin systems. Further analysis revealed evidence for the persistence of the toxin antitoxin systems throughout the oral microbiome. Molecular allometric analysis confirms uneven persistent distribution of the type II TAS. This comprehensive study of new chromosomal type II toxin antitoxin systems found in the oral microbiome provides insights on plasticity of the human oral microbiome and its adaptation to change in the host environment. v TABLE OF CONTENTS 1. LITERATURE REVIEW ........................................................................................................ 1 1.1. Human Oral Microbiome ................................................................................................. 1 1.1.1. Introduction on Human Oral Microbiome ................................................................ 1 1.1.2. Ecology of the Human Oral Microbiome ................................................................. 2 1.1.3. Association of Human Oral Microbiome and Clinical Diseases .............................. 4 1.1.4. Mobile Genetic Elements as Key Members of the Human Oral Microbiome .......... 5 1.2. Toxin Antitoxin Systems .................................................................................................. 8 1.2.1. Introduction on Toxin Antitoxin Systems................................................................. 8 1.2.2. Classification of the Toxin Antitoxin Systems. ........................................................ 9 1.2.3. Roles of the Chromosomal Toxin Antitoxin Systems ............................................ 19 1.2.4. Importance of the Toxin Antitoxin Systems ........................................................... 22 1.3. Objectives ....................................................................................................................... 27 2. METHODOLOGY ...............................................................................................................