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Pseudomonas Aeruginosa Ampr Transcriptional Regulatory Network Deepak Balasubramanian Florida International University, [email protected]

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Pseudomonas Aeruginosa Ampr Transcriptional Regulatory Network Deepak Balasubramanian Florida International University, Deeps66@Gmail.Com Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 3-8-2013 Pseudomonas Aeruginosa AmpR Transcriptional Regulatory Network Deepak Balasubramanian Florida International University, [email protected] DOI: 10.25148/etd.FI13042330 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Bacteria Commons, Bacterial Infections and Mycoses Commons, Bacteriology Commons, Bioinformatics Commons, Genomics Commons, Molecular Genetics Commons, Organismal Biological Physiology Commons, Other Genetics and Genomics Commons, Pathogenic Microbiology Commons, and the Respiratory Tract Diseases Commons Recommended Citation Balasubramanian, Deepak, "Pseudomonas Aeruginosa AmpR Transcriptional Regulatory Network" (2013). FIU Electronic Theses and Dissertations. 863. https://digitalcommons.fiu.edu/etd/863 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida PSEUDOMONAS AERUGINOSA AMPR TRANSCRIPTIONAL REGULATORY NETWORK A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOLOGY by Deepak Balasubramanian 2013 To: Dean Kenneth G. Furton College of Arts and Sciences This dissertation, written by Deepak Balasubramanian, and entitled Pseudomonas aeruginosa AmpR transcriptional regulatory network, having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. _______________________________________________ Stephen Lory _______________________________________________ John Makemson _______________________________________________ Giri Narasimhan _______________________________________________ Fernando Noriega _______________________________________________ Kalai Mathee, Major Professor Date of Defense: March 08, 2013 The dissertation of Deepak Balasubramanian is approved. _______________________________________________ Dean Kenneth G. Furton College of Arts and Sciences _______________________________________________ Dean Lakshmi Reddi University Graduate School Florida International University, 2013 ii DEDICATION To appa, amma and anna for the unconditional love and support iii ACKNOWLEDGMENTS This dissertation is the result of the support of many people. It is difficult to overstate my gratitude to my mentor, Dr. Kalai Mathee. With her enthusiasm, her inspiration, she helped to make science even more fun than it already is. I’m forever in debt! Throughout my stay here, she provided encouragement, good teaching, great company, and lots of ideas. I would have been lost without her. Thanks Kalai! I would like to thank my committee members, Dr. Stephen Lory, Dr. John Makemson, Dr. Giri Narasimhan and Dr. Fernando Noriega for their helpful ideas, guidance, and help with my project. Special thanks to Dr. Lory for allowing me to work in his lab. I learned a lot from Steve and his group of talented postdocs. And I had a lot of fun in Boston! I’m very thankful to Dr. Narasimhan for all the bioinformatics help. I relied heavily on computational analyses for my project, which could not have been possible without the help of Giri and his talented students, Camilo Valdes and Melita Jaric. One of my first classes at FIU was with Dr. Noriega on genomics and proteomics way back when. I thoroughly enjoyed Fernando’s class but little did I know then that my project would be so genomically-skewed (I just made that word up!). Dr. Makemson, thank you for making me study biochemistry for my quals! I’m not a big fan of biochemistry and would’ve never read Lehninger but your quals questions were so much fun to answer (I know I sound like a nerd but whatever!). I am indebted to the Mathee Crew, past and present, for their support. Working in the lab was fun, thanks to them. There are so many people in the Mathee Lab that made my journey through here smooth. The lab ‘adopted’ me as it’s own. I have many fond iv memories with people in the lab, some with the lab members and some with visiting researchers. I especially want to thank Oli, Lisa, Cami, Marios, Ciraj, Senthil, Nat, Mario and the many, many others (that’s what happens when you stay in one place for six years!) for making my stay such a pleasant experience. I had a wonderful time outside the lab, thanks to Wim, Hideaki, Saeed, Senthil, (our camping, canoeing and kayaking trips were awesome!) Ziad, Gorakh, and Jitesh. Ever since she joined the lab, Hansi has been a major positive influence on my research and me. She has been a wonderful friend and my sounding board for science and non-science issues. Her unbiased and outright honest opinions have guided me through some rough patches in research. Thanks re! She and Bhupesh took me into their family and their hearts, and have made me feel at home away from home. We’ve had so much fun on our trips and it is going to continue! Money helps when you are doing science! The Biological Sciences Department and the Herbert Werthiem College of Medicine have supported me through these years and I am grateful for that. I’m also thankful to the Cystic Fibrosis Foundation for the two Student Traineeship awards and to the National Institutes of Health-MRBS RISE program for a Summer Student award. My special thanks to FIU University Graduate School for supporting me at the final critical writing phase with the Dissertation Year Fellowship. Lastly, and most importantly, I would not be where I am today if it were not for the constant support and encouragement of my parents, Balasubramanian and Vasantha, and my brother Satish. My parents put our education and well being above all else through some tough times and made us into what we are. My family supported my decisions and loved me unconditionally. I’m eternally grateful for everything. v ABSTRACT OF THE DISSERTATION PSEUDOMONAS AERUGINOSA AMPR TRANSCRIPTIONAL REGULATORY NETWORK by Deepak Balasubramanian Florida International University, 2013 Miami, Florida Professor Kalai Mathee, Major Professor In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)- regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated using DNA microarrays and RNA-Seq of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion mutant, PAO∆ampR were analyzed. Transcriptome analysis demonstrates that the AmpR regulon is much more extensive than previously thought influencing the differential expression of over 500 genes. In addition to regulating resistance to β-lactam antibiotics via AmpC, AmpR also regulates non-β-lactam antibiotic resistance by modulating the MexEF-OprN efflux pump. Virulence mechanisms including biofilm formation, QS-regulated acute virulence, and diverse physiological processes such as oxidative stress response, heat- vi shock response and iron uptake are AmpR-regulated. Real-time PCR and phenotypic assays confirmed the transcriptome data. Further, Caenorhabditis elegans model demonstrates that a functional AmpR is required for full pathogenicity of P. aeruginosa. AmpR, a member of the core genome, also regulates genes in the regions of genome plasticity that are acquired by horizontal gene transfer. The extensive AmpR regulon included other transcriptional regulators and sigma factors, accounting for the extensive AmpR regulon. Gene expression studies demonstrate AmpR-dependent expression of the QS master regulator LasR that controls expression of many virulence factors. Using a chromosomally tagged AmpR, ChIP-Seq studies show direct AmpR binding to the lasR promoter. The data demonstrates that AmpR functions as a global regulator in P. aeruginosa and is a positive regulator of acute virulence while negatively regulating chronic infection phenotypes. In summary, my dissertation sheds light on the complex regulatory circuit in P. aeruginosa to provide a better understanding of the bacterial response to antibiotics and how the organism coordinately regulates a myriad of virulence factors. vii TABLE OF CONTENTS CHAPTER PAGE CHAPTER 1 ....................................................................................................................... 1 Introduction ..................................................................................................................... 1 The model bacterium, Pseudomonas aeruginosa ....................................................... 2 Antibiotics, antibiotic resistance and AmpR .............................................................. 5 Antibiotic resistance .................................................................................................... 7 Antibiotic resistance in P. aeruginosa ........................................................................ 9 Intrinsic resistance .................................................................................................
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