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Scholarworks@UNO University of New Orleans ScholarWorks@UNO University of New Orleans Theses and Dissertations Dissertations and Theses Summer 8-4-2011 Identification and characterization of enzymes involved in the biosynthesis of different phycobiliproteins in cyanobacteria Avijit Biswas University of New Orleans, [email protected] Follow this and additional works at: https://scholarworks.uno.edu/td Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Biswas, Avijit, "Identification and characterization of enzymes involved in the biosynthesis of different phycobiliproteins in cyanobacteria" (2011). University of New Orleans Theses and Dissertations. 446. https://scholarworks.uno.edu/td/446 This Dissertation-Restricted is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Dissertation-Restricted 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. This Dissertation-Restricted has been accepted for inclusion in University of New Orleans Theses and Dissertations by an authorized administrator of ScholarWorks@UNO. For more information, please contact [email protected]. Identification and characterization of enzymes involved in biosynthesis of different phycobiliproteins in cyanobacteria A Thesis Submitted to the Graduate Faculty of the University of New Orleans in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Chemistry (Biochemistry) By Avijit Biswas B.S. Pharmacy, Utkal University, India, 2001 M.S. Biology, Rutgers, The State University of New Jersey, 2006 ACKNOWLEDGMENT First, I want to thank to my PhD advisor Dr. Wendy Schluchter, she is an excellent mentor with great personality, professionalism, and knowledge. It’s always been a great pleasure working with her and in her lab. She makes me feel the importance of research, gave me every possible chance to learn, make myself better to excel in my career. Her door was always open to discuss about, she knows when to get tough on me and when to hand over helpful advices. Not only she is my advisor also a good friend, she gave chances to entertain myself when I get overwhelmed with lab work. Thank you very much Dr. Schluchter for accepting me to you lab, giving me every opportunity to work and helping me every way in building my career. It always being a great pleasure working in your lab, I feel like my second home. Last but not the least Thanks for arranging a place to stay during hurricane and for the Hornet’s tickets!!!!! Yeah….. Second, I want to thank my mom and dad, for their support and encouragement. Although they have no idea about my research work, still they gave constant motivation in my path of success. Dad, thank you for all you did for me and you are the driving force that made me come to this level of career. Mom, I can’t express in words for your help you did to me for my entire life that make me a perfect person to face the real world. I love you mom and dad. Third, I like to thank my uncle (Subhasis) and aunt (Esther). Thank you very much, for all you guys did for me, helping in every way starting for giving scientific suggestions, helping me with understanding what is the important of research and how to handle the situations. Esther thanks a lot for providing me with opportunity to volunteer in your lab, which helped a lot in getting hands on Molecular Biology/ Biochemistry. ii Now I should spend some time thanking the people who have worked with and helped me in the lab in putting this thesis work together. First, I should thank Yasmin, she had been working with me for 3 yrs and provided a lots of help starting from doing my experiments doing some parts of my thesis. She never told no whenever I asked her to do something for me. I really appreciate her help. Yasmin I wish you good luck with you graduate school at Baylor University. Above all she is a great friend, thanks for checking my mails and baking cakes in my Birthday. Second, I should thank Tierna, she is a great co-worker and friend. She always provided me company, helped with my lab works and provided me moral supports. Thank you very much, Tierna for getting lunch for me all the times. I wish you good luck in your admission to Medical School. Third, I should thank Christina and Corry for helping me out with my clones and other experiments. Thank you, Christina and Corry. Last but not the least I should thank all the undergraduate and high school students who had worked in my project during my years in Dr. Schluchter’s lab. I should thank to my committee members Dr. Zengchang Liu, Dr. Steve Rick and Dr. Edward Stevens, especially Dr. Liu since I got lots of helpful comments about my research. Thanks a lot for providing us with different reagents and chemical, which helps us a lot. Thanks to Dr. Rick and Dr. Stevens for their helpful inputs in putting my thesis together. Now I should thank to all our collaborators who provided us with different plasmids construct and research ideas which helped me in working with new projects and getting papers published in peer reviewed journals. First, Thank you very much to Dr. Bryant, you gave us a lot of help with your research ideas putting my paper together. Thanks to Rick, you helped me a lots with all the cloned you made for us along with research helps. Thanks, to Dr. Frankenberg for providing us with the pebS/ ho1 construct it helped us a lot. Thanks to Dr. Kehoe’s lab iii (Aminesh and Adrian) for making the clones and mutants, which provided me a lot of help in putting this thesis together. I should also express my thanks to one of the most important person in life in my wife Sudeshna Das (Tina), she has always been with me, in my good and bad days. She always listened to my complains, achievements and successes I had in my research. “I love you, Tina” Lastly I should thank to numerous other people; undergraduate, high school students and high school teacher who are involved in this project. iv Table of Contents List of figures .................................................................................................................... iv List of Tables .................................................................................................................... vi Table for abbreviations .................................................................................................. vii Abstract ........................................................................................................................... viii 1.0 Introduction ..................................................................................................................1 1.1 Cyanobacteria: Background and History ...........................................................1 1.2 Phycobilisome: Structure and Function .............................................................2 1.3 Structure elucidation of phycobiliproteins .........................................................7 1.4 Application of fluorescent proteins ..................................................................11 1.4.1 Application of Cyanobacterial phycobiliproteins as fluorescent tags.....11 1.4.2 Application of Cyanobacterial phycobiliproteins as commercial Commodities ...........................................................................................15 1.5 Application of green fluorescent protein .........................................................17 1.6 Bilin: Types and Biosynthetic pathway ...........................................................21 1.7 Bilin addition to phycobiliproteins ..................................................................28 1.7.1 E/F type lyase ..........................................................................................28 1.7.2 SU type lyase ..........................................................................................30 1.7.3 T type lyase .............................................................................................31 1.7.4 Autoctalytic lyase....................................................................................32 1.8 Other posttranslational modifications to phycobiliproteins .............................32 1.9 Chromatic acclimation .....................................................................................33 1.10 Purpose of work .............................................................................................39 2.0 Materials and Methods .............................................................................................41 2.1 Construction of expression vectors ..................................................................41 2.1.1 cpcS-I and cpcU expression construct ....................................................44 2.1.2 cpcT expression construct .......................................................................44 2.1.3 pcyA/ho1 expression constructs ..............................................................44 2.1.4 cpcBA and cpcB expression constructs ...................................................45 2.1.5 apcE expression construct.......................................................................46 2.1.6 cpcEF expression construct ....................................................................46 2.1.7 cpeA expression
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