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Synechocystis Pcc6803 And STUDIES ON THE PHOTOSYNTHETIC MICROORGANISM SYNECHOCYSTIS PCC6803 AND HOW IT RESPONDS TO THE EFFECTS OF SALT STRESS BY BRADLEY LYNN POSTIER Bachelor of Science Oklahoma State University Stillwater, OK 1996 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY December, 2003 STUDIES ON THE PHOTOSYNTHETIC MICROORGANISM SYNECHOCYSTIS PCC6803 AND HOW IT RESPONDS TO THE EFFECTS OF SALT STRESS Thesis approved: Dean of the Graduate College 11 ACKNOWLEDGMENTS I would first like to thank my wife Sheridan for all of her support and motivation. Without her, I may have never even attempted graduate school. Since I met her in 1994, she has been everything I could ask for. I look forward to spending the rest of my life with you and our as of yet unborn son. I would also like to acknowledge all the work and effort put forth by my advisor - Dr. Burnap. Rob made every possible effort to support my research financially. He guided my intellectual'maturation throughout my experience here. I don't think anyone else could have shown the patience necessary to help me achieve my goals. I am truly appreciative for what he has helped me achieve and hope that some day I can do the same for other students working under me. To my parents, I would like to say thank you for all the great support guidance and memories. Y cm have been very supportive through all my years in school, allowing me to make all of the important decisions myself, good or bad. My brothers have provided many opportunities to escape from work when necessary and when not. I thank you for that. It helped keep me in excellent mental condition. I have had many coworkers and made many friends while in graduate school, too many to name.· I would like to thank all of you for your companionship; it has made my experience so much more enjoyable. I will remember the countless lunches at the Hideaway. Finally, I must thank my committee members: Dr. Miller, Dr. Prade, Dr. Melcher, and Dr. Henley. I would like to compliment (did I get it right this time?) you for all the work you have put into correcting my many mistakes. 111 TABLE OF CONTENTS Chapter Page I. Functional and Comparative Genomics of Cyanobacteria ............................ 1 Cyanobacterial Systems ...........................................................2 Genomics ...............................................................................7 Functional Genomics in a Cyanobacterium ...................................22 Outlook and Prospective ....................................................... .43 Bibliography ..................................................................... 4 7 II. The Construction and Use of Bacterial DNA Microarrays Based on an Optimized Two-stage PCR Strategy ................................................... 52 Abstract. .......................................................................... 53 Introduction ...................................................................... 55 Materials and Methods ..........................................................57 Results and Discussion .......................................................... 65 Bibliography ...................................................................... 77 III. Optimization of Fusion PCR for In Vitro Construction of Gene Knockout Fragments .............................................................. 78 Introduction ............................................................................. 79 Methods, Results and Discussion ................................................. 79 Bibliography ......................................................................90 IV. Global gene expression profiling and physiological analysis of salt stress and acclimation in Synechocystis sp PCC6803 ............................... 91 Abstract. ...........................................................................92 Introduction .......................................................................92 Materials and Methods ......................................................... 100 Results ............................................................................ 110 Discussion ....................................................................... 146 Bibliography ..................................................................... 151 iv TABLE OF CONTENTS CONTINUED. Summary............................................................................. 154 Bibliography............................................................... 159 Appendix ............................................................................ 161 Vitae .................................................................................247 .v LIST OF TABLES 1.1 Statistical summary and comparison of cyanobacterial genome sequencing efforts .......................................................................... 12 . 1.2 Abbreviated list of web based genomic information services ........................... 19 1.3 Representative genes induced after one and five hours salt shock from 2mM to 684 mM NaCl in Synechocystis PCC6803 as determined through analysis with sub-genomic DNAmicroarrays .......................... ; ......................... 33 1.4 Synechocystis genes regulated by salt stress after 5 hours of treatement revealed through microarray differential expression profiling.................... 34-35 1.5 Hypothetical genes differentially expressed before and after salt shock. ............. .37 2.1 Construction of DNA microarray ............................................. ;., ............66 2.2 Synthesis and hybridization of fluorescently labeled cDNA derived from sample RNA ............................................................................ ~ .... 72 3 .1 Primer sequences for PCR mutagenesis .................................................... 81 4.1 Genes induced after acclimation to high salt conditions; ............................... 113 4.2 Genes repressed after acclimation to high salt conditions ............................... 120 A-1 Gene expression profiles for Synechocytis PCC6803 after acclimating to high salt conditions ....................................................................... 161 A-2 Gene expression profiles in response to 650 mM NaCl shock treatment By Synechocystis PCC6803 ................................................................................. 202 VI LIST OF FIGURES 1.1 Venn diagram presentation of genome homology clustering with various genome sequencing projects .................................................... 15 1.2 Functional genomics strategy for Synechocystis PCC6803 .............................. 24 1.3 PCR amplification strategy used to develop full genome arrays ........................ .38 2.1 Overall strategy for the production of bacterial DNA microarrays ..................... 59 2.2 Design and use of chimeric bipartite oligonucleotides for PCR amplification of each open reading frame of the genome from Synechocystis PCC6803 ......... 67 2.3 Thermal cycling conditions and resultant products from first and second round amplifications ....................................................................... 69 2.4 Scatter-plot of differential hybridization of fluorescently labeled cDNA from a 3-hour salt shock treated culture versus an untreated sample ................ 74 3 .1 Comparison of fusion PCR strategies for in vitro construction of gene knockout fragments developed in this study and elsewhere ......................... 82 3 .2 Optimization of fusion PCR steps for in vitro construction of gene knockout fragments .................................................................................... 84 3.3 Colony PCRs of Synechocystis with Taq or Herculase DNA polymerases ............ 88 4.1 The effect of an upshift in salt concentration (18 mM--+650 mM NaCl) On the autotrophic growth of Wild-type Synechocystis PCC6803 ............... 111 4.2 Hierarchical clustering of gene expression profiles ............................... 129-132 4.3 Polarographically measured rates of photosynthesis and respiration following salt shock of Synechocystis PCC6803 cells ........................................... 136 4.3 PAM Fluorometer measurements of PSII activity ....................................... 138 4.5 Salt shock reduces quantum efficiency of PSII ........................................... 139 4.6 Impact of salt shock on P700 content and P700+ re-reduction kinetics.; ............. 142 vu LIST OF FIGURES CONTINUED 4.7 Salt shock induced superoxide production ............................................... 143 4.8 Superoxide production during salt shock requires PSII activity during auto trophic growth ....................................................................... 145 Vlll NOMENCLATURE DNA deoxyribonucleic acid RNA ribonucleic acid DCMU 3-(3,4-dichlorophenyl)-1, 1-dimethylurea DCBQ 2,5-dichloro-1,4-benzo-quinone · PSI photosystem I PSII photosystem II DEPC diethyl pyrocarbonate DTT dithiothreitol ATP a:denosine triphosphate GTP guanosine triphosphate TTP thymidine triphosphate CTP cytidine triphosphate aa-dUTP amino-allyl deoxyuridine triphosphate IX CHAPTERI LITERATURE· REVIEW Bradley L. Postier and Robert L. Burnap Functional Geno mies of Plants and Fungi 2 CYANOBACTERIAL SYSTEMS Some of earth's oldest fossils derive from cyanobacteria-dominated mats that filled the shallow Archaean seas over 3.5 billion years ago (52). A significant factor in the ecological success
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