Phycobiliprotein Lyases: Structure of Reconstitution Products and Mechanistic Studies Jun-Ming Tu 2008 MUNICH Phycobiliprotein Lyases: Structure of Reconstitution Products and Mechanistic Studies Jun-Ming Tu Dissertation zur Erlangung des Doktorgrades der Fakultät für Biologie der Ludwig-Maximilians-Universität München Submitted by Jun-Ming Tu 2008 MUNICH 1. Referee: Prof. Dr. Hugo Scheer 2. Referee: Prof. Dr. Lutz Eichacker Date of oral defense: October 29, 2008 Publications: Tu,J.M., Kupka,M., Böhm,S., Plöscher,M., Eichacker,L., Zhao,K.H., and Scheer, H. (2008) Intermediate binding of phycocyanobilin to the lyase, CpeS1, and transfer to apoprotein. Photosynth.Res. 95:163-168. Zhao, K. H., Su, P., Li, J., Tu, J.M., Zhou, M., Bubenzer, C. and Scheer, H. (2006) Chromophore attachment to phycobiliprotein beta-subunits: phycocyanobilin: cysteine-beta84 phycobiliprotein lyase activity of CpeS-like protein from Anabaena sp. PCC7120. J. Biol. Chem. 281: 8573-8581. Zhao,K.H., Su,P., Tu,J.M., Wang,X., Liu,H., Plöscher,M., Eichacker,L., Yang,B., Zhou,M. and Scheer, H. (2007) Phycobilin:cysteine-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins. Proc Natl Acad Sci USA, 104:14300-14305. Zhao,K.H., Zhang,J., Tu,J.M., Böhm,S., Plöscher,M., Eichacker,L., Bubenzer,C., Scheer, H., Wang,X., and Zhou,M. (2007) Lyase activities of CpcS and CpcT-like proteins from Nostoc PCC7120, and sequential reconstitution of binding sites of phycoerythrocyanin and phycocyanin β-subunits. J. Biol. Chem. 282:34093-34103 Acknowledgements This work was performed at the laboratory of Prof. Dr. H. Scheer in the Department I of the Botanical Institute of the Ludwig-Maximilians-University in Munich, Germany and at the laboratory of Prof. Dr.K-H. Zhao in College of Environmental Science and Engineering, Huazhong University of Science and Technology in Wuhan, PR China I am very much grateful to my supervisor Prof. Dr. H. Scheer for theoretical and practical supervision during the work. I would like to thank him for inviting me into his group, for giving me an opportunity to conduct my PhD research in his laboratory and for excellent working conditions. I would like to acknowledge him for his help, continuous support and valuable discussions throughout my PhD study. I am thankful for the advises that he gave me, for careful reading and correction of this thesis and for his helpful comments. I also appreciate a lot his optimism and never-ending enthusiasm. I am thankful to my supervisor in PR China Prof. Dr. K-H.Zhao. Thanks for his support, care, for teaching me at the beginning of my studies in Huazhong University of Science and Technology, for introducing me into molecular biology and providing all of plasmids for this work. My sincere thanks go to Dr. Stephan Böhm for his excellent technical help, support, patience, care and for interesting talks about life. I am grateful to him for his bright personality and for helping me to better understand people of his country My special thanks to Dr. Zhen-Hua Cui for her help, for introducing me into the lab life, for scientific and personal support since my very first days in the lab, for nice discussions and for good time in and outside the lab. Many thanks to Prof. Dr. Lutz Eichacker and Dr. Matthias Plöscher (LMU, Biology Department I, Munich) for the ESI-MS measurements, and to Dr. Rainer Haessner (Technical University Munich, Germany) for NMR measurements. I would like to thank all graduate students and post-docs who used to work or are currently working in this group for their friendly and helpful collaboration, for creating a pleasant working atmosphere and for a nice time. My dear parents, sister and my wife H-X Tong; many, many thanks for your constant and genuine love, care, encouragement, understanding, inspiration and support at each step of my life. Thank you very much! Last but not least, I gratefully acknowledge the Chinese Scholarship Council for a doctoral scholarship. Abbreviations A absorption a.u. arbitrary unit APC allophycocyanin ApcA apoprotein of allophycocyanin α-subunit ApcA2 apoprotein of allophycocyanin α-subunit ApcD apoprotein of allophycocyanin α-subunit ApcB apoprotein of allophycocyanin β-subunit ApcF apoprotein of allophycocyanin β-subunit APS ammonium persulfate bp base pair BSA bovine serum albumin BV IXa biliverdin IXa CD circular dichroism Cpc A apoprotein of C-Phycocyanin α-subunit CpcB apoprotein of C-Phycocyanin β-subunit CpcE, CpcF subunits of Phycocyanobilin-α-Phycocyanin-lyase DNA deoxyribonucleic acid DMSO dimethyl sulfoxide E. coli Escherichia coli EDTA ethylenediaminetetraacetic acid ESI-MS electronspray ٛ ionization mass spectrometry NR ferredoxin NADP+ oxidoreductase hr hour(s) IPTG isopropyl β-D-thiogalactoside k rate constant [s-1] kDa kiloDalton LB Luria-Bertani medium ME 2-mercaptoethanol MHz Megahertz min minute MS mass spectrometry MW molecular weight m/z mass per charge nm nanometer NMR nuclear magnetic resonance NOESY nuclear Overhauser and Exchange Spectroscopy ORF open reading frame PAGE polyacrylamide gel electrophoresis PBS phycobilisome PC phycocyanin PCB phycocyanobilin PCR polymerase chain reaction PE phycoerythrin PEB phycoerythrobilin PEC phycoerythrocyanin PecA apoprotein of phycoerythrocyanin α-subunit PecB apoprotein of phycoerythrocyanin β-subunit PecE and PecF phycoviolobilin-α84-cystein-lyase-isomerase subunits PFB phytochromobilin PK protein kinases PSI photosystem I PSII photosystem II PVB phycoviolobilin (4,5-Dihydro-mesobiliverdin) rpm revolutions per minute SDS sodium dodecyl sulfate TBE tris-borate-EDTA buffer TE Tris-EDTA TEMED N, N, N’, N’-tetramethylethylene diamine TFA trifluoroacetic acid TLC thin layer chromatography tr retention time Tris tris-(hydroxymethyl)-aminomethane TritonX-100 alkylphenyl polyethylenglycol WT wild type v/v volume per volume QVis/UV ratio of maximum absorption in the visible (Vis) and the ultraviolet (UV) spectral region w/v weight per volume Table of Contents TABLE OF CONTENTS 1: Introduction...................................................................................................................................1 1.1 Structures of phycobilisomes ..............................................................................................1 1.2 Biosynthesis of phycobilins ................................................................................................6 1.3 Chromophore attachment....................................................................................................7 1.3.1 Spontaneous attachment...........................................................................................8 1.3.2. Autocatalytic attachment.........................................................................................9 1.3.3. E/F-type lyases........................................................................................................9 1.3.4. Cyanobacterial S/U-type lyases ............................................................................10 1.3.5. Cyanobacterial T-Type lyases................................................................................11 1.4 Lyase mechanisms.............................................................................................................11 1.5 Applications ......................................................................................................................13 1.6 Thesis plan ........................................................................................................................14 2: Materials and Methods................................................................................................................16 2.1 Materials ...........................................................................................................................16 2.1.1 Organisms ..............................................................................................................16 2.1.2 Vectors....................................................................................................................16 2.1.3 Plasmids .................................................................................................................16 2.1.3 Chemicals...............................................................................................................17 2.1.4 Technical devices ...................................................................................................20 2.2 Methods.............................................................................................................................22 2.2.1 General molecular biological methods...................................................................22 2.2.2 Protein isolation .....................................................................................................22 2.2.3 Pigment isolation....................................................................................................25 2.2.4 Phycobiliprotein reconstitution/preparation...........................................................27 2.2.5 Lyase CpcS (Alr0617) reaction assay ....................................................................29 2.2.6 Chromophore adduct assay ....................................................................................29 2.2.7 Spectroscopy ..........................................................................................................30 2.2.8 Websites .................................................................................................................31