Phycobiliprotein lyases [Elektronische Ressource] : structure of reconstitution products and mechanistic studies / submitted by Jun-Ming Tu

Jun-Ming Tu

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2008
• Nombre de lectures: 17
• Langue: English
• Poids de l'ouvrage: 2 Mo

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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 α
ApcD α-subunit
ApcB β
ApcF 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 β
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
-1k rate constant [s ]
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 β
PecE and PecF phycoviolobilin- α84-cystein-lyase-isomerase subunits
PFB phytochromobilin
PK protein kinases
PSI photosystem I
PSII photosystemII
PVB phycoviolobilin (4,5-Dihydro-mesobiliverdin)
rpm revolutions per minute
SDS sodium dodecyl sulfate
TBE tris-borate-EDTAbuffer
TE Tris-EDTA
TEMED N, N, N’, N’-tetramethylethylene diamine
TFA trifluoroacetic acid
TLC thin layer chromatography
t retention time r
Tris tris-(hydroxymethyl)-aminomethane
TritonX-100 alkylphenyl polyethylenglycol
WT wild type
v/v volume per volume
Q ratio of maximum absorption in the visible (Vis) and the Vis/UV
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.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 Chemicals17
2.1.4 Technical devices ...................................................................................................20
2.2 Methods.............................................................................................................................22
2.2.1 General molecular biological methods...................................................................22
2.2.2 Protein isolation ..................................................................................................