Functional analysis of selected DOF transcription factors in the model plant Arabidopsis thaliana [Elektronische Ressource] / von Aleksandra Skirycz

Aleksandra Skirycz

Sujets

• Biologie

Informations

• Publié par: universitat_potsdam
• Publié le: 01 janvier 2007
• Nombre de lectures: 18
• Langue: English
• Poids de l'ouvrage: 6 Mo

Extrait

Max-Planck-Institute für Molekulare Pflanzenphysiologie
Arbeitsgruppe Prof. Dr. Bernd Müller - Röber



Functional analysis of selected DOF transcription factors in the
model plant Arabidopsis thaliana.

Dissertation
zur Erlangung des akademischen Grades
"doctor rerum naturalium"
(Dr. rer. nat.)
in der Wissenschaftsdisziplin "Molekulare Pflanzenphysiologie"


eingereicht an der
Mathematisch-Naturwissenschaftlichen Fakultät
der Universität Potsdam


von Aleksandra Skirycz


Potsdam, den 08.10.2007


i












































Elektronisch veröffentlicht auf dem
Publikationsserver der Universität Potsdam:
http://opus.kobv.de/ubp/volltexte/2008/1698/
urn:nbn:de:kobv:517-opus-16987
[http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-16987] Erklärung
Erklärung

Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig und unter Verwendung keiner
anderen als den von mir angegebenen Quellen und Hilfsmitteln verfasst habe.
Ferner erkläre ich, dass ich bisher weder an der Universität Potsdam noch anderweitig
versucht habe, eine Dissertation einzureichen oder mich einer Doktorprüfung zu unterziehen.

Aleksandra Skirycz Potsdam, 08.10.2007

ii Acknowledgements
Acknowledgements
I would firstly like to thank Prof. Bernd Mueller-Roeber for his excellent supervision. He
allowed me to develop and pursue my own scientific interests but at the same time wisely
guided me through out my PhD project. I would also like to thank Dr. Isabell Witt for
stimulating my interest in the DOF transcription factors, her supervision during the early parts
of my research and support through out my PhD. I would like to acknowledge members of
my PhD Committee: Prof. Ralph Bock, Dr. Renate Schmidt and Dr. Wolf-Ruediger Scheible,
for the excellent discussions and their intellectual input. I am also grateful to the members of
the Institute, particularly my group, for their help, advice and friendship. Special thanks must
go to Camila Caldana, Salma Balazadeh, Rajsree Mungur and Sylwia Bem for useful
discussions, technical suggestions and brilliant company, and to Szymon Jozefczuk and
Joanna Czeszejko for their superb technical assistance. I am also grateful for the excellent
technical support provided by the Institute, in particular to Dr. Eugenia Maximova for help
with microscopy, Karin Koehl and her MPI Green Team for plant care, and Josef Bergstein
for the expert photography. I am grateful to our collaborators; their expertise hugely benefited
the project. I would especially like to thank Dr. Joachim Kopka and Alexander Erban for
metabolite profiling, Dr. Michael Reichelt for glucosinolates measurements, Prof. Maciej
Stobiecki for flavonoid analysis, Wolfgang Busch for sharing secrets of chromatin
immunoprecipitation and Amandine Radziejwoski for the help with ploidy analysis. I
acknowledge the financial support of the Schering Foundation and of the University of
Potsdam. Finally I would like to thank my parents for their excellent support and
encouragement throughout my studies. Special thanks go to Matthew Hannah for his love,
friendship and support throughout this PhD.

iii Table of contents
Table of contents

Title …………………………………………………………………………………………………… i
Erklärung ……………………………………………………………………………………………. ii
Acknowledgements ……..……………………………..…………………………………………… iii
Table of contents …….……………………………………………………………………….......... iv
Abbreviations ………………………………………………………………………………………… vi
1 Summary ............................................................................................................................ 1
2 General introduction ......................... 2
2.1 Transcription factors ……….…………………………………………................................ 2
2.2 DOF transcription factors …..………………................................................................... 4
2.3 Methods for functional characterization of transcription factors …………….………...... 8
2.4 Aim of the thesis ............................................................................................................. 15
3 DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling
glucosinolate biosynthesis in Arabidopsis. ………………………………………………….. 16
3.1 Abstract ......................................................................................................................... 17
3.2 Introduction .................................... 17
3.3 Results .......................................................................................................................... 19
3.4 Discussion ..................................... 30
3.5 Material and methods ………………………………………………………………………... 34
3.6 Acknowledgements ....................................................................................................... 40
3.7 New data ……………………………………………………………………………………… 41
4 Transcription factor AtDOF4;2 affects phenylpropanoid metabolism in Arabidops is
thaliana. ................................................................................................................................. 44
4.1 Abstract ......................................... 45
4.2 Introduction .................................................................................................................... 45
4.3 Results .......................................... 47
4.4 Discussion ..................................................................................................................... 58
4.5 Material and methods ………………………………………………………………………... 62
66 4.6 Acknowledgements .......................................................................................................
68 5 DOF transcription factor OBP1 (AtDof3.4) is involved in cell cycle regulation. ……..
69 5.1 Abstract .........................................................................................................................
69 5.2 Introduction ....................................
72 5.3 Results ..........................................................................................................................
iv Table of contents
85 5.4 Discussion .....................................................................................................................
91 5.5 Material and methods ………………………………………………………………………...
95 5.6 Acknowledgements .......................................................................................................
96 6 General discussion and outlook ………………….....………………………………………..
96 6.1 Overview of the three DOF TFs ………………………………………..
97 6.2 OBP1, OBP2 and AtDOF4;2 within the context of the DOF TF family. …………………
103 6.3 Transcription factors ………………………………………………………………………….
106 7 References ………………….…………...………………….........
124 8 Supplementary materials …………………………………...…………………………............

vii Deutsche Zusammenfassung .................................................................................................
viii Curriculum vitae ......................................
x Publication list .....................................................................................................


v
Abbreviations
Abbreviations

ACT - arabidopsis co-expression tool
CDF1 – cycling DOF factor 1
CDK – cyclin dependent kinase
ChIP – chromatin immunoprecipitation
cry1 – cryptochrome 1
CYC - cyclin
DEX – dexamethasone
DOF – DNA binding with one zinc finger
EMSA – electrophoretic-mobility shift assay
ESR2 – enhanced shoot regeneration 2
GC-MS – gas chromatography coupled to mass spectrometry
GFP – green fluorescent protein
GR – glucocorticoid domain
GS - glucosinolates
GST6 – glutathione S-transferase 6
HPLC – high pressure liquid chromatography
IAA – indole-3-acetic acid
IAOx - indole-3-acetaldoxime
IGS – indole glucosinolates
IOE – inducible over-expression
KRP – Kip related protein
LC-MS – liquid chromatography coupled to mass spectrometry
MeJA - methyl jasmonate
NAA - 1-naphthaleneacetic acid
OBF4 – ocs element binding factor
OBP – OBF4 binding protein
OE – over-expression
PBF – prolamin-box binding factor
PCA - principle component analysis
phyB – phytochrome B
RAM – root apical meristem
SA - salicylic acid
SAGE - serial analysis of gene expression
SELEX - systematic evolution of ligands by exponential enrichment
SAM – shoot apical meristem
Q-PC