Identification of transcription factor genes in plants [Elektronische Ressource] / von Diego Mauricio Riaño-Pachón

Riaño-Pachón, Diego Mauricio

Sujets

• Biologie

Informations

• Publié par: universitat_potsdam
• Publié le: 01 janvier 2008
• Nombre de lectures: 22
• Langue: English
• Poids de l'ouvrage: 6 Mo

Extrait

Institut für Biochemie und Biologie
Arbeitsgruppe Prof. Dr. Bernd Müller-Röber
Identification of transcription factor
genes in plants
Dissertation
zur Erlangung des akademischen Grades
"doctor rerum naturalium"
(Dr. rer. nat.)
in der Wissenschaftdisziplin "Molekularbiologie"
eingereicht an der
Mathematisch-Naturwissenschaftlichen Falkultät
der Universität Potsdam
von
Diego Mauricio Riaño-Pachón
aus Bogotá, Kolumbien
Potsdam-Golm Summer 2008Gutachter: Prof. Dr. Bernd Müller-Röber Prof. Dr. Erich Grotewold
Gutachter: P.D. Dr. Stefan Rensing
thTag der mündlichen Prüfung: November 28 , 2008I love fools’ experiments. I am always making them.
— Charles Darwin
i













































Online published at the
Institutional Repository of the Potsdam University:
http://opus.kobv.de/ubp/volltexte/2008/2700/
urn:nbn:de:kobv:517-opus-27009
[http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-27009] Erklärung
I hereby declare that this Ph.D. thesis is the result of my own work carried out between the
winter semester of 2005 and May 2008 in the group of Prof. Dr. Bernd Mueller-Roeber
at the University of Potsdam in Golm, Germany. It has not been submitted for any degree
or Ph.D. at any other university.
Potsdam, 14.08.2008
Diego Mauricio Riaño Pachón
iiiAcknowledgements
I have managed to spend a bit more than four years working towards a PhD. In that time
I have had the opportunity to interact with many people at the University of Potsdam and
the Max Planck Institute of Molecular Plant Physiology. One of the rewards of finally
finishing it is to take the opportunity to thank them.
First and foremost, to my thesis advisor Prof. Bernd Mueller-Roeber, for giving me
the opportunity to develop my ideas in his group, for his continuous guidance, support
and interest in my varied endeavours. To Judith Lucia Gomez Porras, for letting me know
about the opportunities in Golm and offering her hospitality at my arrival and always
ever since. To Ingo Dreyer, for offering his help and interest in my research, and all the
small annoying ‘favours’ dealing with living in Deutschland. To Slobodan Ruzicic for
fruitful discussions regarding the classification of transcription factors and the aesthetic
appearance of our TF web sites. To Luiz Gustavo Guedes Correa for all the discussions we
had about almost everything, his unconditional help and his friendship. To Marco Ende
and Aixa Baumgärtel for their help regarding computer matters. To Babette Regierer and
all MÜRÖS, for fruitful discussions and interesting joint projects.
The analysis that I present here would have been impossible without public access to
data from different genome sequencing projects, and the effort of the several annotation
communities. I am deeply grateful.
I want to acknowledge the funding agencies and projects through which I was funded
over this years. The Center for Advanced Protein Technologies and the International
PhD programme “Integrative Plant Science” at the University of Potsdam. The European
Union (NICIP; EU CT-2002-00245) for supporting my participation in ISMB 2006 in
Fortaleza, Brazil.
To the Latinamerican connection in Germany: to Flavia for being so loving; to Fer-
nando Arana, María Inés, los Ticos: Rafa y Raúl. To CALEIDOSCOPIO LATINO ‘en
pleno’, for great frienships and good moments.
To my parents Jorge and María, my brother David, my sister Adriana, my niece
Daniela and my nephew Camilo, and to Catalina, for all their love and giving me the
strength to achieve my goals.
vContents
Erklärung iii
Acknowledgements v
Contents vii
List of Figures xi
List of Tables xiii
List of Abbreviations xv
Summary xvii
1 General introduction 1
1.1 Eukaryotic transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Transcriptional regulation . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Transcription factor DNA-binding domains . . . . . . . . . . . . . . . . 4
1.4 Evolution of regulatory programs . . . . . . . . . . . . . . . . . . . . . . 6
1.5 Overview of plant evolutionary relationships . . . . . . . . . . . . . . . . 8
1.5.1 Species studied . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.6 Aims and structure of the thesis . . . . . . . . . . . . . . . . . . . . . . . 11
1.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2 Identification and classification of transcription factors 17
2.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3 Construction and content . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.1 Source datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
viiContents
2.3.2 Identification and classification of transcription factors . . . . . . 19
2.3.3 New HMMs for TFs families . . . . . . . . . . . . . . . . . . . . 22
2.3.4 Database scheme . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.3.5 Web databases . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.3.6 Quality control . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.4 Utility and discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3 Transcription factors inChlamydomonasreinhardtii 29
3.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.3 Materials and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.3.1 Identification of transcription factors . . . . . . . . . . . . . . . . 31
3.3.2 Phylogenetic analysis . . . . . . . . . . . . . . . . . . . . . . . . 31
3.3.3 Identification of orthologues among green plants . . . . . . . . . 31
3.4 Results and discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.4.1 Transcription factors in eukaryotes . . . . . . . . . . . . . . . . . 31
3.4.2 Chlamydomonas transcription factors . . . . . . . . . . . . . . . 33
3.4.3 Transcription factors involved in hormone signaling . . . . . . . . 34
3.4.4 TF families absent from algae . . . . . . . . . . . . . . . . . . . 34
3.4.5 Orthologues across green plants . . . . . . . . . . . . . . . . . . 34
3.4.6 Evolution of photosynthetic networks . . . . . . . . . . . . . . . 36
3.5 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4 bZIP transcription factors in plants 39
4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.2 Results and discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
4.2.1 Groups of homologues of angiosperm bZIP genes . . . . . . . . . 41
4.2.2 Possible groups of orthologues (PoGOs) in angiosperms . . . . . 42
4.2.3 Tracing the origin and diversification of bZIP genes in green plants 45
4.2.4 Ancestral relationships in groups B and C . . . . . . . . . . . . . 48
4.2.5 bZIP evolution in plants . . . . . . . . . . . . . . . . . . . . . . 48
4.3 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.4 Materials and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.4.1 Datasets of bZIP genes . . . . . . . . . . . . . . . . . . . . . . . 49
4.4.2 Phylogenetic analyses . . . . . . . . . . . . . . . . . . . . . . . 50
viii