Funktionelle Promotoranalyse des Glycin-Decarboxylase-PA-Gens (GLDPA) von Flaveria trinervia (C4) [Elektronische Ressource] / Christian Wiludda. Gutachter: Rüdiger Simon. Betreuer: Peter Westhoff

Christian Wiludda

Sujets

• Biologie

Informations

• Publié par: heinrich-heine-universitat_dusseldorf
• Publié le: 01 janvier 2012
• Nombre de lectures: 69
• Langue: English
• Poids de l'ouvrage: 34 Mo

Extrait

Functional analysis of the promoter of the
glycine decarboxylase PA gene (GLDPA)
of Flaveria trinervia (C ) 4



Inaugural-Dissertation

zur Erlangung des Doktorgrades
der Mathematisch-Naturwissenschaftlichen Fakultät
der Heinrich-Heine-Universität Düsseldorf

vorgelegt von

Christian Wiludda
aus Düsseldorf




Düsseldorf, November 2011




aus dem Institut für Entwicklungs- und Molekularbiologie der Pflanzen
der Heinrich-Heine-Universität Düsseldorf
















Gedruckt mit der Genehmigung der
Mathematisch-Naturwissenschaftlichen Fakultät der
Heinrich-Heine-Universität Düsseldorf


Referent: Prof. Dr. P. Westhoff
Koreferent: Prof. Dr. R. Simon

Tag der mündlichen Prüfung: 19.01.2012





Ich habe die vorliegende Dissertation eigenständig und ohne unerlaubte Hilfe angefertigt. Die
Dissertation habe ich in der vorgelegten oder in ähnlicher Form noch bei keiner anderen
Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche unternommen.

Düsseldorf, 17.11.2011


(Christian Wiludda)






















Contents


I. Introduction ...............................................................................................1
1. The biochemistry of C photosynthesis ...................................................................1 4
1.1 The ribulose 1,5-bisphosphate carboxylase/oxygenase – a bifunctional enzyme ...........1
1.2 The CO -concentrating mechanism of C plants suppresses photorespiration ...............2 2 4
1.3 Specific adaptations and characteristics of C plants ......................................................4 4
1.4 The phenomenon of single-cell C photosynthesis .........................................................5 4
1.5 C plants are highly productive in warm habitats ...........................................................5 4
2. Evolution of the C syndrome ..................................................................................6 4
2.1 The polyphyletic origin of C photosynthesis .................................................................6 4
2.2 C photosynthesis as an evolutionary adaptation to counteract photorespiration ...........7 4
2.3 All enzymes involved in C photosynthesis are already present in C plants .................7 4 3
2.4 The stepwise transition from C to C photosynthesis during C evolution ....................8 3 4 4
2.5 The genus Flaveria as model system to study C evolution .........................................12 4
3. The transcriptional control region of eukaryotic protein-coding genes ............12
3.1 Structure of the eukaryotic RNA polymerase II-dependent promoter ..........................12
3.2 Cis-regulatory elements of the core promoter ...............................................................13
3.3 Enhancers, silencers and insulators influence gene expression ....................................15
3.4 The mesophyll expression module 1 for C -specific gene expression ..........................16 4
3.5 The phenomenon of multiple transcription start sites in plants ....................................17
4. The glycine decarboxylase complex ......................................................................18
4.1 Composition and reaction mechanism of the glycine decarboxylase complex ............18
4.2 Function of the glycine decarboxylase complex in plants ............................................19
4.3 The GLDPA gene encodes the P-protein of GDC in the C plant Flaveria trinervia ...20 4
II. Scientific aims ..........................................................................................21
III. Theses .......................................................................................................22
IV.A Summary ..................................................................................................23
IV.B Zusammenfassung ...................................................................................24
V. Literature .................................................................................................26 VI. Manuscripts .............................................................................................33
1. Sascha Engelmann, Christian Wiludda, Janet Burscheidt, Udo Gowik, Ute Schlue,
Maria Koczor, Monika Streubel, Roberto Cossu, Hermann Bauwe, Peter Westhoff
(2008). The gene for the P-subunit of glycine decarboxylase from the C species 4
Flaveria trinervia: Analysis of transcriptional control in transgenic Flaveria
bidentis (C ) and Arabidopsis (C ). Plant Physiology 146: 1773–1785 ...............34 4 3
2. Christian Wiludda, Stefanie Schulze, Udo Gowik, Sascha Engelmann, Maria
Koczor, Monika Streubel, Hermann Bauwe, Peter Westhoff (2011). Regulation of
the photorespiratory GLDPA gene in C Flaveria – an intricate interplay of 4
transcriptional and post-transcriptional processes. Submitted for publication to
The Plant Cell. .........................................................................................................49
VII. Addendum ..............................................................................................100
1. The influence of the 50-bp flanking sequences of P on gene expression ......100 R2
2. Fine mapping of the transcriptional enhancing regions 1 and 3 of the GLDPA
promoter ................................................................................................................103
3. Region 2 of the GLDPA promoter can enhance transcription of P ..............106 R7
4. The position of region 3 influences the output of P .......................................108 R2
5. P -derived RNAs are destabilized in the presence of P ...............................110 R2 R7
6. Material and Methods ..........................................................................................113
7. Literature ..............................................................................................................117












Abbreviations

A Adenine
A. thaliana Arabidopsis thaliana
bp Base pairs
BREd Downstream transcription factor IIB recognition element
BREu Upstream transcription factor IIB recognition element
°C Degree Celsius
C , C , C One-, three-, four-carbon molecule 1 3 4
13C Carbon-13, stable isotope of carbon
C Cytosine
CA Carbonic anhydrase
CO Carbon dioxide 2
DNA Deoxyribonucleic acid
DPE Downstream promoter element
F. Flaveria
Ft Flaveria trinervia
G Guanine
GDC Glycine decarboxylase complex
GLDPA Glycine decarboxylase PA gene of Flaveria trinervia
GUS -glucuronidase
h Hour(s)
- HCO Bicarbonate (hydrogen carbonate) 3
Inr Initiator
kb Kilobases
N Molecular nitrogen 2
NAD Nicotinamide adenine dinucleotide
NADP Nicotinamide adenine dinucleotide phosphate
NH Ammonia 3
MDH Malate dehydrogenase
ME Malic enzyme
MEM1 Mesophyll expression module 1
mRNA Messenger ribonucleic acid
NMD Nonsense-mediated mRNA decay
nt Nucleotides
O Molecular oxygen 2
OAA Oxaloacetate
ORF Open reading frame
PEP Phosphoenolpyruvate
PEPC Phosphoenolpyruvate carboxylase
PEPCK Phosphoenolpyruvate carboxykinase
3PGA 3-Phosphoglycerate
2PG 2-Phosphoglycolate
PPDK Pyruvate, orthophosphate dikinase
P Distal promoter (defined by region 2 of the GLDPA promoter) R2
P Proximal promoter (defined by region 7 of the GLDPA promoter) R7
R Purine (adenine or guanine)
5' RACE Rapid amplification of 5' complementary DNA ends
RNA Ribonucleic acid
Rubisco Ribulose 1,5-bisphosphate carboxylase/oxygenase
RuBP Ribulose 1,5-bisphosphate
SHMT Hydroxymethyltransferase
T Thymine
TBP TATA box-binding protein
T-DNA Transfer DNA
TFII Transcription factor for RNA polymerase II
TF Transcription factor
TSS Transcription start site
uORF Upstream open reading frame
5' UTR 5' Untranslated region
Y Pyrimidine (cytosine or thymine) Introduction 1

I. Introduction

1. The biochemistry of C photosynthesis 4
1.1 The ribulose 1,5-bisphosphate carboxylase/oxygenase – a bifunctional enzyme
Terrestrial plants can convert atmospheric carbon dioxide (CO ) into organic compounds with 2
the energy of the sun by three different pathways. The most common one is represented by C 3
photosynthesis from which C photosynthesis and the crassulacean acid metabolism (CAM) 4
are derived (West-Eberhard et al., 2011; Wang et al., 2011).
The C pathway represents the single largest flux of organic carbon in the majority of 3
photosynthetic organisms leading to the assimilation of about 100 billion tons of carbon
annually, which corresponds to 15% of the atmospheric carbon (Raines, 2011). About 85% of
all plant species assimilate CO by C photosynthesis, including agronomically relevant crops