Functional analysis of Nt-Hypo1 and NtPLC3, two novel pollen-specific proteins from Nicotiana tabacum [Elektronische Ressource] / presented by Diana Helling

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Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg, Germany for the degree of Doctor of Natural Sciences presented by Diana Helling born in: Bielefeld, Germany thOral-examination: December 7 , 2005 Functional Analysis of Nt-Hypo1 and NtPLC3, Two Novel Pollen-Specific Proteins From Nicotiana tabacum Referees: Prof. Dr. Thomas Rausch Prof. Dr. David G. Robinson CONTENTS Contents.................................................................................................................................I Summary .......................................................................................................................... VII Zusammenfassung .............................................................................................................IX 1 Introduction ................................................................................................................. 1 1.1 Pollen tube growth: a model system for polarized plant cell growth .................... 1 1.1.1 Ion gradients and fluxes involved in polarized pollen tube growth .............. 3 1.1.1.1 Calcium...................................................................................................... 3 1.1.1.2 Protons..................................................

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Dissertation
submitted to the
Combined Faculties for the Natural Sciences and for Mathematics
of the Ruperto-Carola University of Heidelberg, Germany
for the degree of
Doctor of Natural Sciences


















presented by
Diana Helling
born in: Bielefeld, Germany
thOral-examination: December 7 , 2005






Functional Analysis of Nt-Hypo1 and NtPLC3,
Two Novel Pollen-Specific Proteins
From Nicotiana tabacum





















Referees: Prof. Dr. Thomas Rausch
Prof. Dr. David G. Robinson
CONTENTS
Contents.................................................................................................................................I
Summary .......................................................................................................................... VII
Zusammenfassung .............................................................................................................IX
1 Introduction ................................................................................................................. 1
1.1 Pollen tube growth: a model system for polarized plant cell growth .................... 1
1.1.1 Ion gradients and fluxes involved in polarized pollen tube growth .............. 3
1.1.1.1 Calcium...................................................................................................... 3
1.1.1.2 Protons....................................................................................................... 4
1.1.1.3 Potassium and chloride.............................................................................. 4
1.1.2 Cytoskeleton and polarized pollen tube growth ............................................ 4
1.1.2.1 Microfilaments........................................................................................... 4
1.1.2.2 Microtubules.............................................................................................. 5
1.2 The role of small GTPases in the control of pollen tube tip growth ..................... 6
1.2.1 The small GTPase superfamily Ras............................................................... 6
1.2.2 The regulation of Rho GTPases..................................................................... 7
1.2.2.1 Rho GTPases and their regulation in plants .............................................. 8
1.2.2.2 The role of Rho GTPases in the regulation of pollen tube growth............ 9
1.2.3 Guanine nucleotide exchange factors.......................................................... 11
1.2.3.1 ange factors in plants ....................................... 13
1.2.3.1.1 Plant-specific Rho GEFs do exist in plants 15
st1.2.4 Aims of the dissertation (1 project) ........................................................... 16
1.3 Phospholipid signaling in pollen tubes................................................................ 17
1.3.1 Phosphoinositides ........................................................................................ 17
1.3.2 Phosphatidylinositol 4,5-bisphosphate synthesis and functions.................. 18
1.3.3 Phospoinositide-specific phospholipases C................................................. 20
1.3.3.1 General overview..................................................................................... 20
1.3.3.2 Molecular domain structure..................................................................... 21
1.3.3.3 Membrane binding................................................................................... 22
1.3.3.4 Phosphoinositide hydrolysis.................................................................... 22
1.3.3.5 Cloning and cellular functions of PI-PLCs in plants............................... 23
1.3.3.5.1 PI-PLCs and their role in pollen tube growth.................................... 25
nd1.3.4 Aims of the dissertation (2 project) .......................................................... 27
2 Results......................................................................................................................... 28
ICONTENTS
2.1 Identification and functional characterization of a new interactor of pollen tube Nt-
Rac5 ......................................................................................................................... 28
2.1.1 Sequence analysis of Nt-Hypo1 and comparison with Arabidopsis thaliana
and Oryza sativa proteins of unknown function .......................................... 31
2.1.2 Analysis of Nt-Hypo1 expression by Northern blotting.............................. 32
2.1.3 Effects of transient expression of Nt-Hypo1 in pollen tubes of Nicotiana
tabacum........................................................................................................ 33
2.1.3.1 Transient over-expression of YFP and Nt-Hypo1................................... 33
2.1.3.2 Subcellular localization of Nt-Hypo1...................................................... 34
2.1.3.3 In vivo interaction of Nt-Hypo1 and Nt-Rac5 ......................................... 35
2.1.4 Over-expression of recombinant Nt-Hypo1 and purification from E. coli.. 36
2.1.4.1 In vitro interaction of Nt-Hypo1 with wild-type and mutant Nt-Rac5.... 36
2.1.4.2 Nt-Hypo1 – antibody production............................................................. 39
2.1.5 Nt-Hypo1 gene-knockout by antisense oligodeoxynucleotides, T-DNA
insertions and RNA interference.................................................................. 39
2.1.5.1 Antisense oligodeoxynucleotides ............................................................ 39
2.1.5.2 T-DNA insertion...................................................................................... 40
2.1.5.3 RNA interference..................................................................................... 40
2.1.6 Identification of novel Nt-Hypo1 interactors by yeast two-hybrid screening .
.....................................................................................................................43
2.2 Identification of novel phosphoinositide-specific phospholipase C isoforms from
Nicotiana tabacum................................................................................................... 47
2.2.1 Identification and sequence analysis of NtPLC3 and NtPLC4.................... 47
2.2.1.1 Phylogenetic analysis of NtPLC3 and NtPLC4....................................... 50
2.2.2 Analysis of NtPLC3 expression by Northern blotting................................. 51
2.2.3 Determination of the enzymatic activity of wild-type and mutant NtPLC3 52
2.2.3.1 Purification of recombinant NtPLC3 over-expressed in E. coli.............. 52
32.2.3.2 In vitro enzyme activity assay using [ H] phosphatidylinositol 4,5-
bisphosphate ............................................................................................ 54
2.2.4 Effects of transient expression of NtPLC3 in pollen tubes of Nicotiana
tabacum........................................................................................................ 56
2.2.4.1 Transient expression of wild-type and mutant NtPLC3 .......................... 56
2.2.4.2 Subcellular localization of NtPLC3......................................................... 58
2.2.4.3 lar localization of NtPLC3 domain-deletion mutants................ 59
IICONTENTS
2.2.4.4 Determination of the specific function of NtPLC3´s catalytic core in
membrane association.............................................................................. 61
2.2.5 Inhibition of PI-PLC activity by U-73122 treatment in vivo....................... 63
2.2.5.1 Complementation of PI-PLC inhibition by NtPLC3 over-expression in
vivo........................................................................................................... 64
2.2.6 Visualization of PI-4,5-P and its implication in pollen tube polarity......... 65 2
2.2.7 Visualization of diacylglycerol and its dependence on PI-PLC activity..... 67
3 Discussion ................................................................................................................... 72
3.1 Identification of a novel pollen-specific protein that interacts with Nt-Rac5 ..... 72
3.1.1 Transient over-expression of Nt-Hypo1 does not affect tobacco pollen tube
growth or morphology ................................................................................. 73
3.1.2 Nt-Hypo1 accumulates in the cytosol of growing pollen tubes................... 73
3.1.3 Interaction of Nt-Hypo1 with Nt-Rac5 cannot be visualized in vivo .......... 73
3.1.4 Nt-Hypo1 interacts with Nt-Rac5 in vitro ................................................... 74
3.1.5 Effects of Nt-Hypo1 gene-knockdown........................................................ 74
3.1.6 Nt-Hypo1 interacts with several pollen tube proteins ................................. 76
3.1.7 Note added in proof ..................................................................................... 79
3.2 Identification of two novel phosphoinositide-specific phospholipases C from
Nicotiana tabacum................................................................................................... 81
3.2.1 NtPLC3 and NtPLC4 are plant-specific PI-PLC isoforms from N. tabacum..
.....................................................................................................................82
3.2.2 NtPLC3 is a pollen-specific PI-PLC isoform..............................................
3.2.3 NtPLC3 hydrolyzes PI-4,5-P in vitro......................................................... 83 2
3.2.4 Transient expression of NtPLC3 in pollen tubes of Nicotiana tabacum..... 88
3.2.4.1 Transient over-expression of NtPLC3 wild-type and mutant versions does
not affect pollen tube growth................................................................... 88
3.2.4.2 NtPLC3 is a plasma membrane-associated enzyme................................ 90
3.2.4.3 EF hand-like domain and C2 domain are essential for membrane
association ............................................................................................... 90
3.2.4.4 The catalytic core is responsible for the absence of NtPLC3 from the
pollen tube tip .......................................................................................... 92
3.2.5 PI-PLCs maintain pollen tube polarity and restrict PI-4,5-P to the tip ...... 93 2
3.2.6 Diacylglycerol, a product of PI-PLC activity, accumulates at the plasma
membrane in the pollen tube tip................................................................... 97
IIICONTENTS
4 Materials and Methods ........................................................................................... 101
4.1 Chemicals, kits, enzymes................................................................................... 101
4.2 Apparatus........................................................................................................... 104
4.3 Bacteria Strains.................................................................................................. 105
4.4 Yeast Strain........................................................................................................ 105
4.5 Plant cultivation................................................................................................. 106
4.5.1 Nicotiana tabacum..................................................................................... 106
4.5.2 Arabidopsis thaliana.................................................................................. 106
4.5.2.1 Sterile cultures ....................................................................................... 106
4.5.2.2 Growth on Soil 106
4.6 Methods related to the treatment of Escherichia coli........................................ 106
4.6.1 E. coli cultivation 106
4.6.2 Chemical transformation of competent E. coli cells (after Inoue et al., 1990)
...................................................................................................................107
4.6.3 Transformation of E. coli via electroporation ...........................................
4.6.4 Colony lift for cDNA library screen.......................................................... 108
4.7 Methods related to the treatment of Agrobacterium tumefaciens...................... 109
4.7.1 Transformation of competent A. tumefaciens............................................ 109
4.8 ent of Saccharomyces cerevisiae........................ 109
4.8.1 S. cerevisiae cultivation............................................................................. 109
4.8.2 Transformation of S. cerevisiae HF7c cells............................................... 110
4.8.2.1 Library scale .......................................................................................... 110
4.8.2.2 Plasmid scale (re-transformation described for 24 probes)................... 111
4.9 DNA-related techniques .................................................................................... 112
4.9.1 Vectors....................................................................................................... 112
4.9.2 Plasmids..................................................................................................... 114
4.9.3 Oligonucleotides........................................................................................ 119
4.9.4 Isolation of plasmid DNA.......................................................................... 121
4.9.4.1 Plasmid DNA isolation from E. coli...................................................... 121
4.9.4.1.1 TELT mini-preparation.................................................................... 121
4.9.4.1.2 Mini- and maxi-preparations ........................................................... 121
4.9.4.2 S. cerevisiae HF7c glycerol stocks and plasmid preparation ................ 121
4.9.5 Isolation of genomic DNA from plants ..................................................... 122
4.9.6 Determination of DNA concentration ....................................................... 122
IVCONTENTS
4.9.7 DNA restriction endonuclease analysis..................................................... 122
4.9.8 DNA dephosphorylation............................................................................ 123
4.9.9 Ligation...................................................................................................... 123
4.9.10 cDNA synthesis ......................................................................................... 123
4.9.11 PCR techniques.......................................................................................... 123
4.9.11.1 Site-directed mutagenesis PCR ......................................................... 124
4.9.12 Purification of PCR products..................................................................... 124
4.9.13 Sequencing................................................................................................. 124
4.9.14 DNA agarose gel-electrophoresis.............................................................. 124
4.9.15 Purification of DNA fragments from agarose gels.................................... 125
4.10 RNA-related techniques .................................................................................... 125
4.10.1 Isolation of total RNA ............................................................................... 125
4.10.2 Determination of RNA concentration........................................................ 125
4.10.3 Northern Blot analysis 125
4.11 Methods related to protein treatment................................................................. 126
4.11.1 Discontinuous SDS polyacrylamide gel-electrophoresis (SDS PAGE;
Laemmli 1970)........................................................................................... 126
4.11.2 Western Blot analysis ................................................................................ 127
4.11.3 Protein over-expression and purification of GST fusion proteins from E. coli
...................................................................................................................128
4.11.4 Antibody preparation................................................................................. 129
4.11.5 In vitro interaction studies ......................................................................... 129
4.12 Transient ballistic transformation of Nicotiana tabacum pollen grains ............ 130
4.12.1 Particle preparation.................................................................................... 130
4.12.2 Pollen bombardment.................................................................................. 130
4.13 Stable transformation of Nicotiana tabacum plants .......................................... 131
4.13.1 Preparation of A. tumefaciens for transformation...................................... 131
4.13.2 Leaf-disc transformation............................................................................ 131
4.13.3 Shoot induction.......................................................................................... 131
4.13.4 From root induction to the flowering plant ............................................... 131
4.13.5 β-galactosidase assay................................................................................. 131
4.13.6 Tobacco transformation media .................................................................. 132
34.14 [ H] PI-4,5-P activity assay.............................................................................. 133 2
4.14.1 Preparation of lipid stock solutions ........................................................... 133
VCONTENTS
4.14.2 Enzyme activity assay ............................................................................... 133
4.15 Microscopy ........................................................................................................ 134
4.15.1 Light microscopy....................................................................................... 134
4.15.2 Epifluorescence microscopy...................................................................... 134
4.15.3 Confocal laser scanning microscopy ......................................................... 134
4.16 Bioinformatic methods ...................................................................................... 135
5 Abbreviations and list of figures and tables.......................................................... 136
6 References................................................................................................................. 142
7 Appendix................................................................................................................... 156
8 Curriculum vitae...................................................................................................... 170
9 List of publications .................................................................................................. 172
10 General Statement ................................................................................................... 173
Danksagung...................................................................................................................... 174


VI
SUMMARY
Pollen tubes are an excellent model system to investigate molecular mechanisms
controlling polar plant cell growth, a process that is essential for cellular and organ
morphogenesis throughout plant development. Pollen tubes are large cells that grow
rapidly in a strictly polar manner through female flower tissue and transport sperm cells
enclosed in their cytoplasm to egg cells. Thus, in only a short time period they grow up to
several centimeters to reach the embryo sac and to ensure fertilization. To guarantee the
highly complex process of polarized growth, several cellular signal transduction cascades
have to be initiated or enhanced in order to guide the pollen tube´s way through the style
and to deliver cell wall and plasma membrane material to the site of maximum growth, the
tip. Although to date only little is known about the mechanisms involved in tip growth, it is
known that plant homologues of the Rho family of small GTPases act in a common
pathway with PI-4,5-P and represent key regulators of polarized cell growth. 2

The present dissertation focused on two independent subjects. The first and minor project
represents the attempt to identify a plant-specific guanine nucleotide exchange factor
(GEF). When the work presented here was initiated, it was unclear how plant Rac/Rop
GTPases are activated and no Rho GEF had been identified in the plant kingdom. In a
yeast two-hybrid screen using a dominant negative mutant of the tobacco small GTPase
Nt-Rac5 as bait, we identified a novel protein of 76 amino acids. This hypothetical protein
interacted with Nt-Rac5 in yeast cells and in in vitro pull-down assays. It was shown to be
a pollen-specific, soluble protein that accumulated in the cytosol of growing pollen tubes.
Loss-of-function mutant plants have been generated by RNA interference and are still
under investigation. Further experiments are in progress to finally solve the question
whether Nt-Hypo1 is a plant-specific GEF or not.

The second and major project of this dissertation represents the identification and
functional characterization of a phosphoinositide-specific phospholipase C from tobacco.
2+PI-PLCs are Ca -dependent enzymes that hydrolyze PI-4,5-P and generate two second 2
messengers: Diacylglycerol remains associated with the plasma membrane, whereas
2+inositol 1,4,5-trisphosphate diffuses to the cytosol where it opens Ca channels and
2+thereby increases the intracellular Ca concentration. PI-4,5-P is known to play an 2
important role in the regulation of polarized pollen tube growth acting together with
Rac/Rop GTPases. In this dissertation we intended to solve the question if PI-PLCs
VIISUMMARY
represent a link between Rac/Rop GTPases, PI-4,5-P and the establishment of a tip-2
2+focused Ca gradient, which all have key functions in the regulation of pollen tube tip
growth.
We identified a novel pollen-specific PI-PLC isoform, NtPLC3, from tobacco by cDNA
library colony hybridization and determined its localization in living pollen tubes by YFP-
tagging. Furthermore, through the generation of single- or multiple-domain deletion
mutants, we showed that two domains, the EF hand and the C2 domain, are both essential
for membrane association of this enzyme. The generation of chimeric constructs,
combining plant and mammalian PI-PLC domains, showed that regions within the catalytic
core of NtPLC3 kept PI-PLCs from associating with the plasma membrane in the pollen
tube tip, whether the enzyme was active or not. We moreover demonstrated that NtPLC3
2+hydrolyzed PI-4,5-P in a Ca -dependent manner in vitro. This activity could be 2
significantly reduced by introducing single amino acid exchanges into the catalytic core of
the enzyme or by treatment with the aminosteroid U-73122. Using the PH domain of the
mammalian PI-PLC δ as a biosensor for PI-4,5-P , we visualized the complementary 1 2
distribution of this lipid, which is a PI-PLC substrate, and of NtPLC3 in vivo. Based on the
experiments and on the observation that PI-4,5-P spreads to a larger area of the plasma 2
membrane at the pollen tube tip after U-73122 treatment, we concluded that PI-PLCs
restrict PI-4,5-P to the pollen tube apex. 2
Our data demonstrate that PI-PLC activity is essential for pollen tube growth. We propose
that a key function of PI-PLCs in pollen tubes is to limit PI-4,5-P distribution to the tip 2
and thereby ensure spatially restricted binding of e.g. actin-binding proteins or proteins that
mediate vesicle fusion with the plasma membrane. Based on this mechanism, pollen tube
PI-PLC activity plays a key role in maintaining polarization of cell expansion.
VIII