Quint Lab:Research

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(natural variation and quantitative genetics of hormone responses)
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===genetics of phytohormone responses===
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<h3><font style="color:#F8B603;">broad research scope</font></h3>
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our knowledge about the mechanisms of signal transduction pathways triggered by plant hormones has dramatically increased within the last decade or so. some pathways, such as auxin signaling seem to be resolved from perception to gene expression (Quint and Gray, [http://www.ncbi.nlm.nih.gov/pubmed/16877027?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Current Opinion in Plant Biology 2006]; Delker et al. [http://www.ncbi.nlm.nih.gov/pubmed/18299888?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Planta 2008]). however, the multitude of different responses triggered by the same molecule is as amazing as it is poorly understood. hormone-induced expression of sometimes hundreds of genes seems to be the key aspect of these responses. but which genes or clusters of genes are responsible for which responses? why do ecotypes from different geographical and climatic backgrounds respond differently to the hormone stimulus ... and what are the genetic factors underlying this variation?
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'''HOW''' do organisms adapt to the environment and how do they react to different biotic and abiotic stimuli? <br>
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the past has shown that understanding hormone action in plants bears great potential for agricultural and horticultural applications. by contributing to the current state of knowledge of hormone biology we hope to participate in this advancement of crop science.
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major players in the conversion of such stimuli into cellular responses are hormones acting as signaling molecules.
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our lab is primarily interested in understanding the genetics and molecular biology of [http://en.wikipedia.org/wiki/Auxin auxin] and other [http://en.wikipedia.org/wiki/Plant_hormone plant hormone] responses in the tiny weed [http://en.wikipedia.org/wiki/Arabidopsis_thaliana arabidopsis thaliana] and related [http://en.wikipedia.org/wiki/Brassicaceae brassicaceae]. the past has shown that understanding hormone action in plants bears great potential for agricultural and horticultural applications. by contributing to the current state of knowledge of hormone biology we hope to participate in the advancement of [http://en.wikipedia.org/wiki/Crop_science crop science]. since several of these hormone-triggered signaling cascades are regulated by the [http://en.wikipedia.org/wiki/Proteasome ubiquitin-proteasome system] SCF-type E3 ubiquitin ligases and functional characterization of their selective f-box protein subunits are another focus of our research activities.<br>
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we apply mostly [http://en.wikipedia.org/wiki/Genomics genomics] approaches, such as:
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*forward [http://en.wikipedia.org/wiki/Genetic_screen genetic screens] and [http://en.wikipedia.org/wiki/Reverse_genetics reverse genetics]
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*whole genome [http://en.wikipedia.org/wiki/Expression_profiling expression profiling]
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*utilizing natural [http://en.wikipedia.org/wiki/Genetic_variation genetic variation] within the global arabidopsis gene pool
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*[http://en.wikipedia.org/wiki/Quantitative_genetics quantitative genetics] → [http://en.wikipedia.org/wiki/Quantitative_trait_locus qtl] mapping
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*evolutionary and [http://en.wikipedia.org/wiki/Population_genomics population genomics]
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*[http://en.wikipedia.org/wiki/Comparative_genomics comparative genomics]<br>
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===natural variation and quantitative genetics of hormone responses===
===natural variation and quantitative genetics of hormone responses===
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we have revealed extensive natural variation for auxin responses in the root in world-wide arabidopsis ecotype collections (delker et al., [http://www.ncbi.nlm.nih.gov/pubmed/18299888?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Planta 2008]) and could recently determine the first quantitative trait loci (QTLs) involved in the inheritance of this genetic variation (as well as QTLs for responses to other phytohormones). To clone the underlying genes we are fine-mapping the target intervals and make use of the vast genetic resources of ''arabidopsis thaliana'' to come up with a reasonable number of candidate genes that can be tested for their ability to functionally complement the differences in auxin response.  
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'''quantitative genetics'''<br>
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[[Image:Thlaspi arvense Blüte1 crop compressed.jpg|280px|right]]we have observed that ecotypes with a high degree of auxin insensitivity in the root do not necessarily display the same insensitivity in other organs like the hypocotyl. hence, it is likely that the various factors responsible for this variation are downstream components and we are therefore also interested in transcriptional differences in response to auxin between ecotypes (delker et al., [http://www.ncbi.nlm.nih.gov/pubmed/20622145 Plant Cell 2010]).
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we have revealed extensive natural variation for auxin responses in the root in world-wide arabidopsis ecotype collections (see delker et al., [http://www.ncbi.nlm.nih.gov/pubmed/18299888?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Planta 2008]). classic genetics tells us that this variation is most likely inherited in a quantitative genetic manner. We are therefore pursuing QTL and association mapping approaches to understand the genetics underlying this variation. Furthermore, we are making an effort to clone selected QTLs with strong effects on auxin-related phenotypes.<br>
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From an evolutionary perspective it will be important to learn about the differences in auxin responses on the physiological and the transcriptional level between species. Comparison of inter-species with intra-species variation may shed new light on the evolutionary development of the auxin response pathway(s). We are using closely related [http://en.wikipedia.org/wiki/Brassicaceae brassicaceae] species such as ''thlaspi arvense'' in this picture for this type of analysis which - in addition to the evolutionary perspective - is most interesting for possible future knowledge transfer to agronomically important species from that family.
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'''population genetics'''<br>
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a possible reason for such natural variation on the physiological level maybe sequence polymorphisms in auxin-associated genes. extensive molecular population genetic analyses allow us to derive selection signatures for the respective gene classes and identify candidate genes which may be the driving forces behind the variation detected.<br>
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'''transcriptional networks'''<br>
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[[Image:Thlaspi arvense Blüte1 crop compressed.jpg|280px|right]]another possible effect contributing to the variation detected are differences on the transcriptional auxin responses between ecotypes. we have observed extensive variation in auxin-induced gene regulation between ecotypes and are using network approaches to understand the causative factors and derive hypotheses thereon (see delker et al., [http://www.ncbi.nlm.nih.gov/pubmed/20622145 Plant Cell 2010]).
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'''evolutionary insights'''<br>
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from an evolutionary perspective it will be important to learn about the differences in auxin responses on the physiological and the transcriptional level between species. Comparison of inter-species with intra-species variation may shed new light on the evolutionary development of the auxin response pathway(s). We are using closely related [http://en.wikipedia.org/wiki/Brassicaceae brassicaceae] species such as thlaspi arvense in this picture for this type of analysis which - in addition to the evolutionary perspective - is most interesting for possible future knowledge transfer to agronomically important species from that family.  
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[[Image:FBP_GFP.gif|150px|right]]‎
 
===f-box proteins===
===f-box proteins===
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the evolutionary conserved f-box motifs can be found in various organisms ranging from fungi, insects, fish, and mammals to plants. f-box proteins are subunits of SCF-type E3 ubiquitin ligases and selectively recruit target proteins via their protein-protein interaction domain for ubiquitination and subsequent proteasomal degradation. therefore, this system represents a straight forward mechanism for simple regulation of signal transduction pathways by removal of target proteins. furthermore, the members of the TIR1 f-box protein family in arabidopsis perceive auxinic compounds and thereby constitute a previously unknown novel class of intracellular receptors for small molecules in eukaryotes. the arabidopsis genome encodes appr. 700 f-box proteins which makes this gene superfamily one of the largest in eukaryotes. however, a biological function has been assigned to less than 30 genes/proteins of the 700 members. a major reason for this seems to be functional redundancy due to evolutionary emergence by gene duplication which disqualifies forward genetics as the approach of choice for the characterization of f-box proteins in plants. we are applying reverse genetic approaches to biologically characterize two subfamilies of f-box proteins
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the evolutionary conserved f-box motifs can be found in various organisms ranging from fungi, insects, fish, and mammals to plants. f-box proteins are subunits of SCF-type E3 ubiquitin ligases and selectively recruit target proteins via their protein-protein interaction domain for ubiquitination and subsequent proteasomal degradation. the arabidopsis genome encodes appr. 700 f-box proteins which makes this gene superfamily one of the largest in eukaryotes. however, a biological function has been assigned to less than 30 genes/proteins of the 700 members. We are generally interested in the evolution and selection patterns acting on f-box proteins (see Schumann et al., 2011 in press) and study a small sub-family to understand the molecular functions of each member.
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to place them into the regulatory networks in which they are active.
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Revision as of 10:10, 25 November 2010

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Contents

broad research scope

HOW do organisms adapt to the environment and how do they react to different biotic and abiotic stimuli?
major players in the conversion of such stimuli into cellular responses are hormones acting as signaling molecules. our lab is primarily interested in understanding the genetics and molecular biology of auxin and other plant hormone responses in the tiny weed arabidopsis thaliana and related brassicaceae. the past has shown that understanding hormone action in plants bears great potential for agricultural and horticultural applications. by contributing to the current state of knowledge of hormone biology we hope to participate in the advancement of crop science. since several of these hormone-triggered signaling cascades are regulated by the ubiquitin-proteasome system SCF-type E3 ubiquitin ligases and functional characterization of their selective f-box protein subunits are another focus of our research activities.
we apply mostly genomics approaches, such as:

natural variation and quantitative genetics of hormone responses

quantitative genetics
we have revealed extensive natural variation for auxin responses in the root in world-wide arabidopsis ecotype collections (see delker et al., Planta 2008). classic genetics tells us that this variation is most likely inherited in a quantitative genetic manner. We are therefore pursuing QTL and association mapping approaches to understand the genetics underlying this variation. Furthermore, we are making an effort to clone selected QTLs with strong effects on auxin-related phenotypes.


population genetics
a possible reason for such natural variation on the physiological level maybe sequence polymorphisms in auxin-associated genes. extensive molecular population genetic analyses allow us to derive selection signatures for the respective gene classes and identify candidate genes which may be the driving forces behind the variation detected.


transcriptional networks

another possible effect contributing to the variation detected are differences on the transcriptional auxin responses between ecotypes. we have observed extensive variation in auxin-induced gene regulation between ecotypes and are using network approaches to understand the causative factors and derive hypotheses thereon (see delker et al., Plant Cell 2010).


evolutionary insights
from an evolutionary perspective it will be important to learn about the differences in auxin responses on the physiological and the transcriptional level between species. Comparison of inter-species with intra-species variation may shed new light on the evolutionary development of the auxin response pathway(s). We are using closely related brassicaceae species such as thlaspi arvense in this picture for this type of analysis which - in addition to the evolutionary perspective - is most interesting for possible future knowledge transfer to agronomically important species from that family.

TIR1-dependent auxin signaling

to identify novel components of SCF complex regulation and/or auxin signaling we used the f-box protein and auxin receptor mutant tir1-1 for a second site forward genetic screen. in a previous screen in bill gray's lab several enhancers of tir1-1-mediated auxin resistance had been identified (see zhang et al., pnas 2008; ito and gray, plant physiology 2006; quint et al., plant journal 2005; chuang et al., plant cell 2004; gray et al., plant cell 2003). Vice versa, we are screening for suppressors of the root growth defect on auxin-supplemented (2,4-D, artificial auxin) media. we identified appr. 15 independent tir1-1 suppressor (tis) mutants that restored the wild-type response and are currently cloning the underlying gene/s and charactarize the physiological and genetic features of the mutants.

f-box proteins

the evolutionary conserved f-box motifs can be found in various organisms ranging from fungi, insects, fish, and mammals to plants. f-box proteins are subunits of SCF-type E3 ubiquitin ligases and selectively recruit target proteins via their protein-protein interaction domain for ubiquitination and subsequent proteasomal degradation. the arabidopsis genome encodes appr. 700 f-box proteins which makes this gene superfamily one of the largest in eukaryotes. however, a biological function has been assigned to less than 30 genes/proteins of the 700 members. We are generally interested in the evolution and selection patterns acting on f-box proteins (see Schumann et al., 2011 in press) and study a small sub-family to understand the molecular functions of each member.

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