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Group de Meaux
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Most of the research effort in this institute is dedicated to the elucidation of central physiological processes necessary to explain the maintenance of plant populations in the wild. In this scientific context, our group is seeking to determine the effect of variation in some of these major processes on the evolutionary success of Arabidopsis thaliana and its close relatives. Our special emphasis is on the relevance of gene regulation for the evolution of these processes.
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What is the evolutionary importance of cis-regulatory DNA?
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Species seem to have the intriguing capacity to adapt to rapid and unpredictable environmental changes. A likely genetic basis of this phenomenon is cis-regulation, because the functional architecture of cis-regulatory regions is simultaneously flexible and robust (Figure 1). However, little is known about the short term evolutionary dynamics of these regions and the extent to which they participate in phenotypic adaptation. This question is our research focus. Our goal is to reconstruct the evolutionary history of recent cis-regulatory changes and to characterize the genetic basis of functional evolution in non-coding DNA regions.
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Figure 1
Gene expression is controlled by the interaction between transcription factors (trans-regulators) and DNA (cis-regulators) in the vicinity of the transcription starting site.
Short nucleotide stretches or Binding-sites are involved in the DNA/protein interaction. These relatively simple features may appear/disappear randomly. Cis-regulatory DNA is thus suspected to evolve faster than coding regions.
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We look at cis-regulatory changes within and among three closely related Arabidopsis species that differ substantially in their life history and ecology: Arabidopsis thaliana, A. halleri and A. lyrata. The Arabidopsis genus provides us with an ecological and evolutionary context in which the functional and historical role of cis-regulatory variation can be addressed (Figure 2).
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Figure 2
Species in the Arabidopsis genus show a rich diversity in morphology, habitat and life history. In our group, we are working with Arabidopsis thaliana, A. lyrata and A. halleri.
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In a first analysis of Chalcone-Synthase cis-regulation, we have developed an allele-specific method to assess functional cis-regulatory variation segregating in F1 heterozygotes (de Meaux et al. 2005). The functional assay was complemented with a survey of nucleotide diversity in the Chalcone-Synthase promoter. This study documents abundant functional variation for Chalcone-synthase cis-regulation in A. thaliana and its relatives (de Meaux et al. 2006). We are now extending this study genome-wide in order to better understand the genetics of expression divergence between species.
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Figure 3
Among other tools, we are using interspecific Arabidopsis hybrids for our investigations. Gene-specific analysis of expression in these individuals reflects the functional cis-regulatory changes that have occurred in the course of speciation.
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Evolution of seed dormancy
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The colonisation of new environments is a key aspect of a species success and requires adaptation to local demands on physiology and ecology. Cis-regulatory regions could play a major role in this process because their functional architecture is thought to allow them to evolve faster than coding regions. However, the extent to which variation in cis-regulatory regions significantly affects the phenotype and actually participates to adaptive evolution is not known. Studying the evolution of seed dormancy in Arabidopsis thaliana provides an optimal strategy to examine this question because a simple evolutionary scenario based on the adaptive value of differences in seed dormancy can be postulated and tested.
Seed dormancy is defined as the inability of a viable seed to germinate under favourable conditions. This characteristic guarantees that the seed does not respond to a transitory bout of favourable conditions and targets the optimal season for germination; it is thus thought to be a trait of adaptive importance. Arabidopsis thaliana is found from the North of Scandinavia down to Northern Africa. This broad geographical range suggests that local demands regarding the control of germination are likely to differ markedly. Because of this, seed dormancy may be a phenotypic trait involved in adaptive differences between northern and southern European A. thaliana populations. Did cis-regulatory changes provide the genetic basis for adaptation to new demands on seed dormancy? Our group addresses the role of cis-regulatory variants in adaptive evolution by the joint analysis of historical, molecular and physiological aspects of both cis-regulatory and coding variation at loci influencing seed dormancy.
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Figure 4:
Non-dormant seeds germinate when conditions are favourable to germination
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Figure 5:
Dormant seeds do not germinate despite environmental conditions favourable to germination are met.
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MicroRNA evolution:
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In plants and animals, gene expression can be down-regulated at the posttranscriptional level by microRNAs (miRNAs), a class of small endogenous RNA. Comparative analysis of miRNA content across species indicates continuous birth and death of these loci in the course of evolution. However, little is known about the microevolutionary dynamics of these genetic elements, especially in plants. In this article we examine polymorphism at two miRNAencoding loci in Arabidopsis thaliana, miR856 and miR824, which are not found in rice or poplar. We compare their diversity to other miRNA-encoding loci conserved across distant taxa. We find that levels of variation vary significantly across loci and that the two recently derived loci harbor patterns of diversity deviating from neutrality. miRNA miR856 shows a weak signature of a selective sweep whereas miR824 displays signs of balancing selection. A detailed examination of structural variation among alleles found at the miR824-encoding locus suggests nonrandom evolution of a thermoresistant substructure in the precursor. Expression analysis of pre-miR824 and its target, AGL16, indicates that these structural differences likely impact the processing of mature miR824. Our work highlights the relevance of RNA structure in precursor sequence evolution, suggesting that the evolutionary dynamics of miRNA-encoding loci is more complex than suggested by the constraints exerted on the interaction between mature miRNA fragments and their target exon.
Although our results clearly point to an adaptive dynamic specific to recently derived miRNA, as was also recently reported in Drosophila, it is too early to elaborate a general scenario. Indeed, patterns of diversity indicate different evolutionary regimes for the two recently derived genes. Within SFB680 in Cologne, we will investigate further the functional consequences of molecular variation at the miRNA encoding loci (http://www.sfb680.uni-koeln.de/). Among other things, this work has motivated a new development in our research: the accurate monitoring of how molecular variation influences fitness in natural environments (PHOTO FIELD ASSAY).
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Under the guidance of Jinyong Hu, Maria Maiz and Falko Frenzel have established a protocole to monitor life-history and fruit production as it occurs in the field |
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Evolution of Innate Immunity
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To sense pathogens, plants have evolved a complex system where i) foreign cells are sensed, ii) basal immune defence processes are triggered and iii) foreign molecules injected into host cells are specifically inactivated. Basal immunity processes are triggered upon detection of flagellin, a well known pathogen associated molecular pattern (PAMP), used by the organism as a signature carried by non-self cells. In plants, detection of flagellin by the FLS2 Receptor-like Protein Kinase (RLK) leads to three concomitant responses: up-regulation of defence related genes, down-regulation of growth related factors and emission of reactive oxygen species (ROS). This basal immune defence system is the primary hurdle met by pathogens to invade the host. It is therefore central to the evolutionary outcome of host pathogen interactions. In close collaboration with the group of  Silke Robatzek, we have begun to investigate the functional consequences of molecular variation at genes controlling plant innate immunity. We find extant functional diversity segregating at the FLS2 locus. Interestingly, this variation correlates with some attributes of the life-cycle. In the near future, we plan to further investigate how flowering time (which varies dramatically across the species range) influences the investment into basal immune competence.
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In liquid culture, A. thaliana seedlings stop growing when they perceive flagellin. |
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© 2011, Max Planck Institute for Plant Breeding Research, Cologne |
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