zur Suche springenzur Navigation springenzum Inhalt springen

Publikationen - Molekulare Signalverarbeitung

Sortieren nach: Erscheinungsjahr Typ der Publikation

Zeige Ergebnisse 1 bis 5 von 5.

Publikation

Raschke, A., Ibañez, C., Ullrich, K., Anwer, M., Becker, S., Glöckner, A., Trenner, J., Denk, K., Saal, B., Sun, X., Ni, M., Davis, S., Delker, C. & Quint, M. Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent auxin response genes BMC Plant Biol. 15, 197, (2015) DOI: 10.1186/s12870-015-0566-6

Background

Perception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis.

Results

We identified GIRAFFE2.1, a major QTL explaining ~18 % of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth.

ConclusionsIn combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod information to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation. 

Publikation

Poeschl, Y., Delker, C., Trenner, J., Ullrich, K. & Quint, M. & Grosse, I. Optimized probe masking for comparative transcriptomics of closely related species. PLOS ONE 8, e78497, (2013)

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are

restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence,

transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more

species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a

microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the

transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due

to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of

non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for

comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts

of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray

designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic

DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting

expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency

and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As

an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides asuperior base for biological interpretation of the measured expression responses.

Publikation

Quint, M., Drost, H-G., Gabel, A., Ullrich, K., Bönner, M. & Grosse, I. A transcriptomic hourglass in plant embryogenesis Nature 490, 98-101, (2012)

Animal and plant development starts with a constituting phase called embryogenesis, which evolved independently in both lineages1. Comparative anatomy of vertebrate developmentbased on the Meckel-Serrès law2 and von Baers laws of embryology3 from the early nineteenth centuryshows that embryos from various taxa appear different in early stages, converge to a similar form during mid-embryogenesis, and again diverge in later stages. This morphogenetic series is known as the embryonic hourglass4, 5, and its bottleneck of high conservation in mid-embryogenesis is referred to as the phylotypic stage6. Recent analyses in zebrafish and Drosophila embryos provided convincing molecular support for the hourglass model, because during the phylotypic stage the transcriptome was dominated by ancient genes7 and global gene expression profiles were reported to be most conserved8. Although extensively explored in animals, an embryonic hourglass has not been reported in plants, which represent the second major kingdom in the tree of life that evolved embryogenesis. Here we provide phylotranscriptomic evidence for a molecular embryonic hourglass in Arabidopsis thaliana, using two complementary approaches. This is particularly significant because the possible absence of an hourglass based on morphological features in plants suggests that morphological and molecular patterns might be uncoupled. Together with the reported developmental hourglass patterns in animals, these findings indicate convergent evolution of the molecular hourglass and a conserved logic of embryogenesis across kingdoms.

Publikation

Schumann, N., Navarro-Quezada, A.R., Ullrich, K., Kuhl, C. & Quint, M. Molecular Evolution and Selection Patterns of Plant F-box Proteins with C-terminal Kelch Repeats Plant Physiol 155, 835-850, (2011)

The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization.

Publikation

Delker, C., Pöschl, Y., Raschke, A., Ullrich, K., Ettingshausen, S., Hauptmann, V., Grosse, I. & Quint, M. Natural variation of transcriptional auxin response networks in Arabidopsis thaliana Plant Cell 22, 2184-2200, (2010)

Natural variation has been observed for various traits in Arabidopsis thaliana. Here, we investigated natural variation in the context of physiological and transcriptional responses to the phytohormone auxin, a key regulator of plant development. A survey of the general extent of natural variation to auxin stimuli revealed significant physiological variation among 20 genetically diverse natural accessions. Moreover, we observed dramatic variation on the global transcriptome level after induction of auxin responses in seven accessions. Although we detect isolated cases of major-effect polymorphisms, sequencing of signaling genes revealed sequence conservation, making selective pressures that favor functionally different protein variants among accessions unlikely. However, coexpression analyses of a priori defined auxin signaling networks identified variations in the transcriptional equilibrium of signaling components. In agreement with this, cluster analyses of genome-wide expression profiles followed by analyses of a posteriori defined gene networks revealed accession-specific auxin responses. We hypothesize that quantitative distortions in the ratios of interacting signaling components contribute to the detected transcriptional variation, resulting in physiological variation of auxin responses among accessions.

IPB Mainnav Search