Publikation
Ibañez, C.; Poeschl, Y.; Peterson, T.; Bellstädt, J.; Denk, K.; Gogol-Döring, A.; Quint, M.; Delker, C. Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana BioRxiv (2017) DOI: 10.1101/017285
Background: Global increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best. Results: Here, we systematically analyze thermomorphogenesis throughout a complete life cycle in ten natural Arabidopsis thaliana accessions grown in four different temperatures ranging from 16 to 28 °C. We used Q 10 , GxE, phenotypic divergence and correlation analyses to assess temperature sensitivity and genotype effects of more than 30 morphometric and developmental traits representing five phenotype classes. We found that genotype and temperature differentially affected plant growth and development with variing strengths. Furthermore, overall correlations among phenotypic temperature responses was relatively low which seems to be caused by differential capacities for temperature adaptations of individual accessions. Conclusion: Genotype-specific temperature responses may be attractive targets for future forward genetic approaches and accession-specific thermomorphogenesis maps may aid the assessment of functional relevance of known and novel regulatory components.
Publikation
Ibañez, C.; Poeschl, Y.; Peterson, T.; Bellstädt, J.; Denk, K.; Gogol-Döring, A.; Quint, M.; Delker, C. Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana BMC Plant Biol 17, 114, (2017) DOI: 10.1186/s12870-017-1068-5
BackgroundGlobal increase in ambient temperatures
constitute a significant challenge to wild and cultivated plant species.
Forward genetic analyses of individual temperature-responsive traits
have resulted in the identification of several signaling and response
components. However, a comprehensive knowledge about temperature
sensitivity of different developmental stages and the contribution of
natural variation is still scarce and fragmented at best.ResultsHere, we
systematically analyze thermomorphogenesis throughout a complete life
cycle in ten natural Arabidopsis thaliana accessions grown under long
day conditions in four different temperatures ranging from 16 to 28 °C.
We used Q10, GxE, phenotypic divergence and correlation analyses to
assess temperature sensitivity and genotype effects of more than 30
morphometric and developmental traits representing five phenotype
classes. We found that genotype and temperature differentially affected
plant growth and development with variing strengths. Furthermore,
overall correlations among phenotypic temperature responses was
relatively low which seems to be caused by differential capacities for
temperature adaptations of individual
accessions.ConclusionGenotype-specific temperature responses may be
attractive targets for future forward genetic approaches and
accession-specific thermomorphogenesis maps may aid the assessment of
functional relevance of known and novel regulatory components.
Publikationen in Druck
Drost, H.-J.; Gabel, A.; Domazet-Lošo, T.; Quint, M.; Grosse, I. Capturing Evolutionary Signatures in Transcriptomes with myTAI BioRxiv (2016) DOI: 10.1101/051565
Combining transcriptome data of biological processes or response to
stimuli with evolutionary information such as the phylogenetic
conservation of genes or their sequence divergence rates enables the
investigation of evolutionary constraints on these processes or
responses. Such phylotranscriptomic analyses recently unraveled that
mid-developmental transcriptomes of fly, fish, and cress were dominated
by evolutionarily conserved genes and genes under negative selection and
thus recapitulated the developmental hourglass on the transcriptomic
level. Here, we present a protocol for performing phylotranscriptomic
analyses on any biological process of interest. When applying this
protocol, users are capable of detecting different evolutionary
constraints acting on different stages of the biological process of
interest in any species. For each step of the protocol, modular and
easy-to-use open-source software tools are provided, which enable a
broad range of scientists to apply phylotranscriptomic analyses to a
wide spectrum of biological questions.
Publikation
Trenner, J.; Poeschl, Y.; Grau, J.; Gogol-Döring, A.; Quint, M.; Delker, C. Auxin-induced expression divergence between Arabidopsis species likely originates within the TIR1/AFB-AUX/IAA-ARF module BioRxiv (2016) DOI: 10.1101/038422
Auxin is an essential regulator of plant growth and development and
auxin signaling components are conserved among land plants. Yet, a
remarkable degree of natural variation in physiological and
transcriptional auxin responses has been described among Arabidopsis
thaliana accessions. As intra-species comparisons offer only limited
genetic variation, we here inspect the variation of auxin responses
between A. thaliana and A. lyrata. This approach allowed the
identification of conserved auxin response genes including novel genes
with potential relevance for auxin biology. Furthermore, promoter
divergences were analyzed for putative sources of variation. De novo
motif discovery identified novel and variants of known elements with
potential relevance for auxin responses, emphasizing the complex, and
yet elusive, code of element combinations accounting for the diversity
in transcriptional auxin responses. Furthermore, network analysis
revealed correlations of inter-species differences in the expression of
AUX/IAA gene clusters and classic auxin-related genes. We conclude that
variation in general transcriptional and physiological auxin responses
may originate substantially from functional or transcriptional
variations in the TIR1/AFB, AUX/IAA, and ARF signaling network. In that
respect, AUX/IAA gene expression divergence potentially reflects
differences in the manner in which different species transduce identical
auxin signals into gene expression responses.
Publikation
Hoehenwarter, W.; Mönchgesang, S.; Neumann, S.; Majovsky, P.; Abel, S.; Müller, J. Comparative expression profiling reveals a role of the root apoplast in local phosphate response BMC Plant Biol 16 , 106, (2016) DOI: 10.1186/s12870-016-0790-8
BackgroundPlant adaptation to limited phosphate availability
comprises a wide range of responses to conserve and remobilize internal
phosphate sources and to enhance phosphate acquisition. Vigorous
restructuring of root system architecture provides a developmental
strategy for topsoil exploration and phosphate scavenging. Changes in
external phosphate availability are locally sensed at root tips and
adjust root growth by modulating cell expansion and cell division. The
functionally interacting Arabidopsis genes, LOW PHOSPHATE RESPONSE 1 and
2 (LPR1/LPR2) and PHOSPHATE DEFICIENCY RESPONSE 2 (PDR2), are key
components of root phosphate sensing. We recently demonstrated that the
LOW PHOSPHATE RESPONSE 1 - PHOSPHATE DEFICIENCY RESPONSE 2 (LPR1-PDR2)
module mediates apoplastic deposition of ferric iron (Fe3+) in the
growing root tip during phosphate limitation. Iron deposition coincides
with sites of reactive oxygen species generation and triggers cell wall
thickening and callose accumulation, which interfere with cell-to-cell
communication and inhibit root growth.ResultsWe took advantage of
the opposite phosphate-conditional root phenotype of the phosphate
deficiency response 2 mutant (hypersensitive) and low phosphate response
1 and 2 double mutant (insensitive) to investigate the phosphate
dependent regulation of gene and protein expression in roots using
genome-wide transcriptome and proteome analysis. We observed an
overrepresentation of genes and proteins that are involved in the
regulation of iron homeostasis, cell wall remodeling and reactive oxygen
species formation, and we highlight a number of candidate genes with a
potential function in root adaptation to limited phosphate availability.
Our experiments reveal that FERRIC REDUCTASE DEFECTIVE 3 mediated,
apoplastic iron redistribution, but not intracellular iron uptake and
iron storage, triggers phosphate-dependent root growth modulation. We
further highlight expressional changes of several cell wall-modifying
enzymes and provide evidence for adjustment of the pectin network at
sites of iron accumulation in the root.ConclusionOur study
reveals new aspects of the elaborate interplay between phosphate
starvation responses and changes in iron homeostasis. The results
emphasize the importance of apoplastic iron redistribution to mediate
phosphate-dependent root growth adjustment and suggest an important role
for citrate in phosphate-dependent apoplastic iron transport. We
further demonstrate that root growth modulation correlates with an
altered expression of cell wall modifying enzymes and changes in the
pectin network of the phosphate-deprived root tip, supporting the
hypothesis that pectins are involved in iron binding and/or phosphate
mobilization.
Publikation
Raschke, A.; Ibañez, C.; Ullrich, K. K.; Anwer, M. U.; Becker, S.; Glöckner, A.; Trenner, J.; Denk, K.; Saal, B.; Sun, X.; Ni, M.; Davis, S. J.; Delker, C.; Quint, M. Natural Variants of ELF3 Affect Thermomorphogenesis by Transcriptionally Modulating PIF4-Dependent Auxin Response Genes BioRxiv (2015) DOI: 10.1101/015305
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. 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. In 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 cues 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
Drost, H.-G.; Bellstädt, J.; Ó'Maoiléidigh, D. S.; Silva, A. T.; Gabel, A.; Weinholdt, C.; Ryan, P. T.; Dekkers, B. J. W.; Bentsink, L.; Hilhorst, H. W. M.; Ligterink, W.; Wellmer, F.; Grosse, I.; Quint, M. Post-embryonic hourglass patterns mark ontogenetic transitions in plant development BioRxiv (2015) DOI: 10.1101/035527
The historic developmental hourglass concept depicts the convergence of
animal embryos to a common form during the phylotypic period. Recently,
it has been shown that a transcriptomic hourglass is associated with
this morphological pattern, consistent with the idea of underlying
selective constraints due to intense molecular interactions during body
plan establishment. Although plants do not exhibit a morphological
hourglass during embryogenesis, a transcriptomic hourglass has
nevertheless been identified in the model plant Arabidopsis thaliana.
Here, we investigated whether plant hourglass patterns are also found
post-embryonically. We found that the two main phase changes during the
life cycle of Arabidopsis, from embryonic to vegetative and from
vegetative to reproductive development, are associated with
transcriptomic hourglass patterns. In contrast, flower development, a
process dominated by organ formation, is not. This suggests that plant
hourglass patterns are decoupled from organogenesis and body plan
establishment. Instead, they may reflect general transitions through
organizational checkpoints.
Publikation
Schilling, S.; Stenzel, I.; von Bohlen, A.; Wermann, M.; Schulz, K.; Demuth, H.-U.; Wasternack, C. Isolation and characterization of the glutaminyl
cyclases from Solanum tuberosum and Arabidopsis thaliana: implications
for physiological functions Biol. Chem 388, 145-153, (2007) DOI: 10.1515/BC.2007.016
0
Publikation
Sharma, V.K.; Monostori, T.; Hause, B.; Maucher, H.; Göbel, C.; Hornung, E.; Hänsch, R.; Bittner, F.; Wasternack, C.; Feussner, I.; Mendel, R.R.; Schulze, J. Genetic transformation of barley to modify expression of a 13-lipoxygenase Acta Biol. Szeged 49, 33-34 , (2005)
Immature scutella of barley were transformed with cDNA coding for a 13-li-poxygenase of barley (LOX-100) via particle bombardment. Regenerated plants were tested by PAT-assay, Western-analysis and PCR-screening. Immunocytochemical assay of T0 plants showed expression of the LOX cDNA both in the chloroplasts and in the cytosol, depending on the presence of the chloroplast signal peptide sequences in the cDNA. A few transgenic plants containing higher amounts of LOX-derived products have been found. These are the candidates for further analysis concerning pathogen resistance.