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.
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
Quint, M.; Drost, H.-G.; Gabel, A.; Ullrich, K. K.; Bönn, M.; Grosse, I. A transcriptomic hourglass in plant embryogenesis Nature 490, 98-101, (2012) DOI: 10.1038/nature11394
Animal and plant development starts with a
constituting phase called embryogenesis, which evolved independently in
both lineages1. Comparative anatomy of vertebrate development—based on
the Meckel-Serrès law2 and von Baer’s laws of embryology3 from the early
nineteenth century—shows 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 ‘hourglass’4,5, 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.
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 Mol Biol Evol 33, 1158-1163, (2016) DOI: 10.1093/molbev/msw039
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 postembryonically. 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.
Ryan,P. T.; Ó’Maoiléidigh, D. S.; Drost, H.-G.; Kwaśniewska, D.; Gabel, A.; Grosse, I.; Graciet, E.; Quint, M.; Wellmer, F. Patterns of gene expression during Arabidopsis flower development from the time of initiation to maturation BMC Genomics 16, 488 , (2015) DOI: 10.1186/s12864-015-1699-6
Background:The formation of flowers is one of the main model systems to elucidate the molecular mechanisms that control developmental processes in plants. Although several studies have explored gene expression during flower development in the model plant Arabidopsis thalianaon a genome-wide scale, a continuous series of expression data from the earliest floral stages until maturation has been lacking. Here, we used a floral induction system to closethis information gap and to generate a reference dataset for stage-specific gene expression during flower formation.Results:Using a floral induction system, we collected floral buds at 14 different stages from the time of initiation until maturation. Using whole-genome microarray analysis, we identified 7,405 genes that exhibit rapid expression changes during flower development. These genes comprise many known floral regulators and we found that the expression profiles for these regulators match their known expression patterns, thus validating the dataset. We analyzed groups ofco-expressed genes for over-represented cellular and developmental functions through Gene Ontology analysis and found that they could be assigned specific patterns of activities, which are in agreement with the progression of flower development. Furthermore, by mapping binding sites of floral organ identity factors onto our dataset, we were able to identify gene groups that are likely predominantly under control of these transcriptional regulators. We furtherfound that the distribution of paralogs among groups of co-expressed genes varies considerably, with genes expressed predominantly at early and intermediate stages of flower development showing the highest proportion of such genes.Conclusions:Our results highlight and describe the dynamic expression changes undergone by a large numberof genes during flower development. They further provide a comprehensive reference dataset for temporal gene expression during flower formation and we demonstrate that it can be used to integrate data from other genomics approaches such as genome-wide localization studies of transcription factor binding sites.
Drost, H.-G.; Gabel, A.; Grosse, I.; Quint, M. Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis Mol Biol Evol 32, 1221-1231, (2015) DOI: 10.1093/molbev/msv012
The developmental hourglass model has been used to describe the morphological transitions of related species throughout embryogenesis. Recently, quantifiable approaches combining transcriptomic and evolutionary information provided novel evidence for the presence of a phylotranscriptomic hourglass pattern across kingdoms. As its biological function is unknown it remains speculative whether this pattern is functional or merely represents a nonfunctional evolutionary relic. The latter would seriously hamper future experimental approaches designed to test hypotheses regarding its function. Here, we address this question by generating transcriptome divergence index (TDI) profiles across embryogenesis of Danio rerio, Drosophila melanogaster, and Arabidopsis thaliana. To enable meaningful evaluation of the resulting patterns, we develop a statistical test that specifically assesses potential hourglass patterns. Based on this objective measure we find that two of these profiles follow a statistically significant hourglass pattern with the most conserved transcriptomes in the phylotypic periods. As the TDI considers only recent evolutionary signals, this indicates that the phylotranscriptomic hourglass pattern is not a rudiment but possibly actively maintained, implicating the existence of some linked biological function associated with embryogenesis in extant species.
Quint, M.; Ito, H.; Zhang, W.; Gray, W.M. Characterization of a novel temperature-sensitive allele of the CUL1/AXR6 subunit of SCF ubiquitin-ligases Plant J 43, 371-383, (2005)
Selective protein degradation by the ubiquitin-proteasome pathway has emerged as a key regulatory mechanism in a wide variety of cellular processes. The selective components of this pathway are the E3 ubiquitin-ligases which act downstream of the ubiquitin-activating and -conjugating enzymes to identify specific substrates for ubiquitinylation. SCF-type ubiquitin-ligases are the most abundant class of E3 enzymes in Arabidopsis. In a genetic screen for enhancers of the tir1-1 auxin response defect, we identified eta1/axr6-3, a recessive and temperature-sensitive mutation in the CUL1 core component of the SCFTIR1 complex. The axr6-3 mutation interferes with Skp1 binding, thus preventing SCF complex assembly. axr6-3 displays a pleiotropic phenotype with defects in numerous SCF-regulated pathways including auxin signaling, jasmonate signaling, flower development, and photomorphogenesis. We used axr6-3 as a tool for identifying pathways likely to be regulated by SCF-mediated proteolysis and propose new roles for SCF regulation of the far-red light/phyA and sugar signaling pathways. The recessive inheritance and the temperature-sensitive nature of the pleiotropically acting axr6-3 mutation opens promising possibilities for the identification and investigation of SCF-regulated pathways in Arabidopsis.
Parry, G.; Calderón Villalobos, L.I.; Prigge, M.; Peret, B.; Dharmasiri, S.; Itoh, H.; Lechner, E.; Gray, W.M.; Bennett, M.; Estelle, M. Complex regulation of the TIR/AFB family of auxin receptors Proc Natl Acad Sci USA 106(52), 22540-22545, (2009) DOI: 10.1073/pnas.0911967106
Auxin regulates most aspects of plant growth and development. The hormone is perceived by the TIR1/AFB family of F-box proteins acting in concert with the Aux/IAA transcriptional repressors. Arabidopsis plants that lack members of the TIR1/AFB family are auxin resistant and display a variety of growth defects. However, little is known about the functional differences between individual members of the family. Phylogenetic studies reveal that the TIR1/AFB proteins are conserved across land plant lineages and fall into four clades. Three of these subgroups emerged before separation of angiosperms and gymnosperms whereas the last emerged before the monocot-eudicot split. This evolutionary history suggests that the members of each clade have distinct functions. To explore this possibility in Arabidopsis, we have analyzed a range of mutant genotypes, generated promoter swap transgenic lines, and performed in vitro binding assays between individual TIR1/AFB and Aux/IAA proteins. Our results indicate that the TIR1/AFB proteins have distinct biochemical activities and that TIR1 and AFB2 are the dominant auxin receptors in the seedling root. Further, we demonstrate that TIR1, AFB2, and AFB3, but not AFB1 exhibit significant posttranscriptional regulation. The microRNA miR393 is expressed in a pattern complementary to that of the auxin receptors and appears to regulate TIR1/AFB expression. However our data suggest that this regulation is complex. Our results suggest that differences between members of the auxin receptor family may contribute to the complexity of auxin response.
Quint, M.; Barkawi, L.S.; Fan, K.T.; Cohen, J.D.; Gray, W.M. Arabidopsis IAR4 modulates auxin response by regulating auxin homeostasis Plant Physiol 150, 748-758, (2009) DOI: 10.1104/pp.109.136671
In a screen for enhancers of tir1-1 auxin resistance, we identified two novel alleles of the putative mitochondrial pyruvate dehydrogenase E1α-subunit, IAA-Alanine Resistant4 (IAR4). In addition to enhancing the auxin response defects of tir1-1, iar4 single mutants exhibit numerous auxin-related phenotypes including auxin-resistant root growth and reduced lateral root development, as well as defects in primary root growth, root hair initiation, and root hair elongation. Remarkably, all of these iar4 mutant phenotypes were rescued when endogenous indole-3-acetic acid (IAA) levels were increased by growth at high temperature or overexpression of the YUCCA1 IAA biosynthetic enzyme, suggesting that iar4 mutations may alter IAA homeostasis rather than auxin response. Consistent with this possibility, iar4 mutants exhibit increased Aux/IAA stability compared to wild type under basal conditions, but not in response to an auxin treatment. Measurements of free IAA levels detected no significant difference between iar4-3 and wild-type controls. However, we consistently observed significantly higher levels of IAA-amino acid conjugates in the iar4-3 mutant. Furthermore, using stable isotope-labeled IAA precursors, we observed a significant increase in the relative utilization of the Trp-independent IAA biosynthetic pathway in iar4-3. We therefore suggest that the auxin phenotypes of iar4 mutants are the result of altered IAA homeostasis.
Zhang, W.; Ito, H.; Quint, M.; Huang, H.; Noël, L.D.; Gray, W.M. Genetic analysis of CAND1-CUL1 interactions in Arabidopsis supports a role for CAND1-mediated cycling of the SCFTIR1 complex Proc Natl Acad Sci 105, 8470-8475, (2008) DOI: 10.1073/pnas.0804144105
SKP1-Cullin1-F-box protein (SCF) ubiquitin-ligases regulate numerous aspects of eukaryotic growth and development. Cullin-Associated and Neddylation-Dissociated (CAND1) modulates SCF function through its interactions with the CUL1 subunit. Although biochemical studies with human CAND1 suggested that CAND1 plays a negative regulatory role by sequestering CUL1 and preventing SCF complex assembly, genetic studies in Arabidopsis have shown that cand1 mutants exhibit reduced SCF activity, demonstrating that CAND1 is required for optimal SCF function in vivo. Together, these genetic and biochemical studies have suggested a model of CAND1-mediated cycles of SCF complex assembly and disassembly. Here, using the SCFTIR1 complex of the Arabidopsis auxin response pathway, we test the SCF cycling model with Arabidopsis mutant derivatives of CAND1 and CUL1 that have opposing effects on the CAND1CUL1 interaction. We find that the disruption of the CAND1CUL1 interaction results in an increased abundance of assembled SCFTIR1 complex. In contrast, stabilization of the CAND1CUL1 interaction diminishes SCFTIR1 complex abundance. The fact that both decreased and increased CAND1CUL1 interactions result in reduced SCFTIR1 activity in vivo strongly supports the hypothesis that CAND1-mediated cycling is required for optimal SCF function.