A photosynthesis operon in the chloroplast genome drives speciation in evening primroses
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ABSTRACT:
PROVIDER: PRJNA728643 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14480033.fastq.gz | Fastqsanger.gz | |||
| SRR14480034.fastq.gz | Fastqsanger.gz | |||
| SRR14480035.fastq.gz | Fastqsanger.gz | |||
| SRR14480036.fastq.gz | Fastqsanger.gz | |||
| SRR14480037.fastq.gz | Fastqsanger.gz |
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Project description:Genetic incompatibility between the cytoplasm and the nucleus is thought to be a major factor in species formation, but mechanistic understanding of this process is poor. In evening primroses (Oenothera spp.), a model plant for organelle genetics and population biology, hybrid offspring regularly display chloroplast-nuclear incompatibility. This usually manifests in bleached plants, more rarely in hybrid sterility. Hence, most of these incompatibilities affect photosynthetic capability, a trait that is under selection in changing environments. Here we show that light-dependent misregulation of the plastid psbB operon, which encodes core subunits of photosystem II and the cytochrome b6f complex, can lead to hybrid incompatibility, and this ultimately drives speciation. This misregulation causes an impaired light acclimation response in incompatible plants. Moreover, as a result of their different chloroplast genotypes, the parental lines differ in photosynthesis performance upon exposure to different light conditions. Significantly, the incompatible chloroplast genome is naturally found in xeric habitats with high light intensities, whereas the compatible one is limited to mesic habitats. Consequently, our data raise the possibility that the hybridization barrier evolved as a result of adaptation to specific climatic conditions.
2021-05-11 | GSE174154 | GEO
Project description:Genetic incompatibility between the cytoplasm and the nucleus is thought to be a major factor in species formation, but mechanistic understanding of this process is poor. In evening primroses (Oenothera spp.), a model plant for organelle genetics and population biology, hybrid offspring regularly display chloroplast-nuclear incompatibility. This usually manifests in bleached plants, more rarely in hybrid sterility or embryonic lethality. Hence, most of these incompatibilities affect photosynthetic capability, a trait that is under selection in changing environments. Here we show that light-dependent misregulation of the plastid psbB operon, which encodes core subunits of photosystem II and the cytochrome b6f complex, can lead to hybrid incompatibility, and this ultimately drives speciation. This misregulation causes an impaired light acclimation response in incompatible plants. Moreover, as a result of their different chloroplast genotypes, the parental lines differ in photosynthesis performance upon exposure to different light conditions. Significantly, the incompatible chloroplast genome is naturally found in xeric habitats with high light intensities, whereas the compatible one is limited to mesic habitats. Consequently, our data raise the possibility that the hybridization barrier evolved as a result of adaptation to specific climatic conditions.
| S-EPMC8408503 | biostudies-literature
Project description:Background: The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts have small genomes, can be easily cultured, and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair has been found, between S. bayanus and S. cerevisiae, comprising the mitochondrially targeted product of a nuclear gene, AEP2, and a mitochondrially encoded locus, OLI1, the 5' region of whose transcript is bound by Aep2. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. Methods: We report here the first detailed genome-wide analysis of rare F2 progeny from an otherwise sterile hybrid, and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions may be responsible for their post-zygotic separation. These interactions most likely involve multiple loci having weak effects, as there were multiple significant pairwise combinations of loci, with no single combination being completely excluded from the viable F2s. Conclusions: The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions, suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that "death by a thousand cuts" leads to speciation, whereby an accumulation of polymorphisms can lead to an incompatibility between the species "transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation. Genotypes for hybrids between S. cerevisiae and S. paradoxus. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's.
2010-06-08 | GSE19683 | GEO
Project description:Photosynthetic capacity is the result of chloroplast biogenesis, but whether photosynthesis itself is required for chloroplast biogenesis has not been investigated. In this study we use 680nm red light to overexcite Photosystem II to disrupt photosynthesis in two conditional mutants (var2 and abc1k1) and demonstrate that this arrests chloroplast biogenesis. During their biogenesis, chloroplasts import the majority of proteins associated with photosynthesis and some are transported further across the thylakoid membrane by the evolutionarily conserved SEC (Secretory) and TAT (Twin Arginine Translocation) pathways, energized by ATP and the proton gradient, respectively. Most luminal thylakoid proteins are synthesized in the cytoplasm with bi-partite, cleavable targeting sequences (first for the chloroplast envelope, second for the thylakoid membrane). Two-step cleavage of these peptides is essential for chloroplast biogenesis. Linked to the photosynthetic defect in var2 and abc1k1 under red light, six incompletely cleaved essential proteins at the thylakoid lumen side of Photosystems I and II accumulated to high levels in the mutants. In summary, the results show that the processing of a specific module of photosynthesis-associated proteins and concomitantly progression of chloroplast biogenesis depend on photosynthesis at the earliest stages of seedling development.
2024-12-13 | PXD050814 | Pride
Project description:Photosynthesis requires chloroplasts, where most proteins are nucleus-encoded and produced via cytoplasmic translation. The translation initiation factor eIF5B gates the transition from initiation (I) to elongation (E), and the Kozak motif is associated with translation efficiency, but their relationship is previously unknown. Here, with ribosome profiling, we determined the genome-wide I-E transition efficiencies. We discovered that the most prevalent Kozak motif is associated with high I-E transition efficiency in Arabidopsis, rice, and wheat, thus implicating the Kozak motif in facilitating the I-E transition. Indeed, the effects of most Kozak motifs, including the most effective ones, depend on HOT3/eIF5B1 in Arabidopsis. HOT3 preferentially promotes the translation of photosynthesis-associated nuclear genes in a Kozak motif-dependent manner, which explains the chloroplast defects of hot3 mutants. Our study reveals an evolutionarily-conserved link between the Kozak motif and eIF5B-mediated translational I-E efficiency and elucidates a HOT3-mediated translational control of nuclear photosynthesis genes for chloroplast biogenesis.
2024-10-03 | GSE212856 | GEO
Project description:Photosynthesis requires chloroplasts, where most proteins are nucleus-encoded and produced via cytoplasmic translation. The translation initiation factor eIF5B gates the transition from initiation (I) to elongation (E), and the Kozak motif is associated with translation efficiency, but their relationship is previously unknown. Here, with ribosome profiling, we determined the genome-wide I-E transition efficiencies. We discovered that the most prevalent Kozak motif is associated with high I-E transition efficiency in Arabidopsis, rice, and wheat, thus implicating the Kozak motif in facilitating the I-E transition. Indeed, the effects of most Kozak motifs, including the most effective ones, depend on HOT3/eIF5B1 in Arabidopsis. HOT3 preferentially promotes the translation of photosynthesis-associated nuclear genes in a Kozak motif-dependent manner, which explains the chloroplast defects of hot3 mutants. Our study reveals an evolutionarily-conserved link between the Kozak motif and eIF5B-mediated translational I-E efficiency and elucidates a HOT3-mediated translational control of nuclear photosynthesis genes for chloroplast biogenesis.
2024-10-03 | GSE212855 | GEO
Project description:Understanding the conditions that promote the evolution of reproductive isolation, and thus speciation. Here we empirically test some of the key predictions of speciation theory (Coyne 2004; Kohn 2005) by experimentally evolving the initial stages of speciation in yeast. After allowing replicate populations to adapt to two divergent environments, we observed the consistent, de novo evolution of two forms of postzygotic isolation: reduced rate of mitotic reproduction and reduced efficiency of meiotic reproduction. In general, divergent selection resulted in greater reproductive isolation than parallel selection, as predicted by ecological speciation theory. Our experimental system allowed for the first controlled comparison of the relative importance of ecological and genetic mechanisms of isolation, and the novel ability to quantify the effects of antagonistic epistasis. For mitotic reproduction, hybrid inferiority was conditional upon the selective environments and was both ecological and genetic in basis. In contrast, isolation associated with meiotic reproduction was unconditional and was caused solely by genetic mechanisms. Overall, our results show that adaption to divergent environments promotes the evolution of isolation through antagonistic epistasis, providing evidence of a plausible common avenue to speciation and adaptive radiation in nature (Schluter 2000,2001: Funk 2006) Keywords: Speciation, antagonistic epistasis, divergent adaptation
2007-06-21 | GSE6870 | GEO
Project description:Plants trigger leaf senescence to relocate energy and nutrients from aging leaves to developing tissues or storage organs to optimize the growth and reproduction under limited nutrients and energy conditions. Jasmonate signaling is one of the major endogenous hormone signals to induced leaf senescence in Arabidopsis. However, whether circadian clock will gate Jasmonate signaling to induce leaf senescence and the underlying precise mechanism is unclear. Here we find that the Evening Complex (EC) of core oscillator closely regulates leaf senescence. To identify the underlying mechanism of EC regulating leaf senescence, we conducted RNA-sequencing. Transcriptomic data reveals Evening complex extensively involves into JA signal transduction and responses. Moreover, the mutants of ELF3, ELF4 and LUX universly display the accelerated JA-induced leaf senescence phenotype, while their overexpression lines act reversely. In accordance with the transcript levels of JA immediate early induced JA-responsive gene MYC2 are up-regulated in lux mutants. Futhermore we demonstrated LUX can bind to to the promoter of MYC2 in vivo to represses its transcription. In addition, the accelerated JA-induced leaf senescence in mutants of evening complex can be overturned by myc2, myc3 and myc4 mutants redundantly. Collectively, our findings demonstrated the underlying molecular basis for circadian clock gating jasmonate signaling to induce leaf senescence through the module of evening complex to directly repressing MYC2 transcription. This novel established molecular module also refines complicated nodes between circadian clock and jasmonate signal in Arabidopsis.
2018-02-06 | GSE99290 | GEO
Project description:To determine how clock components are integrated with cellular pathways, affinity purification and mass spectrometry (AP-MS) were used to identify proteins that co-precipitate with the evening complex, which is critical regulator of clock, growth, light and flowering pathways.
2016-03-15 | PXD002606 | Pride
Project description:A pluripotent inducible cell line was generated from Arabidopsis to address the limitations of traditional in planta dicot systems and to develop a well-controlled experimental setup where the individual regulatory check points of chloroplast development could be defined. Following light exposure, this cell line was shown to differentiate into photosynthetically active cells with functional chloroplasts providing an experimental system with a temporal gradient of chloroplast development. Using this unique cell line from the dicot Arabidopsis we could demonstrate that the development from a proplastid to a functional chloroplast, and thereby the establishment of photosynthesis, is dependent on a regulatory mechanism involving two distinct phases. First, light exposure triggers an initial change in gene expression, metabolite profile, chlorophyll accumulation and plastid structure. Secondly, a second signal, most likely triggered by activation of the chloroplast, is required for full transition to a functional chloroplast and the shift from heterotrophic to photoautotrophic metabolism.
2018-05-12 | E-MTAB-5777 | biostudies-arrayexpress