Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration

Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pretreatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pretreatments reduced this damage. Ethylene pretreatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.

Zinc Finger Artificial Transcription Factor-Mediated Chloroplast Genome Interrogation in Arabidopsis thaliana

The large majority of core photosynthesis proteins in plants are encoded by nuclear genes, but a small portion have been retained in the plastid genome. These plastid-encoded chloroplast proteins fulfill essential roles in the process of photochemistry. Here, we report the use of nuclear-encoded, chloroplast-targeted zinc finger artificial transcription factors (ZF-ATFs) with effector domains of prokaryotic origin to modulate the expression of chloroplast genes, and to enhance the photochemical activity and growth characteristics of Arabidopsis thaliana plants. This technique was named chloroplast genome interrogation. Using this novel approach, we obtained evidence that ZF-ATFs can indeed be translocated to chloroplasts of Arabidopsis plants, can modulate their growth and operating light use efficiency of PSII, and finally can induce statistically significant changes in the expression levels of several chloroplast genes. Our data suggest that the distortion of chloroplast gene expression might be a feasible approach to manipulate the efficiency of photosynthesis in plants.

Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control

Floral induction in Tulipa gesneriana and Lilium longiflorum is triggered by contrasting temperature conditions, high and low temperature, respectively. In Arabidopsis, the floral integrator FLOWERING LOCUS T (FT), a member of the PEBP (phosphatidyl ethanolamine-binding protein) gene family, is a key player in flowering time control. In this study, one PEBP gene was identified and characterized in lily (LlFT) and three PEBP genes were isolated from tulip (TgFT1, TgFT2 and TgFT3). Overexpression of these genes in Arabidopsis thaliana resulted in an early flowering phenotype for LlFT and TgFT2, but a late flowering phenotype for TgFT1 and TgFT3. Overexpression of LlFT in L. longiflorum also resulted in an early flowering phenotype, confirming its proposed role as a flowering time-controlling gene. The tulip PEBP genes TgFT2 and TgFT3 have a similar expression pattern in tulip, but show opposite effects on the timing of flowering in Arabidopsis. Therefore, the difference between these two proteins was further investigated by interchanging amino acids thought to be important for the FT function. This resulted in the conversion of phenotypes in Arabidopsis upon overexpressing the substituted TgFT2 and TgFT3 genes, revealing the importance of these interchanged amino acid residues. Based on all obtained results, we hypothesize that LlFT is involved in creating meristem competence to flowering-related cues in lily, and TgFT2 is considered to act as a florigen involved in the floral induction in tulip. The function of TgFT3 remains unclear, but, based on our observations and phylogenetic analysis, we propose a bulb-specific function for this gene.

Molecular Regulation of Temperature-Dependent Floral Induction in Tulipa gesneriana

The vegetative-to-reproductive phase change in tulip (Tulipa gesneriana) is promoted by increasing temperatures during spring. The warm winters of recent years interfere with this process and are calling for new adapted cultivars. A better understanding of the underlying molecular mechanisms would be of help, but unlike the model plant Arabidopsis (Arabidopsis thaliana), very little is known about floral induction in tulip. To shed light on the gene regulatory network controlling flowering in tulip, RNA sequencing was performed on meristem-enriched tissue collected under two contrasting temperature conditions, low and high. The start of reproductive development correlated with rounding of the shoot apical meristem and induction of TGSQA expression, a tulip gene with a high similarity to Arabidopsis APETALA1 Gene Ontology enrichment analysis of differentially expressed genes showed the overrepresentation of genes potentially involved in floral induction, bulb maturation, and dormancy establishment. Expression analysis revealed that TERMINAL FLOWER1 (TgTFL1) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1-like1 (TgSOC1-like1) might be repressors, whereas TgSOC1-like2 likely is an activator, of flowering. Subsequently, the flowering time-associated expression of eight potential flowering time genes was confirmed in three tulip cultivars grown in the field. Additionally, heterologous functional analyses in Arabidopsis resulted in flowering time phenotypes in line with TgTFL1 being a floral repressor and TgSOC1-like2 being a floral activator in tulip. Taken together, we have shown that long before morphological changes occur in the shoot apical meristem, the expression of floral repressors in tulip is suppressed by increased ambient temperatures, leading either directly or indirectly to the activation of potential flowering activators shortly before the commencement of the phase change.

Elucidating and mining the Tulipa and Lilium transcriptomes

Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser ( http://www.bioinformatics.nl/bulbs/db/species/index ). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.

Reduced seed germination in Arabidopsis over-expressing SWI/SNF2 ATPase genes

In the life of flowering plants, seed germination is a critical step to ensure survival into the next generation. Generally the seed prior to germination has been in a dormant state with a low rate of metabolism. In the transition from a dormant seed to a germinating seed, various epigenetic mechanisms play a regulatory role. Here, we demonstrate that the over-expression of chromatin remodeling ATPase genes (AtCHR12 or AtCHR23) reduced the frequency of seed germination in Arabidopsis thaliana up to 30% relative to the wild-type seeds. On the other hand, single loss-of-function mutations of the two genes did not affect seed germination. The reduction of germination in over-expressing mutants was more pronounced in stress conditions (salt or high temperature), showing the impact of the environment. Reduced germinations upon over-expression coincided with increased transcript levels of seed maturation genes and with reduced degradation of their mRNAs stored in dry seeds. Our results indicate that repression of AtCHR12/23 gene expression in germinating wild-type Arabidopsis seeds is required for full germination. This establishes a functional link between chromatin modifiers and regulatory networks towards seed maturation and germination.

Transfer of knowledge about flowering and vegetative propagation from model species to bulbous plants

The extensive characterization of plant genes and genome sequences summed to the continuous development of biotechnology tools, has played a major role in understanding biological processes in plant model species. The challenge for the near future is to generate methods and pipelines for an efficient transfer of this knowledge to economically important crops and other plant species. In the case of flower bulbs, which are economically very important for the ornamental industry, flowering time control and vegetative propagation constitute the most relevant processes for agronomical improvements. Those processes have been reasonably studied in reference species, making them excellent candidates for translational investigations in bulbous plant species. The approaches that can be taken for the transfer of biological knowledge from model to non-model species can be roughly categorized as "bottom-up" or "top-down". The former approach usually goes from individual genes to systems, also known as a "gene-by-gene" approach. It assumes conservation of molecular pathways and therefore makes use of sequence homology searches to identify candidate genes. "Top-down" methodologies go from systems to genes, and are e.g. based on large scale transcriptome profiling via heterologous microarrays or RNA sequencing, followed by the identification of associations between phenotypes, genes, and gene expression patterns and levels. In this review, examples of the various knowledge-transfer approaches are provided and pros and cons are discussed. Due to the latest developments in transgenic research and next generation sequencing and the emerging of systems biology as a matured research field, transfer of knowledge concerning flowering time and vegetative propagation capacity in bulbous species are now within sight.

Prevalence of transcription factors in ascomycete and basidiomycete fungi

Background

Gene regulation underlies fungal physiology and therefore is a major factor in fungal biodiversity. Analysis of genome sequences has revealed a large number of putative transcription factors in most fungal genomes. The presence of fungal orthologs for individual regulators has been analysed and appears to be highly variable with some regulators widely conserved and others showing narrow distribution. Although genome-scale transcription factor surveys have been performed before, no global study into the prevalence of specific regulators across the fungal kingdom has been presented.

Results

In this study we have analysed the number of members for 37 regulator classes in 77 ascomycete and 31 basidiomycete fungal genomes and revealed significant differences between ascomycetes and basidiomycetes. In addition, we determined the presence of 64 regulators characterised in ascomycetes across these 108 genomes. This demonstrated that overall the highest presence of orthologs is in the filamentous ascomycetes. A significant number of regulators lacked orthologs in the ascomycete yeasts and the basidiomycetes. Conversely, of seven basidiomycete regulators included in the study, only one had orthologs in ascomycetes.

Conclusions

This study demonstrates a significant difference in the regulatory repertoire of ascomycete and basidiomycete fungi, at the level of both regulator class and individual regulator. This suggests that the current regulatory systems of these fungi have been mainly developed after the two phyla diverged. Most regulators detected in both phyla are involved in central functions of fungal physiology and therefore were likely already present in the ancestor of the two phyla.