Role of Arabidopsis AtPI4Kγ3, a type II phosphoinositide 4-kinase, in abiotic stress responses and floral transition

Transcriptomic insights into the epigenetic modulation of turnip mosaic virus evolution in Arabidopsis thaliana

BACKGROUND

Plant-virus interaction models propose that a virus's ability to infect a host genotype depends on the compatibility between virulence and resistance genes. Recently, we conducted an evolution experiment in which lineages of turnip mosaic virus (TuMV) were passaged in Arabidopsis thaliana genotypes carrying mutations in components of the DNA methylation and the histone demethylation epigenetic pathways. All evolved lineages increased infectivity, virulence and viral load in a host genotype-dependent manner.

RESULTS

To better understand the underlying reasons for these evolved relationships, we delved into the transcriptomic responses of mutant and WT plant genotypes in mock conditions and infected with either the ancestral or evolved viruses. Such a comparison allowed us to classify every gene into nine basic expression profiles. Regarding the targets of viral adaptation, our analyses allowed the identification of common viral targets as well as host genotype-specific genes and categories of biological processes. As expected, immune response-related genes were found to be altered upon infection. However, we also noticed the pervasive over-representation of other functional groups, suggesting that viral adaptation was not solely driven by the level of expression of plant resistance genes. In addition, a significant association between the presence of transposable elements within or upstream the differentially expressed genes was observed. Finally, integration of transcriptomic data into a virus-host protein-protein interaction network highlighted the most impactful interactions.

CONCLUSIONS

These findings shed extra light on the complex dynamics between plants and viruses, indicating that viral infectivity depends on various factors beyond just the plant's resistance genes.

The MADS-box genes SOC1 and AGL24 antagonize XAL2 functions in Arabidopsis thaliana root development

MADS-domain transcription factors play pivotal roles in numerous developmental processes in Arabidopsis thaliana. While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (XAL2, SOC1 and AGL24) in primary root development. By analyzing loss-of-function and overexpression lines, we found that SOC1 and AGL24, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either SOC1 or AGL24 partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant xal2-2. Furthermore, we observed that the simultaneous overexpression of AGL24 and SOC1 leads to short-root phenotypes, affecting meristem cell number and fully elongated cell size, whereas SOC1 overexpression is sufficient to affect columella stem cell differentiation. Additionally, qPCR analyses revealed that these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. We identified 100 differentially expressed genes in xal2-2 roots by RNA-seq. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the xal2-2 mutant, reverted to WT levels in the absence of SOC1 or AGL24.

S-nitrosylation of RABG3E positively regulates vesicle trafficking to promote salt tolerance

Nitric oxide (NO) is a key signaling molecule affecting the response of plants to salt stress; however, the underlying molecular mechanism is poorly understood. In this study, we conducted a phenotype analysis and found that the small GTPase RABG3E (RAB7) promotes salt tolerance in Arabidopsis thaliana. NO promotes the S-nitrosylation of RAB7 at Cys-171, which in turn helps maintain the ion balance in salt-stressed plants. Furthermore, the S-nitrosylation of RAB7 at Cys-171 enhances the enzyme's GTPase activity, thereby promoting vesicle trafficking and increasing its interaction with phosphatidylinositol phosphates-especially phosphatidylinositol-4-phosphate (PI4P). Exogenously applied PI4P increases vesicle trafficking and promotes salt tolerance depending on the S-nitrosylation of RAB7 at Cys-171. These findings illustrate a unique mechanism in salt tolerance, by which NO regulates vesicle trafficking and ion homeostasis through the S-nitrosylation of RAB7 and its interaction with PI4P.

Functional diversity of microbial eukaryotes in a meromictic lake: Coupling between metatranscriptomic and a trait-based approach

The advent of high-throughput sequencing has led to the discovery of a considerable diversity of microbial eukaryotes in aquatic ecosystems, nevertheless, their function and contribution to the trophic food web functioning remain poorly characterized especially in freshwater ecosystems. Based on metabarcoding data obtained from a meromictic lake ecosystem (Pavin, France), we performed a morpho-physio-phenological traits-based approach to infer functional groups of microbial eukaryotes. Metatranscriptomic data were also analysed to assess the metabolic potential of these groups across the diel cycle, size fraction, sampling depth, and periods. Our analysis highlights a huge microbial eukaryotic diversity in the monimolimnion characterized by numerous saprotrophs expressing transcripts related to sulfur and nitrate metabolism as well as dissolved and particulate organic matter degradation. We also describe strong seasonal variations of microbial eukaryotes in the mixolimnion, especially for parasites and mixoplankton. It appears that the water mixing (occurring during spring and autumn) which benefits photosynthetic host communities also promotes parasitic fungi dissemination and over-expression of genes involved in the zoospore phototaxis and stage transition in the parasitic cycle. Mixoplanktonic haptophytes over-expressing photosynthesis-, endocytosis- and phagosome-linked genes under nutrient limitation also suggest that phagotrophy may provide them an advantage over non-phagotrophic phytoplankton.

Enhanced meristem development, tolerance to oxidative stress and hyposensitivity to nitric oxide in the hypermorphic vq10-H mutant in AtVQ10 gene

Nitric oxide (NO) and reactive oxygen are common factors in multiple plant responses to stress, and their involvement in hypoxia-triggered responses is key to ensure growth under adverse environmental conditions. Here, we analyse the regulatory functions exerted by hypoxia-, NO- and oxidative stress-inducible Arabidopsis gene coding for the VQ motif-containing protein 10 (VQ10). A hypermorphic vq10-H mutant allowed identifying VQ10-exerted regulation on root and shoot development as well as its role in regulating responses to NO and oxidative stress. Enhanced VQ10 expression in vq10-H plants led to enhanced elongation of the primary root, and increased root cell division and meristem size during early postgermination development. In shoots, VQ10 activation of cell division was counteracted by WRKY33-exerted repression, thus leading to a dwarf bushy phenotype in plants with enhanced VQ10 expression in a wrky33 knock-out background. Low number of differentially expressed genes were identified when vq10-H versus Col-0 plants were compared either under normoxia or hypoxia. vq10-H and VQ10ox plants displayed less tolerance to submergence but, in turn, were more tolerant to oxidative stress and less sensitive to NO than wild-type plants. VQ10 could be a node integrating redox-related regulation on development and stress responses.

Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis

Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.

The Bro1-like domain-containing protein, AtBro1, modulates growth and abiotic stress responses in Arabidopsis

Abscisic acid (ABA) affects plant physiology by altering gene expression, enabling plants to adapt to a wide range of environments. Plants have evolved protective mechanisms to allow seed germination in harsh conditions. Here, we explore a subset of these mechanisms involving the AtBro1 gene, which encodes one of a small family of poorly characterised Bro1-like domain-containing proteins, in Arabidopsis thaliana plants subjected to multiple abiotic stresses. AtBro1 transcripts were upregulated by salt, ABA and mannitol stress, while AtBro1-overexpression lines demonstrated robust tolerance to drought and salt stress. Furthermore, we found that ABA elicits stress-resistance responses in loss-of-function bro1-1 mutant plants and AtBro1 regulates drought resistance in Arabidopsis. When the AtBro1 promoter was fused to the β-glucuronidase (GUS) gene and introduced into plants, GUS was expressed mainly in rosette leaves and floral clusters, especially in anthers. Using a construct expressing an AtBro1-GFP fusion protein, AtBro1 was found to be localized in the plasma membrane in Arabidopsis protoplasts. A broad RNA-sequencing analysis revealed specific quantitative differences in the early transcriptional responses to ABA treatment between wild-type and loss-of-function bro1-1 mutant plants, suggesting that ABA stimulates stress-resistance responses via AtBro1. Additionally, transcripts levels of MOP9.5, MRD1, HEI10, and MIOX4 were altered in bro1-1 plants exposed to different stress conditions. Collectively, our results show that AtBro1 plays a significant role in the regulation of the plant transcriptional response to ABA and the induction of resistance responses to abiotic stress.

Phosphoinositides in plant-pathogen interaction: trends and perspectives

Phosphoinositides are important regulatory membrane lipids, with a role in plant development and cellular function. Emerging evidence indicates that phosphoinositides play crucial roles in plant defence and are also utilized by pathogens for infection. In this review, we highlight the role of phosphoinositides in plant-pathogen interaction and the implication of this remarkable convergence in the battle against plant diseases.

A de novo gene originating from the mitochondria controls floral transition in Arabidopsis thaliana

De novo genes created in the plant mitochondrial genome have frequently been transferred into the nuclear genome via intergenomic gene transfer events. Therefore, plant mitochondria might be a source of de novo genes in the nuclear genome. However, the functions of de novo genes originating from mitochondria and the evolutionary fate remain unclear. Here, we revealed that an Arabidopsis thaliana specific small coding gene derived from the mitochondrial genome regulates floral transition. We previously identified 49 candidate de novo genes that induce abnormal morphological changes on overexpression. We focused on a candidate gene derived from the mitochondrial genome (sORF2146) that encodes 66 amino acids. Comparative genomic analyses indicated that the mitochondrial sORF2146 emerged in the Brassica lineage as a de novo gene. The nuclear sORF2146 emerged following an intergenomic gene transfer event in the A. thaliana after the divergence between Arabidopsis and Capsella. Although the nuclear and mitochondrial sORF2146 sequences are the same in A. thaliana, only the nuclear sORF2146 is transcribed. The nuclear sORF2146 product is localized in mitochondria, which may be associated with the pseudogenization of the mitochondrial sORF2146. To functionally characterize the nuclear sORF2146, we performed a transcriptomic analysis of transgenic plants overexpressing the nuclear sORF2146. Flowering transition-related genes were highly regulated in the transgenic plants. Subsequent phenotypic analyses demonstrated that the overexpression and knockdown of sORF2146 in transgenic plants resulted in delayed and early flowering, respectively. These findings suggest that a lineage-specific de novo gene derived from mitochondria has an important regulatory effect on floral transition.

Data-driven, participatory characterization of farmer varieties discloses teff breeding potential under current and future climates

In smallholder farming systems, traditional farmer varieties of neglected and underutilized species (NUS) support the livelihoods of millions of growers and consumers. NUS combine cultural and agronomic value with local adaptation, and transdisciplinary methods are needed to fully evaluate their breeding potential. Here, we assembled and characterized the genetic diversity of a representative collection of 366 Ethiopian teff (Eragrostis tef) farmer varieties and breeding materials, describing their phylogenetic relations and local adaptation on the Ethiopian landscape. We phenotyped the collection for its agronomic performance, involving local teff farmers in a participatory variety evaluation. Our analyses revealed environmental patterns of teff genetic diversity and allowed us to identify 10 genetic clusters associated with climate variation and with uneven spatial distribution. A genome-wide association study was used to identify loci and candidate genes related to phenology, yield, local adaptation, and farmers’ appreciation. The estimated teff genomic offset under climate change scenarios highlighted an area around lake Tana where teff cropping may be most vulnerable to climate change. Our results show that transdisciplinary approaches may efficiently propel untapped NUS farmer varieties into modern breeding to foster more resilient and sustainable cropping systems.

Small farms support the livelihoods of about two billion people worldwide. Smallholder farmers often rely on local varieties of crops and use less irrigation and fertilizer than large producers. But smallholdings can be vulnerable to weather events and climate change. Data-driven research approaches may help to identify the needs of farmers, taking into account traditional knowledge and cultural practices to enhance the sustainability of certain crops.

Teff is a cereal crop that plays a critical role in the culture and diets of Ethiopian communities. It is also a super food appreciated on international markets for its nutritional value. Rural smallholder farmers in Ethiopia rely on the crop for subsistence and income and make up the bulk of the country’s agricultural system. Many grow local varieties with tremendous genetic diversity. Scientists, in collaboration with farmers, could tap that diversity to produce more productive or climate-resilient types of teff, both for national and international markets.

Woldeyohannes, Iohannes et al. produced the first large-scale genetic, agronomic and climatic study of traditional teff varieties. In the experiments, Woldeyohannes and Iohannes et al. sequenced the genomes of 366 Ethiopian teff varieties and evaluated their agronomic value in common gardens. The team collaborated with 35 local farmers to understand their preference of varieties and traits. They then conducted a genome-wide association study to assess the crops’ productivity and their adaptations to local growing conditions and farmer preferences. Genetic changes that speed up teff maturation and flowering time could meet small farmers’ needs to secure teff harvest. Woldeyohannes, Iohannes et al. also identified a region in Ethiopia, where local teff varieties may struggle to adapt to climate change. Genetic modifications may help the crop to adapt to frequent droughts that may be a common characteristic of future climates.

The experiments reveal the importance of incorporating traditional knowledge from smallholder farmers into data-driven crop improvement efforts considering genetics and climate science. This multidisciplinary approach may help to improve food security and protect local genetic diversity on small farms. It may also help to ensure that agricultural advances fairly and equitably benefit small farmers.

An Arabidopsis mutant deficient in phosphatidylinositol-4-phosphate kinases ß1 and ß2 displays altered auxin-related responses in roots

Phosphatidylinositol 4-kinases (PI4Ks) are the first enzymes that commit phosphatidylinositol into the phosphoinositide pathway. Here, we show that Arabidopsis thaliana seedlings deficient in PI4Kβ1 and β2 have several developmental defects including shorter roots and unfinished cytokinesis. The pi4kβ1β2 double mutant was insensitive to exogenous auxin concerning inhibition of root length and cell elongation; it also responded more slowly to gravistimulation. The pi4kß1ß2 root transcriptome displayed some similarities to a wild type plant response to auxin. Yet, not all the genes displayed such a constitutive auxin-like response. Besides, most assessed genes did not respond to exogenous auxin. This is consistent with data with the transcriptional reporter DR5-GUS. The content of bioactive auxin in the pi4kß1ß2 roots was similar to that in wild-type ones. Yet, an enhanced auxin-conjugating activity was detected and the auxin level reporter DII-VENUS did not respond to exogenous auxin in pi4kß1ß2 mutant. The mutant exhibited altered subcellular trafficking behavior including the trapping of PIN-FORMED 2 protein in rapidly moving vesicles. Bigger and less fragmented vacuoles were observed in pi4kß1ß2 roots when compared to the wild type. Furthermore, the actin filament web of the pi4kß1ß2 double mutant was less dense than in wild-type seedling roots, and less prone to rebuilding after treatment with latrunculin B. A mechanistic model is proposed in which an altered PI4K activity leads to actin filament disorganization, changes in vesicle trafficking, and altered auxin homeostasis and response resulting in a pleiotropic root phenotypes.

Importance of inositols and their derivatives in cowpea under root dehydration: An omics perspective

This work presents a robust analysis of the inositols (INSs) and raffinose family oligosaccharides (RFOs) pathways, using genomic and transcriptomic tools in cowpea under root dehydration. Nineteen (~70%) of the 26 scrutinized enzymes presented transcriptional up-regulation in at least one treatment time. The transcriptional orchestration allowed categorization of the analyzed enzymes as time-independent (those showing the same regulation throughout the assay) and time-dependent (those showing different transcriptional regulation over time). It is suggested that up-regulated time-independent enzymes (INSs: myo-inositol oxygenase, inositol-tetrakisphosphate 1-kinase 3, phosphatidylinositol 4-phosphate 5-kinase 4-like, 1-phosphatidylinositol-3-phosphate 5-kinase, phosphoinositide phospholipase C, and non-specific phospholipase C; RFOs: α-galactosidase, invertase, and raffinose synthase) actively participate in the reorganization of cowpea molecular physiology under the applied stress. In turn, time-dependent enzymes, especially those up-regulated in some of the treatment times (INSs: inositol-pentakisphosphate 2-kinase, phosphatidylinositol 4-kinase, phosphatidylinositol synthase, multiple inositol polyphosphate phosphatase 1, methylmalonate-semialdehyde dehydrogenase, triosephosphate isomerase, myo-inositol-3-phosphate synthase, phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and protein-tyrosine-phosphatase, and phosphatidylinositol 3-kinase; RFOs: galactinol synthase) seem to participate in fine-tuning of the molecular physiology, helping the cowpea plants to acclimatize under dehydration stress. Not all loci encoding the studied enzymes were expressed during the assay; most of the expressed ones exhibited a variable transcriptional profile in the different treatment times. Genes of the INSs and RFOs pathways showed high orthology with analyzed Phaseoleae members, suggesting a relevant role within this legume group. Regarding the promoter regions of INSs and RFOs genes, some bona fide cis-regulatory elements were identified in association with seven transcription factor families (AP2-EFR, Dof-type, MADS-box, bZIP, CPP, ZF-HD, and GATA-type). Members of INSs and RFOs pathways potentially participate in other processes regulated by these proteins in cowpea.

A novel sweetpotato RING-H2 type E3 ubiquitin ligase gene IbATL38 enhances salt tolerance in transgenic Arabidopsis

Arabidopsis Toxicos en Levadura (ATL) proteins compose a subfamily of E3 ubiquitin ligases and play major roles in regulating plant growth, cold, drought, oxidative stresses response and pathogen defense in plants. However, the role in enhancing salt tolerance has not been reported to date. Here, we cloned a novel RING-H2 type E3 ubiquitin ligase gene, named IbATL38, from sweetpotato cultivar Lushu 3. This gene was highly expressed in the leaves of sweetpotato and strongly induced by NaCl and abscisic acid (ABA). This IbATL38 was localized to nucleus and plasm membrane and possessed E3 ubiquitin ligase activity. Overexpression of IbATL38 in Arabidopsis significantly enhanced salt tolerance, along with inducible expression of a series of stress-responsive genes and prominently decrease of H₂O₂ content. These results suggest that IbATL38 as a novel E3 ubiquitin ligase may play an important role in salt stress response.

Isoprenoid-Derived Metabolites and Sugars in the Regulation of Flowering Time: Does Day Length Matter?

In plants, a diverse set of pathways regulate the transition to flowering, leading to remarkable developmental flexibility. Although the importance of photoperiod in the regulation of flowering time is well known, increasing evidence suggests the existence of crosstalk among the flowering pathways regulated by photoperiod and metabolic pathways. For example, isoprenoid-derived phytohormones (abscisic acid, gibberellins, brassinosteroids, and cytokinins) play important roles in regulating flowering time. Moreover, emerging evidence reveals that other metabolites, such as chlorophylls and carotenoids, as well as sugar metabolism and sugar accumulation, also affect flowering time. In this review, we summarize recent findings on the roles of isoprenoid-derived metabolites and sugars in the regulation of flowering time and how day length affects these factors.

Low Mannitol Concentrations in Arabidopsis thaliana Expressing Ectocarpus Genes Improve Salt Tolerance

Mannitol is abundant in a wide range of organisms, playing important roles in biotic and abiotic stress responses. Nonetheless, mannitol is not produced by a vast majority of plants, including many important crop plants. Mannitol-producing transgenic plants displayed improved tolerance to salt stresses though mannitol production was rather low, in the µM range, compared to mM range found in plants that innately produce mannitol. Little is known about the molecular mechanisms underlying salt tolerance triggered by low concentrations of mannitol. Reported here is the production of mannitol in Arabidopsis thaliana, by expressing two mannitol biosynthesis genes from the brown alga Ectocarpus sp. strain Ec32. To date, no brown algal genes have been successfully expressed in land plants. Expression of mannitol-1-phosphate dehydrogenase and mannitol-1-phosphatase genes was associated with the production of 42.3–52.7 nmol g⁻¹ fresh weight of mannitol, which was sufficient to impart salinity and temperature stress tolerance. Transcriptomics revealed significant differences in the expression of numerous genes, in standard and salinity stress conditions, including genes involved in K⁺ homeostasis, ROS signaling, plant development, photosynthesis, ABA signaling and secondary metabolism. These results suggest that the improved tolerance to salinity stress observed in transgenic plants producing mannitol in µM range is achieved by the activation of a significant number of genes, many of which are involved in priming and modulating the expression of genes involved in a variety of functions including hormone signaling, osmotic and oxidative stress, and ion homeostasis.

Transcriptomic analysis of poco1, a mitochondrial pentatricopeptide repeat protein mutant in Arabidopsis thaliana

BACKGROUND

Flowering is a crucial stage during plant development. Plants may respond to unfavorable conditions by accelerating reproductive processes like flowering. In a recent study, we showed that PRECOCIOUS1 (POCO1) is a mitochondrial pentatricopeptide repeat (PPR) protein involved in flowering time and abscisic acid (ABA) signaling in Arabidopsis thaliana. Here, we use RNA-seq data to investigate global gene expression alteration in the poco1 mutant.

RESULTS

RNA-seq analysis was performed during different developmental stages for wild-type and poco1 plants. The most profound differences in gene expression were found when wild-type and poco1 plants of the same developmental stage were compared. Coverage analysis confirmed the T-DNA insertion in POCO1, which was concomitant with truncated transcripts. Many biological processes were found to be enriched. Several flowering-related genes such as FLOWERING LOCUS T (FT), which may be involved in the early-flowering phenotype of poco1, were differentially regulated. Numerous ABA-associated genes, including the core components of ABA signaling such as ABA receptors, protein phosphatases, protein kinases, and ABA-responsive element (ABRE) binding proteins (AREBs)/ABRE-binding factors (ABFs) as well as important genes for stomatal function, were mostly down-regulated in poco1. Drought and oxidative stress-related genes, including ABA-induced stress genes, were differentially regulated. RNA-seq analysis also uncovered differentially regulated genes encoding various classes of transcription factors and genes involved in cellular signaling. Furthermore, the expression of stress-associated nuclear genes encoding mitochondrial proteins (NGEMPs) was found to be altered in poco1. Redox-related genes were affected, suggesting that the redox state in poco1 might be altered.

CONCLUSION

The identification of various enriched biological processes indicates that complex regulatory mechanisms underlie poco1 development. Differentially regulated genes associated with flowering may contribute to the early-flowering phenotype of poco1. Our data suggest the involvement of POCO1 in the early ABA signaling process. The down-regulation of many ABA-related genes suggests an association of poco1 mutation with the ABA signaling deficiency. This condition further affects the expression of many stress-related, especially drought-associated genes in poco1, consistent with the drought sensitivity of poco1. poco1 mutation also affects the expression of genes associated with the cellular regulation, redox, and mitochondrial perturbation.

LPIAT, a lyso-Phosphatidylinositol Acyltransferase, Modulates Seed Germination in Arabidopsis thaliana through PIP Signalling Pathways and is Involved in Hyperosmotic Response

Lyso-lipid acyltransferases are enzymes involved in various processes such as lipid synthesis and remodelling. Here, we characterized the activity of an acyltransferase from Arabidopsis thaliana (LPIAT). In vitro, this protein, expressed in Escherichia coli membrane, displayed a 2-lyso-phosphatidylinositol acyltransferase activity with a specificity towards saturated long chain acyl CoAs (C16:0- and C18:0-CoAs), allowing the remodelling of phosphatidylinositol. In planta, LPIAT gene was expressed in mature seeds and very transiently during seed imbibition, mostly in aleurone-like layer cells. Whereas the disruption of this gene did not alter the lipid composition of seed, its overexpression in leaves promoted a strong increase in the phosphatidylinositol phosphates (PIP) level without affecting the PIP2 content. The spatial and temporal narrow expression of this gene as well as the modification of PIP metabolism led us to investigate its role in the control of seed germination. Seeds from the lpiat mutant germinated faster and were less sensitive to abscisic acid (ABA) than wild-type or overexpressing lines. We also showed that the protective effect of ABA on young seedlings against dryness was reduced for lpiat line. In addition, germination of lpiat mutant seeds was more sensitive to hyperosmotic stress. All these results suggest a link between phosphoinositides and ABA signalling in the control of seed germination.

Nicotiana benthamiana phosphatidylinositol 4-kinase type II regulates chilli leaf curl virus pathogenesis

Geminiviruses are single-stranded DNA viruses that can cause significant losses in economically important crops. In recent years, the role of different kinases in geminivirus pathogenesis has been emphasized. Although geminiviruses use several host kinases, the role of phosphatidylinositol 4-kinase (PI4K) remains obscure. We isolated and characterized phosphatidylinositol 4-kinase type II from Nicotiana benthamiana (NbPI4KII) which interacts with the replication initiator protein (Rep) of a geminivirus, chilli leaf curl virus (ChiLCV). NbPI4KII-mGFP was localized into cytoplasm, nucleus or both. NbPI4KII-mGFP was also found to be associated with the cytoplasmic endomembrane systems in the presence of ChiLCV. Furthermore, we demonstrated that Rep protein directly interacts with NbPI4KII protein and influenced nuclear occurrence of NbPI4KII. The results obtained in the present study revealed that NbPI4KII is a functional protein kinase lacking lipid kinase activity. Downregulation of NbPI4KII expression negatively affects ChiLCV pathogenesis in N. benthamiana. In summary, NbPI4KII is a susceptible factor, which is required by ChiLCV for pathogenesis.

The effect of plant stress on phosphoinositides

Phosphoinositides are very versatile molecules with a plethora of functions such as cytokinesis, chemotaxis, cell survival, and cell death. Their functions depend on the proteins with which they interact. Thus, when interacting with phospholipases, phosphatases, or kinases, they can be precursors of second messengers in different signalling pathways. They could be second messengers themselves and interact directly with other proteins to modulate their functions trough changing its localization and activity or enhancing its synthesis rate. Because they are more abundant in animal cells and their importance in diseases such as cancer has taken priority, the study of the phosphoinositides in plants has not evolved to the same extent. Nevertheless, several studies have shown the significance of these lipids in plant cells viability and environmental response. This review focuses on phosphoinositides response to abiotic and biotic stress, showing their implication in plant survival during different stages of development. SIGNIFICANCE OF THE STUDY: This review is focused on plant PIPs functions in stress, highlighting in the main differences between plant and mammal PIPs and the novel interactions that could be extrapolated to animal models to contribute in a better understanding of these pivotal molecules.

EARLY FLOWERING IN SHORT DAYS (EFS) regulates the seed size in Arabidopsis

Post-transcriptional modifications, including histone modifications and DNA methylation, alter the chromatin landscape to regulate gene expression, thus control various cellular processes in plants. EARLY FLOWERING IN SHORT DAYS (EFS) is the major contributor for H3K36 methylation in Arabidopsis and is important for plant development. Here, we find that EFS is expressed in different stages of embryo morphogenesis, and the efs mutant produces larger embryo that results in enlarged seeds. Further analysis reveals that an imprinted gene MOP9.5 is hypomethylated at the promoter region and its expression is derepressed in efs mutant. MOP9.5 promoter is marked by various epigenetic modifications, and we find that following the increase of H3K36me3, H3K27me3 and H3K9me2 levels are reduced in efs mutant. This data indicates an antagonistic regulation between H3K36me3 and DNA methylation, and/or H3K27me3 at MOP9.5. Our results further show that both maternal and paternal EFS alleles are responsible for the seed size regulation, which unraveled a novel function of EFS in plant development.