Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum

Gene regulatory networks underlying sulfate deficiency responses in plants

Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate-the primary form of S accessible to plants in soil-has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency.

Transcriptional and metabolic profiling of sulfur starvation response in two monocots

BACKGROUND

Sulfur (S) is a mineral nutrient essential for plant growth and development, which is incorporated into diverse molecules fundamental for primary and secondary metabolism, plant defense, signaling, and maintaining cellular homeostasis. Although, S starvation response is well documented in the dicot model Arabidopsis thaliana, it is not clear if the same transcriptional networks control the response also in the monocots.

RESULTS

We performed series of physiological, expression, and metabolite analyses in two model monocot species, one representing the C3 plants, Oryza sativa cv. kitaake, and second representing the C4 plants, Setaria viridis. Our comprehensive transcriptomic analysis revealed twice as many differentially expressed genes (DEGs) in S. viridis than in O. sativa under S-deficiency, consistent with a greater loss of sulfur and S-containing metabolites under these conditions. Surprisingly, most of the DEGs and enriched gene ontology terms were species-specific, with an intersect of only 58 common DEGs. The transcriptional networks were different in roots and shoots of both species, in particular no genes were down-regulated by S-deficiency in the roots of both species.

CONCLUSIONS

Our analysis shows that S-deficiency seems to have different physiological consequences in the two monocot species and their nutrient homeostasis might be under distinct control mechanisms.

Alleviation of Adverse Effects of Drought Stress on Growth and Nitrogen Metabolism in Mungbean (Vigna radiata) by Sulphur and Nitric Oxide Involves Up-Regulation of Antioxidant and Osmolyte Metabolism and Gene Expression

The influence of drought induced by polyethylene glycol (PEG) and the alleviatory effect of nitric oxide (50 µM) and sulphur (S, 1 mM K2SO4) were studied in Vigna radiata. Drought stress reduced plant height, dry weight, total chlorophylls, carotenoids and the content of nitrogen, phosphorous, potassium and sulphur. The foliar applications of NO and sulphur each individually alleviated the decline, with a greater alleviation observed in seedlings treated with both NO and sulphur. The reduction in intermediates of chlorophyll synthesis pathways and photosynthesis were alleviated by NO and sulphur. Oxidative stress was evident through the increased hydrogen peroxide, superoxide and activity of lipoxygenase and protease which were significantly assuaged by NO, sulphur and NO + sulphur treatments. A reduction in the activity of nitrate reductase, glutamine synthetase and glutamate synthase was mitigated due to the application of NO and the supplementation of sulphur. The endogenous concentration of NO and hydrogen sulphide (HS) was increased due to PEG; however, the PEG-induced increase in NO and HS was lowered due to NO and sulphur. Furthermore, NO and sulphur treatments to PEG-stressed seedlings further enhanced the functioning of the antioxidant system, osmolytes and secondary metabolite accumulation. Activities of γ-glutamyl kinase and phenylalanine ammonia lyase were up-regulated due to NO and S treatments. The treatment of NO and S regulated the expression of the Cu/ZnSOD, POD, CAT, RLP, HSP70 and LEA genes significantly under normal and drought stress. The present study advocates for the beneficial use of NO and sulphur in the mitigation of drought-induced alterations in the metabolism of Vigna radiata.

A Revised View of the LSU Gene Family: New Functions in Plant Stress Responses and Phytohormone Signaling

LSUs (RESPONSE TO LOW SULFUR) are plant-specific proteins of unknown function that were initially identified during transcriptomic studies of the sulfur deficiency response in Arabidopsis. Recent functional studies have shown that LSUs are important hubs of protein interaction networks with potential roles in plant stress responses. In particular, LSU proteins have been reported to interact with members of the brassinosteroid, jasmonate signaling, and ethylene biosynthetic pathways, suggesting that LSUs may be involved in response to plant stress through modulation of phytohormones. Furthermore, in silico analysis of the promoter regions of LSU genes in Arabidopsis has revealed the presence of cis-regulatory elements that are potentially responsive to phytohormones such as ABA, auxin, and jasmonic acid, suggesting crosstalk between LSU proteins and phytohormones. In this review, we summarize current knowledge about the LSU gene family in plants and its potential role in phytohormone responses.

Transcriptomic analysis provides insight into defensive strategies in response to continuous cropping in strawberry (Fragaria × ananassa Duch.) plants

BACKGROUND

Strawberries are an important economic fruit crop world-wide. In strawberry cultivation, continuous cropping (CC) can seriously threaten yield and quality. However, our understanding of the gene expression changes in response to CC and during subsequent defense processes is limited. In this study, we analyzed the impact of CC on the transcriptome of strawberry roots using RNA-Seq technology to elucidate the effect of CC and the subsequent molecular changes.

RESULTS

We found that CC significantly affects the growth of strawberry plants. The transcriptome analysis identified 136 differentially expressed genes (DEGs), including 49 up-regulated and 87 down-regulated DEGs. A Gene Ontology (GO) analysis indicated that the up-regulated DEGs were mainly assigned to defense-related GO terms, and most down-regulated DEGs were assigned to nutrient-related GO terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the responsive DEGs were classified in a large number of important biological pathways, such as phenylalanine metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, glutathione metabolism and plant-pathogen interaction. We also found that four WRKY transcription factors and three peroxidase genes involved in plant defense pathways were up-regulated in the roots of strawberry plants subjected to CC.

CONCLUSION

Several unigenes involved in plant defense processes, such as CNGCs, WRKY transcription factors, PR1, and peroxidase genes with highly variable expression levels between non-CC and CC treatments may be involved in the regulation of CC in strawberry. These results indicate that strawberry roots reallocate development resources to defense mechanisms in response to CC. This study will further deepen our understanding of the fundamental regulatory mechanisms of strawberry resource reallocation in response to CC.

Evolutionary and Gene Expression Analyses Reveal New Insights into the Role of LSU Gene-Family in Plant Responses to Sulfate-Deficiency

LSU proteins belong to a plant-specific gene family initially characterized by their strong induction in response to sulfate (S) deficiency. In the last few years, LSUs have arisen as relevant hubs in protein–protein interaction networks, in which they play relevant roles in the response to abiotic and biotic stresses. Most of our knowledge on LSU genomic organization, expression and function comes from studies in Arabidopsis and tobacco, while little is known about the LSU gene repertoire and evolution of this family in land plants. In this work, a total of 270 LSU family members were identified using 134 land plant species with whole-genome sequences available. Phylogenetic analysis revealed that LSU genes belong to a Spermatophyta-specific gene family, and their homologs are distributed in three major groups, two for dicotyledons and one group for monocotyledons. Protein sequence analyses showed four new motifs that further support the subgroup classification by phylogenetic analyses. Moreover, we analyzed the expression of LSU genes in one representative species of each phylogenetic group (wheat, tomato and Arabidopsis) and found a conserved response to S deficiency, suggesting that these genes might play a key role in S stress responses. In summary, our results indicate that LSU genes belong to the Spermatophyta-specific gene family and their response to S deficiency is conserved in angiosperms.

Transcriptomic, Metabolomic and Ionomic Analyses Reveal Early Modulation of Leaf Mineral Content in Brassica napus under Mild or Severe Drought

While it is generally acknowledged that drought is one of the main abiotic factors affecting plant growth, how mineral nutrition is specifically and negatively affected by water deficit has received very little attention, other than being analyzed as a consequence of reduced growth. Therefore, Brassica napus plants were subjected to a gradual onset of water deficits (mild, severe, or severe extended), and leaves were analyzed at the ionomic, transcriptomic and metabolic levels. The number of Differentially Expressed Genes (DEGs) and of the most differentially accumulated metabolites increased from mild (525 DEGs, 57 metabolites) to severe (5454 DEGs, 78 metabolites) and severe extended (9346 DEGs, 95 metabolites) water deficit. Gene ontology enrichment analysis of the 11,747 DEGs identified revealed that ion transport was one of the most significant processes affected, even under mild water deficit, and this was also confirmed by the shift in ionomic composition (mostly micronutrients with a strong decrease in Mo, Fe, Zn, and Mn in leaves) that occurred well before growth reduction. The metabolomic data and most of the transcriptomic data suggested that well-known early leaf responses to drought such as phytohormone metabolism (ABA and JA), proline accumulation, and oxidative stress defense were induced later than repression of genes related to nutrient transport.

Comparative Omics Analysis of Brassica napus Roots Subjected to Six Individual Macronutrient Deprivations Reveals Deficiency-Specific Genes and Metabolomic Profiles

The early and specific diagnosis of a macronutrient deficiency is challenging when seeking to better manage fertilizer inputs in the context of sustainable agriculture. Consequently, this study explored the potential for transcriptomic and metabolomic analysis of Brassica napus roots to characterize the effects of six individual macronutrient deprivations (N, Mg, P, S, K, and Ca). Our results showed that before any visual phenotypic response, all macronutrient deprivations led to a large modulation of the transcriptome and metabolome involved in various metabolic pathways, and some were common to all macronutrient deprivations. Significantly, comparative transcriptomic analysis allowed the definition of a subset of 3282, 2011, 6325, 1384, 439, and 5157 differentially expressed genes (DEGs) specific to N, Mg, P, S, K, and Ca deprivations, respectively. Surprisingly, gene ontology term enrichment analysis performed on this subset of specific DEGs highlighted biological processes that are common to a number of these macronutrient deprivations, illustrating the complexity of nutrient interactions. In addition, a set of 38 biochemical compounds that discriminated the macronutrient deprivations was identified using a metabolic approach. The opportunity to use these specific DEGs and/or biochemical compounds as potential molecular indicators to diagnose macronutrient deficiency is discussed.

Transcriptome Analysis of Seed Weight Plasticity in Brassica napus

A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including Brassica napus. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source-sink (S-S) ratios in order to examine the relationship between SW and SN under different field conditions. A multifactorial analysis of the RNA-seq data was used to identify a group of 1014 genes exclusively regulated by the S-S ratio. We found that a reduction in the S-S ratio during seed filling induces the expression of genes involved in sucrose transport, seed weight, and stress responses. Moreover, we identified five co-expression modules that are positively correlated with SW and negatively correlated with SN. Interestingly, one of these modules was significantly enriched in transcription factors (TFs). Furthermore, our network analysis predicted several NAC TFs as major hubs underlying SW and SN compensation. Taken together, our study provides novel insights into the molecular factors associated with the SW-SN relationship in rapeseed and identifies TFs as potential targets when improving crop yield.

The Dynamic Responses of Oil Palm Leaf and Root Metabolome to Phosphorus Deficiency

Inorganic phosphate (Pi) starvation is an important abiotic constraint that affects plant cellular homeostasis, especially in tropical regions with high acidic soil and less solubilizable Pi. In the current work, oil palm seedlings were hydroponically maintained under optimal Pi-supply and no Pi-supply conditions for 14 days, and metabolites were measured by gas chromatography-mass spectrometry (GC-MS), from leaves and roots, after seven and 14 days of treatment, to investigate biochemical pathways in relation to P-utilizing strategy. After seven days of limited Pi, plant leaves showed increased levels of most soluble sugars, and after 14 days, the sugars' level decrease, except for erythritol, mannose, fructose, and glucose, which showed the highest levels. Rather in root samples, there were different but overlapping alterations, mainly on sugars, amino acids, and organic acids. The leaf sample was shown to have the highest response of sugars with myo-inositol playing a vital role in the redistribution of sugars, while maltose levels increased, indicating active degradation of starch in the root. High levels of glycerol and stearate in both roots and leaves suggest the metabolism of storage lipids for cellular energy during Pi-deficient conditions.

Sulfur Homeostasis in Plants

Sulfur (S) is an essential macronutrient for plant growth and development. S is majorly absorbed as sulfate from soil, and is then translocated to plastids in leaves, where it is assimilated into organic products. Cysteine (Cys) is the first organic product generated from S, and it is used as a precursor to synthesize many S-containing metabolites with important biological functions, such as glutathione (GSH) and methionine (Met). The reduction of sulfate takes place in a two-step reaction involving a variety of enzymes. Sulfate transporters (SULTRs) are responsible for the absorption of SO42- from the soil and the transport of SO42- in plants. There are 12-16 members in the S transporter family, which is divided into five categories based on coding sequence homology and biochemical functions. When exposed to S deficiency, plants will alter a series of morphological and physiological processes. Adaptive strategies, including cis-acting elements, transcription factors, non-coding microRNAs, and phytohormones, have evolved in plants to respond to S deficiency. In addition, there is crosstalk between S and other nutrients in plants. In this review, we summarize the recent progress in understanding the mechanisms underlying S homeostasis in plants.