Arabidopsis Phosphatidic Acid Phosphohydrolases Are Essential for Growth under Nitrogen-Depleted Conditions

Phosphatidic acid phosphohydrolase modulates glycerolipid synthesis in Marchantia polymorpha and is crucial for growth under both nutrient-replete and -deficient conditions

MAIN CONCLUSION

The phosphatidic acid phosphohydrolase of Marchantia polymorpha modulates plastid glycolipid synthesis through the ER pathway and is essential for normal plant development regardless of nutrient availability. Membrane lipid remodeling is one of the strategies plant cells use to secure inorganic phosphate (Pi) for plant growth, but many aspects of the molecular mechanism and its regulation remain unclear. Here we analyzed membrane lipid remodeling using a non-vascular plant, Marchantia polymorpha. The lipid composition and fatty acid profile during Pi starvation in M. polymorpha revealed a decrease in phospholipids and an increase in both galactolipids and betaine lipids. In Arabidopsis thaliana, phosphatidic acid phosphohydrolase (PAH) is involved in phospholipid degradation and is crucial for tolerance to both Pi and nitrogen starvation. We produced two M. polymorpha PAH (MpPAH) knockout mutants (Mppah-1 and Mppah-2) and found that, unlike Arabidopsis mutants, Mppah impaired plant growth with shorter rhizoids compared with wild-type plants even under nutrient-replete conditions. Mutation of MpPAH did not significantly affect the mole percent of each glycerolipid among total membrane glycerolipids from whole plants under both Pi-replete and Pi-deficient conditions. However, the fatty acid composition of monogalactosyldiacylglycerol indicated that the amount of plastid glycolipids produced through the endoplasmic reticulum pathway was suppressed in Mppah mutants. Phospholipids accumulated in the mutants under N starvation. These results reveal that MpPAH modulates plastid glycolipid synthesis through the endoplasmic reticulum pathway more so than what has been observed for Arabidopsis PAH; moreover, unlike Arabidopsis, MpPAH is crucial for M. polymorpha growth regardless of nutrient availability.

Role of SEC14-like phosphatidylinositol transfer proteins in membrane identity and dynamics

Membrane identity and dynamic processes, that act at membrane sites, provide important cues for regulating transport, signal transduction and communication across membranes. There are still numerous open questions as to how membrane identity changes and the dynamic processes acting at the surface of membranes are regulated in diverse eukaryotes in particular plants and which roles are being played by protein interaction complexes composed of peripheral and integral membrane proteins. One class of peripheral membrane proteins conserved across eukaryotes comprises the SEC14-like phosphatidylinositol transfer proteins (SEC14L-PITPs). These proteins share a SEC14 domain that contributes to membrane identity and fulfills regulatory functions in membrane trafficking by its ability to sense, bind, transport and exchange lipophilic substances between membranes, such as phosphoinositides and diverse other lipophilic substances. SEC14L-PITPs can occur as single-domain SEC14-only proteins in all investigated organisms or with a modular domain structure as multi-domain proteins in animals and streptophytes (comprising charales and land plants). Here, we present an overview on the functional roles of SEC14L-PITPs, with a special focus on the multi-domain SEC14L-PITPs of the SEC14-nodulin and SEC14-GOLD group (PATELLINs, PATLs in plants). This indicates that SEC14L-PITPs play diverse roles from membrane trafficking to organism fitness in plants. We concentrate on the structure of SEC14L-PITPs, their ability to not only bind phospholipids but also other lipophilic ligands, and their ability to regulate complex cellular responses through interacting with proteins at membrane sites.

RNA-seq profiling in leaf tissues of two soybean (Glycine max [L.] Merr.) cultivars that show contrasting responses to drought stress during early developmental stages

Drought stress is the major environment constraint on soybean yield, and a variety of pathways underlie drought tolerance mechanisms. Transcriptomic profiling of two soybean cultivars, drought-tolerant SS2-2 and drought-sensitive Taekwang, was performed under normal and drought conditions to identify genes involved in drought tolerance. This revealed large differences in water loss during drought treatment. Genes involved in signaling, lipid metabolism, phosphorylation, and gene regulation were overrepresented among genes that were differentially expressed between cultivars and between treatments in each cultivar. The analysis revealed transcription factors from six families, including WRKYs and NACs, showed significant SS2-2-specific upregulation. Genes involved in stress defense pathways, including MAPK signaling, Ca2+ signaling, ROS scavenging, and NBS-LRR, were also identified. Expression of non-specific phospholipases, phospholipase D, and PHOSPHATIDYL INOSITOL MONOPHOSPHATE 5 KINASE (PIP5K), which act in the lipid-signaling pathway, was greatly increased in SS2-2. The roles of PIP5K in drought stress tolerance were confirmed in Arabidopsis thaliana. Arabidopsis pip5k mutants had significantly lower survival rates under drought stress than wild-type plants. This study identified additional elements in the mechanisms used by plants to protect themselves from drought stress and provides valuable information for the development of drought-tolerant soybean cultivars.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01385-1.

Distinctly localized lipid phosphate phosphatases mediate endoplasmic reticulum glycerolipid metabolism in Arabidopsis

Inter-organelle communication is an integral subcellular process in cellular homeostasis. In plants, cellular membrane lipids are synthesized in the plastids and endoplasmic reticulum (ER). However, the crosstalk between these organelles in lipid biosynthesis remains largely unknown. Here, we show that a pair of lipid phosphate phosphatases (LPPs) with differential subcellular localizations is required for ER glycerolipid metabolism in Arabidopsis (Arabidopsis thaliana). LPPα2 and LPPε1, which function as phosphatidic acid phosphatases and thus catalyze the core reaction in glycerolipid metabolism, were differentially localized at ER and chloroplast outer envelopes despite their similar tissue expression pattern. No mutant phenotype was observed in single knockout mutants; however, genetic suppression of these LPPs affected pollen growth and ER phospholipid biosynthesis in mature siliques and seeds with compromised triacylglycerol biosynthesis. Although chloroplast-localized, LPPε1 was localized close to the ER and ER-localized LPPα2. This proximal localization is functionally relevant, because overexpression of chloroplastic LPPε1 enhanced ER phospholipid and triacylglycerol biosynthesis similar to the effect of LPPα2 overexpression in mature siliques and seeds. Thus, ER glycerolipid metabolism requires a chloroplast-localized enzyme in Arabidopsis, representing the importance of inter-organelle communication in membrane lipid homeostasis.

Longer Duration of Active Oil Biosynthesis during Seed Development Is Crucial for High Oil Yield-Lessons from Genome-Wide In Silico Mining and RNA-Seq Validation in Sesame

Sesame, one of the ancient oil crops, is an important oilseed due to its nutritionally rich seeds with high protein content. Genomic scale information for sesame has become available in the public databases in recent years. The genes and their families involved in oil biosynthesis in sesame are less studied than in other oilseed crops. Therefore, we retrieved a total of 69 genes and their translated amino acid sequences, associated with gene families linked to the oil biosynthetic pathway. Genome-wide in silico mining helped identify key regulatory genes for oil biosynthesis, though the findings require functional validation. Comparing sequences of the SiSAD (stearoyl-acyl carrier protein (ACP)-desaturase) coding genes with known SADs helped identify two SiSAD family members that may be palmitoyl-ACP-specific. Based on homology with lysophosphatidic acid acyltransferase (LPAAT) sequences, an uncharacterized gene has been identified as SiLPAAT1. Identified key regulatory genes associated with high oil content were also validated using publicly available transcriptome datasets of genotypes contrasting for oil content at different developmental stages. Our study provides evidence that a longer duration of active oil biosynthesis is crucial for high oil accumulation during seed development. This underscores the importance of early onset of oil biosynthesis in developing seeds. Up-regulating, identified key regulatory genes of oil biosynthesis during early onset of seed development, should help increase oil yields.

Autophagy triggered by iron-mediated ER stress is an important stress response to the early phase of Pi starvation in plants

Inorganic phosphate (Pi) is essential for plant growth. However, Pi is often limiting in soil. Hence, plants have established several mechanisms of response to Pi starvation. One of the important mechanisms is Pi recycling, which includes membrane lipid remodeling and plastid DNA degradation via catabolic enzymes. However, the involvement of other degradation systems in Pi recycling remains unclear. Autophagy, a system for degradation of intracellular components, contributes to recycling of some nutrients, such as nitrogen, carbon, and zinc, under starvation. In the present study, we found that autophagy-deficient mutants depleted Pi early and exhibited severe leaf growth defects under Pi starvation. The main cargo of autophagy induced by early Pi depleted conditions was the endoplasmic reticulum (ER), indicating that ER-phagy, a type of autophagy that selectively degrades the ER, is involved in the response to the early phase of Pi starvation for contribution to Pi recycling. This ER-phagy was suppressed in an INOSITOL-REQUIRING ENZYME 1 double mutant, ire1a ire1b, in which ER stress responses are defective, suggesting that the early Pi starvation induced ER-phagy is induced by ER stress. Furthermore, iron limitation and inhibition of lipid-reactive oxygen species accumulation suppressed the ER-phagy. Interestingly, membrane lipid remodeling, a response to late Pi starvation, was accelerated in the ire1a ire1b under early Pi-depleted conditions. Our findings reveal the existence of two different phases of responses to Pi starvation (i.e. early and late) and indicate that ER stress-mediated ER-phagy is involved in Pi recycling in the early phase to suppress acceleration of the late phase.

RCB-mediated chlorophagy caused by oversupply of nitrogen suppresses phosphate-starvation stress in plants

Inorganic phosphate (Pi) and nitrogen (N) are essential nutrients for plant growth. We found that a five-fold oversupply of nitrate rescues Arabidopsis (Arabidopsis thaliana) plants from Pi-starvation stress. Analyses of transgenic plants that overexpressed GFP-AUTOPHAGY8 showed that an oversupply of nitrate induced autophagy flux under Pi-depleted conditions. Expression of DIN6 and DIN10, the carbon (C) starvation-responsive genes, was upregulated when nitrate was oversupplied under Pi starvation, which suggested that the plants recognized the oversupply of nitrate as C starvation stress because of the reduction in the C/N ratio. Indeed, formation of Rubisco-containing bodies (RCBs), which contain chloroplast stroma and are induced by C starvation, was enhanced when nitrate was oversupplied under Pi starvation. Moreover, autophagy-deficient mutants did not release Pi (unlike wild-type plants), exhibited no RCB accumulation inside vacuoles, and were hypersensitive to Pi starvation, indicating that RCB-mediated chlorophagy is involved in Pi starvation tolerance. Thus, our results showed that the Arabidopsis response to Pi starvation is closely linked with N and C availability and that autophagy is a key factor that controls plant growth under Pi starvation.

Epigenetic Variation at a Genomic Locus Affecting Biomass Accumulation under Low Nitrogen in Arabidopsis thaliana

Nitrogen (N) is a macronutrient determining crop yield. The application of N fertilisers can substantially increase the yield, but excess use also causes the nitrate pollution of water resources and increases production costs. Increasing N use efficiency (NUE) in crop plants is an important step to implement low-input agricultural systems. We used Arabidopsis thaliana as model system to investigate the natural genetic diversity in traits related to NUE. Natural variation was used to study adaptive growth patterns and changes in gene expression associated with limited nitrate availability. A genome-wide association study revealed an association of eight SNP markers on Chromosome 1 with shoot growth under limited N. The identified linkage disequilibrium (LD) interval includes the DNA sequences of three cysteine/histidine-rich C1 domain proteins in tandem orientation. These genes differ in promoter structure, methylation pattern and expression level among accessions, correlating with growth performance under N deficiency. Our results suggest the involvement of epigenetic regulation in the expression of NUE-related traits.

Overexpression of soybean GmPLDγ enhances seed oil content and modulates fatty acid composition in transgenic Arabidopsis

Phospholipase D (PLD) hydrolyzes the phosphodiester bond of glycerophospholipids to yield phosphatidic acid (PA) and a free headgroup. PLDs are important for plant growth, development, and responses to external stresses. However, their roles in triacylglycerol (TAG) synthesis are still unclear. Here, we report that a soybean (Glycine max) PLDγ (GmPLDγ) is involved in glycerolipid turnover and seed oil production. GmPLDγ was targeted to mitochondria and exhibited PLD activity that was activated by oleate and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2]. Overexpression of GmPLDγ (abbreviated GmPLDγ-OE) in Arabidopsis thaliana resulted in enhanced seed weight, elevated levels of TAGs with 18-, 20-, and 22-carbon fatty acids (FAs), and altered oil-body morphology. Furthermore, the levels of membrane lipids in vegetative tissues decreased significantly, whereas no overt changes were found in mature seeds except for a decrease in the digalactosyldiacylglycerol (DGDG) level in the GmPLDγ-OE lines. Additionally, the expression of genes involved in glycerolipid metabolism was significantly upregulated in developing siliques in GmPLDγ-OE lines. Together, our data indicate a regulatory role for GmPLDγ in TAG synthesis and fatty-acid remodeling, highlighting the importance of mitochondria-directed glycerophospholipid homeostasis in seed oil accumulation.