Comprehensive genomic analysis and expression profiling of diacylglycerol kinase gene family in Malus prunifolia (Willd.) Borkh

Exploring lipid signaling in plant physiology: From cellular membranes to environmental adaptation

Lipids have evolved as versatile signaling molecules that regulate a variety of physiological processes in plants. Convincing evidence highlights their critical role as mediators in a wide range of plant processes required for survival, growth, development, and responses to environmental conditions such as water availability, temperature changes, salt, pests, and diseases. Understanding lipid signaling as a critical process has helped us expand our understanding of plant biology by explaining how plants sense and respond to environmental cues. Lipid signaling pathways constitute a complex network of lipids, enzymes, and receptors that coordinate important cellular responses and stressing plant biology's changing and adaptable traits. Plant lipid signaling involves a wide range of lipid classes, including phospholipids, sphingolipids, oxylipins, and sterols, each of which contributes differently to cellular communication and control. These lipids function not only as structural components, but also as bioactive molecules that transfer signals. The mechanisms entail the production of lipid mediators and their detection by particular receptors, which frequently trigger downstream cascades that affect gene expression, cellular functions, and overall plant growth. This review looks into lipid signaling in plant physiology, giving an in-depth look and emphasizing its critical function as a master regulator of vital activities.

Genome-Wide Characterization of Differentially Expressed Scent Genes in the MEP Control Network of the Flower of Lilium 'Sorbonne'

Fragrance is an important feature of ornamental lilies. Components of volatile substances and important genes for monoterpene synthesis in the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway were examined in this study. Twenty volatile compounds (2 in the budding stage, 3 in the initial flowering stage, 7 in the semi-flowering stage, 17 in the full-flowering stage, and 5 in withering stage) were detected in the Oriental lily 'Sorbonne' using gas chromatography-mass spectrometry. The semi- and full-flowering stages were key periods for volatile substance production and enzyme function. Sequence assembly from samples collected during all flowering stages resulted in the detection of 274,849 genes and 129,017 transcripts. RNA sequencing and heatmapping led to the detection of genes in the MEP monoterpene metabolism pathway. Through gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we extracted key genes (LiDXS2, LiLIS, and LiMYS) and transcription factors (in the bHLH, MYB, HD-ZIP, and NAC families) associated with the MEP pathway. Tissue localization revealed that LiDXS2, LiLIS, and LiMYS were expressed in Lilium 'Sorbonne' petals in the full-flowering stage. Genes regulating the 1-deoxy-D-X-lignone-5-phosphate synthase family of rate-limiting enzymes, involved in the first step of monoterpene synthesis, showed high expression in the semi- and full-flowering stages. LiDXS2 was cloned and localized in chloroplast subcells. The relative expression of terpene-related genes in the MEP and mevalonic acid pathways of wild-type and LiLIS/LiMYS transgenic Arabidopsis thaliana, and changes in chemical composition, confirmed that LiLIS/LiMYS regulates the monoterpene synthesis pathway. The results of this study provide a theoretical basis for the synthesis of lily aromatic substances and the cultivation of new garden flower varieties.

Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses

Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.

The Role of Genetic Factors in the Differential Invasion Success of Two Spartina Species in China

Biological invasions have become one of the greatest threats to global biodiversity and ecosystem conservation. Most previous studies have revealed how successful invasive species adapt to new environments and climate change through phenotypic and genetic evolution. Some researchers suggested that understanding unsuccessful or less successful biological invasions might be important for understanding the relationships between invasion adaptability and climate factors. We compared the sexual reproduction ability, genetic diversity, and gene × environment interaction in two intentionally introduced alien species in China (Spartina anglica and Spartina alterniflora) based on restriction site-associated DNA (RAD) sequencing. After more than 50 years, the distribution of S. alterniflora has rapidly expanded, while S. anglica has experienced extreme dieback. A total of 212,939 single nucleotide polymorphisms (SNPs) for the two Spartina species were used for analysis. The multilocus genotype (MLG) analysis revealed that clonal reproduction was the prevalent mode of reproduction in both species, indicating that a change in the mode of reproduction was not the key factor enabling successful invasion by Spartina. All genetic diversity indicators (He, Ho, π) in S. alterniflora populations were at least two times higher than those in S. anglica populations, respectively (p < 0.001). Furthermore, the population genetic structure and stronger patterns of climate-associated loci provided support for rapid adaptive evolution in the populations of S. alterniflora in China. Altogether, our results highlight the importance of genetic diversity and local adaptation, which were driven by multiple source populations, in increasing the invasiveness of S. alterniflora.

Combined Transcriptome and Lipidomic Analyses of Lipid Biosynthesis in Macadamia ternifolia Nuts

Macadamia nuts are considered a high-quality oil crop worldwide. To date, the lipid diversity and the genetic factors that mediate storage lipid biosynthesis in Macadamia ternifolia are poorly known. Here, we performed a comprehensive transcriptomic and lipidomic data analysis to understand the mechanism of lipid biosynthesis by using young, medium-aged, and mature fruit kernels. Our lipidomic analysis showed that the M. ternifolia kernel was a rich source of unsaturated fatty acids. Moreover, different species of triacylglycerols, diacylglycerol, ceramides, phosphatidylethanolamine, and phosphatidic acid had altered accumulations during the developmental stages. The transcriptome analysis revealed a large percentage of differently expressed genes during the different stages of macadamia growth. Most of the genes with significant differential expression performed functional activity of oxidoreductase and were enriched in the secondary metabolite pathway. The integration of lipidomic and transcriptomic data allowed for the identification of glycerol-3-phosphate acyltransferase, diacylglycerol kinase, phosphatidylinositols, nonspecific phospholipase C, pyruvate kinase 2, 3-ketoacyl-acyl carrier protein reductase, and linoleate 9S-lipoxygenase as putative candidate genes involved in lipid biosynthesis, storage, and oil quality. Our study found comprehensive datasets of lipidomic and transcriptomic changes in the developing kernel of M. ternifolia. In addition, the identification of candidate genes provides essential prerequisites to understand the molecular mechanism of lipid biosynthesis in the kernel of M. ternifolia.

Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat

The inositol phospholipid signaling system mediates plant growth, development, and responses to adverse conditions. Diacylglycerol kinase (DGK) is one of the key enzymes in the phosphoinositide-cycle (PI-cycle), which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGKs have not been reported in wheat. In this study, 24 DGK gene family members from the wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and an accessory domain. The analyses of phylogenetic and gene structure analyses revealed that each TaDGK gene could be grouped into clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation of functional domains, for example, of gene structure and amino acid sequences. Four coding sequences were then cloned from Chinese Spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification across wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated under salt and drought stresses, suggesting their possible roles in dealing with adverse environmental conditions. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. These results provide valuable information for understanding the putative functions of DGKs in wheat and support deeper functional analysis of this pivotal gene family. The 24 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

Turnover of diacylglycerol kinase 4 by cytoplasmic acidification induces vacuole morphological change and nuclear DNA degradation in the early stage of pear self-incompatibility response

Pear has an S-RNase-based gametophytic self-incompatibility (SI) system. Nuclear DNA degradation is a typical feature of incompatible pollen tube death, and is among the many physiological functions of vacuoles. However, the specific changes that occur in vacuoles, as well as the associated regulatory mechanism in pear SI, are currently unclear. Although research in tobacco has shown that decreased activity of diacylglycerol kinase (DGK) results in the morphological change of pollen tube vacuole, whether DGK regulates the pollen tube vacuole of tree plants and whether it occurs in SI response, is currently unclear. We found that DGK activity is essential for pear pollen tube growth, and DGK4 regulates pollen tube vacuole morphology following its high expression and deposition at the tip and shank edge of the pollen tube of pear. Specifically, incompatible S-RNase may induce cytoplasmic acidification of the pollen tube by inhibiting V-ATPase V₀ domain a1 subunit gene expression as early as 30 min after treatment, when the pollen tube is still alive. Cytoplasmic acidification induced by incompatible S-RNase results in reduced DGK4 abundance and deposition, leading to morphological change of the vacuole and fragmentation of nuclear DNA, which indicates that DGK4 is a key factor in pear SI response.

Increased Drought Resistance 1 Mutation Increases Drought Tolerance of Upland Rice by Altering Physiological and Morphological Traits and Limiting ROS Levels

To discover new mutants conferring enhanced tolerance to drought stress, we screened a mutagenized upland rice (Oryza sativa) population (cv. IAPAR9) and identified a mutant, named idr1-1 (increased drought resistance 1-1), with obviously increased drought tolerance under upland field conditions. The idr1-1 mutant possessed a significantly enhanced ability to tolerate high-drought stresses. Map-based cloning revealed that the gene LOC_Os05g26890, residing in the mapping region of IDR1 locus, carried a single-base deletion in the idr1-1 mutant. IDR1 encodes the Gα subunit of the heterotrimeric G protein (also known as RGA1), and this protein was localized in nucleus and to plasma membrane or cell periphery. Further investigations indicated that the significantly increased drought tolerance in idr1-1 mutants stemmed from a range of physiological and morphological changes, including greater leaf potentials, increased proline contents, heightened leaf thickness and upregulation of antioxidant-synthesizing and drought-induced genes, under drought-stressed conditions. Especially, reactive oxygen species (ROS) production might be remarkably impaired, while ROS-scavenging ability appeared to be markedly enhanced due to significantly elevated expression of ROS-scavenging enzyme genes in idr1-1 mutants under drought-stressed conditions. In addition, idr1-1 mutants showed reduced expression of OsBRD1. Altogether, these results suggest that mutation of IDR1 leads to alterations in multiple layers of regulations, which ultimately leads to changes in the physiological and morphological traits and limiting of ROS levels, and thereby confers obviously increased drought tolerance to the idr1-1 mutant.

Genome-wide identification and comparative analysis of diacylglycerol kinase (DGK) gene family and their expression profiling in Brassica napus under abiotic stress

BACKGROUND

Diacylglycerol kinases (DGKs) are signaling enzymes that play pivotal roles in response to abiotic and biotic stresses by phosphorylating diacylglycerol (DAG) to form phosphatidic acid (PA). However, no comprehensive analysis of the DGK gene family had previously been reported in B. napus and its diploid progenitors (B. rapa and B. oleracea).

RESULTS

In present study, we identified 21, 10, and 11 DGK genes from B. napus, B. rapa, and B. oleracea, respectively, which all contained conserved catalytic domain and were further divided into three clusters. Molecular evolutionary analysis showed that speciation and whole-genome triplication (WGT) was critical for the divergence of duplicated DGK genes. RNA-seq transcriptome data revealed that, with the exception of BnaDGK4 and BnaDGK6, BnaDGK genes have divergent expression patterns in most tissues. Furthermore, some DGK genes were upregulated or downregulated in response to hormone treatment and metal ion (arsenic and cadmium) stress. Quantitative real-time PCR analysis revealed that different BnaDGK genes contribute to seed oil content.

CONCLUSIONS

Together, our results indicate that DGK genes have diverse roles in plant growth and development, hormone response, and metal ion stress, and in determining seed oil content, and lay a foundation for further elucidating the roles of DGKs in Brassica species.

Comprehensive Genomic Analysis and Expression Profiling of Diacylglycerol Kinase (DGK) Gene Family in Soybean (Glycine max) under Abiotic Stresses

Diacylglycerol kinase (DGK) is an enzyme that plays a pivotal role in abiotic and biotic stress responses in plants by transforming the diacylglycerol into phosphatidic acid. However, there is no report on the characterization of soybean DGK genes in spite of the availability of the soybean genome sequence. In this study, we performed genome-wide analysis and expression profiling of the DGK gene family in the soybean genome. We identified 12 DGK genes (namely GmDGK1-12) which all contained conserved catalytic domains with protein lengths and molecular weights ranging from 436 to 727 amino acids (aa) and 48.62 to 80.93 kDa, respectively. Phylogenetic analyses grouped GmDGK genes into three clusters-cluster I, cluster II, and cluster III-which had three, four, and five genes, respectively. The qRT-PCR analysis revealed significant GmDGK gene expression levels in both leaves and roots coping with polyethylene glycol (PEG), salt, alkali, and salt/alkali treatments. This work provides the first characterization of the DGK gene family in soybean and suggests their importance in soybean response to abiotic stress. These results can serve as a guide for future studies on the understanding and functional characterization of this gene family.

Diacylglycerol Kinases Are Widespread in Higher Plants and Display Inducible Gene Expression in Response to Beneficial Elements, Metal, and Metalloid Ions

Diacylglycerol kinases (DGKs) are pivotal signaling enzymes that phosphorylate diacylglycerol (DAG) to yield phosphatidic acid (PA). The biosynthesis of PA from phospholipase D (PLD) and the coupled phospholipase C (PLC)/DGK route is a crucial signaling process in eukaryotic cells. Next to PLD, the PLC/DGK pathway is the second most important generator of PA in response to biotic and abiotic stresses. In eukaryotic cells, DGK, DAG, and PA are implicated in vital processes such as growth, development, and responses to environmental cues. A plethora of DGK isoforms have been identified so far, making this a rather large family of enzymes in plants. Herein we performed a comprehensive phylogenetic analysis of DGK isoforms in model and crop plants in order to gain insight into the evolution of higher plant DGKs. Furthermore, we explored the expression profiling data available in public data bases concerning the regulation of plant DGK genes in response to beneficial elements and other metal and metalloid ions, including silver (Ag), aluminum (Al), arsenic (As), cadmium (Cd), chromium (Cr), mercury (Hg), and sodium (Na). In all plant genomes explored, we were able to find DGK representatives, though in different numbers. The phylogenetic analysis revealed that these enzymes fall into three major clusters, whose distribution depends on the composition of structural domains. The catalytic domain conserves the consensus sequence GXGXXG/A where ATP binds. The expression profiling data demonstrated that DGK genes are rapidly but transiently regulated in response to certain concentrations and time exposures of beneficial elements and other ions in different plant tissues analyzed, suggesting that DGKs may mediate signals triggered by these elements. Though this evidence is conclusive, further signaling cascades that such elements may stimulate during hormesis, involving the phosphoinositide signaling pathway and DGK genes and enzymes, remain to be elucidated.