Isolation and characterization of S-Adenosylmethionine synthase gene from cucumber and responsive to abiotic stress

Tandem mass tag (TMT)-based quantitative proteomics analysis reveals the different responses of contrasting alfalfa varieties to drought stress

BACKGROUND

Drought stress restricts the growth, distribution and productivity of alfalfa (Medicago sativa L.). In order to study the response differences of alfalfa cultivars to drought stress, we previously carried out physiological and molecular comparative analysis on two alfalfa varieties with contrasting drought resistance (relatively drought-tolerant Longdong and drought-sensitive Algonquin). However, the differences in proteomic factors of the two varieties in response to drought stress still need to be further studied. Therefore, TMT-based quantitative proteomic analysis was performed using leaf tissues of the two alfalfa cultivars to identify and uncover differentially abundant proteins (DAPs).

RESULTS

In total, 677 DAPs were identified in Algonquin and 277 in Longdong under drought stress. Subsequently, we conducted various bioinformatics analysis on these DAPs, including subcellular location, functional classification and biological pathway enrichment. The first two main COG functional categories of DAPs in both alfalfa varieties after drought stress were 'Translation, ribosomal structure and biogenesis' and 'Posttranslational modification, protein turnover, chaperones'. According to KEGG database, the DAPs of the two alfalfa cultivars after drought treatment were differentially enriched in different biological pathways. The DAPs from Algonquin were enriched in 'photosynthesis' and 'ribosome'. The pathways of 'linoleic acid metabolism', 'protein processing in endoplasmic reticulum' and 'RNA transport' in Longdong were significantly enriched. Finally, we found significant differences in DAP enrichment and expression patterns between Longdong and Algonquin in glycolysis/glycogenesis, TCA cycle, photosynthesis, protein biosynthesis, flavonoid and isoflavonoid biosynthesis, and plant-pathogen interaction pathway after drought treatment.

CONCLUSIONS

The differences of DAPs involved in various metabolic pathways may explain the differences in the resistance of the two varieties to drought stress. These DAPs can be used as candidate proteins for molecular breeding of alfalfa to cultivate new germplasm with more drought tolerance to adapt to unfavorable environments.

Research Advancements in Salt Tolerance of Cucurbitaceae: From Salt Response to Molecular Mechanisms

Soil salinization severely limits the quality and productivity of economic crops, threatening global food security. Recent advancements have improved our understanding of how plants perceive, signal, and respond to salt stress. The discovery of the Salt Overly Sensitive (SOS) pathway has been crucial in revealing the molecular mechanisms behind plant salinity tolerance. Additionally, extensive research into various plant hormones, transcription factors, and signaling molecules has greatly enhanced our knowledge of plants' salinity tolerance mechanisms. Cucurbitaceae plants, cherished for their economic value as fruits and vegetables, display sensitivity to salt stress. Despite garnering some attention, research on the salinity tolerance of these plants remains somewhat scattered and disorganized. Consequently, this article offers a review centered on three aspects: the salt response of Cucurbitaceae under stress; physiological and biochemical responses to salt stress; and the current research status of their molecular mechanisms in economically significant crops, like cucumbers, watermelons, melon, and loofahs. Additionally, some measures to improve the salt tolerance of Cucurbitaceae crops are summarized. It aims to provide insights for the in-depth exploration of Cucurbitaceae's salt response mechanisms, uncovering the roles of salt-resistant genes and fostering the cultivation of novel varieties through molecular biology in the future.

CRISPR-Cas9-mediated construction of a cotton CDPK mutant library for identification of insect-resistance genes

Calcium-dependent protein kinases (CDPKs) act as key signal transduction enzymes in plants, especially in response to diverse stresses, including herbivory. In this study, a comprehensive analysis of the CDPK gene family in upland cotton revealed that GhCPKs are widely expressed in multiple cotton tissues and respond positively to various biotic and abiotic stresses. We developed a strategy for screening insect-resistance genes from a CRISPR-Cas9 mutant library of GhCPKs. The library was created using 246 single-guide RNAs targeting the GhCPK gene family to generate 518 independent T0 plants. The average target-gene coverage was 86.18%, the genome editing rate was 89.49%, and the editing heritability was 82%. An insect bioassay in the field led to identification of 14 GhCPK mutants that are resistant or susceptible to insects. The mutant that showed the clearest insect resistance, cpk33/74 (in which the homologous genes GhCPK33 and GhCPK74 were knocked out), was selected for further study. Oral secretions from Spodoptera litura induced a rapid influx of Ca2+ in cpk33/74 leaves, resulting in a significant increase in jasmonic acid content. S-adenosylmethionine synthase is an important protein involved in plant stress response, and protein interaction experiments provided evidence for interactions of GhCPK33 and GhCPK74 with GhSAMS1 and GhSAM2. In addition, virus-induced gene silencing of GhSAMS1 and GhSAM2 in cotton impaired defense against S. litura. This study demonstrates an effective strategy for constructing a mutant library of a gene family in a polyploid plant species and offers valuable insights into the role of CDPKs in the interaction between plants and herbivorous insects.

Genome-wide identification of SAMS gene family in Cucurbitaceae and the role of ClSAMS1 in watermelon tolerance to abiotic stress

S-Adenosyl-L-methionine (SAM) is widely involved in plant growth, development, and abiotic stress response. SAM synthetase (SAMS) is the key enzyme that catalyzes the synthesis of SAM from methionine and ATP. However, the SAMS gene family has not been identified and their functions have not been characterized in most Cucurbitaceae plants. Here, a total of 30 SAMS genes were identified in nine Cucurbitaceae species and they were categorized into 3 subfamilies. Physicochemical properties and gene structure analysis showed that the SAMS protein members are tightly conserved. Further analysis of the cis-regulatory elements (CREs) of SAMS genes' promoter implied their potential roles in stress tolerance. To further understand the molecular functions of SAMS genes, watermelon SAMSs (ClSAMSs) were chosen to analyze the expression patterns in different tissues and under various abiotic stress and hormone responses. Among the investigated genes, ClSAMS1 expression was observed in all tissues and found to be up-regulated by abiotic stresses including salt, cold and drought treatments as well as exogenous hormone treatments including ETH, SA, MeJA and ABA. Furthermore, knockdown of ClSAMS1 via virus-induced gene silencing (VIGS) decreased SAM contents in watermelon seedings. The pTRSV2-ClSAMS1 plants showed reduced susceptibility to drought, cold and NaCl stress, indicating a positive role of ClSAMS1 in abiotic stresses tolerance. Those results provided candidate SAMS genes to regulate plant resistance against abiotic stresses in Cucurbitaceae plants.

Integrative physiological, metabolomic, and transcriptomic analysis reveals the drought responses of two apple rootstock cultivars

BACKGROUND

Drought is considered the main environmental factor restricting apple production and thus the development of the apple industry. Rootstocks play an important role in enhancing the drought tolerance of apple plants. Studies of the physiology have demonstrated that 'ZC9-3' is a strong drought-resistant rootstock, whereas 'Jizhen-2' is a weak drought-resistant rootstock. However, the metabolites in these two apple rootstock varieties that respond to drought stress have not yet been characterized, and the molecular mechanisms underlying their responses to drought stress remain unclear.

RESULTS

In this study, the physiological and molecular mechanisms underlying differences in the drought resistance of 'Jizhen-2' (drought-sensitive) and 'ZC9-3' (drought-resistant) apple rootstocks were explored. Under drought stress, the relative water content of the leaves was maintained at higher levels in 'ZC9-3' than in 'Jizhen-2', and the photosynthetic, antioxidant, and osmoregulatory capacities of 'ZC9-3' were stronger than those of 'Jizhen-2'. Metabolome analysis revealed a total of 95 and 156 differentially accumulated metabolites in 'Jizhen-2' and 'ZC9-3' under drought stress, respectively. The up-regulated metabolites in the two cultivars were mainly amino acids and derivatives. Transcriptome analysis revealed that there were more differentially expressed genes and transcription factors in 'ZC9-3' than in 'Jizhen-2' throughout the drought treatment. Metabolomic and transcriptomic analysis revealed that amino acid biosynthesis pathways play key roles in mediating drought resistance in apple rootstocks. A total of 13 metabolites, including L-α-aminoadipate, L-homoserine, L-threonine, L-isoleucine, L-valine, L-leucine, (2S)-2-isopropylmalate, anthranilate, L-tryptophan, L-phenylalanine, L-tyrosine, L-glutamate, and L-proline, play an important role in the difference in drought resistance between 'ZC9-3' and 'Jizhen-2'. In addition, 13 genes encoding O-acetylserine-(thiol)-lyase, S-adenosylmethionine synthetase, ketol-acid isomeroreductase, dihydroxyacid dehydratase, isopropylmalate isomerase, branched-chain aminotransferase, pyruvate kinase, 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase, N-acetylglutamate-5-P-reductase, and pyrroline-5-carboxylate synthetase positively regulate the response of 'ZC9-3' to drought stress.

CONCLUSIONS

This study enhances our understanding of the response of apple rootstocks to drought stress at the physiological, metabolic, and transcriptional levels and provides key insights that will aid the cultivation of drought-resistant apple rootstock cultivars. Especially, it identifies key metabolites and genes underlying the drought resistance of apple rootstocks.

The plant cytosolic m6A RNA methylome stabilizes photosynthesis in the cold

The sessile lifestyle of plants requires an immediate response to environmental stressors that affect photosynthesis, growth, and crop yield. Here, we showed that three abiotic perturbations-heat, cold, and high light-triggered considerable changes in the expression signatures of 42 epitranscriptomic factors (writers, erasers, and readers) with putative chloroplast-associated functions that formed clusters of commonly expressed genes in Arabidopsis. The expression changes under all conditions were reversible upon deacclimation, identifying epitranscriptomic players as modulators in acclimation processes. Chloroplast dysfunctions, particularly those induced by the oxidative stress-inducing norflurazon in a largely GENOME UNCOUPLED-independent manner, triggered retrograde signals to remodel chloroplast-associated epitranscriptomic expression patterns. N6-methyladenosine (m6A) is known as the most prevalent RNA modification and impacts numerous developmental and physiological functions in living organisms. During cold treatment, expression of components of the primary nuclear m6A methyltransferase complex was upregulated, accompanied by a significant increase in cellular m6A mRNA marks. In the cold, the presence of FIP37, a core component of the writer complex, played an important role in positive regulation of thylakoid structure, photosynthetic functions, and accumulation of photosystem I, the Cytb6f complex, cyclic electron transport proteins, and Curvature Thylakoid1 but not that of photosystem II components and the chloroplast ATP synthase. Downregulation of FIP37 affected abundance, polysomal loading, and translation of cytosolic transcripts related to photosynthesis in the cold, suggesting m6A-dependent translational regulation of chloroplast functions. In summary, we identified multifaceted roles of the cellular m6A RNA methylome in coping with cold; these were predominantly associated with chloroplasts and served to stabilize photosynthesis.

cGMP functions as an important messenger involved in SlSAMS1-regulated salt stress tolerance in tomato

Salt stress adversely affects the growth, development, and yield of tomato (Solanum lycopersicum). SAM Synthetase (SAMS), which is responsible for the biosynthesis of S-adenosylmethionine (SAM, a precursor of polyamine biosynthesis), participates in plant response to abiotic stress. However, the regulatory mechanism of SAMS-mediated salt stress tolerance remains elusive. In this study, we characterized a SAMS homologue SlSAMS1 in tomato. We found that SlSAMS1 is highly expressed in tomato roots, and its expression can be induced by salt stress. Crucially, overexpression of SlSAMS1 in tomato enhances salt stress tolerance. Through metabolomic profiling, we identified some differentially accumulated metabolites, especially, a secondary messenger guanosine 3',5'-cyclic monophosphate (cGMP) which may play a key role in SlSAMS1-regulated salt tolerance. A series of physiological and biochemical data suggest that cGMP alleviates salt stress-induced growth inhibition, and potentially acts downstream of the polyamine-nitric oxide (PA-NO) signaling pathway to trigger H2O2 signaling in response to salt stress. Taken together, the study reveals that SlSAMS1 regulates tomato salt tolerance via the PA-NO-cGMP-H2O2 signal module. Our findings elucidate the regulatory pathway of SlSAMS1-induced plant response to salt stress and indicate a pivotal role of cGMP in salt tolerance.

SlSAMS1 enhances salt tolerance through regulation DNA methylation of SlGI in tomato

S-adenosylmethionine (SAM), which is synthesized from methionine and ATP catalyzed by S-adenosylmethionine synthetase (SAMS), is an important methyl donor in plants. SAMS and DNA methylation play an important role in the plant response to abiotic stresses. Previous studies have shown that SAMS improves salt tolerance in tomato plants, but it is not clear whether the DNA methylation pathway mediates SAMS-induced salt tolerance. This study confirmed that SlSAMS1-overexpressing plants exhibited improved salt tolerance. Through whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing (RNA-seq) analysis, the study screened the circadian rhythm pathway and identified the gene SlGI in this pathway, which was regulated by SlSAMS1. The gene body region of SlGI, the core gene of the circadian rhythm pathway, was hypermethylated in SlSAMS1-overexpressing plants, and its expression level was significantly increased. Furthermore, the SlGI-overexpressing plants showed higher salt tolerance, less reduction in plant height and fresh weight, lower electrolyte leakage, malondialdehyde and H2O2 content, and higher antioxidant enzyme activity compared to wild type plants. Therefore, SlSAMS1-overexpressing plants regulated significant changes in CHG-type methylation sites of the SlGI gene body and its expression levels, leading to an enhanced salt tolerance of tomato plants.

The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress

Masson pine (Pinus massoniana Lamb.) is a major fast-growing woody tree species and pioneer species for afforestation in barren sites in southern China. However, the regulatory mechanism of gene expression in P. massoniana under drought remains unclear. To uncover candidate microRNAs, their expression profiles, and microRNA-mRNA interactions, small RNA-seq was used to investigate the transcriptome from seedling roots under drought and rewatering in P. massoniana. A total of 421 plant microRNAs were identified. Pairwise differential expression analysis between treatment and control groups unveiled 134, 156, and 96 differential expressed microRNAs at three stages. These constitute 248 unique microRNAs, which were subsequently categorized into six clusters based on their expression profiles. Degradome sequencing revealed that these 248 differentially expressed microRNAs targeted 2069 genes. Gene Ontology enrichment analysis suggested that these target genes were related to translational and posttranslational regulation, cell wall modification, and reactive oxygen species scavenging. miRNAs such as miR482, miR398, miR11571, miR396, miR166, miRN88, and miRN74, along with their target genes annotated as F-box/kelch-repeat protein, 60S ribosomal protein, copper-zinc superoxide dismutase, luminal-binding protein, S-adenosylmethionine synthase, and Early Responsive to Dehydration Stress may play critical roles in drought response. This study provides insights into microRNA responsive to drought and rewatering in Masson pine and advances the understanding of drought tolerance mechanisms in Pinus.

Physiological and proteomic analyses reveal the important role of arbuscular mycorrhizal fungi on enhancing photosynthesis in wheat under cadmium stress

Arbuscular mycorrhizal fungi (AMF) are important in the phytoremediation of cadmium (Cd). Improving photosynthesis under Cd stress helps to increase crop yields. However, the molecular regulatory mechanisms of AMF on photosynthetic processes in wheat (Triticum aestivum) under Cd stress remain unclear. This study utilized physiological and proteomic analyses to reveal the key processes and related genes of AMF that regulate photosynthesis under Cd stress. The results showed that AMF promoted the accumulation of Cd in the roots of wheat but significantly reduced the content of Cd in the shoots and grains. The photosynthetic rates, stomatal conductance, transpiration rates, chlorophyll content, and accumulation of carbohydrates under Cd stress were increased by AMF symbiosis. Proteomic analysis showed that AMF significantly induced the expression of two enzymes involved in the chlorophyll biosynthetic pathway (coproporphyrinogen oxidase and Mg-protoporphyrin IX chelatase), improved the expression of two proteins related to CO₂ assimilation (ribulose-1,5-bisphosphate carboxylase and malic enzyme), and increased the expression of S-adenosylmethionine synthase, which positively regulates abiotic stress. Therefore, AMF may regulate photosynthesis under Cd stress by promoting chlorophyll biosynthesis, carbon assimilation, and S-adenosylmethionine metabolism.

Harnessing enzyme cofactors and plant metabolism: an essential partnership

Cofactors are fundamental to the catalytic activity of enzymes. Additionally, because plants are a critical source of several cofactors (i.e., including their vitamin precursors) within the context of human nutrition, there have been several studies aiming to understand the metabolism of coenzymes and vitamins in plants in detail. For example, compelling evidence has been brought forth regarding the role of cofactors in plants; specifically, it is becoming increasingly clear that an adequate supply of cofactors in plants directly affects their development, metabolism, and stress responses. Here, we review the state-of-the-art knowledge on the significance of coenzymes and their precursors with regard to general plant physiology and discuss the emerging functions attributed to them. Furthermore, we discuss how our understanding of the complex relationship between cofactors and plant metabolism can be used for crop improvement.

Roles of S-Adenosylmethionine and Its Derivatives in Salt Tolerance of Cotton

Salinity is a major abiotic stress that restricts cotton growth and affects fiber yield and quality. Although studies on salt tolerance have achieved great progress in cotton since the completion of cotton genome sequencing, knowledge about how cotton copes with salt stress is still scant. S-adenosylmethionine (SAM) plays important roles in many organelles with the help of the SAM transporter, and it is also a synthetic precursor for substances such as ethylene (ET), polyamines (PAs), betaine, and lignin, which often accumulate in plants in response to stresses. This review focused on the biosynthesis and signal transduction pathways of ET and PAs. The current progress of ET and PAs in regulating plant growth and development under salt stress has been summarized. Moreover, we verified the function of a cotton SAM transporter and suggested that it can regulate salt stress response in cotton. At last, an improved regulatory pathway of ET and PAs under salt stress in cotton is proposed for the breeding of salt-tolerant varieties.

Interactions of Polyamines and Phytohormones in Plant Response to Abiotic Stress

Numerous environmental conditions negatively affect plant production. Abiotic stresses, such as salinity, drought, temperature, and heavy metals, cause damage at the physiological, biochemical, and molecular level, and limit plant growth, development, and survival. Studies have indicated that small amine compounds, polyamines (PAs), play a key role in plant tolerance to various abiotic stresses. Pharmacological and molecular studies, as well as research using genetic and transgenic approaches, have revealed the favorable effects of PAs on growth, ion homeostasis, water maintenance, photosynthesis, reactive oxygen species (ROS) accumulation, and antioxidant systems in many plant species under abiotic stress. PAs display a multitrack action: regulating the expression of stress response genes and the activity of ion channels; improving the stability of membranes, DNA, and other biomolecules; and interacting with signaling molecules and plant hormones. In recent years the number of reports indicating crosstalk between PAs and phytohormones in plant response to abiotic stresses has increased. Interestingly, some plant hormones, previously known as plant growth regulators, can also participate in plant response to abiotic stresses. Therefore, the main goal of this review is to summarize the most significant results that represent the interactions between PAs and plant hormones, such as abscisic acid, brassinosteroids, ethylene, jasmonates, and gibberellins, in plants under abiotic stress. The future perspectives for research focusing on the crosstalk between PAs and plant hormones were also discussed.

Identification of cucumber S-adenosylmethionine decarboxylase genes and functional analysis of CsSAMDC3 in salt tolerance

As one of the key enzymes in the biosynthesis of polyamines, S-adenosylmethionine decarboxylase (SAMDC) plays an important role in plant stress resistance. In this study, four SAMDC genes (CsSAMDC1-4) were identified in cucumber (Cucumis sativus L.) and divided into three groups (I, II, and III) by phylogenetic analysis. Motif analysis suggested the existence of many conserved motifs, which is compatible with SAMDC protein classification. Gene structure analysis revealed that CsSAMDC2 and CsSAMDC3 in group I have no intron, which showed a similar response to salt stress by gene expression analysis. CsSAMDC3 responded differently to hormone and stress treatments, and was more susceptible to salt stress. Compared with wild-type (WT) tobacco, the activities of superoxide dismutase, peroxidase, and catalase were increased in CsSAMDC3-overexpressing tobacco under salt stress, but the content of electrolyte leakage, malondialdehyde, and hydrogen peroxide were decreased, which alleviated the inhibition of growth induced by salt stress. Under salt stress, overexpression of CsSAMDC3 in transgenic tobacco plants exhibited salt tolerance, mainly in the form of a significant increase in dry and fresh weight, the maximal quantum yield of PSII photochemistry, the net photosynthetic rate and the content of spermidine and spermine, while the content of putrescine was reduced. In addition, the expression levels of antioxidase-related coding genes (NtSOD, NtPOD, NtCAT) and PAs metabolism-related coding genes (NtSAMS, NtSPDS, NtSPMS, NtPAO) in transgentic plants was lower than WT under salt stress, which suggested that overexpression of CsSAMDC3 affected the expression of these genes. In summary, our results showed that CsSAMDC3 could be used as a potential candidate gene to improve salt tolerance of cucumber by regulating polyamine and antioxidant metabolism.

Ethylene: A Master Regulator of Plant-Microbe Interactions under Abiotic Stresses

The plant phytohormone ethylene regulates numerous physiological processes and contributes to plant-microbe interactions. Plants induce ethylene production to ward off pathogens after recognition of conserved microbe-associated molecular patterns (MAMPs). However, plant immune responses against pathogens are essentially not different from those triggered by neutral and beneficial microbes. Recent studies indicate that ethylene is an important factor for beneficial plant-microbial association under abiotic stress such as salt and heat stress. The association of beneficial microbes with plants under abiotic stresses modulates ethylene levels which control the expression of ethylene-responsive genes (ERF), and ERFs further regulate the plant transcriptome, epi-transcriptome, Na⁺/K⁺ homeostasis and antioxidant defense mechanisms against reactive oxygen species (ROS). Understanding ethylene-dependent plant-microbe interactions is crucial for the development of new strategies aimed at enhancing plant tolerance to harsh environmental conditions. In this review, we underline the importance of ethylene in beneficial plant-microbe interaction under abiotic stresses.

ROS scavenging and ion homeostasis is required for the adaptation of halophyte Karelinia caspia to high salinity

The halophyte Karelinia caspia has not only fodder and medical value but also can remediate saline-alkali soils. Our previous study showed that salt-secreting by salt glands is one of main adaptive strategies of K. caspia under high salinity. However, ROS scavenging, ion homeostasis, and photosynthetic characteristics responses to high salinity remain unclear in K. caspia. Here, physio-biochemical responses and gene expression associated with ROS scavenging and ions transport were tested in K. caspia subjected to 100-400 mM NaCl for 7 days. Results showed that both antioxidant enzymes (SOD, APX) activities and non-enzymatic antioxidants (chlorogenic acid, α-tocopherol, flavonoids, polyamines) contents were significantly enhanced, accompanied by up-regulating the related enzyme and non-enzymatic antioxidant synthesis gene (KcCu/Zn-SOD, KcAPX6, KcHCT, KcHPT1, Kcγ-TMT, KcF3H, KcSAMS and KcSMS) expression with increasing concentrations of NaCl. These responses are beneficial for removing excess ROS to maintain a stable level of H2O2 and O2 - without lipid peroxidation in the K. caspia response to high salt. Meanwhile, up-regulating expression of KcSOS1/2/3, KcNHX1, and KcAVP was linked to Na+ compartmentalization into vacuoles or excretion through salt glands in K. caspia. Notably, salt can improve the function of PSII that facilitate net photosynthetic rates, which is helpful to growing normally in high saline. Overall, the findings suggested that ROS scavenging systems and Na+/K+ transport synergistically contributed to redox equilibrium, ion homeostasis, and the enhancement of PSII function, thereby conferring high salt tolerance.

Bidirectional mRNA transfer between Cuscuta australis and its hosts

The holoparasitic dodder (Cuscuta spp.) is able to transfer mRNA and certain plant pathogens (e.g., viruses and bacteria) from the host plant. "Candidatus Liberibacter asiaticus," the phloem-limited causative agent of citrus Huanglongbing, can be transferred from citrus to periwinkle (Catharanthus roseus) mediated by dodder. However, characterization of mRNA transport between dodder and citrus/periwinkle remains unclear. In this study, we sequenced transcriptomes of dodder and its parasitizing host, sweet orange (Citrus sinensis "Newhall") and periwinkle (Catharanthus roseus), to identify and characterize mRNA transfer between dodder and the host plant during parasitism. The mRNA transfer between dodder and citrus/periwinkle was bidirectional and most of the transfer events occurred in the interface tissue. Compared with the citrus-dodder system, mRNA transfer in the periwinkle-dodder system was more frequent. Function classification revealed that a large number of mRNAs transferred between dodder and citrus/periwinkle were involved in secondary metabolism and stress response. Dodder transcripts encoding proteins associated with microtubule-based processes and cell wall biogenesis were transferred to host tissues. In addition, transcripts involved in translational elongation, plasmodesmata, and the auxin-activated signaling pathway were transmitted between dodder and citrus/periwinkle. In particular, transcripts involved in shoot system development and flower development were transferred between the host and dodder in both directions. The high abundance of dodder-origin transcripts, encoding MIP aquaporin protein, and S-adenosylmethionine synthetase 1 protein, in citrus and periwinkle tissues indicated they could play an important biological role in dodder-host interaction. In addition, the uptake of host mRNAs by dodder, especially those involved in seed germination and flower development, could be beneficial for the reproduction of dodder. The results of this study provide new insights into the RNA-based interaction between dodder and host plants.

Identification and Functional Analysis of the Caffeic Acid O-Methyltransferase (COMT) Gene Family in Rice (Oryza sativa L.)

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.

Physiological and multi-omics responses of Neoporphyra haitanensis to dehydration-rehydration cycles

BACKGROUND

Seaweeds in the upper intertidal zone experience extreme desiccation during low tide, followed by rapid rehydration during high tide. Porphyra sensu lato are typical upper intertidal seaweeds. Therefore, it is valuable to investigate the adaptive mechanisms of seaweed in response to dehydration-rehydration stress.

RESULTS

A reduction in photosynthetic capacity and cell shrinkage were observed when N. haitanensis was dehydrated, and such changes were ameliorated once rehydrated. And the rate and extent of rehydration were affected by the air flow speed, water content before rehydration, and storage temperature and time. Rapid dehydration at high air-flow speed and storage at - 20 °C with water content of 10% caused less damage to N. haitanensis and better-protected cell activity. Moreover, proteomic and metabolomic analyses revealed the abundance members of the differentially expressed proteins (DEPs) and differentially abundant metabolites (DAMs) mainly involved in antioxidant system and osmotic regulation. The ascorbic acid-glutathione coupled with polyamine antioxidant system was enhanced in the dehydration response of N. haitanensis. The increased soluble sugar content, the accumulated polyols, but hardly changed (iso)floridoside and insignificant amount of sucrose during dehydration indicated that polyols as energetically cheaper organic osmolytes might help resist desiccation. Interestingly, the recovery of DAMs and DEPs upon rehydration was fast.

CONCLUSIONS

Our research results revealed that rapid dehydration and storage at - 20 °C were beneficial for recovery of N. haitanensis. And the strategy to resist dehydration was strongly directed toward antioxidant activation and osmotic regulation. This work provided valuable insights into physiological changes and adaptative mechanism in desiccation, which can be applied for seaweed farming.

Differential protein abundance of vetiver grass in response to acid mine drainage

Acid mine drainage (AMD) is an acidic and metalliferous discharge that imposes oxidative stress on living things through bioaccumulation and physical exposure. The abandoned Tab-Simco mining site of Southern Illinois generates highly acidic AMD with elevated sulfate (SO₄ ^2- ) and various metals. Vetiver grass (Chrysopogon zizanioides) is effective for the remediation of Tab-Simco AMD at both mesocosm and microcosm levels over extended periods. In this study, we conducted a proteomic investigation of vetiver shoots under short and long-term exposure to AMD. Our objective was to decipher the physiological responses of vetiver to the combined abiotic stresses of AMD (metal and low pH). Differential regulation was observed for longer-term (56 days) exposure to AMD, which resulted in 17 upregulated and nine downregulated proteins, whereas shorter-term (7 days) exposure led to 14 upregulated and 14 downregulated proteins. There were significant changes to photosynthesis, including upregulation of electron transport chain proteins for light-dependent reactions after 56 days, whereas differential regulation of enzymes relating to C₄ carbon fixation was observed after 7 days. Significant changes in amino acid and nitrogen metabolism, including upregulation of ethylene and flavonoid biosynthesis, along with plant response to nitrogen starvation, were observed. Short-term changes also included upregulation of glutathione reductase and methionine sulfoxide reductase, whereas longer-term changes included changes in protein misfolding and ER-associated protein degradation for stress management and acclimation.

CsCDPK6, a CsSAMS1-Interacting Protein, Affects Polyamine/Ethylene Biosynthesis in Cucumber and Enhances Salt Tolerance by Overexpression in Tobacco

S-adenosylmethionine synthetase (SAMS) plays a crucial role in regulating stress responses. In a recent study, we found that overexpression of the cucumber gene CsSAMS1 in tobacco can affect the production of polyamines and ethylene, as well as enhancing the salt stress tolerance of tobacco, but the exact underlying mechanisms are elusive. The calcium-dependent protein kinase (CDPK) family is ubiquitous in plants and performs different biological functions in plant development and response to abiotic stress. We used a yeast two-hybrid system to detect whether the protein CDPK6 could interact with SAMS1 and verified their interaction by bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (Co-IP) assays. To further explore the function of cucumber CDPK6, we isolated and characterized CsCDPK6 in cucumber. CsCDPK6 is a membrane protein that is highly expressed under various abiotic stresses, including salt stress. It was also observed that ectopic overexpression of CsCDPK6 in tobacco enhanced salt tolerance. Under salt stress, CsCDPK6-overexpressing lines enhanced the survival rate and reduced stomatal apertures in comparison to wild-type (WT) lines, as well as lowering malondialdehyde (MDA) and hydrogen peroxide (H2O2) contents and causing less relative electrolyte leakage. Moreover, repression of CsCDPK6 expression by virus-induced gene silencing (VIGS) in cucumber seedling cotyledons under salt stress increased ethylene production and promoted the transformation from putrescine (Put) to spermidine (Spd) and spermine (Spm). These findings shed light on the interaction of CsSAMS1 and CsCDPK6, which functions positively to regulate salt stress in plants.

Metabolism and Regulatory Functions of O-Acetylserine, S-Adenosylmethionine, Homocysteine, and Serine in Plant Development and Environmental Responses

The metabolism of an organism is closely related to both its internal and external environments. Metabolites can act as signal molecules that regulate the functions of genes and proteins, reflecting the status of these environments. This review discusses the metabolism and regulatory functions of O-acetylserine (OAS), S-adenosylmethionine (AdoMet), homocysteine (Hcy), and serine (Ser), which are key metabolites related to sulfur (S)-containing amino acids in plant metabolic networks, in comparison to microbial and animal metabolism. Plants are photosynthetic auxotrophs that have evolved a specific metabolic network different from those in other living organisms. Although amino acids are the building blocks of proteins and common metabolites in all living organisms, their metabolism and regulation in plants have specific features that differ from those in animals and bacteria. In plants, cysteine (Cys), an S-containing amino acid, is synthesized from sulfide and OAS derived from Ser. Methionine (Met), another S-containing amino acid, is also closely related to Ser metabolism because of its thiomethyl moiety. Its S atom is derived from Cys and its methyl group from folates, which are involved in one-carbon metabolism with Ser. One-carbon metabolism is also involved in the biosynthesis of AdoMet, which serves as a methyl donor in the methylation reactions of various biomolecules. Ser is synthesized in three pathways: the phosphorylated pathway found in all organisms and the glycolate and the glycerate pathways, which are specific to plants. Ser metabolism is not only important in Ser supply but also involved in many other functions. Among the metabolites in this network, OAS is known to function as a signal molecule to regulate the expression of OAS gene clusters in response to environmental factors. AdoMet regulates amino acid metabolism at enzymatic and translational levels and regulates gene expression as methyl donor in the DNA and histone methylation or after conversion into bioactive molecules such as polyamine and ethylene. Hcy is involved in Met-AdoMet metabolism and can regulate Ser biosynthesis at an enzymatic level. Ser metabolism is involved in development and stress responses. This review aims to summarize the metabolism and regulatory functions of OAS, AdoMet, Hcy, and Ser and compare the available knowledge for plants with that for animals and bacteria and propose a future perspective on plant research.

The key cyclic electron flow protein PGR5 associates with cytochrome b6f, and its function is partially influenced by the LHCII state transition

In plants and algae, PGR5-dependent cyclic electron flow (CEF) is an important regulator of acclimation to fluctuating environments, but how PGR5 participates in CEF is unclear. In this work, we analyzed two PGR5s in cucumber (Cucumis sativus L.) under different conditions and found that CsPGR5a played the dominant role in PGR5-dependent CEF. The results of yeast two-hybrid, biomolecular fluorescence complementation (BiFC), blue native PAGE, and coimmunoprecipitation (CoIP) assays showed that PGR5a interacted with PetC, Lhcb3, and PsaH. Furthermore, the intensity of the interactions was dynamic during state transitions, and the abundance of PGR5 attached to cyt b₆f decreased during the transition from state 1 to state 2, which revealed that the function of PGR5a is related to the state transition. We proposed that PGR5 is a small mobile protein that functions when attached to protein complexes.

Phosphoproteomic Profiling Reveals Early Salt-Responsive Mechanisms in Two Foxtail Millet Cultivars

Excess soluble salts in saline soils are harmful to most plants. Understanding the biochemical responses to salts in plants and studying the salt tolerance-associated genetic resources in nature will contribute to the improvement of salt tolerance in crops. As an emerging model crop, foxtail millet (Setaria italica L.) has been regarded as a novel species for stress resistance investigation. Here, the dynamic proteomic and phosphoproteomic profiling of two foxtail millet varieties of An04 and Yugu2 with contrasting salt tolerance characteristics were investigated under salt stress. In total, 10,366 sites representing to 2,862 proteins were detected and quantified. There were 759 and 990 sites corresponding to 484 and 633 proteins identified under salinity in An04 and Yugu2, respectively, and 1,264 and 1,131 phosphorylation sites corresponding to 789 and 731 proteins were identified between these two varieties before and after salt stress, respectively. The differentially-regulated phosphoproteins (DRPPs) were mainly involved in signal transduction, regulation of gene expression, translation, ion transport, and metabolism processes. Yugu2 possessed signal perception and transduction capabilities more rapidly and had a more intense response compared with An04 upon salinity. The sucrose metabolism pathway, in particularly, might play a vital role in salt response in foxtail millet, which not only provides UDP-glucose for the cellulose synthesis and energy production, but also promotes flavonoid related synthesis to enhance the salt tolerance ability. Over-expressing the phospho-mimic sucrose synthase (SuS) (SuS ^S10D ) in soybean roots enhanced salt tolerance compared with over-expressing SuS lines. The knowledge of this research will shed light on elucidating the mechanisms of salt response, and pave the way for crop varieties innovation and cultivation under salinity and stresses.

The regulation of ethylene biosynthesis: a complex multilevel control circuitry

The gaseous plant hormone ethylene is produced by a fairly simple two-step biosynthesis route. Despite this pathway's simplicity, recent molecular and genetic studies have revealed that the regulation of ethylene biosynthesis is far more complex and occurs at different layers. Ethylene production is intimately linked with the homeostasis of its general precursor S-adenosyl-l-methionine (SAM), which experiences transcriptional and posttranslational control of its synthesising enzymes (SAM synthetase), as well as the metabolic flux through the adjacent Yang cycle. Ethylene biosynthesis continues from SAM by two dedicated enzymes: 1-aminocyclopropane-1-carboxylic (ACC) synthase (ACS) and ACC oxidase (ACO). Although the transcriptional dynamics of ACS and ACO have been well documented, the first transcription factors that control ACS and ACO expression have only recently been discovered. Both ACS and ACO display a type-specific posttranslational regulation that controls protein stability and activity. The nonproteinogenic amino acid ACC also shows a tight level of control through conjugation and translocation. Different players in ACC conjugation and transport have been identified over the years, however their molecular regulation and biological significance is unclear, yet relevant, as ACC can also signal independently of ethylene. In this review, we bring together historical reports and the latest findings on the complex regulation of the ethylene biosynthesis pathway in plants.

Stage-specific protein regulation during somatic embryo development of Carica papaya L. 'Golden'

Somatic embryogenesis is an important biotechnological technique for large-scale propagation of elite genotypes. Identifying stage-specific compounds associated with somatic embryo development can help elucidate the ontogenesis of Carica papaya L. somatic embryos and improve tissue culture protocols. To identify the stage-specific proteins that are present during the differentiation of C. papaya somatic embryos, proteomic analyses of embryos at the globular, heart, torpedo and cotyledonary developmental stages were performed. Mass spectrometry data have been deposited in the ProteomeXchange with the dataset identifier PXD021107. Comparative proteomic analyses revealed a total of 801 proteins, with 392 classified as differentially accumulated proteins in at least one of the developmental stages. The globular-staged presented a higher number of unique proteins (16), and 7 were isoforms of 60S ribosomal proteins, suggesting high translational activity at the beginning of somatic embryogenesis. Proteins related to mitochondrial metabolism accumulated to a high degree at the early developmental stages and then decreased with increasing development, and they contributed to cell homeostasis in early somatic embryos. A progressive increase in the accumulation of vicilin, late embryogenesis abundant proteins and chloroplastic proteins that lead to somatic embryo maturation was also observed. The differential accumulation of acetylornithine deacetylase and S-adenosylmethionine synthase 2 proteins was correlated with increases in putrescine and spermidine contents, which suggests that both polyamines should be tested to determine whether they increase the conversion rates of globular- to cotyledonary-staged somatic embryos. Taken together, the results showed that somatic embryo development in C. papaya is regulated by the differential accumulation of proteins, with ribosomal and mitochondrial proteins more abundant during the early somatic embryo stages and seed maturation proteins more abundant during the late stages.

S-Adenosyl-l-Methionine Promotes Metabolism of Fungicides in Cabernet Sauvignon (Vitis vinifera L.) Berries

Fungicides are commonly used to prevent and treat grape (Vitis vinifera L.) diseases; however, they are potentially toxic to humans. Herein, we show that the application of S-adenosyl-l-methionine (SAM) accelerated the metabolism of various fungicides in Cabernet Sauvignon berries. The substances and enzymes involved in the metabolism of fungicides were analyzed to elucidate the effects of SAM. Results showed that SAM improved the production rate of superoxide anion, the hydrogen peroxide content, and the activities of superoxide dismutase, catalase, and peroxidase in azoxystrobin-treated berries. Additionally, SAM had a positive effect on the content of reduced glutathione and on the activities of glutathione S-transferase, glutathione reductase, and glutathione peroxidase. Importantly, the stimulatory effect of SAM on fungicide metabolism was also observed for metalaxyl and thiophanate-methyl. These results suggest that SAM can be used to improve food safety.

Gibberellin mediates spermidine-induced salt tolerance and the expression of GT-3b in cucumber

Numerous studies have demonstrated that spermidine (Spd) plays a critical role in salt tolerance in plants, but the associated mechanism remains largely unknown. In this study, we investigated the role of gibberellin (GA) in Spd-induced salt tolerance and the expression of GT-3b transcription factor in cucumber. The results showed that exogenous Spd significantly increased the salt tolerance of cucumber plants, while its effects were compromised in the presence of methylglyoxal bis-guanylhydrazone (MGBG), an inhibitor of Spd biosynthesis. Interestingly, the expression of GT-3b was significantly induced by Spd under salt stress, and the promoter sequence of GT-3b was predicted to contain cis-acting regulatory elements that could respond to phytohormones, such as GA, salicylic acid (SA), and methyl jasmonate (MeJA). The application of GA3, SA and MeJA as foliar spray could induce the expression of GT-3b. In addition, exogenous Spd dramatically increased the expression of genes related to GA biosynthesis, the activity of gibberellin oxidase, and the accumulation of GA3, whereas these effects were attenuated in the MGBG-treated plants. Furthermore, the application of GA3 increased GT-3b expression and salt tolerance, whereas these effects were blocked when the plants were treated with paclobutrazol (PAZ), a GA biosynthesis inhibitor. Similarly, the Spd-induced salt tolerance was compromised in the PAZ-treated plants. Our results suggest that GA mediates Spd-induced salt tolerance and the expression of GT-3b in cucumber. These results provide a new perspective for understanding the molecular mechanism of Spd-regulated salt tolerance in plants.

Characterization of the CsPNG1 gene from cucumber and its function in response to salinity stress

Peptide: N-glycanase (PNGase; EC 3.5.1.52) is a deglycosylation enzyme that is responsible for deglycosylating misfolded glycoproteins in the endoplasmic reticulum. However, the role of PNGase in plants is largely unknown. Here, we cloned and characterized the function of peptide: N-glycanase (CsPNG1) from cucumber. The amino acid encoded by CsPNG1 gene contained a typical transglutaminase (TGase) catalytic triad domain and belonged to the "TGase superfamily". Subcellular localization showed that CsPNG1 was located in the cell membrane and nucleus. Promoter sequence analysis and qPCR tests showed that CsPNG1 could respond to a variety of abiotic stresses and hormone treatments. Yeast one-hybrid assays revealed the interaction between the transcription factor CsGT-3b and CsPNG1 promoter. Importantly, overexpression of CsPNG1 in tobacco increased the tolerance to salt stress of transgenic plants. In addition, CsPNG1 interacted with CsRAD23 family proteins and the C-terminal UBA domain of CsRAD23 protein was responsible for binding to CsPNG1, indicating that CsPNG1 was involved in the ER-associated degradation pathway (ERAD). Taken together, our study demonstrated that CsPNG1 plays a positive role in improving plant salt tolerance, and these findings might provide a basis for further functional analysis of CsPNG1 genes in abiotic stress and ERAD.

Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

BACKGROUND

Little is known about the molecular basis of seed size formation in endospermic seed of dicotyledons. The seed of castor bean (Ricinus communis L.) is considered as a model system in seed biology studies because of its persistent endosperms throughout seed development.

RESULTS

We compared the size of endosperm and endospermic cells between ZB107 and ZB306 and found that the larger seed size of ZB107 resulted from a higher cell count in the endosperm, which occupy a significant amount of the total seed volume. In addition, fresh weight, dry weight, and protein content of seeds were remarkably higher in ZB107 than in ZB306. Comparative proteomic and transcriptomic analyses were performed between large-seed ZB107 and small-seed ZB306, using isobaric tags for relative and absolute quantification (iTRAQ) and RNA-seq technologies, respectively. A total of 1416 protein species were identified, of which 173 were determined as differentially abundant protein species (DAPs). Additionally, there were 9545 differentially expressed genes (DEGs) between ZB306 and ZB107. Functional analyses revealed that these DAPs and DEGs were mainly involved in cell division and the metabolism of carbohydrates and proteins.

CONCLUSIONS

These findings suggest that both cell number and storage-component accumulation are critical for the formation of seed size, providing new insight into the potential mechanisms behind seed size formation in endospermic seeds.