Transcriptome and Metabolome Analyses Reveal an Insight of Chlorophyll, Photosynthesis, Metal Ion and Phenylpropanoids Related Pathways in Sugarcane Ratoon Chlorosis

BackgroundRatoon sugarcane (Saccharum officinarum) is susceptible to chlorosis, significantly reducing production. The molecular mechanism underlying this phenomenon remains unknown. We analyzed the transcriptome and metabolome of chlorotic and non-chlorotic sugarcane leaves from the same field to gain insight into the symptom. ResultsThe agronomic traits, like plant height, leaf number, stalk nod number, and tiller number, declined in chlorotic sugarcane. The chlorophyll content in chlorosis leaves was significantly lower than non-chlorotic leaves. A total of 11,776 differentially expressed genes (DEGs) were discovered in transcriptome analysis. In the KEGG enriched chlorophyll metabolism pathway, sixteen DEGs were found, eleven of which were down-regulated. Two photosynthesis pathways were also enriched, with 32 genes downregulated and four genes upregulated. Among the 81 enriched GO biological processes, there were four categories related to metal ion homeostasis and three related to metal ion transport. Approximately 400 metabolites were identified in metabolome analysis. The thirteen classified differentially expressed metabolites (DEMs) were found all down-regulated. The phenylpropanoid biosynthesis pathway was enriched in DEGs and DEMs, indicating phenylpropanoids' vital role in chlorosis. ConclusionsAccording to our study, chlorophyll production, metal ion metabolism, photosynthesis, and some secondary metabolites of the phenylpropanoid biosynthesis pathway, were considerably altered in chlorotic ratoon sugarcane. Our finding revealed the relation between chlorosis and these pathways, which would further the understanding of the mechanism of ratoon sugarcane chlorosis.

iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism of Golden-Yellow Leaf Mutant in Hybrid Paper Mulberry

Plant growth and development relies on the conversion of light energy into chemical energy, which takes place in the leaves. Chlorophyll mutant variations are important for studying certain physiological processes, including chlorophyll metabolism, chloroplast biogenesis, and photosynthesis. To uncover the mechanisms of the golden-yellow phenotype of the hybrid paper mulberry plant, this study used physiological, cytological, and iTRAQ-based proteomic analyses to compare the green and golden-yellow leaves of hybrid paper mulberry. Physiological results showed that the mutants of hybrid paper mulberry showed golden-yellow leaves, reduced chlorophyll, and carotenoid content, and increased flavonoid content compared with wild-type plants. Cytological observations revealed defective chloroplasts in the mesophyll cells of the mutants. Results demonstrated that 4766 proteins were identified from the hybrid paper mulberry leaves, of which 168 proteins displayed differential accumulations between the green and mutant leaves. The differentially accumulated proteins were primarily involved in chlorophyll synthesis, carotenoid metabolism, and photosynthesis. In addition, differentially accumulated proteins are associated with ribosome pathways and could enable plants to adapt to environmental conditions by regulating the proteome to reduce the impact of chlorophyll reduction on growth and survival. Altogether, this study provides a better understanding of the formation mechanism of the golden-yellow leaf phenotype by combining proteomic approaches.

Yeast β-Glucan Altered Intestinal Microbiome and Metabolome in Older Hens

The prebiotics- and probiotics-mediated positive modulation of the gut microbiota composition is considered a useful approach to improve gut health and food safety in chickens. This study explored the effects of yeast β-glucan (YG) supplementation on intestinal microbiome and metabolites profiles as well as mucosal immunity in older hens. A total of 256 43-week-old hens were randomly assigned to two treatments, with 0 and 200 mg/kg of YG. Results revealed YG-induced downregulation of toll-like receptors (TLRs) and cytokine gene expression in the ileum without any effect on the intestinal barrier. 16S rRNA analysis claimed that YG altered α- and β-diversity and enriched the relative abundance of class Bacilli, orders Lactobacillales and Enterobacteriales, families Lactobacillaceae and Enterobacteriaceae, genera Lactobacillus and Escherichia–Shigella, and species uncultured bacterium-Lactobacillus. Significant downregulation of cutin and suberin, wax biosynthesis, atrazine degradation, vitamin B6 metabolism, phosphotransferase system (PTS), steroid degradation, biosynthesis of unsaturated fatty acids, aminobenzoate degradation and quorum sensing and upregulation of ascorbate and aldarate metabolism, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism, pentose and glucuronate interconversions, steroid biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, sesquiterpenoid and triterpenoid biosynthesis, lysine degradation, and ubiquinone and other terpenoid-quinone biosyntheses were observed in YG-treated hens, as substantiated by the findings of untargeted metabolomics analysis. Overall, YG manifests prebiotic properties by altering gut microbiome and metabolite profiles and can downregulate the intestinal mucosal immune response of breeder hens.

Quantitative Proteome Profiling of a S-Nitrosoglutathione Reductase (GSNOR) Null Mutant Reveals a New Class of Enzymes Involved in Nitric Oxide Homeostasis in Plants

Nitric oxide (NO) is a short-lived radical gas that acts as a signaling molecule in all higher organisms, and that is involved in multiple plant processes, including germination, root growth, and fertility. Regulation of NO-levels is predominantly achieved by reaction of oxidation products of NO with glutathione to form S-nitrosoglutathione (GSNO), the principal bioactive form of NO. The enzyme S-nitrosoglutathione reductase (GSNOR) is a major route of NADH-dependent GSNO catabolism and is critical to NO homeostasis. Here, we performed a proteomic analysis examining changes in the total leaf proteome of an Arabidopsis thaliana GSNOR null mutant (hot5-2/gsnor1-3). Significant increases or decreases in proteins associated with chlorophyll metabolism and with redox and stress metabolism provide insight into phenotypes observed in hot5-2/gsnor1-3 plants. Importantly, we identified a significant increase in proteins that belong to the aldo-keto reductase (AKR) protein superfamily, AKR4C8 and 9. Because specific AKRs have been linked to NO metabolism in mammals, we expressed and purified A. thaliana AKR4C8 and 9 and close homologs AKR4C10 and 11 and determined that they have NADPH-dependent activity in GSNO and S-nitroso-coenzyme A (SNO-CoA) reduction. Further, we found an increase of NADPH-dependent GSNO reduction activity in hot5-2/gsnor1-3 mutant plants. These data uncover a new, NADPH-dependent component of NO metabolism that may be integrated with NADH-dependent GSNOR activity to control NO homeostasis in plants.

Comparative Transcriptomic Analysis Provides Novel Insights into the Blanched Stem of Oenanthe javanica

In the agricultural field, blanching is a technique used to obtain tender, sweet, and delicious water dropwort stems by blocking sunlight. The physiological and nutritional parameters of blanched water dropwort have been previously investigated. However, the molecular mechanism of blanching remains unclear. In the present study, we investigated transcriptomic variations for different blanching periods in the stem of water dropwort (pre, mid, post-blanching, and control). The results showed that many genes in pathways, such as photosynthesis, carbon fixation, and phytohormone signal transduction as well as transcription factors (TFs) were significantly dysregulated. Blanched stems of water dropwort showed the higher number of downregulated genes in pathways, such as photosynthesis, antenna protein, carbon fixation in photosynthetic organisms, and porphyrin and chlorophyll metabolism, which ultimately affect the photosynthesis in water dropwort. The genes of hormone signal transduction pathways (ethylene, jasmonic acid, brassinosteroid, and indole-3-acetic acid) showed upregulation in the post-blanched water dropwort plants. Overall, a higher number of genes coding for TFs, such as ERF, BHLH, MYB, zinc-finger, bZIP, and WRKY were overexpressed in blanched samples in comparison with the control. These genes and pathways participate in inducing the length, developmental processes, pale color, and stress tolerance of the blanched stem. Overall, the genes responsive to blanching, which were identified in this study, provide an effective foundation for further studies on the molecular mechanisms of blanching and photosynthesis regulations in water dropwort and other species.

Comparative Physiological and Proteomic Analyses Reveal the Mechanisms of Brassinolide-Mediated Tolerance to Calcium Nitrate Stress in Tomato

Secondary salinization caused by the overaccumulation of calcium nitrate [Ca(NO3)2] in soils due to excessive fertilization has become one of the major handicaps of protected vegetable production. Brassinolide, a bioactive plant steroid hormone, plays an important role in improving abiotic stress tolerance in plants. However, whether and how brassinolide (BR) can alleviate Ca(NO3)2 stress remains elusive. Here, we investigated the effects of exogenous BR on hydroponically grown tomato (Solanum lycopersicum L.) plants under Ca(NO3)2 stress through proteomics combined with physiological studies. Proteomics analysis revealed that Ca(NO3)2 stress affected the accumulation of proteins involved in photosynthesis, stress responses, and antioxidant defense, however, exogenous BR increased the accumulation of proteins involved in chlorophyll metabolism and altered the osmotic stress responses in tomatoes under Ca(NO3)2 stress. Further physiological studies supported the results of proteomics and showed that the exogenous BR-induced alleviation of Ca(NO3)2 stress was associated with the improvement of photosynthetic efficiency, levels of soluble sugars and proteins, chlorophyll contents, and antioxidant enzyme activities, leading to the reduction in the levels of reactive oxygen species and membrane lipid peroxidation, and promotion of the recovery of photosynthetic performance, energy metabolism, and plant growth under Ca(NO3)2 stress. These results show the importance of applying BR in protected agriculture as a means for the effective management of secondary salinization.

Effects of Long-Term Non-Pruning on Main Quality Constituents in ‘Dancong’ Tea (Camellia sinensis) Leaves Based on Proteomics and Metabolomics Analysis

‘Dancong’ tea is a famous traditional Oolong tea. In order to keep the original taste of “ancient tea trees”, most of the ’Dancong’ tea plants are planted in a single plant pattern without pruning. The objective of this study was to explore the effects of long-term non-pruning on main quality constituents in ‘Dancong’ tea. The results showed that the contents of free amino acids, chlorophylls, and floral-honey aromatic substances in tea leaves of unpruned tea plants were higher than those in every year pruned tea plants, while the catechin content in leaves of pruned tea plants was higher than that in leaves of unpruned tea plants. Quantitative proteomics analysis showed that most enzymes involved in biosynthesis of catechins were downregulated in leaves of unpruned tea plants. Five proteins involved in chlorophyll metabolism and 12 proteins related to photosynthesis were upregulated, and the results suggested that higher chlorophyll content and more efficient photosynthetic energy conversion may be important for the higher accumulation of special quality components in leaves of unpruned tea plants. The findings of this study will advance our understanding of the mechanism of formation of different metabolites in leaves of unpruned and pruned tea plants.

Adaptability to High Temperature and Stay-Green Genotypes Associated With Variations in Antioxidant, Chlorophyll Metabolism, and γ-Aminobutyric Acid Accumulation in Creeping Bentgrass Species

High temperature limits the cultivation and utilization of cool-season plants in many regions worldwide. Recently, extreme hot waves swept across the globe in summer, leading to enormous economic loss. The evaluation and identification of genotypic variation in thermotolerance within species are critical to breeding for environmental adaptation and also provide potential materials to explore thermo-resistant mechanism in plants. Forty-two accessions of creeping bentgrass (Agrostis stolonifera), which is a cool-season perennial grass for turf and ecological remediation, were collected from 15 different countries. Physiological traits, namely, chlorophyll (Chl) content, electrolyte leakage, photochemical efficiency, performance index on absorption basis, leaf relative water content, and osmotic potential were used to evaluate the heat tolerance of these materials in controlled growth chambers and field during summer. Stay-green and early-aging genotypes were selected to further reveal the potential mechanism of tolerance to senescence and heat damage associated with alterations in Chl metabolism, antioxidant and photosynthetic capacity, and endogenous γ-aminobutyric acid (GABA). Findings showed that there were significant genetic variations in physiological traits among 41 materials in response to high temperature stress. The 13M, PROVIDENCE, and LOFTS L-93 were the top three accessions with superior tolerance to heat and summer stress than other materials in terms of laboratory and field tests. In response to heat stress, the stay-green genotype PROVIDENCE exhibited significantly higher photochemical efficiency, net photosynthetic rate, transpiration rate, and water use efficiency than the heat-susceptible W6 6570. Delayed leaf senescence in relation to less Chl loss was detected in the PROVIDENCE associated with maintenance of significantly higher expression levels of Chl-anabolic genes (AsCHLH, AsPBGD, and AsPOR) and lower Chl-catabolic gene AsPPH under heat stress. Genetic attributes, such as better capacity to scavenge reactive oxygen species and higher endogenous GABA content could play positive roles in alleviating heat-induced senescence, oxidative damage, and metabolic disturbance in the PROVIDENCE.

Unravelling the Role of Piriformospora indica in Combating Water Deficiency by Modulating Physiological Performance and Chlorophyll Metabolism-Related Genes in Cucumis sativus

Water stress is the most critical aspect restricting the development of agriculture in regions with scarce water resources, which requires enhancing irrigation water-saving strategies. The current work discusses the potential application of the plant-strengthening root endophyte Piriformospora indica against moderate (25% less irrigation water) and severe (50% less irrigation water) water stress in comparison to the optimum irrigation conditions of greenhouse cucumbers. P. indica improved growth, nutrient content, and photosynthesis apparatus under normal or water-stress conditions. On the other hand, moderate and severe water stress reduced yield up to 47% and 83%, respectively, in non-colonized cucumber plants, while up to 28 and 78%, respectively, in P. indica-colonized plants. In terms of water-use efficiency (WUE), P. indica improved the WUE of colonized cucumber plants grown under moderate (26 L/kg) or severe stress (73 L/kg) by supporting colonized plants in producing higher yield per unit volume of water consumed by the crop in comparison to non-colonized plants under the same level of moderate (43 L/kg) or severe (81 L/kg) water stress. Furthermore, P. indica increased the indole-3-acetic acid (IAA) content, activity levels of catalase (CAT) and peroxidase (POD) with an apparent clear reduction in the abscisic acid (ABA), ethylene, malondialdehyde (MDA), proline contents and stomatal closure compared to non-stressed plants under both water-stress levels. In addition, chlorophyll a, b, a + b contents were increased in the leaves of the colonized plants under water-stress conditions. This improvement in chlorophyll content could be correlated with a significant increment in the transcripts of chlorophyll biosynthesis genes (protochlorophyllide oxidoreductase [POR], chlorophyll a oxygenase [CAO]) and a reduction in the chlorophyll degradation genes (PPH, pheophorbide a oxygenase [PAO], and red chlorophyll catabolite reductase [RCCR]). In conclusion, P. indica has the potential to enhance the cucumber yield grown under moderate water stress rather than severe water stress by improving WUE and altering the activity levels of antioxidant enzymes and chlorophyll metabolism-related genes.

Identification, Molecular Characteristic, and Expression Analysis of PIFs Related to Chlorophyll Metabolism in Tea Plant (Camellia sinensis)

The phytochrome-interacting factors (PIFs) proteins belong to the subfamily of basic helix–loop–helix (bHLH) transcription factors and play important roles in chloroplast development and chlorophyll biosynthesis. Currently, knowledge about the PIF gene family in Camellia sinensis remains very limited. In this study, seven PIF members were identified in the C. sinensis genome and named based on homology with AtPIF genes in Arabidopsis thaliana. All C. sinensis PIF (CsPIF) proteins have both the conserved active PHYB binding (APB) and bHLH domains. Phylogenetic analysis revealed that CsPIFs were clustered into four groups—PIF1, PIF3, PIF7, and PIF8—and most CsPIFs were clustered in pairs with their corresponding orthologs in Populus tremula. CsPIF members in the same group tended to display uniform or similar exon–intron distribution patterns and motif compositions. CsPIF genes were differentially expressed in C. sinensis with various leaf colors and strongly correlated with the expression of genes involved in the chlorophyll metabolism pathway. Promoter analysis of structural genes related to chlorophyll metabolism found DNA-binding sites of PIFs were abundant in the promoter regions. Protein–protein interaction networks of CsPIFs demonstrated a close association with phytochrome, PIF4, HY5, TOC1, COP1, and PTAC12 proteins. Additionally, subcellular localization and transcriptional activity analysis suggested that CsPIF3b was nuclear localized protein and possessed transcriptional activity. We also found that CsPIF3b could activate the transcription of CsHEMA and CsPOR in Nicotiana benthamiana leaves. This work provides comprehensive research of CsPIFs and would be helpful to further promote the regulation mechanism of PIF on chlorophyll metabolism in C. sinensis.