Combination of Transcriptomic, Proteomic, and Metabolomic Analysis Reveals the Ripening Mechanism of Banana Pulp

Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis

Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.

Transcriptomic and metabolomic analyses provide new insights into the appropriate harvest period in regenerated bulbs of Fritillaria hupehensis

INTRODUCTION

The bulb of Fritillaria hupehensis, a traditional cough and expectorant medicine, is usually harvested from June to September according to traditional cultivation experience, without practical scientific guidance. Although steroidal alkaloid metabolites have been identified in F. hupehensis, the dynamic changes in their levels during bulb development and their molecular regulatory mechanisms are poorly understood.

METHODS

In this study, integrative analyses of the bulbus phenotype, bioactive chemical investigations, and metabolome and transcriptome profiles were performed to systematically explore the variations in steroidal alkaloid metabolite levels and identify the genes modulating their accumulation and the corresponding regulatory mechanisms.

RESULTS

The results showed that weight, size, and total alkaloid content of the regenerated bulbs reached a maximum at IM03 (post-withering stage, early July), whereas peiminine content reached a maximum at IM02 (withering stage, early June). There were no significant differences between IM02 and IM03, indicating that regenerated bulbs could be harvested appropriately in early June or July. Peiminine, peimine, tortifoline, hupehenine, korseveramine, delafrine, hericenone N-oxide, korseveridine, puqiedinone, pingbeinone, puqienine B, puqienine E, pingbeimine A, jervine, and ussuriedine levels were upregulated in IM02 and IM03, compared with IM01 (vigorous growth stage, early April). The Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the accumulation of steroidal alkaloid metabolites mainly occurred prior to IM02. HMGR1, DXR, CAS1, CYP 90A1, and DET2 may play a positive role in peiminine, peimine, hupehenine, korseveramine, korseveridine, hericenone N-oxide, puqiedinone, delafrine, tortifoline, pingbeinone, puqienine B, puqienine E, pingbeimine A, jervine, and ussuriedine biosynthesis, whereas the downregulation of FPS1, SQE and 17-DHCR may lead to a reduction in peimisine levels. Weighted gene correlation network analysis showed that CYP 74A2-1, CYP 74A2-2, CYP 71A26-1, CYP 71A26-2, and CYP74A were negatively correlated with peiminine and pingbeimine A, whereas CYP R and CYP707A1 were positively correlated. . CYP 74A2-1 and CYP 74A2-2 may play a negative role in peimine and korseveridine biosynthesis, whereas CYP R plays a positive role. In addition, the highly expressed C2H2, HSF, AP2/ERF, HB, GRAS, C3H, NAC, MYB-related transcription factors (TFs), GARP-G2-like TFs, and WRKY may play positive roles in the accumulation of peiminine, peimine, korseveridine, and pingbeimine A.

DISCUSSION

These results provide new insights into scientific harvesting of F. hupehensis.

Role of integrated omics in unravelling fruit stress and defence responses during postharvest: A review

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Postharvest treatment and storage conditions influenced transcriptomic, proteomic and metabolomic profile of fruit.

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Multi-omics techniques can be used to identify biomarkers linked topostharvest changes and physiological responses.

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Omics techniques showed great potential to explore antagonistic fruit and pathogen interactions.

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Studies using multi-omics approach for fruit postharvest were explored in-depth..

Fruit are susceptible to quality loss and deterioration after harvest due to high metabolic and physiological activities. Over the last four decades various postharvest treatments have ensured maintenance of quality, control of diseases or decay by slowing down the postharvest ripening and senesce. The fruit quality change during postharvest however, has been mostly explored using physicochemical characteristics. Considering the complexity of fruit physiology and metabolism, the application of omics techniques could aid the in-depth analysis and understanding of fruit quality change during postharvest treatment. Therefore, this review presents recent information on the application of integrated omics (transcriptomics, proteomics, and metabolomics) in postharvest research, with an overview on fruit quality and safety. Trends in omics data analysis for fruit during postharvest handling was highlighted. The role of integrated omics in improving our understanding of fruit response during natural postharvest progression (towards decay) during storage, as well as in case of induced responses due to the application of biocontrols was discussed. The article concluded with the outlooks of future studies on the application of integrated omics as the catalyst for innovative postharvest solutions.

From fruit growth to ripening in plantain: a careful balance between carbohydrate synthesis and breakdown

In this study, we aimed to investigate for the first time different fruit development stages in plantain banana in order gain insights into the order of appearance and dominance of specific enzymes and fluxes. We examined fruit development in two plantain banana cultivars during the period between 2-12 weeks after bunch emergence using high-throughput proteomics, quantification of major metabolites, and analyses of metabolic fluxes. Starch synthesis and breakdown are processes that take place simultaneously. During the first 10 weeks fruits accumulated up to 48% of their dry weight as starch, and glucose 6-phosphate and fructose were important precursors. We found a unique amyloplast transporter and hypothesize that it facilitates the import of fructose. We identified an invertase originating from the Musa balbisiana genome that would enable carbon flow back to growth and starch synthesis and maintain a high starch content even during ripening. Enzymes associated with the initiation of ripening were involved in ethylene and auxin metabolism, starch breakdown, pulp softening, and ascorbate biosynthesis. The initiation of ripening was cultivar specific, with faster initiation being particularly linked to the 1-aminocyclopropane-1-carboxylate oxidase and 4-alpha glucanotransferase disproportionating enzymes. Information of this kind is fundamental to determining the optimal time for picking the fruit in order to reduce post-harvest losses, and has potential applications for breeding to improve fruit quality.

Combined Transcriptome and Metabolome Analyses Reveal Candidate Genes Involved in Tangor (Citrus reticulata × Citrus sinensis) Fruit Development and Quality Formation

Tangor, an important citrus type, is a hybrid of orange and mandarin and possesses their advantageous characteristics. Fruit quality is an important factor limiting the development of the citrus industry and highly depends on fruit development and ripening programs. However, fruit development and quality formation have not been completely explored in mandarin-orange hybrids. We sequenced the metabolome and transcriptome of three mandarin-orange hybrid cultivars at the early fruiting [90 days after full bloom (DAFB)], color change (180 DAFB), and ripening (270 DAFB) stages. Metabolome sequencing was performed to preliminarily identify the accumulation patterns of primary and secondary metabolites related to fruit quality and hormones regulating fruit development. Transcriptome analysis showed that many genes related to primary metabolism, secondary metabolism, cell wall metabolism, phytohormones, and transcriptional regulation were up-regulated in all three cultivars during fruit development and ripening. Additionally, multiple key genes were identified that may play a role in sucrose, citric acid and flavonoid accumulation, cell wall modification, and abscisic acid signaling, which may provide a valuable resource for future research on enhancement of fruit quality of hybrid citrus. Overall, this study provides new insights into the molecular basis of pulp growth and development regulation and fruit quality formation in mandarin-orange hybrids.

Changes in Homogalacturonan Metabolism in Banana Peel during Fruit Development and Ripening

Though numerous studies have focused on the cell wall disassembly of bananas during the ripening process, the modification of homogalacturonan (HG) during fruit development remains exclusive. To better understand the role of HGs in controlling banana fruit growth and ripening, RNA-Seq, qPCR, immunofluorescence labeling, and biochemical methods were employed to reveal their dynamic changes in banana peels during these processes. Most HG-modifying genes in banana peels showed a decline in expression during fruit development. Four polygalacturonase and three pectin acetylesterases showing higher expression levels at later developmental stages than earlier ones might be related to fruit expansion. Six out of the 10 top genes in the Core Enrichment Gene Set were HG degradation genes, and all were upregulated after softening, paralleled to the significant increase in HG degradation enzyme activities, decline in peel firmness, and the epitope levels of 2F4, CCRC-M38, JIM7, and LM18 antibodies. Most differentially expressed alpha-1,4-galacturonosyltransferases were upregulated by ethylene treatment, suggesting active HG biosynthesis during the fruit softening process. The epitope level of the CCRC-M38 antibody was positively correlated to the firmness of banana peel during fruit development and ripening. These results have provided new insights into the role of cell wall HGs in fruit development and ripening.

Proteomic and physiological analysis provides an elucidation of Fusarium proliferatum infection causing crown rot on banana fruit

Fusarium proliferatum causes the crown rot of harvested banana fruit but the underling infection mechanism remains unclear. Here, proteomic changes of the banana peel with and without inoculation of F. proliferatum were evaluated. In addition, we investigated the effects of F. proliferatum infection on cell structure, hormone content, primary metabolites and defense-related enzyme activities in the banana peel. Our results showed that F. proliferatum infection mainly affects cell wall components and inhibits the activities of polyphenoloxidase, peroxidase, and chitinase. Gel free quantitative proteomic analysis showed 92 down-regulated and 29 up-regulated proteins of banana peel after F. proliferatum infection. These proteins were mainly related to defense response to biotic stress, chloroplast structure and function, JA signaling pathway, and primary metabolism. Although jasmonic acid (JA) content and JA signaling component coronatine-insensitive (COI) protein were induced by F. proliferatum infection, JA-responsible defense genes/proteins were downregulated. In contrast, expression of senescence-related genes was induced by F. proliferatum, indicating that F. proliferatum modulated the JA signaling to accelerate the senescence of banana fruit. Additionally, salicylic acid (SA) content and SA signaling for resistance acquisition were inhibited by F. proliferatum. Taken together, these results suggest that F. proliferatum depolymerizes the cell wall barrier, impairs the defense system in banana fruit, and activates non-defensive JA-signaling pathway accelerated the senescence of banana fruit. This study provided the elucidation of the prominent pathways disturbed by F. proliferatum in banana fruit, which will facilitate the development of a new strategy to control crown rot of banana fruit and improvement of banana cultivars.

Pre-Anthesis Cytokinin Applications Increase Table Grape Berry Firmness by Modulating Cell Wall Polysaccharides

The use of plant growth regulators (PGRs) is widespread in commercial table grape vineyards. The synthetic cytokinin CPPU is a PGR that is extensively used to obtain higher quality grapes. However, the effect of CPPU on berry firmness is not clear. The current study investigated the effects of pre-anthesis applications (BBCH15 and BBCH55 stages) of CPPU on 'Thompson Seedless' berry firmness at harvest through a combination of cytological, morphological, and biochemical analyses. Ovaries in CPPU-treated plants presented morphological changes related to cell division and cell wall modification at the anthesis stage (BBCH65). Moreover, immunofluorescence analysis with monoclonal antibodies 2F4 and LM15 against pectin and xyloglucan demonstrated that CPPU treatment resulted in cell wall modifications at anthesis. These early changes have major repercussions regarding the hemicellulose and pectin cell wall composition of mature fruits, and are associated with increased calcium content and a higher berry firmness at harvest.

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.

Systems Biology Applied to the Study of Papaya Fruit Ripening: The Influence of Ethylene on Pulp Softening

Papaya is a fleshy fruit that undergoes fast ethylene-induced modifications. The fruit becomes edible, but the fast pulp softening is the main factor that limits the post-harvest period. Papaya fast pulp softening occurs due to cell wall disassembling coordinated by ethylene triggering that massively expresses pectinases. In this work, RNA-seq analysis of ethylene-treated and non-treated papayas enabled a wide transcriptome overview that indicated the role of ethylene during ripening at the gene expression level. Several families of transcription factors (AP2/ERF, NAC, and MADS-box) were differentially expressed. ACO, ACS, and SAM-Mtase genes were upregulated, indicating a high rate of ethylene biosynthesis after ethylene treatment. The correlation among gene expression and physiological data demonstrated ethylene treatment can indeed simulate ripening, and regulation of changes in fruit color, aroma, and flavor could be attributed to the coordinated expression of several related genes. Especially about pulp firmness, the identification of 157 expressed genes related to cell wall metabolism demonstrated that pulp softening is accomplished by a coordinated action of several different cell wall-related enzymes. The mechanism is different from other commercially important fruits, such as strawberry, tomato, kiwifruit, and apple. The observed behavior of this new transcriptomic data confirms ethylene triggering is the main event that elicits fast pulp softening in papayas.

Integrating proteomics and metabolomics approaches to elucidate the ripening process in white Psidium guajava

Psidium guajava (guava) exhibits a high content of biomolecules with nutraceutical properties. However, the biochemistry and molecular foundation of guava ripening is unknown. We performed comparative proteomics and metabolomics studies in different fruit tissues at two ripening stages to understand this process in white guava. Our results, suggest the positive contribution of ethylene and abscisic acid (ABA) signaling to the regulation of biochemical changes during guava ripening. We characterized the modulation of several metabolic pathways, including those of sugar and chlorophyll metabolism, abiotic and biotic stress responses, and biosynthesis of carotenoids and secondary metabolites, among others. In addition to ethylene and ABA, we also found a differential accumulation of other growth regulators such as brassinosteroids, cytokinin, methyl-jasmonate, gibberellins and proteins, and discuss their possible implications in the intricate biochemical network associated with guava ripening process. This integrative approach represents a global overview of the metabolic pathway dynamics during guava ripening.

Postharvest senescent dark spot development mechanism of Musa acuminata ("Khai" banana) peel associated with chlorophyll degradation and stomata cell death

The occurrence of the postharvest physiological disorder of dark spots on the peel of the ripened "Khai" banana has led to a reduction in its commercial value. The objective of the present study was to investigate the development mechanisms of senescence dark spots of the "Khai" (Musa AA group) banana peel in relation to chlorophyll degradation and stomata cell death. Freshly harvested bananas (commercial mature green stage) were let to ripened at 25 ± 2°C (90%-95% RH). Peel color, senescent spots, DNA degradation, chlorophyll content, chlorophyll-degrading enzyme activities were assessed. The senescent dark spots developed on the ripened bananas right after 6 days of storage, which coincided with remarkably increased DNA degradation, and a rapid decreased of hue angle value and total chlorophyll content which indicated the chlorophyll degradation. The activities of chlorophyllase, chlorophyll-degrading peroxidase and pheophytinase increased gradually to the highest point where the chlorophyll content drastically reduced and the appearance of the dark spots was first recorded after 6 days of storage. These dark spots were observed to be surrounded with a bright luminescent ring of hypermodified fluorescent chlorophyll catabolites (FCCs), the product of chlorophyll breakdown. Additionally, the scanning electron microscope (SEM) revealed that the dark spots were found to have originated from the collapsed cells around the stomata of the ripened banana peel whereby the chlorophyll was entirely diminished. PRACTICAL APPLICATIONS: This research revealed the senescent dark spot development mechanisms of the "Khai" banana peel. The dark spot development symptom on the banana peel surface was caused by the senescence and cell death of the relevant stomata, further associated with chlorophyll degradation. Therefore, any further research into minimizing the dark spot symptom must focus on preventing or delaying stomata senescence and cell death.

Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples

In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.

Purified cellobiose dehydrogenase of Termitomyces sp. OE147 fuels cellulose degradation resulting in the release of reducing sugars

Termitomyces sp. OE 147 is one of the active cellulose degraders in the ecosphere and produces large amount of cellobiose dehydrogenase (CDH) and β-glucosidases when cultivated on cellulose. In order to investigate its effect on cellulose, a highly purified preparation of CDH was obtained from the culture supernatant of the fungus cultivated on cellulose. A combination of ultrafiltration, ion-exchange and gel-filtration chromatography was used to purify CDH by ∼172-fold to a high specific activity of ∼324 U/mg protein on lactose which was used for routine measurement of enzyme activity. The enzyme displayed a pH optimum of 5.0 and stability between pH 5.0 and 8.0 with maximum catalytic efficiency (k_cat/K_m) of 397 mM^-1 s^-1 on cellobiose. Incubation of microcrystalline cellulose with the purified CDH led to production of reducing sugars which was accelerated by the addition of FeCl₃ during the early stages of incubation. A mass spectrometric analysis revealed fragmentation products of cellulose which were concluded to be cellodextrins, sugars, and corresponding aldonic acids suggesting that CDH can release reducing sugars in the absence of externally added lytic polysaccharide monooxygenases. Polymerized products of glucose were also detected at low intensity.

Nutritional component changes in Xiangfen 1 banana at different developmental stages

Banana is an essential food resource in many tropical and subtropical countries. Metabolites in banana greatly influence its nutritional value and flavor. However, metabolic changes that occur in different developmental stages have not been comprehensively evaluated. In this study, widely targeted metabolomics based on multiple reaction monitoring was used in investigating dynamic changes in metabolites at three stages of fruit development. A total of 655 metabolites were identified in all the stages. A hierarchical cluster analysis of metabolites showed six clear expression patterns at the three developmental stages, and 69 up-regulated differential metabolites were identified in mature fruits compared with young and mature green fruits. A metabolic pathway analysis of differential metabolites showed significant enrichment of the flavonoid biosynthesis pathway and the phenylalanine, tyrosine, and tryptophan biosynthesis pathways. These results may serve as a reference for the isolation and identification of functional compounds from banana and for their sufficient utilization in the future.

Potential mechanisms of action of celastrol against rheumatoid arthritis: Transcriptomic and proteomic analysis

The clinical efficacy for treating of celastrol rheumatoid arthritis (RA) has been well-documented, but its mechanism of action remains unclear. Here we explored through what proteins and processes celastrol may act in activated fibroblast-like synoviocytes (FLS) from RA patients. Differential expression of genes and proteins after celastrol treatment of FLS was examined using RNA sequencing, label-free relatively quantitative proteomics and molecular docking. In this paper, expression of 26,565 genes and 3,372 proteins was analyzed. Celastrol was associated with significant changes in genes that respond to oxidative stress and oxygen levels, as well as genes that stabilize or synthesize components of the extracellular matrix. These results identify several potential mechanisms through which celastrol may inhibit inflammation in RA.