Integrated proteomic and metabolomic analysis suggests high rates of glycolysis are likely required to support high carotenoid accumulation in banana pulp

15-cis-Phytoene Desaturase and 15-cis-Phytoene Synthase Can Catalyze the Synthesis of β-Carotene and Influence the Color of Apricot Pulp

Fruit color affects its commercial value. β-carotene is the pigment that provides color for many fruits and vegetables. However, the molecular mechanism of β-carotene metabolism during apricot ripening is largely unknown. Here, we investigated whether β-carotene content affects apricot fruit color. First, the differences in β-carotene content between orange apricot 'JTY' and white apricot 'X15' during nine developmental stages (S1-S9) were compared. β-carotene contents highly significantly differed between 'JTY' and 'X15' from S5 (color transition stage) onwards. Whole-transcriptome analysis showed that the β-carotene synthesis genes 15-cis-phytoene desaturase (PaPDS) and 15-cis-phytoene synthase (PaPSY) significantly differed between the two cultivars during the color transition stage. There was a 5 bp deletion in exon 11 of PaPDS in 'X15', which led to early termination of amino acid translation. Gene overexpression and virus-induced silencing analysis showed that truncated PaPDS disrupted the β-carotene biosynthesis pathway in apricot pulp, resulting in decreased β-carotene content and a white phenotype. Furthermore, virus-induced silencing analysis showed that PaPSY was also a key gene in β-carotene biosynthesis. These findings provide new insights into the molecular regulation of apricot carotenoids and provide a theoretical reference for breeding new cultivars of apricot.

High-quality genome assemblies for two Australimusa bananas (Musa spp.) and insights into regulatory mechanisms of superior fiber properties

Bananas (Musa spp.) are monocotyledonous plants with high genetic diversity in the Musaceae family that are cultivated mainly in tropical and subtropical countries. The fruits are a popular food, and the plants themselves have diverse uses. Four genetic groups (genomes) are thought to have contributed to current banana cultivars: Musa acuminata (A genome), Musa balbisiana (B genome), Musa schizocarpa (S genome), and species of the Australimusa section (T genome). However, the T genome has not been effectively explored. Here, we present the high-quality TT genomes of two representative accessions, Abaca (Musa textilis), with high-quality natural fiber, and Utafun (Musa troglodytarum, Fe'i group), with abundant β-carotene. Both the Abaca and Utafun assemblies comprise 10 pseudochromosomes, and their total genome sizes are 613 Mb and 619 Mb, respectively. Comparative genome analysis revealed that the larger size of the T genome is likely attributable to rapid expansion and slow removal of transposons. Compared with those of Musa AA or BB accessions or sisal (Agava sisalana), Abaca fibers exhibit superior mechanical properties, mainly because of their thicker cell walls with a higher content of cellulose, lignin, and hemicellulose. Expression of MusaCesA cellulose synthesis genes peaks earlier in Abaca than in AA or BB accessions during plant development, potentially leading to earlier cellulose accumulation during secondary cell wall formation. The Abaca-specific expressed gene MusaMYB26, which is directly regulated by MusaMYB61, may be an important regulator that promotes precocious expression of secondary cell wall MusaCesAs. Furthermore, MusaWRKY2 and MusaNAC68, which appear to be involved in regulating expression of MusaLAC and MusaCAD, may at least partially explain the high accumulation of lignin in Abaca. This work contributes to a better understanding of banana domestication and the diverse genetic resources in the Musaceae family, thus providing resources for Musa genetic improvement.

Carotenoids in Health as Studied by Omics-Related Endpoints

Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor κB and nuclear factor erythroid 2-related factor 2. Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor and peroxisome proliferator-activated receptors, which play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes and proteins implicated in oxidative stress and inflammation, antioxidation, and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)omics-related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, as well as metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells, or other tissue cellular extracts. In this review, we highlight the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.

Magnesium accelerates changes in the fruit ripening and carotenoid accumulation in Satsuma Mandarin pulp

This study aims to further examine the effect of Magnesium (Mg) application on fruit quality and carotenoid metabolism in Satsuma mandarin pulp. For this, a field experiment was using 20-year-old Satsuma mandarin (C. unshiu Marc.) for two treatment; (1) CK treatment (without Mg), (2) Mg fertilizer treatment (200 g MgO plant-1). Compared with CK, Mg treatment substantially raised the Mg content in pulp at 90 to 150 DAF (the fruit expansion period), increasing by 15.69%-21.74%. Mg treatment also increased fruit TSS content by 15.84% and 9.88%, decreased fruit TA content in by 34.25% and 33.26% at 195 DAF and 210 DAF (the fruit ripening period). Moreover, at 120 to 195 DAF, Mg treatment significantly increased the levels of lutein, β-cryptoxanthin, zeaxanthin and violaxanthin in the pulp. This can be explained by the increased expression of important biosynthetic genes, including CitPSY, CitPDS, CitLCYb1, CitLCYb2, CitLCYe, CitHYb, and CitZEP, that played a role in altering the carotenoid composition. The findings of this research offer a novel approach for augmenting both the economic and nutritional worth of citrus fruits.

Linolenic Acid-Derived Oxylipins Inhibit Aflatoxin Biosynthesis in Aspergillus flavus through Activation of Imizoquin Biosynthesis

Oxylipins play important signaling roles in aflatoxin (AF) biosynthesis in Aspergillus flavus. We previously showed that exogenous supply of autoxidated linolenic acid (AL) inhibited AF biosynthesis in A. flavus via oxylipins, but the molecular mechanism is still unknown. Here, we performed multiomics analyses of A. flavus grown in media with or without AL. Targeted metabolite analyses and quantitative reverse transcription (qRT)-polymerase chain reaction (PCR) showed that the imizoquin (IMQ) biosynthetic pathway was distinctly upregulated in the presence of AL. ¹³C-glucose labeling confirmed in parallel that the tricarboxylic acid cycle was also enhanced by AL, consistent with observed increases in mycelial growth. Moreover, we integrated thermal proteome profiling and molecular dynamics simulations to identify a potential receptor of AL; AL was found to interact with a transporter (ImqJ) located in the IMQ gene cluster, primarily through hydrophobic interactions. Further analyses of strains with an IMQ pathway transcription factor overexpressed or knocked out confirmed that this pathway was critical for AL-mediated inhibition of AF biosynthesis. Comparison of 22 assembled A. flavus and Aspergillus oryzae genomes showed that genes involved in the IMQ pathway were positively selected in A. oryzae. Taken together, the results of our study provide novel insights into oxylipin-mediated regulation of AF biosynthesis and suggest potential methods for preventing AF contamination of crops.

Starch and sugars as determinants of postharvest shelf life and quality: some new and surprising roles

Starch and sugars account for most of the dry weight of horticultural crops and in many species, are known determinants of quality. However, we posit that these carbohydrates often have less-obvious roles in plant tissues with direct implications for the postharvest quality and produce shelf life. The latter has not been given as much attention, but with the recent interest in reducing the scale of postharvest waste and loss, we highlight how dynamic changes in the spatial-temporal accumulation of carbohydrates, can influence myriads of biological processes affecting postharvest attributes. Versatile roles, some surprising, that carbohydrates play in determining produce of high value to consumers, are highlighted, and gene targets for biotechnological improvement are specified.

Metabolomics and proteomics reveal the molecular basis of colour formation in the pericarp of Chinese wild rice (Zizania latifolia)

Chinese wild rice (Zizania latifolia) is rich in flavonoids and the characteristic colour of its pericarp is attributed to the flavonoids. In this study, the molecular basis of the colour change in the pericarp of Chinese wild rice was studied using metabolomics and proteomics. Whole seeds in three developmental stages (10, 20, and 30 days after flowering) were characterised based on phenolic contents, free amino acids (FAAs), and the expression level and activities of enzymes critical in flavonoid biosynthesis. The total phenolic and proanthocyanidin contents of Chinese wild rice increased gradually, whereas total flavonoid and FAA contents decreased during seed development. Metabolomic analysis revealed gradual upward trends for 57 flavonoids (sub classes 1, 3, and 10) related to colour change in the pericarp. Proteomic analysis showed that the phenylpropanoid biosynthesis metabolic pathway was enriched with differentially expressed proteins and was associated with flavonoid biosynthesis. Proteomic data suggested that leucoanthocyanidin reductase and WD40 repeat protein may be involved in flavonoid biosynthesis in Chinese wild rice, which was also verified by real-time quantitative PCR. Our results provide new insights into the understanding of the colour formation in the pericarp of Chinese wild rice.

Spatially resolved metabolomics reveals variety-specific metabolic changes in banana pulp during postharvest senescence

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Both post-ripening stages and banana varieties contribute to metabolite variation.

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AuNP-assisted LDI-MSI was firstly used in mapping functional metabolites in pulps.

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AAs and monoamines exclusively accumulated in the middle region near the seed zone.

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Monosaccharides locate in whole pulps but enrich in the intermediate microregion.

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Di/trisaccharides exhibit different accumulation patterns as monosaccharides.

Banana is one of most popular fruits globally due to health-promoting and disease-preventing effects, yet little is known about in situ metabolic changes across banana varieties. Here, we integrated gold nanoparticle (AuNP)-assisted laser desorption/ionization mass spectrometry imaging (LDI-MSI) and metabolomics to investigate the spatiotemporal distribution and levels of metabolites within Brazil and Dongguan banana pulps during postharvest senescence. Metabolomics results indicated that both postripening stages and banana varieties contribute to metabolite levels. Benefiting from improved ionization efficiency of small-molecule metabolites and less peak interference, we visualized the spatiotemporal distribution of sugars, amino acids (AAs) and monoamines within pulps using AuNP-assisted LDI-MSI for the first time, revealing that AAs and monoamines exclusively accumulated in the middle region near the seed zone. Monosaccharides and di/trisaccharides were generally distributed across entire pulps but exhibited different accumulation patterns. These findings provide a guide for breeding new varieties and improving extraction efficiency of bioactive compounds.

The Musa troglodytarum L. genome provides insights into the mechanism of non-climacteric behaviour and enrichment of carotenoids

BACKGROUND

Karat (Musa troglodytarum L.) is an autotriploid Fe'i banana of the Australimusa section. Karat was domesticated independently in the Pacific region, and karat fruit are characterized by a pink sap, a deep yellow-orange flesh colour, and an abundance of β-carotene. Karat fruit showed non-climacteric behaviour, with an approximately 215-day bunch filling time. These features make karat a valuable genetic resource for studying the mechanisms underlying fruit development and ripening and carotenoid biosynthesis.

RESULTS

Here, we report the genome of M. troglodytarum, which has a total length of 603 Mb and contains 37,577 predicted protein-coding genes. After divergence from the most recent common ancestors, M. troglodytarum (T genome) has experienced fusion of ancestral chromosomes 8 and 9 and multiple translocations and inversions, unlike the high synteny with few rearrangements found among M. schizocarpa (S genome), M. acuminata (A genome) and M. balbisiana (B genome). Genome microsynteny analysis showed that the triplication of MtSSUIIs due to chromosome rearrangement may lead to the accumulation of carotenoids and ABA in the fruit. The expression of duplicated MtCCD4s is repressed during ripening, leading to the accumulation of α-carotene, β-carotene and phytoene. Due to a long terminal repeat (LTR)-like fragment insertion upstream of MtERF11, karat cannot produce large amounts of ethylene but can produce ABA during ripening. These lead to non-climacteric behaviour and prolonged shelf-life, which contributes to an enrichment of carotenoids and riboflavin.

CONCLUSIONS

The high-quality genome of M. troglodytarum revealed the genomic basis of non-climacteric behaviour and enrichment of carotenoids, riboflavin, flavonoids and free galactose and provides valuable resources for further research on banana domestication and breeding and the improvement of nutritional and bioactive qualities.

Recent advances in proteomics and metabolomics in plants

Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.

Analyses of key gene networks controlling carotenoid metabolism in Xiangfen 1 banana

BACKGROUND

Banana fruits are rich in various high-value metabolites and play a key role in the human diet. Of these components, carotenoids have attracted considerable attention due to their physiological role and human health care functions. However, the accumulation patterns of carotenoids and genome-wide analysis of gene expression during banana fruit development have not been comprehensively evaluated.

RESULTS

In the present study, an integrative analysis of metabolites and transcriptome profiles in banana fruit with three different development stages was performed. A total of 11 carotenoid compounds were identified, and most of these compounds showed markedly higher abundances in mature green and/or mature fruit than in young fruit. Results were linked to the high expression of carotenoid synthesis and regulatory genes in the middle and late stages of fruit development. Co-expression network analysis revealed that 79 differentially expressed transcription factor genes may be responsible for the regulation of LCYB (lycopene β-cyclase), a key enzyme catalyzing the biosynthesis of α- and β-carotene.

CONCLUSIONS

Collectively, the study provided new insights into the understanding of dynamic changes in carotenoid content and gene expression level during banana fruit development.

Metabolomics of Chlorophylls and Carotenoids: Analytical Methods and Metabolome-Based Studies

Chlorophylls and carotenoids are two families of antioxidants present in daily ingested foods, whose recognition as added-value ingredients runs in parallel with the increasing number of demonstrated functional properties. Both groups include a complex and vast number of compounds, and extraction and analysis methods evolved recently to a modern protocol. New methodologies are more potent, precise, and accurate, but their application requires a better understanding of the technical and biological context. Therefore, the present review compiles the basic knowledge and recent advances of the metabolomics of chlorophylls and carotenoids, including the interrelation with the primary metabolism. The study includes material preparation and extraction protocols, the instrumental techniques for the acquisition of spectroscopic and spectrometric properties, the workflows and software tools for data pre-processing and analysis, and the application of mass spectrometry to pigment metabolomics. In addition, the review encompasses a critical description of studies where metabolomics analyses of chlorophylls and carotenoids were developed as an approach to analyzing the effects of biotic and abiotic stressors on living organisms.

Identification of Key Genes Controlling Carotenoid Metabolism during Apricot Fruit Development by Integrating Metabolic Phenotypes and Gene Expression Profiles

To explore the metabolic basis of carotenoid accumulation in different developmental periods of apricot fruits, targeted metabonomic and transcriptomic analyses were conducted in four developmental periods (S1-S4) in two cultivars (Prunus armeniaca cv. "Kuchebaixing" with white flesh and P. armeniaca cv. "Shushangganxing" with orange flesh) with different carotenoid contents. 14 types of carotenes and 27 types of carotene lipids were identified in apricot flesh in different developmental periods. In S3 and S4, the carotenoid contents of the two cultivars were significantly different, and β-carotene and (E/Z)-phytoene were the key metabolites that caused the difference in the total carotenoid content between the examined cultivars. Twenty-five structural genes (including genes in the methylerythritol 4-phosphate and carotenoid biosynthesis pathways) related to carotenoid biosynthesis were identified among the differentially expressed genes in different developmental periods of the two cultivars, and a carotenoid metabolic pathway map of apricot fruits was drawn according to the KEGG pathway map. The combined analysis of carotenoid metabolism data and transcriptome data showed that PSY, NCED1, and CCD4 were the key genes leading to the great differences in the total carotenoid content. The results provide a new approach to study the synthesis and accumulation of carotenoids in apricot fruits.

Exploring the differential stages of the pigment metabolism by pre-harvest bagging and post-harvest ethylene de-greening of Eureka lemon peel

Pre-harvest bagging or post-harvest ethylene treatments on lemons are commonly applied to change the surface color from green to favorable yellow. In this study, the differential mechanisms of the pigment metabolism by the two treatments were investigated by pigments contents and related genetic expression. The results showed that both treatments reduced the number of chloroplasts and the content of chlorophyll. The differential expression of PSY1 and PSY2 were observed, causing the different accumulation of the main carotenoid phytoene content. The differential expression of NYC resulted in altered contents of chlorophyll a and chlorophyll b, and further led to the difference in a* value. More interestingly, the degradation of chlorophyll uncovered the color of carotenoids, leading to the color changed from green to yellow.

Sugar Signaling During Fruit Ripening

Sugars play a key role in fruit quality, as they directly influence taste, and thus consumer acceptance. Carbohydrates are the main resources needed by the plant for carbon and energy supply and have been suggested to be involved in all the important developmental processes, including embryogenesis, seed germination, stress responses, and vegetative and reproductive growth. Recently, considerable progresses have been made in understanding regulation of fruit ripening mechanisms, based on the role of ethylene, auxins, abscisic acid, gibberellins, or jasmonic acid, in both climacteric and non-climacteric fruits. However, the role of sugar and its associated molecular network with hormones in the control of fruit development and ripening is still poorly understood. In this review, we focus on sugar signaling mechanisms described up to date in fruits, describing their involvement in ripening-associated processes, such as pigments accumulation, and their association with hormone transduction pathways, as well as their role in stress-related responses.

Banana MaSPL16 Modulates Carotenoid Biosynthesis during Fruit Ripening through Activating the Transcription of Lycopene β-Cyclase Genes

Carotenoids are a class of bioactive compounds that exhibit health-promoting properties for humans, but their regulation in bananas during fruit ripening remains largely unclear. Here, we found that the total carotenoid content continued to be elevated along the course of banana ripening and peaked at the ripening stage followed by a decrease, which is presumably caused by the transcript abundances of carotenoid biosynthetic genes MaLCYB1.1 and MaLCYB1.2. Moreover, a ripening-inducible transcription factor MaSPL16 was characterized, which was a nuclear protein with transactivation activity. Transient transformation of MaSPL16 in banana fruits led to enhanced transcript levels of MaLCYB1.1 and MaLCYB1.2 and hence the total carotenoid accumulation. Importantly, MaSPL16 stimulated the transcription of MaLCYB1.1 and MaLCYB1.2 through directly binding to their promoters. Collectively, our findings indicate that MaSPL16 behaves as an activator to modulate banana carotenoid biosynthesis, which may provide a new target for molecular improvement of the nutritional and bioactive qualities of agricultural crops that accumulate carotenoids.