Tandem Mass Tag Based Quantitative Proteomics of Developing Sea Buckthorn Berries Reveals Candidate Proteins Related to Lipid Metabolism

Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid

BACKGROUND

To determine how abscisic acid (ABA) affects tomato fruit ripening at the protein level, mature green cherry tomato fruit were treated with ABA, nordihydroguaiaretic acid (NDGA) or sterile water (control, CK). The proteomes of treated fruit were analyzed and quantified using tandem mass tags (TMTs) at 7 days after treatment, and the gene transcription abundances of differently expressed proteins (DEPs) were validated with quantitative real-time polymerase chain reaction.

RESULTS

Postharvest tomato fruit underwent faster color transformation and ripening than the CK when treated with ABA. In total, 6310 proteins were identified among the CK and treatment groups, of which 5359 were quantified. Using a change threshold of 1.2 or 0.83 times, 1081 DEPs were identified. Among them, 127 were upregulated and 127 were downregulated in the ABA versus CK comparison group. According to KEGG and protein-protein interaction network analyses, the ABA-regulated DEPs were primarily concentrated in the photosynthesis system and sugar metabolism pathways, and 102 DEPs associated with phytohormones biosynthesis and signal transduction, pigment synthesis and metabolism, cell wall metabolism, photosynthesis, redox reactions, allergens and defense responses were identified in the ABA versus CK and NDGA versus CK comparison groups.

CONCLUSION

ABA affects tomato fruit ripening at the protein level to some extent. The results of this study provided comprehensive insights and data for further research on the regulatory mechanism of ABA in tomato fruit ripening. © 2023 Society of Chemical Industry.

The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review

Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.

Multi-Omics Elucidates Difference in Accumulation of Bioactive Constituents in Licorice (Glycyrrhiza uralensis) under Drought Stress

Licorice is a frequently applied herb with potential edible and medicinal value based on various flavonoids and triterpenes. However, studies on detailed flavonoid and triterpene metabolism and the molecular basis of their biosynthesis in licorice are very limited, especially under drought conditions. In the present study, we carried out transcriptome, proteome, and metabolome experiments. To ultimately combine three omics for analysis, we performed a bioinformatics comparison, integrating transcriptome data and proteome data through a Cloud platform, along with a simplified biosynthesis of primary flavonoids and triterpenoids in the KEGG pathway based on metabolomic results. The biosynthesis pathways of triterpenes and flavonoids are enriched at both gene and protein levels. Key flavonoid-related genes (PAL, 4CL, CHS, CHI, CYP93C, HIDH, HI4OMT, and CYP81E1_7) and representative proteins (HIDH, CYP81E1_7, CYP93C, and VR) were obtained, which all showed high levels after drought treatment. Notably, one R2R3-MYB transcription factor (Glyur000237s00014382.1), a critical regulator of flavonoid biosynthesis, achieved a significant upregulated expression as well. In the biosynthesis of glycyrrhizin, both gene and protein levels of bAS and CYP88D6 have been found with upregulated expression under drought conditions. Most of the differentially expressed genes (DEGs) and proteins (DEPs) showed similar expression patterns and positively related to metabolic profiles of flavonoid and saponin. We believe that suitable drought stress may contribute to the accumulation of bioactive constituents in licorice, and our research provides an insight into the genetic study and quality breeding in this plant.

Exploring metabolic dynamics during the fermentation of sea buckthorn beverage: comparative analysis of volatile aroma compounds and non-volatile metabolites using GC-MS and UHPLC-MS

Sea buckthorn has a high nutritional value, but its sour taste and foul odor make it unpalatable for consumers. In this study, we analyzed the metabolite changes occurring during the yeast-assisted fermentation of sea buckthorn juice using the HeadSpace Solid-Phase Microextraction Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS) and Ultra-High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) techniques. A total of 86 volatile aroma compounds were identified during the fermentation process. The content of total volatiles in sea buckthorn juice increased by 3469.16 μg/L after 18 h of fermentation, with 22 compounds showing elevated levels. Notably, the total content of esters with fruity, floral, and sweet aromas increased by 1957.09 μg/L. We identified 379 non-volatile metabolites and observed significant increases in the relative abundance of key active ingredients during fermentation: glycerophosphorylcholine (increased by 1.54), glutathione (increased by 1.49), L-glutamic acid (increased by 2.46), and vanillin (increased by 0.19). KEGG pathway analysis revealed that amino acid metabolism and lipid metabolism were the primary metabolic pathways involved during fermentation by Saccharomyces cerevisiae. Fermentation has been shown to improve the flavor of sea buckthorn juice and increase the relative content of bioactive compounds. This study provides novel insights into the metabolic dynamics of sea buckthorn juice following yeast fermentation through metabolomics analysis. These findings could serve as a theoretical foundation for further studies on the factors influencing differences in yeast fermentation.

Identification of Key Lipogenesis Stages and Proteins Involved in Walnut Kernel Development

Walnuts are abundant in oil content, especially for polyunsaturated fatty acids, but the understanding of their formation is limited. We collected walnut (Juglans regia L.) kernels at 60, 74, 88, 102, 116, 130, and 144 days after pollination (designated S1-S7). The ultrastructure and accumulation of oil bodies (OBs) were observed using transmission electron microscopy (TEM), and the oil content, fatty acid composition, and proteomic changes in walnut kernels were determined. The oil content and OB accumulation increased during the development and rose sharply from S1 to S3 stages, which are considered the key lipogenesis stage. A total of 5442 proteins were identified and determined as differentially expressed proteins (DEPs) using label-free proteomic analysis. Fatty acid desaturases (FAD) 2, FAD3, oleosin, and caleosin were essential and upregulated from the S1 to S3 stages. Furthermore, the highly expressed oleosin gene JrOLE14.7 from walnuts was cloned and overexpressed in transgenic Brassica napus. The overexpression of JrOLE14.7 increased the oil content, diameter, hundred weight of seeds and changed the fatty acid composition and OB size of Brassica napus seeds. These findings provide insights into the molecular mechanism of oil biosynthesis and the basis for the genetic improvement of walnuts.

Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice

The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either CRY1C gene on chromosome 11 or CRY2A gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits. Using 512 microsatellite markers, the three transgenic lines inherited 2.9-4.3% of the Minghui 63 donor genome and 96.3-97.1% of the CH891 recurrent parent genome. As compared with the recurrent parent, the number of upregulated and down-regulated proteins in the three transgenic lines varied from 169 to 239 and from 131 to 199, respectively. Most DEPs were associated with the secondary metabolites biosynthesis transport and catabolism, carbohydrate transport and metabolism, post-translational modification, and signal transduction mechanisms. Although several differentially expressed proteins were observed between transgenic rice and its recurrent parent, the differences may not have been associated with grain yield and most other phenotypic traits in transgenic rice.

Medicinal and edible plants in the treatment of dyslipidemia: advances and prospects

Dyslipidemia is an independent risk factor of cardiovascular diseases (CVDs), which lead to the high mortality, disability, and medical expenses in the worldwide. Based on the previous researches, the improvement of dyslipidemia could efficiently prevent the occurrence and progress of cardiovascular diseases. Medicinal and edible plants (MEPs) are the characteristics of Chinese medicine, and could be employed for the disease treatment and health care mostly due to their homology of medicine and food. Compared to the lipid-lowering drugs with many adverse effects, such as rhabdomyolysis and impaired liver function, MEPs exhibit the great potential in the treatment of dyslipidemia with high efficiency, good tolerance and commercial value. In this review, we would like to introduce 20 kinds of MEPs with lipid-lowering effect in the following aspects, including the source, function, active component, target and underlying mechanism, which may provide inspiration for the development of new prescription, functional food and complementary therapy for dyslipidemia.

Application of quantitative proteomics to investigate fruit ripening and eating quality

The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.

Identification of the key flavonoid and lipid synthesis proteins in the pulp of two sea buckthorn cultivars at different developmental stages

BACKGROUND

Sea buckthorn is an economically important woody plant for desertification control and water soil conservation. Its berry pulp is rich in flavonoids and unsaturated fatty acids. Cultivars containing high oil and flavonoid contents have higher economic value and will increase in the planting area. However, the cause of the differences in oil and flavonoid contents among cultivars is still unclear. The influence of key enzymes in the lipid and flavonoid synthesis pathways on their content needs to be explored and clarified.

RESULTS

The flavonoid content in XE (Xin'e 3) was 54% higher than that in SJ (Suiji 1). Rutin was the main flavonoid in sea buckthorn pulp, and the differences in the rutin content could cause flavonoid differences between the two cultivars. The oil content of XE was 31.58% higher than that of SJ, and the difference in oil content was highest at 50-70 DAF. High-throughput proteomics was used to quantify key enzymes of flavonoid and lipid synthesis pathways in two cultivars at three developmental stages. By functional annotation and KEGG analysis, 41 key enzymes related to phenylpropanoid biosynthesis, flavonoid biosynthesis, flavone and flavonol biosynthesis, fatty acid biosynthesis and TAG biosynthesis were quantified. CHS, F3H, ANS, fabD, FATA, FAB2, LPIN and plcC showed significant differences between the two cultivars. In addition, we quantified 6 oleosins. With the exception of a 16 kDa oleosin, the other oleosins in the two cultivars were positively correlated with oil content.

CONCLUSIONS

In the flavonoid synthesis pathway, CHS and F3H were the main enzymes responsible for the difference in flavonoid content between the two cultivars. In the lipid synthesis pathway, LPIN, plcC and MGD were the main enzymes with different contents in the middle to late stages. Higher contents of LPIN and plcC in XE than in SJ could cause DAG to generate TAG from PC, since the difference in DGAT between the two cultivars was not significant. Investigating the causes of flavonoid and oil content differences among different cultivars from the perspective of proteomics, could provide a basis for understanding the regulatory mechanism of flavonoids and lipid synthesis in sea buckthorn pulp.

Comparative Proteomic Analysis of Two Contrasting Maize Hybrids’ Responses to Low Nitrogen Stress at the Twelve Leaf Stage and Function Verification of ZmTGA Gene

Nitrogen is one of the essential nutrients for plant growth and development. However, large amounts of nitrogen fertilizer not only increase the production costs, but also lead to serious environmental problems. Therefore, it is particularly important to reduce the application of nitrogen fertilizer and develop maize varieties with low nitrogen tolerance. The aim of this study was to determine the phenotypic and proteomic alterations of maize affected by nitrogen deficiency and to elucidate the molecular and physiological mechanisms underpinning maize tolerance to low nitrogen. Two maize hybrids with contrasting low nitrogen tolerance were used as the experimental materials. Maize plants were grown under different nitrogen application levels (N0 and N240) and proteomic analysis performed to analyze leaf differentially abundant proteins (DAPs) under different nitrogen conditions. The results showed that under the nitrogen deficiency condition, the nitrogen content, leaf dry weight, leaf area, and leaf area index of XY335 decreased by 15.58%, 8.83%, 3.44%, and 3.44%, respectively. However, in the variety HN138, the same parameters decreased by 56.94%, 11.97%, 8.79%, and 8.79%, respectively. Through proteomic analysis, we found that the low nitrogen tolerance variety responded to low nitrogen stress through lignin biosynthesis, ubiquitin-mediated proteolysis, and stress defense proteins. Transmembrane transporters were differentially expressed in both hybrids after low nitrogen treatment, suggesting that this was a common response to low nitrogen stress. Using bioinformatics analysis, we selected the key candidate gene (ZmTGA) that was assumed to respond to low nitrogen stress, and its function was characterized by maize mutants. The results showed that when compared with normal nitrogen treatment, the root length of the mutants under low nitrogen treatment increased by 10.1%, while that of the wild-type increased by 14.8%; the root surface area of the wild type under low nitrogen treatment increased by 9.6%, while that of the mutants decreased by 5.2%; the root surface area of the wild type was higher than that of the mutant at both nitrogen levels; and the activities of glutathione and guaiacol peroxidase enzymes in the mutant were lower than those in the wild-type under low nitrogen treatment. In summary, the mutant was less adaptable to a low nitrogen environment than the wild type. Our results provide maize genetic resources and a new direction for a further understanding of maize response to low nitrogen stress.

Label-free quantitative proteomics analysis of jujube (Ziziphus jujuba Mill.) during different growth stages

Chinese jujube (Zizyphus jujuba Mill.), a member of the Rhamnaceae family with favorable nutritional and flavor quality, exhibited characteristic climacteric changes during its fruit growth stage. Therefore, fruit samples were harvested at four developmental stages on days 55 (young fruits), 76 (white-mature fruits), 96 (half-red fruits), and 116 (full-red fruits) after flowering (DAF). This study then investigated those four growth stage changes of the jujube proteome using label-free quantification proteomics. The results identified 4762 proteins in the samples, of which 3757 proteins were quantified. Compared with former stages, the stages examined were designated as "76 vs. 55 DAF" group, "96 vs. 76 DAF" group, and "116 vs. 96 DAF" group. Gene Ontology (GO) and KEGG annotation and enrichment analysis of the differentially expressed proteins (DEPs) showed that 76 vs. 55 DAF group pathways represented amino sugar, nucleotide sugar, ascorbate, and aldarate metabolic pathways. These pathways were associated with cell division and resistance. In the study, the jujube fruit puffing slowed down and attained a stable growth stage in the 76 vs. 55 DAF group. However, fatty acid biosynthesis and phenylalanine metabolism was mainly enriched in the 96 vs. 76 DAF group. Fatty acids are precursors of aromatic substances and fat-soluble pigments in fruit. The upregulation of differential proteins at this stage indicates that aromatic compounds were synthesized in large quantities at this stage and that fruit would enter the ripening stage. During the ripening stage, 55 DEPs were identified to be involved in photosynthesis and flavonoid biosynthesis in the 116 vs. 96 DAF group. Also, the fruit entered the mature stage, which showed that flavonoids were produced in large quantities. Furthermore, the color of jujube turned red, and photosynthesis was significantly reduced. Hence, a link was established between protein profiles and growth phenotypes, which will help improve our understanding of jujube fruit growth at the proteomic level.

Proteomic Analysis of the Hemolymph After Metschnikowia bicuspidata Infection in the Chinese Mitten Crab Eriocheir sinensis

The “milky disease” of the Chinese mitten crab, Eriocheir sinensis, is a highly lethal fungal disease caused by Metschnikowia bicuspidata infection. To elucidate the immune responses of the hemolymph of E. sinensis to M. bicuspidata infection, a comparative analysis of the hemolymph of E. sinensis infected with M. bicuspidata and that treated with phosphate buffered saline was performed using label-free quantitative proteomics. A total of 429 proteins were identified. Using a 1.5-fold change in expression as a physiologically significant benchmark, 62 differentially expressed proteins were identified, of which 38 were significantly upregulated and 24 were significantly downregulated. The upregulated proteins mainly included cytoskeleton-related proteins (myosin regulatory light chain 2, myosin light chain alkali, tubulin α-2 chain, and tubulin β-1 chain), serine protease and serine protease inhibitor (clip domain-containing serine protease, leukocyte elastase inhibitor, serine protein inhibitor 42Dd), catalase, transferrin, and heat shock protein 70. Upregulation of these proteins indicated that phenoloxidase system, phagocytosis and the ROS systems were induced by M. bicuspidata. The downregulated proteins were mainly organ and tissue regeneration proteins (PDGF/VEGF-related factor protein, integrin-linked protein kinase homing pat-4 gene) and hemagglutination-associated proteins (hemolymph clottable protein, hemocyte protein-glutamine gamma-glutamyltransferase). Downregulation of these proteins indicated that M. bicuspidata inhibited hemocyte regeneration and hemolymph agglutination. Fifteen differentially expressed proteins related to immunity were verified using a parallel reaction monitoring method. The expression trend of these proteins was similar to that of the proteome. To the best of our knowledge, this is the first report on the proteome of E. sinensis in response to M. bicuspidata infection. These results not only provide new and important information on the immune response of crustaceans to yeast infection but also provide a basis for further understanding the molecular mechanism of complex host pathogen interactions between crustaceans and fungi.

Quantitative proteomic analysis of Xanthoceras sorbifolium Bunge seedlings in response to drought and heat stress

Yellowhorn (Xanthoceras sorbifolium Bunge) is a woody oil species that is widely distributed in northwestern China. To investigate the molecular mechanisms underlying the drought and heat tolerance response of yellowhorn seedlings, changes in protein abundance were analyzed via comparative proteomics. Drought and heat treatment of seedlings was applied in growth chamber, and the leaves were harvested after 7 days of treatment. The total protein was extracted, and comparative proteomic analysis was performed via isobaric tag for relative and absolute quantitation (iTRAQ). The abundance of most of the proteins associated with oxidative phosphorylation, NADH dehydrogenase and superoxide dismutase (SOD) was reduced. The differential proteins associated with photosynthesis enzymes indicated that stress had different effects on photosystem I (PSI) and photosystem II (PSII). After comprehensively analyzing the results, we speculated that drought and heat stress could hinder the synthesis of riboflavin, reducing NADH dehydrogenase content, which might further have an impact on energy utilization. Yellowhorn seedlings relied on Fe-Mn SOD enzymes rather than Cu/Zn SOD enzymes to remove reactive oxygen species (ROS). In addition, heat-shock proteins (HSPs) had significant increase and played a key role in stress response, which could be divided into two categories according to their transcription and translation efficiency. Over all, the results can provide a basis for understanding the molecular mechanism underlying resistance to drought and heat stress in yellowhorn and for subsequent research of posttranslational modification-related omics of key proteins.

Tandem Mass Tag-Based Quantitative Proteome Analysis of Porcine Deltacoronavirus (PDCoV)-Infected LLC Porcine Kidney Cells

Porcine deltacoronavirus (PDCoV) is a newly emerging porcine pathogenic enteric coronavirus that can cause diarrhea, vomiting, dehydration, and a high mortality rate in piglets. At present, the understanding of PDCoV pathogenesis is very limited, which seriously hinders effective prevention and control. In this study, liquid chromatography tandem-mass spectrometry (LC-MS/MS) combined with tandem mass tag (TMT) labeling was performed to compare the differential expression of proteins in PDCoV-infected and mock-infected LLC-PK cells at 18 h post-infection (hpi). In addition, the parallel reaction monitoring (PRM) technique was used to verify the quantitative proteome data. A total of 4624 differentially expressed proteins (DEPs) were quantitated, of which 128 were significantly upregulated, and 147 were significantly downregulated. Bioinformatics analysis revealed that these DEPs were involved mainly in the defense response, apoptosis, and the immune system, and several DEPs may be related to interferon-stimulated genes and the immune system. Based on DEP bioinformatics analysis, we propose that PDCoV infection may utilize the apoptosis pathway of host cells to achieve maximum viral replication. Meanwhile, the host may be able to stimulate the transcription of interferon-stimulated genes (ISGs) through the JAK/STAT signaling pathway to resist the virus. Overall, in this study, we presented the first application of proteomics analysis to determine the protein profile of PDCoV-infected cells, which provides valuable information with respect to better understanding the host response to PDCoV infection and the specific pathogenesis of PDCoV infection.

Role of hydrogen cyanamide (HC) in grape bud dormancy release: proteomic approach

In the present study, we identified changes in protein expression patterns of grapevine buds when treated with hydrogen cyanamide (HC). HC induced a shift of more than 2-folds in the expression of 1250 proteins out of approximately 7000 detected proteins. The majority of the differentially expressed proteins (DEPs) were localized in the chloroplast (419) and cytoplasm (347). Most of the detected DEPs were linked with energy metabolism, redox activity, hormone, and stress signaling. Particularly, the DEPs associated with defense and sugar metabolism showed significantly higher expression in HC-treated buds. Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed significant enrichment for circadian rhythm, ribosome, and metabolic pathways. Moreover, the antioxidant activity of peroxidase (POD) increased at initial stages but declined at later stages (18 days post-treatment). This study identified several dormancy-related proteins that regulated signaling, as well as metabolic pathways upon HC application. The outcome of this study provides insights into the role of HC in dormancy release for grapevine production, hence useful to alleviate yield losses in mild winter regions.

Comparative Proteomic Analysis Reveals the Molecular Mechanisms Underlying the Accumulation Difference of Bioactive Constituents in Glycyrrhiza uralensis Fisch under Salt Stress

Licorice (Glycyrrhiza uralensis Fisch) possesses a substantial share of the global markets for its unique sweet flavor and diverse pharmacological compounds. Cultivated licorice is widely distributed in northwest regions of China, covered with land with a broad range of salinities. A preliminary study indicated that suitable salt stress significantly increased the content of bioactive constituents in licorice. However, the molecular mechanisms underlying the influence of salinity on the accumulation of these constituents remain unclear, which hinders quality breeding of cultivated licorice. In our study, flavonoid-related structural genes were obtained, and most of them, such as phenylalanine ammonia-lyases, cinnamate 4-hydroxylases, 4-coumarate: CoA ligases, chalcone synthases, chalcone-flavanone isomerase, and flavonol synthase, showed high levels after salt treatment. In the biosynthesis of glycyrrhizin, three key enzymes (bAS, CYP88D6, and CYP72A154) were identified as differentially expressed proteins and remarkably upregulated in the salt-stressed group. Combining these results with the contents of 14 bioactive constituents, we also found that the expression patterns of those structural proteins were logically consistent with changes in bioactive constituent profiles. Thus, we believe that suitable salt stress increased the accumulation of bioactive constituents in licorice by upregulating proteins involved in the related biosynthesis pathways. This work provided valuable proteomic information for unraveling the molecular mechanism of flavonoid and glycyrrhizin metabolism and offered fundamental resources for quality breeding in licorice.