OBJECTIVE:To investigate the underlying protein molecular mechanisms of"Qi stagnation and blood stasis syndrome"(QS)and"Qi deficiency and blood stasis syndrome"(QD),as two subtypes of coronary artery disease(CAD)in Traditional Chinese Medicine(TCM),following percutaneous coronary intervention(PCI). METHODS:In this study,a total of 227 CAD patients with QS and 211 CAD patients with QD were enrolled;all participants underwent PCI.Label-free quantification proteomics were employed to analyze the changes in serum in two subtypes of CAD patients before and 6 months after PCI,aiming to elucidate the intervention mechanism of PCI in treating CAD characterized by two different TCM syndromes. RESULTS:Biochemical analysis revealed significant changes in tumor necrosis factor-α,high density lipoprotein cholesterol,blood stasis clinical symptoms observation,and Gensini levels in both patient groups post-PCI;Proteomic analysis identified 79 and 95 differentially expressed proteins in the QS and QD patient groups,respectively,compared to their control groups.complement C8 alpha chain,complement factor H,apolipoprotein H,apolipoprotein B,plasminogen,carbonic anhydrase 2,and complement factor I were altered in both comparison groups.Furthermore,enrichment analysis demonstrated that cell adhesion and connectivity-related processes underwent changes in QS patients post-PCI,whereas lipid metabolism-related pathways,including the peroxisome proliferator-activated receptor signaling pathway and extracellular matrix receptor interaction,underwent changes in the QD group.The protein-protein interaction network analysis further enriched 52 node proteins,including apolipoprotein B,lipoprotein(a),complement C5,apolipoprotein A4,complement C8 alpha chain,complement C8 beta chain,complement C8 gamma chain,apolipoprotein H,apolipoprotein A-Ⅱ,albumin,complement C4-B,apolipoprotein C3,among others.The functional network of these proteins is posited to contribute to the pathophysiology of CAD characterized by TCM syndromes. CONCLUSION:The current quantitative proteomic study has preliminarily identified biomarkers of CAD in different TCM subtypes treated with PCI,potentially laying the groundwork for understanding the protein profiles associated with the treatment of various TCM subtypes of CAD.

Objective: Astragali Radix (AR, Huangqi in Chinese) has a neuroprotective effect on cerebral infarction (CI). In order to explore the biological basis and therapeutic mechanism of AR in CI, a double-blind randomized controlled trial was established in this study, and proteomics analysis was carried out on serum samples of patients. Methods: The patients were divided into the AR group (n = 35) and the control group (n = 30). The curative effect was evaluated by the traditional Chinese medicine (TCM) syndrome score and clinical indicators, and the serum of the two groups was analyzed by proteomics. Based on bioinformatics analysis methods, the changes in differential proteins between two groups of samples were explored, and the key proteins were validated through enzyme-linked immunosorbent assay (ELISA). Results: The results of this study showed that the scores of deficiency of vital energy (DVE), blood stasis (BS), and NIH Stroke Scale (NIHSS) decreased significantly (p < 0.05), while the scores of the Barthel Index (BI) increased, indicating that AR could significantly improve the symptoms of CI patients. In addition, we found that compared with the control group, AR upregulated 43 proteins and downregulated 20 proteins, especially focusing on anti-atherosclerosis and neuroprotective effects. Moreover, ELISA indicated the levels of IL-6, TNF-α, VCAM-1, MCP-1, and ICAM-1 were significantly decreased in the serum of the AR group (p < 0.05, p < 0.01). Conclusion: This study found that AR can significantly recover the clinical symptoms of CI. Serum proteomics research results show that AR may act on IL-6, TNF-α, VCAM-1, MCP-1, and ICAM-1, and play anti-atherosclerosis and neuroprotective roles. Clinical Trial Registration: [clinicaltrials.gov], identifier [NCT02846207].

Drought severely affects the yield of wheat (Triticum aestivum L.), which is mainly grown in arid and semi-arid regions. Melatonin plays an important role in various types of stress resistance in plants, including drought resistance. However, the molecular mechanism through which melatonin affects drought tolerance remains largely unknown. In this study, we revealed that melatonin (100 μM) significantly improved drought resistance during the maturation stage of Chinese Spring, Shi4185, and Hanxuan10 varieties, but not Chang6878. Further physiological, transcriptomic, and proteomic data analysis at the wheat seedling stage revealed that melatonin increased jasmonic acid (JA) content, upregulating the expression of JA genes (LOX1.5 and LOX2.1) and two transcription factors (HY5 and MYB86) under drought conditions. It also upregulated genes related to lignin biosynthesis (4CL2, P5CS1, and CCR2) as well as starch and sucrose metabolism (PME53 and SUS4). Additionally, melatonin alleviated photosynthetic and cell membrane damage caused by drought stress through maintaining low levels of hydrogen peroxide. The current results elucidate melatonin-regulated pathways in wheat and provide evidence for using melatonin as a potential biostimulant to improve wheat drought resistance under field conditions in the future.

Nitrogen is an important nutrient for the growth and yield of wheat. However, in practical production, wheat suffers from nitrogen stress. In this study, we generated wheat plants with improved low nitrogen (LN) tolerance by introducing AtbZIP69, a gene encoding a basic leucine zipper domain transcription factor, into the wheat variety Shi 4056. We observed that AtbZIP69 expression in transgenic wheat was induced by LN and drought stress. AtbZIP69 localised in the nucleus and activated transcription. A greenhouse trial revealed that, compared to wild type (WT) wheat, the AtbZIP69 transgenic wheat showed significantly increased drought and LN stress tolerance. A two-year field trial demonstrated that the yield and number of spikes of transgenic wheat were significantly higher than those of WT wheat under LN conditions. By investigating nitrogen use-related traits, we discovered that overexpression of AtbZIP69 altered nitrogen distribution by allocating more nitrogen to grains under LN conditions. In addition, the expression of nitrogen transporter protein genes (such as TaNRT2.1, TaNRT2.5, and TaNR1) was higher in AtbZIP69 transgenic wheat than in WT wheat under LN conditions. Overall, AtbZIP69 overexpression increased nitrogen content of the transgenic line grains under LN conditions by regulating the expression of nitrogen-related transporter protein genes, potentially leading to increased grain yield. As a result, a new candidate gene for improving LN stress tolerance in the field was identified using heterologous expression analysis of wheat.

Wheat is a staple crop in China’s arid and semi-arid regions. Drought and low nitrogen (LN) are two major constraints to wheat growth and production. However, the molecular mechanism underlying wheat response to both drought and LN stress remains unknown. Accordingly, we conducted a proteomic study on the roots of two wheat varieties, Chang6878 (drought tolerant) and Shi4185 (drought sensitive) and compared the differences between drought and combined drought and LN stress treatments. In total, 5143 proteins were identified, of which 163 differentially abundant proteins (DAPs) were uniquely upregulated under drought and LN stress in Chang6878. Enrichment analysis showed that DAPs were mainly involved in mitogen-activated protein kinase signaling, phenylpropanoid biosynthesis, glutathione metabolism, ethylene biosynthesis, ethylene signal transduction, and oxidation–reduction reactions. These DAPs were verified via parallel reaction monitoring and quantitative real-time polymerase chain reaction. Chang6878 was treated with the ethylene synthesis precursor 1-aminocyclopropanecarboxylic acid, and its resistance to drought and LN stress improved. After treatment with the ethylene synthesis inhibitor silver nitrate and ethylene signal transduction inhibitor 1-methylcyclopropene, drought and LN stress resistance reduced. These results provide novel insights into the tolerance mechanisms of Chang6878 to drought and LN stress by altering ethylene synthesis and signal transduction. This study provides a reference for breeding drought- and low-nitrogen-tolerant wheat germplasm resources and a theoretical basis for maintaining food security in arid, barren areas.

Metabolomics, which mainly studies the metabolite components of organisms, tissues, cells and their dynamic changes, is an emerging omics technology following genomics and proteomics. Metabolites are the final products of cellular regulation, and the concentration of metabolites is considered to be the ultimate response of a biological system to genetic or environmental changes. Secondary metabolites with chemical diversity are widely present in living organisms, thus accurate quantification of secondary metabolites through appropriate analytical platforms is an important task of metabolomics. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is the most commonly used method for the detection of metabolites, providing a basis for the wide application of plant secondary metabolites. This review summarizes the advances of using LC-MS/MS techniques for the detection of phytohormone, folic acid, flavonoids and other secondary metabolites.

Drought is the major limiting factor that directly or indirectly inhibits the growth and reduces the productivity of sorghum (Sorghum bicolor (L.) Moench). As the main vegetative organ of sorghum, the response mechanism of the leaf to drought stress at the proteomic level has not been clarified. In the present study, nano-scale liquid chromatography mass spectrometry (nano-LC-MS/MS) technology was used to compare the changes in the protein expression profile of the leaves of drought-sensitive (S4 and S4-1) and drought-resistant (T33 and T14) sorghum varieties at the seedling stage under 25% PEG-6000 treatment for 24 h. A total of 3927 proteins were accurately quantitated and 46, 36, 35, and 102 differentially abundant proteins (DAPs) were obtained in the S4, S4-1, T14, and T33 varieties, respectively. Four proteins were randomly selected for parallel reaction monitoring (PRM) assays, and the results verified the reliability of the mass spectrometry (MS) results. The response mechanism of the drought-sensitive sorghum leaves to drought was attributed to the upregulation of proteins involved in the tyrosine metabolism pathway with defense functions. Drought-resistant sorghum leaves respond to drought by promoting the TCA cycle, enhancing sphingolipid biosynthesis, interfering with triterpenoid metabolite synthesis, and influencing aminoacyl-tRNA biosynthesis. The 17 screened important candidate proteins related to drought stress were verified by quantitative real-time PCR (qRT-PCR), the results of which were consistent with the results of the proteomic analysis. This study lays the foundation for revealing the drought-resistance mechanism of sorghum at the protein level. These findings will help us cultivate and improve new drought-resistant sorghum varieties.

Mycobacterium sp. 16 F can degrade 94% of pyrene (20 ppm) in 4 days. To investigate its pyrene degradation mechanism, proteomic changes were analyzed using two-dimensional differential gel electrophoresis (2DE-DIGE). Comparative analysis of differential proteins revealed 91 differentially expressed protein spots after pyrene exposure. Among these, 65 spots were identified as 57 proteins. Further analysis revealed that 13 spots were involved in the pyrene degradation pathway, and most of these were dioxygenases and dehydrogenases. Further, 16 up-regulated expression protein spots were associated with four pathways that may be related to pyrene degradation. Bioinformatics analysis further revealed that the pentose phosphate and glycolytic pathways led to the production of amino acids and nucleotide precursors in pyrene-induced cells. The metabolites from these processes then entered the shikimate pathway via the beta-ketoadipate pathway in conjunction with the pyrene degradation pathway. This study provides a new model for the pyrene degradation pathway in Mycobacteria.

Compound Renshen Buqi Granules have been widely used to treat chronic heart failure(CHF) due to Qi deficiency and blood stasis, but the mechanism of action remains unclear. This paper explored the pathogenesis of CHF due to Qi deficiency and blood stasis and the intervention mechanism of Compound Renshen Buqi Granules based on quantitative proteomics for uncovering the biological basis. SD rats were divided into the normal control(N) group, normal+Compound Renshen Buqi Granules(ND) group, model(M) group, model+Compound Renshen Buqi Granules(D) group, and positive control(Y) group. The rat model of CHF due to Qi deficiency and blood stasis was established by ligation of the left anterior descending(LAD) coronary artery and chronic sleep deprivation. The rats in the ND group and D group were provided with Compound Renshen Buqi Granules, while those in the Y group received valsartan. Six weeks later, the serum was sampled and the data-dependent acquisition(DDA) was employed for the non-targeted quantitative proteomics analysis of the differences in protein expression among groups, followed by the targeted analysis of differentially expressed proteins(DEPs) generated by data-independent acquisition(DIA). Compared with the N group, the rats in the M group pre-sented with decreased body weight, grip strength, and pulse amplitude and increased RGB value on the tongue surface. The pathomorphological examination revealed inflammatory cell infiltration, cell degeneration and necrosis, tissue fibrosis, etc. After the intervention with Compound Renshen Buqi Granules, multiple indicators were reversed. As demonstrated by proteomics results, there were 144 and 111 DEPs found in the M group and ND group in comparison with the N group. Compared with the M group, 107 and 194 DEPs were found in the D group and the Y group, respectively. Compared with the ND group, 119 DEPs were detected in the D group. As illustrated by DIA-based verification, the quantitative results of six proteins in each group were consistent with those by DDA. The syndrome indicators and pathomorphological examination results demonstrated that the protein expression profile of rats with CHF due to Qi deficiency and blood stasis changed obviously. However, Compound Renshen Buqi Granules were able to reverse the differential expression of immune proteins to regulate CHF of Qi deficiency and blood stasis syndrome, which has provided clues for figuring out the pathogenesis of CHF due to Qi deficiency and blood stasis and the intervention mechanism of Compound Renshen Buqi Granules.

BACKGROUND:Heterosis refers to superior traits exhibiting in a hybrid when compared with both parents. Generally, the hybridization between parents can change the expression pattern of some proteins such as non-additive proteins (NAPs) which might lead to heterosis. 'Zhongdan808' (ZD808) and 'Zhongdan909' (ZD909) are excellent maize hybrids in China, however, the heterosis mechanism of them are not clear. Proteomics has been wildly used in many filed, and comparative proteomic analysis of hybrid and its parents is helpful for understanding the mechanism of heterosis in the two maize hybrids.RESULTS:Over 2000 protein groups were quantitatively identified from second seedling leaves of two hybrids and their parents by label-free quantification. Statistical analysis of total identified proteins, differentially accumulated proteins (DAPs) and NAPs of the two hybrids revealed that both of them were more similar to their female parents. In addition, most of DAPs were up-regulated and most of NAPs were high parent abundance or above-high parent abundance in ZD808, while in ZD909, most of DAPs were down-regulated and most of NAPs were low parent abundance or below-low parent abundance. Pathway enrichment analysis showed that more of stress response-related NAPs in ZD808 were high parent abundance or above-high parent abundance, and most of PS related NAPs in ZD909 were high parent abundance or above-high parent abundance. Finally, four stress response-related proteins and eight proteins related to PS were verified by PRM, ten of them had significant differences between hybrid and midparent value.CONCLUSIONS:Even though every one of the two hybrids were more similar to its female parent at proteome level, the biological basis of heterosis is different in the two maize hybrids. In comparison with their parents, the excellent agronomic traits of hybrid ZD808 is mainly correlated with the high expression levels of some proteins related to stress responses and metabolic functions, while traits of ZD909 is mainly correlated with high expressed proteins related to photosynthesis. Our proteomics results support previous physiological and morphological research and have provided useful information in understanding the reason of valuable agronomic traits.

Developing an effective method to improve the quality of Pu-erh tea is of great scientific and commercial interest. In this work, Penicillium chrysogenum P1 isolated from Pu-erh tea was inoculated in sterilized or unsterilized sun-dreid green tea leaves to develop pure-culture fermentation (PF) and enhanced fermentation (EF) of Pu-erh tea. Spectrophotometry and high performance liquid chromatography determined that contents of free amino acids (FAA), total tea polyphenols and eight polyphenolic compounds in PF were significantly lower than these in non-inoculation control test (CK) (P < 0.05), whereas the contents of soluble sugars and theabrownins (TB) in PF were significantly higher (P < 0.05) than in CK. A total of 416 volatile compounds were detected by headspace solid-phase micro-extraction combined with gas chromatography-mass spectrometry. Comparison to CK, 124 compounds in PF were degraded or decreased significantly [Variable importance in projection [(VIP) > 1.0, P < 0.05, fold change (FC) < 0.5], whereas 110 compounds in PF were formed or increased significantly (VIP > 1.0, P < 0.05, FC > 2). Compared with normal fermentation (NF), the levels of gallic acid, (+)-catechin, (-)-epicatechin and 64 volatile compounds in EF were significantly lower (VIP > 1.0, P < 0.05, FC < 0.5), whereas the levels of FAA and 39 volatile compounds were significantly higher (VIP > 1.0, P < 0.05, FC > 2). Amplicon sequencing of fungal internal transcribed spacer 1 (ITS1) revealed that P. chrysogenum P1 didn't become the dominant fungus in EF; while the fungal communities in EF were different from those in NF, in that the relative abundances of Blastobotrys bambusae and P. chrysogenum in EF were higher, and the relative abundances of Aspergillus niger and Kluyveromyces marxianus in EF were lower. Overall, inoculation of P. chrysogenum in unsterilized sun-dreid green tea leaves changed the the fungal communities in fermentation of Pu-erh tea, and chemical compounds in fermented tea leaves, i.e., the levels of TB and the compounds responsible for the stale flavor, e.g., 2-amino-4-methoxybenzothiazole were increased, resulting in improvement of the sensory quality, including mellower taste and stronger stale flavor.

Although genetically modified (GM) glyphosate-resistant soybeans with cp4-epsps gene have been widely planted all over the world, their proteomic characteristics are not very clear. In this study, the soybean seeds of a GM soybean line H06-698 (H) with cp4-epsps gene and its non-transgenic counterpart Mengdou12 (M), which were collected from two experiment fields in two years and used as 4 sample groups, were analyzed with label-free proteomics technique. A total of 1706 proteins were identified quantitatively by label-free quantification, and a total of 293 proteins were detected as common differential abundance proteins (DAPs, FC is not less than 1.5) both in two groups or more. Functional enrichment analysis of common DAPs identified from four groups, shows that most up-regulated proteins were clustered into stress response, carbon and energy metabolism, and genetic information processing. Further documentary analysis shows that 15 proteins play important roles in shikimate pathways, reactive oxygen species (ROS) and stress response. These results indicated that the change of protein abundance in different samples were affected by various factors, but except shikimate and branched pathways related proteins, only ROS and stress-related proteins were found to be stably regulated by cp4-epsps gene, and no unexpected and safety-related proteins such as antinutritional factors, allergenic proteins, and toxic proteins were found as DAPs. The influence of foreign genes in genetically modified plants is worthy of attention and this work provides new clues for exploring the regulated proteins and pathways in GM plants.

Post-fermented Pu-erh tea (PFPT) is a microbially-fermented tea with distinct sensory qualities and multiple health benefits. Aspergillus are the dominant fungi in the fermentation and the main contributors to the characteristics of PFPT, so their underlying functions warrant detailed study. Here, tea leaves were fermented by Aspergillus niger, Aspergillus tamarii and Aspergillus fumigatus, and resulting samples (designated as Asn, Ast and Asf, respectively) were analyzed by proteomic and metabolomic methods. Changes to the composition of flavonoids, glycerophospholipids, organo-oxygen compounds and fatty acids resulting from Aspergillus fermentation were observed. Carbohydrate-active enzymes, e.g., endoglucanases and cellulases, for degradation of cellulose, starch, lignin, pectin, xylan and xyloglucan were identified. Glycoside hydrolase, glycosyltransferases, tannase, laccases, vanillyl-alcohol oxidases and benzoquinone reductase were identified and hypothesized to catalyze hydrolysis, oxidation, polymerization and degradation of phenolic compounds. Together, functions of Aspergillius were demonstrated as production of enzymes to change concentrations and compositions of metabolites in tea leaves.

Leaf color mutants are ideal materials for chloroplast development and photosynthetic mechanism research. Here, we characterized an EMS (ethyl methane sulfonate)-mutagenized sorghum (Sorghum bicolor) mutant, sbe6-a1, in which the severe disruption in chloroplast structure and a chlorophyll deficiency promote an albino leaf phenotype and lead to premature death. The proteomic analyses of mutant and its progenitor wild-type (WT) were performed using a Q Exactive plus Orbitrap mass spectrometer and 4,233 proteins were accurately quantitated. The function analysis showed that most of up-regulated proteins in mutant sbe6-a1 had not been well characterized. GO-enrichment analysis of the differentially abundant proteins (DAPs) showed that up-regulated DAPs were significantly enriched in catabolic process and located in mitochondria, while down regulated DAPs were located in chloroplasts and participated in photosynthesis and some other processes. KEGG pathway-enrichment analyses indicated that the degradation and metabolic pathways of fatty acids, as well as some amino acids and secondary metabolites, were significantly enhanced in the mutant sbe6-a1, while photosynthesis-related pathways, some secondary metabolites' biosynthesis and ribosomal pathways were significantly inhibited. Analysis also shows that some DAPs, such as FBAs, MDHs, PEPC, ATP synthase, CABs, CHLM, PRPs, pathogenesis-related protein, sHSP, ACP2 and AOX may be closely associated with the albino phenotype. Our analysis will promote the understanding of the molecular phenomena that result in plant albino phenotypes.

Sleep is an essential and fundamental physiological process that plays crucial roles in the balance of psychological and physical health. Sleep disorder may lead to adverse health outcomes. The effects of sleep deprivation were extensively studied, but its mechanism is still not fully understood. The present study aimed to identify the alterations of serum proteins associated with chronic sleep deprivation, and to seek for potential biomarkers of sleep disorder mediated diseases. A label-free quantitative proteomics technology was used to survey the global changes of serum proteins between normal rats and chronic sleep deprivation rats. A total of 309 proteins were detected in the serum samples and among them, 117 proteins showed more than 1.8-folds abundance alterations between the two groups. Functional enrichment and network analyses of the differential proteins revealed a close relationship between chronic sleep deprivation and several biological processes including energy metabolism, cardiovascular function and nervous function. And four proteins including pyruvate kinase M1, clusterin, kininogen1 and profilin-1were identified as potential biomarkers for chronic sleep deprivation. The four candidates were validated via parallel reaction monitoring (PRM) based targeted proteomics. In addition, protein expression alteration of the four proteins was confirmed in myocardium and brain of rat model. In summary, the comprehensive proteomic study revealed the biological impacts of chronic sleep deprivation and discovered several potential biomarkers. This study provides further insight into the pathological and molecular mechanisms underlying sleep disorders at protein level.

As a plant growth regulator which functionally resembles a kind of plant hormone Brassinosteroids (BRs), 2,4-Epibrassinolide (EBR) has been widely studied and applied in different aspects. EBR can enhance plant's cold tolerance effectively, but the proteomic characteristics of the effect of EBR on rice seedings response to cold stress are still unclear. In this study, the germinating seeds of rice Nipponbare were treated with 0.1 mg L–1 EBR and distilled water before they were cultivated at 4°C or 26°C, and then the total protein of each group of seedlings was extracted. Finally, proteomes of rice seedings were analyzed by label-free quantitative mass spectrometry, and some important proteins were verified by parallel reaction monitoring technique (PRM). A total of 5778 protein groups were identified by qualitative method and 4834 protein groups were accurately quantitated. Among them, 401 up-regulated and 220 down-regulated proteins were related to the effect of EBR on rice seedings response to cold stress. The up-regulated proteins were mainly related to molecular function of RNA binding and hydrolase activity, and mainly enriched in the pathways of carbon metabolism, folic acid synthesis and amino acid biosynthesis. The down-regulated proteins were mainly related to catalytic activity and oxidoreductase activity, and mainly enriched in the pathways of porphyrin and chlorophyll metabolism and other metabolic pathways. PRM validation and literature analysis showed that NADP-malic acidase, peroxidase, 3-phosphoglycerate dehydrogenase, enolase, glyceraldehyde-3-phosphate dehydrogenase and pyruvate kinase, which are distributed in the pathways of carbon metabolism and phenylpropanol metabolism and others, take part in the regulation of EBR on rice seedlings response to cold stress, suggesting that BRs can affect rice seedlings response to cold stress through a variety of pathways.