Catechin gallate acts as a key metabolite induced by trypsin in Hylocereus undatus during storage indicated by omics

(-)-Epicatechin gallate prevented atherosclerosis by reducing abnormal proliferation of VSMCs and oxidative stress of AML 12 cells

(-)-Epicatechin gallate (ECG) is beneficial to the treatment of cardiovascular diseases (CVDs), especially atherosclerosis (AS) through antioxidant stress, but there is a lack of detailed mechanism research. In this study, the therapeutic target of ECG was determined by crossing the drug target and disease target of CVDs and AS. The combination ability of ECG with important targets was verified by Discovery Studio software. The abnormal proliferation of vascular smooth muscle cells (VSMCs) induced by Ang-II and the oxidative damage of AML 12 induced by H2O2 were established to verify the reliability of ECG intervention on the target protein. A total of 120 ECG targets for the treatment of CVDs-AS were predicted by network pharmacology. The results of molecular docking showed that ECG has strong binding force with VEGFA, MMP-9, CASP3 and MMP-2 domains. In vitro experiments confirmed that ECG significantly reduced the expression of VEGFA, MMP-9, CASP3 and MMP-2 in Ang-II-induced VSMCs, and also blocked the abnormal proliferation, oxidative stress and inflammatory reaction of VSMCs by inhibiting the phosphorylation of PI3K signaling pathway. At the same time, ECG also interfered with H2O2-induced oxidative damage of AML 12 cells, decreased the expression of ROS and MDA and cell foaming, and increased the activities of antioxidant enzymes such as SOD, thus playing a protective role.

Single-cell and spatial RNA sequencing reveal the spatiotemporal trajectories of fruit senescence

The senescence of fruit is a complex physiological process, with various cell types within the pericarp, making it highly challenging to elucidate their individual roles in fruit senescence. In this study, a single-cell expression atlas of the pericarp of pitaya (Hylocereus undatus) is constructed, revealing exocarp and mesocarp cells undergoing the most significant changes during the fruit senescence process. Pseudotime analysis establishes cellular differentiation and gene expression trajectories during senescence. Early-stage oxidative stress imbalance is followed by the activation of resistance in exocarp cells, subsequently senescence-associated proteins accumulate in the mesocarp cells at late-stage senescence. The central role of the early response factor HuCMB1 is unveiled in the senescence regulatory network. This study provides a spatiotemporal perspective for a deeper understanding of the dynamic senescence process in plants.

CsMYC2 is involved in the regulation of phenylpropanoid biosynthesis induced by trypsin in cucumber (Cucumis sativus) during storage

Trypsin has a new activity of scavenging superoxide anion and generating hydrogen peroxide. Trypsin can significantly improve the storage quality of C. sativus. To illustrate the mechanism of trypsin-induced resistance in fruits and vegetables, an integrated analysis of widely targeted metabolomics and transcriptomics was carried out. Transcriptomic results showed that 1068 genes highly related to phenylpropanoid biosynthesis gathered in the brown module were obtained by WGCNA. In KEGG analysis, differentially expressed genes (DEGs) were also highly enriched in EIP (Environmental Information Processing) pathways "Plant hormone signal transduction (map04075)" and "MAPK signaling pathway-plant (map04016)". Next, 87 genes were identified as the leading edge by GSEA analysis. So far, CsMYC2 was highlighted as a key transcription factor that regulates phenylpropanoid biosynthesis identified by GSEA and WGCNA. Furthermore, the major route of biosynthesis of phenylpropanoid compounds including coumarins, lignins, chlorogenic acid, flavonoids, and derivatives regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Results of O2PLS showed that CsMYC2 was positively correlated with Rosmarinic acid-3-O-glucoside, Epigallocatechin, Quercetin-3-O-sophoroside (Baimaside), and so on. Correlation between CsMYC2, phenylpropanoid related genes, and metabolites in C. sativus was illustrated by co-expression networks. Roles of CsMYC2 were further checked in C. sativus by VIGS. The results of this study might give new insight into the exploration of the postharvest resistance mechanism of C. sativus induced by trypsin and provide useful information for the subsequent mining of resistance genes in C. sativus.

Transcriptome analyses and virus-induced gene silencing identify HuWRKY40 acting as a hub transcription factor in the preservation of Hylocereus undatus by trypsin

Trypsin can significantly improve the storage quality of Hylocereus undatus (H. undatus). To verify the hub WRKY gene of H. undatus in trypsin preservation, joint analysis of transcriptome and protein-protein interaction (PPI) network was carried out, and virus-induced gene silencing (VIGS) was conducted. In the transcriptome of H. undatus, GO directed acyclic graph (DAG) showed that the GO terms of 55 WRKY genes were mainly enriched in sequence-specific DNA binding, DNA binding transcription factor activity, and so on. The GO enrichment chord diagram showed that HuWRKY40 was significantly up-regulated in the enriched top10 GO terms. KEGG enrichment analysis showed that 55 WRKY genes were mainly enriched in plant-pathogen interaction and MAPK pathway. The results of PPI network showed that HuWRKY40 was a hub protein of WRKY transcription factors (TFs) family regulated by trypsin, which was consistent with the results of transcriptome analysis. Bioinformatics analysis showed that HuWRKY40 of H. undatus had the highest homology with Beta vulgaris L. and Spinacia oleracea L. The function of the core regulatory protein HuWRKY40 was further clarified by VIGS technology. The results of VIGS showed that there was a big difference between the phenotype of the pTRV2-HuWRKY40 group and that of the control group. Finally, it was confirmed that HuWRKY40 accelerated the synthesis of flavonoids and improved the fruit quality during the storage of H. undatus. This study found that trypsin may regulate HuWRKY40 activity through the MAPK cascade pathway, affect the participation of flavonoid synthesis, and then delay fruit corruption. PRACTICAL APPLICATIONS: With attention of people to the safety and freshness of fruits and vegetables, biological preservation technology has become one of the hotspots in the field of preservation in recent years. Trypsin can significantly improve the antioxidant capacity of fruits and vegetables. As a new biological preservative, it is convenient to operate and economical. In the current work, the mechanism of trypsin on the WRKY TFs during H. undatus storage was investigated. The application of trypsin would provide a new strategy for the storage quality control of fruits and vegetables.

EuRBG10 involved in indole alkaloids biosynthesis in Eucommia ulmoides induced by drought and salt stresses

Alkaloids are natural products with many important medicinal activities. To explore the mechanism of abiotic stress promoting alkaloid biosynthesis in Eucommia ulmoides, transcriptomic analysis and metabonomic analysis were used, virus-induced gene silencing (VIGS) lines of target gene were constructed. The results showed that drought and salt stress caused wilting and blackening of leaves, decreased chlorophyll level, and significantly induced MDA and relative conductivity. To resist the damage of stress to cells, the level of secondary metabolites such as alkaloids increased significantly with the extension of stress time. Transcriptomic results showed that, were. Six alkaloid related genes (AWGs) were gathered in five modules positively correlated with either salt stress or alkaloid contents by WGCNA. Results of GO and KEGG enrichment revealed that biosynthesis of alkaloid, especially indole alkaloid was induced, and degradation of alkaloid was inhibited under salt stress. Combining the results of transcriptome and metabolomics, it was suggested that EuRBG10 promotes the production of indole alkaloids and EuAMO5 inhibits the degradation of alkaloids, which may be the core mechanism of the indole alkaloid biosynthesis pathway (map00901) induced by salt stress. The results of these hub proteins were also consistent with the chordal graph of KEGG enrichment. Hub roles of EuRGB10 was checked in E. ulmoides by VIGS. Our findings provide a preliminary understanding of abiotic stress regulating secondary metabolites such as alkaloids, and propose hub genes that can be used to improve the level of bioactive components in medicinal plant.

Mechanism of trypsin activation by pulsed electric field treatment revealed based on chemical experiments and molecular dynamics simulations

A pulsed electric field (PEF) treatment exhibits different effects on trypsin; however, the mechanism of enzyme activation remains unclear. Herein, chemical experiments combined with molecular dynamics simulations revealed the mechanism of trypsin activation by PEF treatment at the molecular level. The results indicated that compared with the values at 0 kV/cm, the enzyme activity, Vmax, and Kcat at 20 kV/cm increased by 9.30%, 4.74%, and 4.30%, respectively, and Km decreased by 11.14%, indicating an improved interaction between the enzyme and substrate. The simulation results revealed that PEF treatment increased the number of molecular hydrogen bonds and the solvent-accessible surface area, while decreasing the rotation radius and random coil content by 5.00% and 3.37%, respectively. Molecular docking indicated that PEF treatment altered the active center and increased the affinity between the enzyme and substrate. The simulation results were consistent with those of the spectroscopic experiments conducted on trypsin after PEF treatment.

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.

LsrB, the hub of ABC transporters involved in the membrane damage mechanisms of heavy ion irradiation in Escherichia coli

BACKGROUND

Ionizing radiation, especially heavy ion (HI) beams, has been widely used in biology and medicine. However, the mechanism of membrane damage by such radiation remains primarily uncharacterized.

PURPOSE

Transcriptomic profiles of Escherichia coli (E. coli) treated with HI illustrated the response mechanisms of the membrane, mainly ABC transporters, related genes regulated by antibiotics treatment through enrichment analyses of GO and KEGG. The networks of protein-protein interactions indicated that LsrB was the crucial one among the ABC transporters specially regulated by HI through the calculation of plugins MCODE and cytoHubba of Cytoscape. Finally, the expression pattern, GO/KEGG enrichment terms, and the interaction between nine LuxS/AI-2 quorum sensing system members were investigated.

CONCLUSIONS

Above all, results suggested that HI might perform membrane damage through regulated material transport, inhibited LuxS/AI-2 system, finally impeded biofilm formation. This work provides further evidence for the role of ABC transporters, especially LsrB, in membrane damage of E. coli to HI. It will provide new strategies for improving the precise application of HI.