scholarly journals Comparative Transcriptomic Analyses Provide Insights into the Enzymatic Browning Mechanism of Fresh-Cut Sand Pear Fruit

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 502
Author(s):  
Jing Fan ◽  
Wei Du ◽  
Qi-Liang Chen ◽  
Jing-Guo Zhang ◽  
Xiao-Ping Yang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Transcript Level ◽  
Enzymatic Browning ◽  
Rna Seq ◽  
Pear Fruit ◽  
Total Polyphenol ◽  
Phenylpropanoid Biosynthesis ◽  
Key Enzyme ◽  
Fresh Cut ◽  
High Level

Pear (Pyrus spp.) is one of the most commonly consumed temperate fruits, having considerable economic and health importance. Fresh-cut or processed pear fruits are prone to browning because of the abundant phenolic compounds; however, little is known about the molecular mechanisms underlying enzymatic browning of fresh-cut sand pear fruit. In this study, fruits of two sand pear genotypes (low browning cultivar ‘Eli No.2′ and high browning cultivar ‘Weiningdahuangli’) were used to analyze the molecular mechanism of enzymatic browning by SMRT-seq and RNA-seq. The results generated 69,122 consensus isoforms, 21,336 new transcripts, 7105 alternative splicing events, and 254 long non-coding RNAs (lncRNAs). Furthermore, five genes related to enzymatic browning were predicted to be targets of six lncRNAs, and 9930 differentially expressed genes (DEGs) were identified between two different flesh browning cultivars. Meanwhile, most DEGs (e.g., PAL, 4CL, CAD, CCR, CHS, and LAR) involved in the phenylpropanoid biosynthesis pathway were up-regulated, and the expression of PPO and POD were highly expressed in the high-browning cultivar. Interestingly, the transcript level of PbrPPO4 (Pbr000321.4) was significantly higher than other PPO and POD genes, and a high level of total polyphenol and PPO activity were observed in the high browning cultivar. We found that the expression of lncRNA PB.156.1 was significantly positively correlated with the target gene PbrPPO4 (Pbr000321.4). The results suggest that PbrPPO4 might act as a major contributor and a key enzyme encoding gene in regulating fresh-cut sand pear fruit enzymatic browning; the expression of PbrPPO4 was probably regulated by lncRNA PB.156.1. Altogether, the transcriptomic and physiological analyses expand the knowledge of sand pear flesh enzymatic browning at the molecular level and provide a foundation for germplasm resources for molecular breeding of high polyphenol and low browning cultivars in sand pears.

scholarly journals Transcriptome Profiling Reveals Potential Genes Involved in Browning of Fresh-cut Eggplant (Solanum Melongena L.)

2020 ◽  
Author(s):  
Xiaohui Liu ◽  
Jing Shang ◽  
Aidong Zhang ◽  
Zongwen Zhu ◽  
Dingshi Zha ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Fruits And Vegetables ◽  
Molecular Mechanisms ◽  
Solanum Melongena ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Enzymatic Browning ◽  
Fruit Samples ◽  
Phenylpropanoid Biosynthesis ◽  
Fresh Cut

Abstract Background: Fresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the appearance of products and impacts their nutrition. We used the RNA-Seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant (Solanum melongena L.) fruit samples from a browning-sensitive cultivar and a browning-resistant cultivar to investigate the genes and molecular mechanisms involved in browning. Results: A total of 111.55 GB of high-quality reads were generated, the genomes of each sample were compared, and 83.50%–95.14% of the data was mapped to the eggplant reference genome. Furthermore, a total of 19631 differentially expressed genes were identified, among which 12 genes and two WRKY transcription factors were identified as potentially involved in enzymatic browning in fresh-cut eggplant fruit. Moreover, the 14 differentially expressed genes associated with browning were verified using qRT-PCR. Conclusions: Several genes associated with phenolic oxidation, phenylpropanoid biosynthesis, and flavonoid biosynthesis were found to be differentially regulated between the eggplant cultivars with different browning sensitivities. This work is of great theoretical significance, as it provides a basis for future molecular studies and improvement of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.

scholarly journals Systems Biology Unraveled the Relationship of lncRNA OIP5-AS1 with CD25 and its Co-Expression Analysis in Cancers

2020 ◽  
Author(s):  
Moein Dehbashi ◽  
Zohreh Hojati ◽  
Majid Motovali-bashi ◽  
C. S. Cho ◽  
Akihiro Shimosaka ◽  
...  
Keyword(s):  
Systems Biology ◽  
Signaling Pathways ◽  
Expression Analysis ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Treg Cells ◽  
Rna Seq ◽  
Cd25 Expression ◽  
High Level ◽  
The Relationship

Abstract Background: Treg cells function in the immune homeostasis, these cells express high level of CD25. Even though the molecular mechanisms of CD25-mediated signaling pathways has been reported, some questions are still unclear, e.g. the relationship and function of the relative lncRNA. It is known that the CD25 expression levels are various among different cancers. Thus, we intended to dissect systems biology of a lncRNA pertained to CD25 and CD25 protein interactors-targeting miRNAs. Methods: Apart from using the available RNA-seq data, the co-expression analysis of the lncRNA pertained to some cancers was performed. Our analysis was done for protein interactors of CD25 by STRING 11.0, ShinyGO v0.60 and KEGG web servers were used for enrichment and network analysis of CD25. TargetScan 7.2, miRTargetLink Human and mirDIP were applied for determining the CD25 and CD25 interactors-targeting miRNAs. To find the lncRNA-miRNA and lncRNA-protein interactions, starBase v3.0, LncBase Predicted v.2 and SFPEL-LPI were recruited, respectively. Also, using Co-LncRNA, the co-expressed lncRNA analysis and the relative signaling pathways in some cancers including bladder, breast, head and neck, kidney, liver, lung, prostate and thyroid cancers using RNA-seq data were achieved. Results: OIP5-AS1 was shown to have the interaction with CD25 and CD25 protein interactors-targeting miRNAs. In addition, the co-expression of OIP5-AS1 in cancers and their signaling pathways was identified. Conclusions: Possibly, OIP5-AS1 can effect on CD25 expression in all relative signaling pathways of these cancers.

scholarly journals Transcriptome Co-expression Network Analysis Identifies Key Genes Regulating Conchosporangia Maturation of Pyropia haitanensis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yinghui Lin ◽  
Kai Xu ◽  
Yan Xu ◽  
Dehua Ji ◽  
Changsheng Chen ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Network Analysis ◽  
Molecular Mechanisms ◽  
Transcript Level ◽  
Pyropia Haitanensis ◽  
Rna Seq ◽  
Hub Genes ◽  
Early Maturing ◽  
Pigment Contents ◽  
Rapid Amplification

Conchosporangia maturation is crucial for the yield of Pyropia/Porphyra. However, the molecular mechanisms underlying this process are poorly understood. In this study, we selected two strains of Pyropia haitanensis that show significant differences in conchosporangia maturation as materials to produce RNA-Seq libraries. Then, we identified key molecular pathways and genes involved in conchosporangia maturation by conducting a weighted gene co-expression network analysis. Two specific modules were identified, and included functions such as phosphorus metabolism, lipid metabolism, and the phosphatidylinositol signaling system. The hub genes that responded positively during conchosporangia maturation encoded diacylglycerol kinase (DGK) and phosphatidylinositol-3-phosphate-5-kinase, which are involved in the synthesis of phosphatidic acid, a key component of lipid metabolism. A full-length DGK sequence of P. haitanensis, designated as PhDGK1, was obtained by rapid-amplification of cDNA ends. Conserved motif and phylogenetic tree analyses showed that PhDGK1 belongs to DGK Cluster II. The transcript level of PhDGK1 increased during conchosporangia maturation in both strains, but increased earlier, and to higher levels, in the early-maturing strain than in the late-maturing strain. This pattern of gene expression was consistent with the patterns of maturity and changes in pigment contents. These results indicate that lipid metabolism plays a key role in regulating conchosporangia maturation in Pyropia spp., and that PhDGK1 might be a useful molecular marker for breeding new early-maturing strains.

scholarly journals Transcriptome profiling reveals potential genes involved in browning of fresh-cut eggplant (Solanum melongena L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiaohui Liu ◽  
Aidong Zhang ◽  
Jie Zhao ◽  
Jing Shang ◽  
Zongwen Zhu ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Fruits And Vegetables ◽  
Molecular Mechanisms ◽  
Solanum Melongena ◽  
Transcriptome Profiling ◽  
Gene Families ◽  
Enzymatic Browning ◽  
Specific Expression ◽  
Fruit Samples ◽  
Fresh Cut

AbstractFresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the product appearance and impacts their nutrition. We used RNA-sequencing to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant fruit samples from both browning-sensitive and browning-resistant cultivars to investigate the molecular mechanisms involved in browning. A total of 8347 differentially expressed genes were identified, of which 62 genes were from six gene families (i.e., PPO, PAL, POD, CAT, APX, and GST) potentially associated with enzymatic browning. Furthermore, using qRT-PCR, we verified 231 differentially regulated transcription factors in fresh-cut eggplant fruits. The enzyme activities of PPO, POD, PAL, and CAT in ‘36’ were significantly higher than those of ‘F’ fresh-cut for 15 min. Both PPO and POD play a major role in the browning of eggplant pulp and might therefore act synergistically in the browning process. Meanwhile, qPCR results of 18 browning related genes randomly screened in 15 eggplant materials with different browning tolerance showed variant-specific expression of genes. Lastly, gene regulatory networks were constructed to identify the browning-related genes. This work provides a basis for future molecular studies of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.

scholarly journals Comparative metabolomics and transcriptomics of pistils, stamens and pistilloid stamens widen key knowledge of pistil and stamen development in wheat.

2019 ◽  
Vol 56 (No. 1) ◽  
pp. 24-33
Author(s):  
Yan Yu ◽  
Zheng Song Peng ◽  
Ji Peng Qu ◽  
Zhen Yong Chen ◽  
Shu Hong Wei ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Molecular Mechanisms ◽  
Acc Synthase ◽  
Gas Chromatography Mass Spectrometry ◽  
Ethylene Synthesis ◽  
Stamen Development ◽  
Chromatography Mass Spectrometry ◽  
Phenylpropanoid Biosynthesis ◽  
Key Enzyme ◽  
Pistil Development

To examine the role of metabolites in wheat stamen and pistil development, metabolomic analyses of pistilloid stamens (PS), pistils (P), and stamens (S) from a novel wheat mutant homologous transformation sterility-1 (HTS-1) and controls from their sib-line CSTP were conducted using base gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). Then, the metabolomic data were integrated with previously published transcriptomic data and analysed. In total, 141 annotated metabolites were determined from P, PS and S tissues by comparison with reference standards. A total of 90, 93 and 18 different metabolites were identified in S vs. PS, S vs. P and P vs. PS, respectively. Among the different metabolites, 80 may be associated with stamen and pistil growth. Using integration evaluations of both the previous transcriptome data and the 80 various metabolites, we found two perturbed pathways that significantly affect flower development in plants, namely, the phenylpropanoid biosynthesis and cysteine and methionine metabolism. The ethylene synthesis pathway, one key branch of the cysteine and methionine metabolic pathways, could have a pivotal role in pistillody growth involving HTS-1. We found two key enzyme genes in the ethylene synthesis pathway (the SAM synthase gene and the ACC synthase gene) that have higher expression levels in stamens than in pistilloid stamens or pistils. We speculate, that the decrease in ethylene content during stamen development leads to pistillody traits in HTS-1. This study helps elucidate the molecular mechanisms underlying stamen and pistil growth in wheat.

scholarly journals Effects of melatonin treatment on the enzymatic browning and nutritional quality of fresh-cut pear fruit

2019 ◽  
Vol 299 ◽  
pp. 125116 ◽  
Author(s):  
Huanhuan Zheng ◽  
Wei Liu ◽  
Shuai Liu ◽  
Changhong Liu ◽  
Lei Zheng
Keyword(s):  
Nutritional Quality ◽  
Enzymatic Browning ◽  
Pear Fruit ◽  
Melatonin Treatment ◽  
Fresh Cut

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

Comprehensive Analysis of Transcriptomics and Metabolomics between the Heads and Tails of Angelica Sinensis: Genes Related to Phenylpropanoid Biosynthesis Pathway

2020 ◽  
Vol 23 ◽  
Author(s):  
Jie Yang ◽  
Chi Zhang ◽  
Wei-Hong Li ◽  
Tian-Er Zhang ◽  
Guang-Zhong Fan ◽  
...  
Keyword(s):  
Ferulic Acid ◽  
Metabolic Regulation ◽  
Comprehensive Analysis ◽  
Angelica Sinensis ◽  
Rna Seq ◽  
Targeted Metabolomics ◽  
Kegg Pathways ◽  
Qrt Pcr ◽  
Phenylpropanoid Biosynthesis ◽  
Combined Strategy

Background:: In Traditional Chinese Medicine (TCM), the heads and tails of Angelica sinensis (Oliv.) Diels (AS) is used in treating different diseases due to their different pharmaceutical efficacies. The underline mechanisms, however, have not been fully explored. Objective:: Novel mechanisms responsible for the discrepant activities between AS heads and tails were explored by a combined strategy of transcriptomes and metabolomics. Method:: Six pairs of the heads and tails of AS roots were collected in Min County, China. Total RNA and metabolites, which were used for RNA-seq and untargeted metabolomics analysis, were respectively isolated from each AS sample (0.1 g) by Trizol and methanol reagent. Subsequently, differentially expressed genes (DEGs) and discrepant pharmaceutical metabolites were identified for comparing AS heads and tails. Key DEGs and metabolites were quantified by qRT-PCR and targeted metabolomics experiment. Results:: Comprehensive analysis of transcriptomes and metabolomics results suggested that five KEGG pathways with significant differences included 57 DEGs. Especially, fourteen DEGs and six key metabolites were relation to the metabolic regulation of Phenylpropanoid biosynthesis (PB) pathway. Results of qRT-PCR and targeted metabolomics indicated that higher levels of expression of crucial genes in PB pathway, such as PAL, CAD, COMT and peroxidase in the tail of AS were positively correlated with levels of ferulic acid-related metabolites. The average content of ferulic acid in tails (569.58162.39 nmol/g) was higher than those in the heads (168.73  67.30 nmol/g) (P˂0.01); Caffeic acid in tails (3.82  0.88 nmol/g) vs heads (1.37  0.41 nmol/g) (P˂0.01), and Cinnamic acid in tails (0.24  0.09 nmol/g) vs heads (0.14  0.02 nmol/g) (P˂0.05). Conclusion:: Our work demonstrated that overexpressed genes and accumulated metabolites derived from PB pathway might be responsible for the discrepant pharmaceutical efficacies between AS heads and tails.

Enzymatic browning and its control in fresh-cut produce

2007 ◽  
Vol 3 (6) ◽  
pp. 1-7 ◽  
Author(s):  
Qiang He ◽  
Yaguang Luo
Keyword(s):  
Enzymatic Browning ◽  
Fresh Cut
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