Melaleuca alternifolia oil can delay nutrient damage of grapes caused by aspergillus ochraceus through regulation of key genes and metabolites in metabolic pathways

2020 ◽  
Vol 164 ◽  
pp. 111152 ◽  
Author(s):  
Qingjun Kong ◽  
Jianrui Qi ◽  
Peipei An ◽  
Rongrong Deng ◽  
Jiahui Meng ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Aspergillus Ochraceus ◽  
Melaleuca Alternifolia ◽  
Key Genes

A comprehensive integrated transcriptome and metabolome analyses to reveal key genes and essential metabolic pathways involved in CMS in kenaf

2020 ◽  
Author(s):  
Meiqiong Tang ◽  
Zengqiang Li ◽  
Dengjie Luo ◽  
Fan Wei ◽  
Muhammad Haneef Kashif ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Key Genes

Exploration and engineering of biosynthetic pathways in the marine actinomycete Salinispora tropica

2009 ◽  
Vol 81 (6) ◽  
pp. 1075-1084 ◽  
Author(s):  
Markus Nett ◽  
Bradley S. Moore
Keyword(s):  
Natural Products ◽  
Metabolic Pathways ◽  
Anticancer Agent ◽  
Complex Molecules ◽  
Dna Cleaving ◽  
Metabolic Plasticity ◽  
Salinosporamide A ◽  
Salinispora Tropica ◽  
Marine Actinomycete ◽  
Key Genes

In recent years, members of the marine actinomycete genus Salinispora have proven to be a precious source of structurally diverse secondary metabolites, including the potent anticancer agent salinosporamide A and the enediyne-derived sporolides. The tremendous potential of these marine-dwelling microbes for natural products biosynthesis, however, was not fully realized until sequencing of the Salinispora tropica genome revealed the presence of numerous orphan biosynthetic loci besides a plethora of rare metabolic pathways. This contribution summarizes the biochemical exploration of this prolific organism, highlighting studies in which genome-based information was exploited for the discovery of new enzymatic processes and the engineering of unnatural natural products. Inactivation of key genes within the salinosporamide pathway has expanded its inherent metabolic plasticity and enabled access to various salinosporamide derivatives by mutasynthesis. New insights into the biosynthesis of the sporolides allowed us to increase production titers of these structurally complex molecules, thereby providing the means to search for the DNA cleaving presporolide enediyne.

scholarly journals Enhanced β-carotene production by promoting the multivesicular body (MVB) pathway in Yarrowia lipolytica

2020 ◽  
Author(s):  
Fan Yang ◽  
Liang Liu ◽  
Shan Qiang ◽  
Ching Yuan Hu ◽  
Ying Li ◽  
...  
Keyword(s):  
Protein Level ◽  
Metabolic Pathways ◽  
Multivesicular Body ◽  
Carotene Content ◽  
Key Enzymes ◽  
New Strategy ◽  
Key Genes ◽  
Complex Regulatory Network ◽  
Β Carotene ◽  
Carotene Synthesis

Abstract Background: β-carotene is a precursor of vitamin A and has great commercial value as an additive in foods and feeds. Many pathways not directly related to the β-carotene synthesis affect β-carotene production since the interactions among metabolic fluxes of cells confer a complex regulatory network. Engineered Y. lipolytica strain has excellent potential for β-carotene production as oleaginous yeast. Optimizing indirectly metabolic pathways in Y. lipolytica may offer a new strategy for making the β-carotene production achieve a commercially viable yield.Results: In this study, we found that the proper promotion of the multivesicular body (MVB) sorting pathway elevated the production of β-carotene by 1.58 fold when overexpressing one copy of the Did2 gene in Y. lipolytica. Through the measurement of ATP, NADPH, the mRNA, and protein level of key genes in the β-carotene synthesis pathway, the reason for β-carotene elevated was deuced that the protein level of the key enzymes (tHMG and CarA) was increased. When overexpressing two copies of the Did2 gene, the transcription level of the key genes was all elevated. However, the protein level of key enzymes in the β-carotene synthesis pathway was reduced compared with the overexpressing one copy of the Did2 gene, which resulted in reduced β-carotene content.Conclusion: This study suggests that the MVB sorting pathway is not responsible for sorting protein but has a crucial regulating effect on protein abundance in cells. Engineering the MVB sorting pathway could potentially increase the production of other high-value products. Moreover, manipulation of indirectly related metabolic pathways also is a critical strategy in synthetic biology research.

scholarly journals Using Transcriptome Analysis to Screen for Key Genes and Pathways Related to Cytoplasmic Male Sterility in Cotton (Gossypium hirsutum L.)

2019 ◽  
Vol 20 (20) ◽  
pp. 5120 ◽  
Author(s):  
Yuqing Li ◽  
Tengfei Qin ◽  
Chunyan Wei ◽  
Jialiang Sun ◽  
Tao Dong ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Energy Metabolism ◽  
Male Sterility ◽  
Carbohydrate Metabolism ◽  
Metabolic Pathways ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Anther Development ◽  
Gossypium Hirsutum L ◽  
Key Genes

Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Cytoplasmic male sterility (CMS) is an excellent breeding system for exploitation of heterosis, which has great potential to increase crop yields. To understand the molecular mechanism of CMS in cotton, we compared transcriptome, cytomorphological, physiological and bioinformatics data between the CMS line C2P5A and its maintainer line C2P5B. By using high-throughput sequencing technology, 178,166 transcripts were assembled and 2013 differentially expression genes (DEGs) were identified at three different stages of C2P5A anther development. In this study, we identified DEGs associated with reactive oxygen species (ROS), peroxisomes, aldehyde dehydrogenases (ALDH), cytochrome oxidase subunit VI, and cytochrome P450, and DEGs associated with tapetum development, Jojoba acyl-CoA reductase-related male sterility protein, basic helix-loop-helix (bHLH) and MYB transcription factors. The abnormal expression of one of these genes may be responsible for the CMS C2P5A line. In gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, DEGs were mainly related to carbohydrate metabolism, amino acid metabolism, transport and catabolism, and signal transduction. Carbohydrate metabolism provides energy for anther development, starch and sucrose metabolism, fatty acid biosynthesis and metabolism and ascorbate and aldarate metabolism. These results showed that numerous genes and multiple complex metabolic pathways regulate cotton anther development. Weighted correlation network analysis (WGCNA) indicated that three modules, ‘turquoise,’ ‘blue,’ and ‘green,’ were specific for the CMS C2P5A line. The ‘turquoise’ and ‘blue’ modules were mainly related to carbohydrate metabolism, amino acid metabolism, energy metabolism, peroxisomes, pyruvate metabolism as well as fatty acid degradation. The ‘green’ module was mainly related to energy metabolism, carbon metabolism, translation, and lipid metabolism. RNA-sequencing and WGCNA polymerization modules were screened for key genes and pathways related to CMS in cotton. This study presents a new perspective for further research into the metabolic pathways of pollen abortion in the CMS C2P5A line and also provides a theoretical basis for its breeding and production.

scholarly journals Identification of the Roles of a Stemness Index Based on mRNA Expression in the Prognosis and Metabolic Reprograming of Pancreatic Ductal Adenocarcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Rong Tang ◽  
Xiaomeng Liu ◽  
Wei Wang ◽  
Jie Hua ◽  
Jin Xu ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mrna Expression ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Metabolic Pathways ◽  
Gene Set Enrichment Analysis ◽  
Metabolic Reprogramming ◽  
Ductal Adenocarcinoma ◽  
Independent Gene ◽  
Gene Modules ◽  
Key Genes

BackgroundCancer stem cells (CSCs) are widely thought to contribute to the dismal prognosis of pancreatic ductal adenocarcinoma (PDAC). CSCs share biological features with adult stem cells, such as longevity, self-renewal capacity, differentiation, drug resistance, and the requirement for a niche; these features play a decisive role in cancer progression. A prominent characteristic of PDAC is metabolic reprogramming, which provides sufficient nutrients to support rapid tumor cell growth. However, whether PDAC stemness is correlated with metabolic reprogramming remains unknown.MethodRNA sequencing data of PDAC, including read counts and fragments per kilobase of transcript per million mapped reads (FPKM), were collected from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA-PAAD) database. Single-sample gene set enrichment analysis (GSEA) was used to calculate the relative activities of metabolic pathways in each PDAC sample. Quantitative real-time PCR was performed to validate the expression levels of genes of interest.ResultsThe overall survival (OS) of patients with high mRNA expression-based stemness index (mRNAsi) values was significantly worse than that of their counterparts with low mRNAsi values (P = 0.003). This survival disadvantage was independent of baseline clinical characteristics. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and GSEA showed that the differentially expressed genes between patients with high and low mRNAsi values were mainly enriched in oncogenic and metabolic pathways. Weighted gene coexpression network analysis (WGCNA) revealed 8 independent gene modules that were significantly associated with mRNAsi and 12 metabolic pathways. Unsupervised clustering based on the key genes in each module identified two PDAC subgroups characterized by different mRNAsi values and metabolic activities. Univariate Cox regression analysis identified 14 genes beneficial to OS from 95 key genes selected from the eight independent gene modules from WGCNA. Among them, MAGEH1, MAP3K3, and PODN were downregulated in both pancreatic tissues and cell lines.ConclusionThe present study showed that PDAC samples with high mRNAsi values exhibited aberrant activation of multiple metabolic pathways, and the patients from whom these samples were obtained had a poor prognosis. Future studies are expected to investigate the underlying mechanism based on the crosstalk between PDAC stemness and metabolic rewiring.

scholarly journals Identification of Heat-Responsive Genes in Guar [Cyamopsis tetragonoloba (L.) Taub]

2020 ◽  
Vol 2020 ◽  
pp. 1-17
Author(s):  
Aref Alshameri ◽  
Fahad Al-Qurainy ◽  
Abdel-Rhman Gaafar ◽  
Salim Khan ◽  
Mohammad Nadeem ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Heat Stress ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Heat Tolerance ◽  
Metabolic Pathways ◽  
Cyamopsis Tetragonoloba ◽  
Protein Families ◽  
New Genes ◽  
Key Genes

The threat of heat stress on crop production increased dramatically due to global warming leading to the rise on the demand of heat-tolerant crops and understanding their tolerance. The leguminous forage crop Guar [Cyamopsis tetragonoloba (L.) Taub] is a high-temperature tolerant plant with numerous works on its tolerance at morph-physiological levels but lack on molecular thermotolerance level. In the current study, the differential gene expression and the underlying metabolic pathways induced by heat treatment were investigated. An RNA-Seq study on Guar leaves was carried out to estimate gene abundance and identify genes involved in heat tolerance to better understand the response mechanisms to heat stress. The results uncovered 1551 up- and 1466 downregulated genes, from which 200 and 72 genes with unknown function could be considered as new genes specific to guar. The upregulated unigenes were associated with 158 enzymes and 102 KEGG pathways. Blast2GO, InterProScan, and Kyoto Encyclopaedia of Genes and Genomes packages were utilized to search the functional annotation, protein analysis, enzymes, and metabolic pathways and revealed hormone signal transduction were enriched during heat stress tolerance. A total of 301 protein families, 551 domains, 15 repeats, and 3 sites were upregulated and matched to those unigenes. A batch of heat-regulated transcription factor transcripts were identified using the PlantTFDB database, which may play roles in heat response in Guar. Interestingly, several heat shock protein families were expressed in response to exposure to stressful conditions for instance small HSP20, heat shock transcription factor family, heat shock protein Hsp90 family, and heat shock protein 70 family. Our results revealed the expressional changes associated with heat tolerance and identified potential key genes in the regulation of this process. These results will provide a good start to dissect the molecular behaviour of plants induced by heat stress and could identify the key genes in stress response for marker-assisted selection in Guar and reveal their roles in stress adaptation in plants.

scholarly journals Transcriptome and Metabolome-based Analysis of Anthocyanidin Biosynthesis in Purple Pepper

2021 ◽  
Author(s):  
Yaning Meng ◽  
Hongxiao Zhang ◽  
Yanqin Fan ◽  
Libin Yan
Keyword(s):  
Metabolic Pathways ◽  
Promoter Region ◽  
Biosynthetic Pathway ◽  
Transcriptome Data ◽  
Structural Genes ◽  
Green Pepper ◽  
Color Formation ◽  
Kegg Analysis ◽  
Key Genes ◽  
Metabolome Data

Abstract In order to clarify the profile of gene expression and metabolites for color formation and the molecular mechanism of anthocyanidin accumulation in purple pepper fruits, we analyzed the anthocyanidin metabolome data of the fruits of 2 purple pepper lines and 1 green pepper line and detected a total of 5 anthocyanidin-like metabolites, of which delphin chloride was unique to purple pepper fruits and 3 other anthocyanidin-like substances shared the metabolic pathway ko00942 and were up-regulated. Based on the transcriptome data, three pathways (ko00360, ko00400, and ko00941) related to anthocyanidin metabolism were identified through KEGG analysis. Three enzymes (DFR, ANS, and UFGT) and three transcription factors (MYB, BHLH, and WD40) in the purple pepper anthocyanidin biosynthetic pathway were up-regulated. We proposed a model to explain the regulation of pepper anthocyanidin biosynthesis: MYB, BHLH, and WD40 formed a ternary complex and bound to the specific cis-acting elements in the promoter region of the structural genes related to anthocyanidin biosynthesis to directly regulate their transcription, which resulted in the accumulation of a large amount of anthocyanidin metabolites including delphinidin 3-O-glucoside, delphinidin 3-O-rutinoside, and delphin chloride, giving color to pepper fruits. This study clarified the metabolic pathways and key genes affecting the color of purple pepper fruits and provided new insights into the synthesis and accumulation of anthocyanidins in pepper fruits.

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