scholarly journals Transcriptome and metabolome analysis to reveal major genes of saikosaponin biosynthesis in Bupleurum chinense

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yilian He ◽  
Hua Chen ◽  
Jun Zhao ◽  
Yuxia Yang ◽  
Bin Yang ◽  
...  
Keyword(s):  
Medicinal Plant ◽  
Biosynthetic Pathway ◽  
Gene Families ◽  
Integrated Analysis ◽  
Cytochrome P450 Enzymes ◽  
Bioactive Constituents ◽  
Metabolome Analysis ◽  
Coa Transferase ◽  
Liquid Chromatography Tandem Mass ◽  
Coa Reductase

Abstract Background Bupleurum chinense DC. is a widely used traditional Chinese medicinal plant. Saikosaponins are the major bioactive constituents of B. chinense, but relatively little is known about saikosaponin biosynthesis. In the present study, we performed an integrated analysis of metabolic composition and the expressed genes involved in saikosaponin biosynthetic pathways among four organs (the root, flower, stem, and leaf) of B. chinense to discover the genes related to the saikosaponin biosynthetic pathway. Results Transcript and metabolite profiles were generated through high-throughput RNA-sequencing (RNA-seq) data analysis and liquid chromatography tandem mass spectrometry, respectively. Evaluation of saikosaponin contents and transcriptional changes showed 152 strong correlations (P < 0.05) over 3 compounds and 77 unigenes. These unigenes belonged to eight gene families: the acetoacetyl CoA transferase (AACT) (6), HMG-CoA synthase (HMGS) (2), HMG-CoA reductase (HMGR) (2), mevalonate diphosphate decarboxylase (MVD) (1), 1-deoxy-D-xylulose-5-phosphate synthase (DXS) (3), farnesyl diphosphate synthase (FPPS) (11), β-amyrin synthase (β-AS) (13) and cytochrome P450 enzymes (P450s) (39) families. Conclusions Our results investigated the diversity of the saikosaponin triterpene biosynthetic pathway in the roots, stems, leaves and flowers of B. chinese by integrated transcriptomic and metabolomic analysis, implying that manipulation of P450s genes such as Bc95697 and Bc35434 might improve saikosaponin biosynthesis. This is a good candidate for the genetic improvement of this important medicinal plant.

scholarly journals Identification of a Unique Type of Isoflavone O-Methyltransferase, GmIOMT1, Based on Multi-Omics Analysis of Soybean under Biotic Stress

2020 ◽  
Vol 61 (11) ◽  
pp. 1974-1985
Author(s):  
Kai Uchida ◽  
Yuji Sawada ◽  
Koji Ochiai ◽  
Muneo Sato ◽  
Jun Inaba ◽  
...  
Keyword(s):  
Biotic Stress ◽  
Biosynthetic Pathway ◽  
Metabolome Analysis ◽  
Gene Encoding ◽  
Unique Type ◽  
Soybean Seedlings ◽  
Genes Encoding ◽  
Liquid Chromatography Tandem Mass ◽  
Key Enzyme ◽  
Fungal Inoculation

Abstract Isoflavonoids are commonly found in leguminous plants. Glycitein is one of the isoflavones produced by soybean. The genes encoding the enzymes in the isoflavone biosynthetic pathway have mostly been identified and characterized. However, the gene(s) for isoflavone O-methyltransferase (IOMT), which catalyzes the last step of glycitein biosynthesis, has not yet been identified. In this study, we conducted multi-omics analyses of fungal-inoculated soybean and indicated that glycitein biosynthesis was induced in response to biotic stress. Moreover, we identified a unique type of IOMT, which participates in glycitein biosynthesis. Soybean seedlings were inoculated with Aspergillus oryzae or Rhizopus oligosporus and sampled daily for 8 d. Multi-omics analyses were conducted using liquid chromatography–tandem mass spectrometry and RNA sequencing. Metabolome analysis revealed that glycitein derivatives increased following fungal inoculation. Transcriptome co-expression analysis identified two candidate IOMTs that were co-expressed with the gene encoding flavonoid 6-hydroxylase (F6H), the key enzyme in glycitein biosynthesis. The enzymatic assay of the two IOMTs using respective recombinant proteins showed that one IOMT, named as GmIOMT1, produced glycitein. Unlike other IOMTs, GmIOMT1 belongs to the cation-dependent OMT family and exhibited the highest activity with Zn2+ among cations tested. Moreover, we demonstrated that GmIOMT1 overexpression increased the levels of glycitein derivatives in soybean hairy roots when F6H was co-expressed. These results strongly suggest that GmIOMT1 participates in inducing glycitein biosynthesis in response to biotic stress.

scholarly journals Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Hong-Lei Li ◽  
Lin Wu ◽  
Zhaoming Dong ◽  
Yusong Jiang ◽  
Sanjie Jiang ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Southwest China ◽  
Reference Genome ◽  
Zingiber Officinale ◽  
Gene Families ◽  
Chromosome Conformation ◽  
Long Reads ◽  
Transcription Factor Networks ◽  
Species Specific ◽  
Haplotype 1

AbstractGinger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger ‘Zhugen’, a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3’H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.

scholarly journals Molecular Characterization of a Poly-β-Hydroxybutyrate-Producing Microbacterium Isolate

2015 ◽  
Vol 3 (2) ◽  
pp. 143-150 ◽  
Author(s):  
Yehia A. Osman ◽  
Ahmed Abd Elrazak ◽  
Wesam Khater ◽  
EL-Shahat Nashy ◽  
Attia Mohamadeen
Keyword(s):  
Biosynthetic Pathway ◽  
Nitrogen Deficiency ◽  
Rrna Gene ◽  
Excess Carbon ◽  
Controlling Elements ◽  
Tree Data ◽  
Microbacterium Paraoxydans ◽  
Coa Reductase ◽  
Beta Hydroxybutyrate

Bacterial poly-β-hydroxybutyrate (PHB) is a natural, biodegradable polymer, which is accumulated in the cells as an energy reserve materialdue to depletion of nitrogen or phosphorous in the presence of excess carbon source. This polymer is foreseen to possess high industrialpotentiality and excellent alternative to the non-degradable petroleum-based plastics. In this study, we isolated and characterized a localbacterial strain WA81 which accumulated 18mg/L PHB after 72 h growth in mineral salt medium under nitrogen deficiency. The PHB granuleswere detected in the cells using TEM and the genes encode for this polymer were detected by oligonucleotide primers using PCR technology.The 16S rRNA gene nucleotide sequence for this isolate was used to construct a phylogentic tree against all available sequences in the GenBank.The phylogenetic tree data suggested that the closest type strain to the local bacterium is the Microbacterium paraoxydans CF36T and hencewe named it Microbacterium sp. strain WA81. Moreover, the set of enzymes responsible for the PHB biosynthetic pathway and their controllingelements were detected in this local isolate using PCR. The genes encode for the biosynthesis enzymes are phbA (β-ketothiolase), phbB(acetoacetly CoA reductase), phbC (PHB polymerase), while the genes encode for the controlling elements are phbP (phasin), phbZ (PHBdepolymerase). The novelty of this local bacterium lies in its ability to accumulate huge amounts of PHB in its cytoplasm and the presence ofa whole set of genes encode for the PHB biosynthetic and catabolic pathways of this polymer.Int J Appl Sci Biotechnol, Vol 3(2): 143-150 DOI: http://dx.doi.org/10.3126/ijasbt.v3i2.12277 

scholarly journals Interactions between gastric microbiota and metabolites in gastric cancer

2021 ◽  
Vol 12 (12) ◽  
Author(s):  
Daofeng Dai ◽  
Yan Yang ◽  
Jieqing Yu ◽  
Tianfeng Dang ◽  
Wenjing Qin ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Amino Acids ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Metabolome Analysis ◽  
Tumor Tissues ◽  
Liquid Chromatography Tandem Mass ◽  
Ultrahigh Performance Liquid Chromatography ◽  
Rrna Gene Sequencing ◽  
Gastric Microbiota

AbstractThe development and progression of gastric cancer (GC) is greatly influenced by gastric microbiota and their metabolites. Here, we characterized the gastric microbiome and metabolome profiles of 37 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and ultrahigh performance liquid chromatography tandem mass spectrometry, respectively. Microbial diversity and richness were higher in GC tumor tissues than in non-tumor tissues. The abundance of Helicobacter was increased in non-tumor tissues, while the abundance of Lactobacillus, Streptococcus, Bacteroides, Prevotella, and 6 additional genera was increased in the tumor tissues. The untargeted metabolome analysis revealed 150 discriminative metabolites, among which the relative abundance of the amino acids, carbohydrates and carbohydrate conjugates, glycerophospholipids, and nucleosides was higher in tumor tissues compared to non-tumor tissues. The targeted metabolome analysis further demonstrated that the combination of 1-methylnicotinamide and N-acetyl-D-glucosamine-6-phosphate could serve as a robust biomarker for distinction between GC tumors and non-tumor tissues. Correlation analysis revealed that Helicobacter and Lactobacillus were negatively and positively correlated with the majority of differential metabolites in the classes of amino acids, carbohydrates, nucleosides, nucleotides, and glycerophospholipids, respectively, suggesting that Helicobacter and Lactobacillus might play a role in degradation and synthesis of the majority of differential metabolites in these classes, respectively. Acinetobacter, Comamonas, Faecalibacterium, Sphingomonas, and Streptococcus were also significantly correlated with many differential amino acids, carbohydrates, nucleosides, nucleotides, and glycerophospholipids. In conclusion, the differences in metabolome profiles between GC tumor and matched non-tumor tissues may be partly due to the collective activities of Helicobacter, Lactobacillus, and other bacteria, which eventually affects GC carcinogenesis and progression.

P207 Synergetic effect of amino acid and ketone metabolism underlies empagliflozin-mediated cardioprotection in the type 2 diabetic heart

2020 ◽  
Vol 41 (Supplement_1) ◽  
Author(s):  
H Kouzu ◽  
H Oshima ◽  
T Miki ◽  
A Kuno ◽  
T Sato ◽  
...  
Keyword(s):  
Amino Acid ◽  
Survival Rate ◽  
Molecular Mechanisms ◽  
Synergetic Effect ◽  
Tca Cycle ◽  
Oxidative Capacity ◽  
Metabolome Analysis ◽  
Coa Transferase ◽  
The Tca Cycle

Abstract Funding Acknowledgements Boehringer Ingelheim Background  Although emerging evidence has indicated that sodium glucose cotransporter 2 (SGLT2) inhibitors restore impaired cardiac energetics in type 2 diabetes mellitus (T2DM), the underlying molecular mechanisms have yet to be established.  Augmented utilization of ketone is one proposed hypothesis, but depletion of succinyl-CoA triggered by the conversion of ketone back to acetyl-CoA by SCOT (succinyl-CoA:3-oxoacid CoA transferase) may hamper oxidative capacity of the tricarboxylic acid (TCA) cycle, which also requires succinyl-CoA.  The recent finding that empagliflozin augments systemic amino acid metabolism in patients with T2DM led us to hypothesize that the anaplerotic effect of amino acid on the TCA cycle complements ketone oxidation. Methods and Results  Myocardial infarction (MI) was induced in T2DM rats (OLETF) and control rats (LETO).  Survival rate at 48 hours after MI was significantly lower in OLETF than in LETO (40% vs 84%), and empagliflozin treatment (10 mg/kg/day, 14 days) before MI improved the survival rate in OLETF to 70%.  Metabolome analysis was performed using heart tissues from the non-infarct region 12 hours after MI.  Using principal component analysis, data from 92 metabolites that were detected were compressed into 2 dimensions, and the first component (PC1) clearly separated empagliflozin-treated OLETF from non-treated LETO and OLETF.  Analysis of factor loading of each metabolite for PC1 revealed that branched chain amino acids leucine, isoleucine and valine, the latter two of which can be oxidized to succynyl-CoA, and β-hydroxybutyrate were the top four metabolites that characterized empagliflozin treatment.  Furthermore, in comparison to LETO, OLETF treated with empagliflozin showed 50% higher levels of glutamine and glutamate, both of which can replenish the TCA cycle at the level of α-ketoglutarate.  In OLETF, empagliflozin significantly increased the TCA cycle intermediates citrate, cis-aconitate and malate by 74%, 119% and 59%, respectively.  OLETF showed 86% higher lactate and 38% lower ATP than those in LETO, but levels of the metabolites were normalized by empagliflozin, suggesting improved glucose oxidation. Conclusions   The present analyses showed that amino acid and ketone metabolism are metabolic pathways that are most affected by empagliflozin.  Coordination of these "starvation-induced pathways" may underlie the favorable metabolic effect of empagliflozin in T2DM hearts.

scholarly journals Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 47 ◽  
Author(s):  
Oleg Gorshkov ◽  
Tatyana Chernova ◽  
Natalia Mokshina ◽  
Natalia Gogoleva ◽  
Dmitry Suslov ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Leucine Zipper ◽  
Target Genes ◽  
Expression Profiles ◽  
Gene Families ◽  
Fiber Development ◽  
Integrated Analysis ◽  
Target Point ◽  
Family Protein ◽  
Phloem Fibers

Phloem fibers are important elements of plant architecture and the target product of many fiber crops. A key stage in fiber development is intrusive elongation, the mechanisms of which are largely unknown. Integrated analysis of miRNA and mRNA expression profiles in intrusivelygrowing fibers obtained by laser microdissection from flax (Linum usitatissimum L.) stem revealed all 124 known flax miRNA from 23 gene families and the potential targets of differentially expressed miRNAs. A comparison of the expression between phloem fibers at different developmental stages, and parenchyma and xylem tissues demonstrated that members of miR159, miR166, miR167, miR319, miR396 families were down-regulated in intrusively growing fibers. Some putative target genes of these miRNA families, such as those putatively encoding growth-regulating factors, an argonaute family protein, and a homeobox-leucine zipper family protein were up-regulated in elongating fibers. miR160, miR169, miR390, and miR394 showed increased expression. Changes in the expression levels of miRNAs and their target genes did not match expectations for the majority of predicted target genes. Taken together, poorly understood intrusive fiber elongation, the key process of phloem fiber development, was characterized from a miRNA-target point of view, giving new insights into its regulation.

scholarly journals Distribution Patterns for Bioactive Constituents in Pericarp, Stalk and Seed of Forsythiae Fructus

Molecules ◽  
2020 ◽  
Vol 25 (2) ◽  
pp. 340 ◽  
Author(s):  
Lifang Wei ◽  
Yuqi Mei ◽  
Lisi Zou ◽  
Jiali Chen ◽  
Mengxia Tan ◽  
...  
Keyword(s):  
Phenolic Acids ◽  
Folk Medicine ◽  
Plant Secondary Metabolites ◽  
Distribution Patterns ◽  
Scientific Data ◽  
Bioactive Constituents ◽  
Phenylethanoid Glycosides ◽  
Liquid Chromatography Tandem Mass ◽  
Phytochemical Profiles ◽  
One Way Anova

Forsythiae Fructus (FF) is a widely used folk medicine in China, Japan, and Korea. The distribution of bioactive constituents throughout the fruit segments has rarely been addressed, although mounting evidence suggests that plant secondary metabolites are synthesized and distributed regularly. The phytochemical profiles of three segments of FF (pericarp, stalk and seed) were firstly revealed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based quantitative analysis of twenty-one bioactive constituents, including three phenylethanoid glycosides, five lignans, eight flavonoids, and five phenolic acids to explore the spatial distribution of bioactive constituents. Furthermore, the hierarchical clustering analysis (HCA) and one-way analysis of variance (one-way ANOVA) were conducted to visualize and verify the distribution regularity of twenty-one analytes among three segments. The results showed that phytochemical profiles of the three segments were similar, i.e., phenylethanoid glycosides covering the most part were the predominant compounds, followed by lignans, flavonoids and phenolic acids. Nevertheless, the abundance of twenty-one bioactive constituents among three segments was different. Specifically, phenylethanoid glycosides were highly expressed in the seed; lignans were primarily enriched in the stalk; flavonoids were largely concentrated in the pericarp, while the contents of phenolic acids showed no much difference among various segments. The research improves our understanding of distribution patterns for bioactive constituents in FF, and also complements some scientific data for further exploring the quality formation mechanism of FF.

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