Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae)

Abstract Background Bletilla striata is one of the important species belonging to the Bletilla genus of Orchidaceae. Since its extracts have an astringent effect on human tissues, B. striata is widely used for hemostasis and healing. Recently, some other beneficial effects have also been uncovered, such as antioxidation, antiinflammation, antifibrotic, and immunomodulatory activities. As a key step towards a thorough understanding on the medicinal ingredient production in B. striata, deciphering the regulatory codes of the metabolic pathways becomes a major task. Results In this study, three organs (roots, tubers and leaves) of B. striata were analyzed by integrating transcriptome sequencing and untargeted metabolic profiling data. Five different metabolic pathways, involved in polysaccharide, sterol, flavonoid, terpenoid and alkaloid biosynthesis, were investigated respectively. For each pathway, the expression patterns of the enzyme-coding genes and the accumulation levels of the metabolic intermediates were presented in an organ-specific way. Furthermore, the relationships between enzyme activities and the levels of the related metabolites were partially inferred. Within the biosynthetic pathways of polysaccharides and flavonoids, long-range phytochemical transportation was proposed for certain metabolic intermediates and/or the enzymes. Conclusions The data presented by this work could strengthen the molecular basis for further studies on breeding and medicinal uses of B. striata.

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Traditional uses and beneficial effects of various species of berry-producing plants in eastern Canada

Botany ◽

10.1139/cjb-2021-0086 ◽

2021 ◽

Author(s):

John Thomas Weber

Keyword(s):

Current Knowledge ◽

Short Review ◽

Food Sources ◽

Eastern Canada ◽

Potential Health ◽

Important Species ◽

Medicinal Uses ◽

Beneficial Effects ◽

Traditional Uses ◽

Contemporary Medicine

There are many different types of berry plants that grow throughout North America. These various species of plants produce berries known by their common names such as blueberry, lingonberry, cranberry, crowberry, blackberry, bunchberry, bearberry and strawberry. The berry fruits are important food sources and can be eaten fresh or preserved. The leaves of several species can also be enjoyed in teas. Contemporary medicine has demonstrated many potential health benefits of berries, due to their antioxidant and anti-inflammatory activity. Indigenous Peoples have not only utilized berries as food, likely over many centuries, but have also passed down knowledge on the medicinal uses of various parts of these plants, including the fruits, leaves and roots. This short review provides a synopsis of some of the major species of berry-producing plants that are prevalent in Canada, particularly eastern Canada. Current knowledge and traditional uses of important species of berry-producing plants are discussed.

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Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

BMC Genomics ◽

10.1186/s12864-021-07434-3 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shuo Wei ◽

Wen Zhang ◽

Rao Fu ◽

Yang Zhang

Keyword(s):

Metabolic Pathways ◽

Developmental Stages ◽

Expression Patterns ◽

Growth Cycle ◽

Model Organisms ◽

Gibberellin Biosynthesis ◽

Type I ◽

Multiple Model ◽

Genome Wide ◽

Tomato Growth

Abstract Background 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato. Results A total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity. Conclusions Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones.

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An Overview of Metabolic Activity, Beneficial and Pathogenic Aspects of Burkholderia Spp

Metabolites ◽

10.3390/metabo11050321 ◽

2021 ◽

Vol 11 (5) ◽

pp. 321

Author(s):

Hazem S. Elshafie ◽

Ippolito Camele

Keyword(s):

Secondary Metabolites ◽

Plant Growth ◽

Biochemical Characterization ◽

Bacterial Species ◽

Promoting Effect ◽

Important Species ◽

Beneficial Effects ◽

Plant Growth Promoting ◽

Rhizosphere Competence

Burkholderia is an important bacterial species which has different beneficial effects, such as promoting the plant growth, including rhizosphere competence for the secretion of allelochemicals, production of antibiotics, and siderophores. In addition, most of Burkholderia species have demonstrated promising biocontrol action against different phytopathogens for diverse crops. In particular, Burkholderia demonstrates significant biotechnological potential as a source of novel antibiotics and bioactive secondary metabolites. The current review is concerned with Burkholderia spp. covering the following aspects: discovering, classification, distribution, plant growth promoting effect, and antimicrobial activity of different species of Burkholderia, shedding light on the most important secondary metabolites, their pathogenic effects, and biochemical characterization of some important species of Burkholderia, such as B. cepacia, B. andropogonis, B. plantarii, B. rhizoxinica, B. glumae, B. caryophylli and B. gladioli.

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A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽

10.3390/molecules26133924 ◽

2021 ◽

Vol 26 (13) ◽

pp. 3924

Author(s):

Maria Leonor Santos ◽

Mariaelena D’Ambrosio ◽

Ana P. Rodrigo ◽

A. Jorge Parola ◽

Pedro M. Costa

Keyword(s):

Metabolic Pathways ◽

Molecular Networks ◽

Bile Pigments ◽

Rna Seq ◽

The Past ◽

Wide Range ◽

Genes Encoding ◽

Organ Specific ◽

Bright Green ◽

Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

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Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng and Eleven Flowering Plants

Molecules ◽

10.3390/molecules24010015 ◽

2018 ◽

Vol 24 (1) ◽

pp. 15 ◽

Cited By ~ 2

Author(s):

He Su ◽

Yang Chu ◽

Junqi Bai ◽

Lu Gong ◽

Juan Huang ◽

...

Keyword(s):

Transcription Factors ◽

Panax Ginseng ◽

Expression Patterns ◽

Flowering Plants ◽

Functional Development ◽

Wide Range ◽

Organ Specific ◽

Genome Level ◽

Negative Links ◽

Global Platform

Herb genomics and comparative genomics provide a global platform to explore the genetics and biology of herbs at the genome level. Panax ginseng C.A. Meyer is an important medicinal plant for a variety of bioactive chemical compounds of which the biosynthesis may involve transport of a wide range of substrates mediated by oligopeptide transporters (OPT). However, information about the OPT family in the plant kingdom is still limited. Only 17 and 18 OPT genes have been characterized for Oryza sativa and Arabidopsis thaliana, respectively. Additionally, few comprehensive studies incorporating the phylogeny, gene structure, paralogs evolution, expression profiling, and co-expression network between transcription factors and OPT genes have been reported for ginseng and other species. In the present study, we performed those analyses comprehensively with both online tools and standalone tools. As a result, we identified a total of 268 non-redundant OPT genes from 12 flowering plants of which 37 were from ginseng. These OPT genes were clustered into two distinct clades in which clade-specific motif compositions were considerably conservative. The distribution of OPT paralogs was indicative of segmental duplication and subsequent structural variation. Expression patterns based on two sources of RNA-Sequence datasets suggested that some OPT genes were expressed in both an organ-specific and tissue-specific manner and might be involved in the functional development of plants. Further co-expression analysis of OPT genes and transcription factors indicated 141 positive and 11 negative links, which shows potent regulators for OPT genes. Overall, the data obtained from our study contribute to a better understanding of the complexity of the OPT gene family in ginseng and other flowering plants. This genetic resource will help improve the interpretation on mechanisms of metabolism transportation and signal transduction during plant development for Panax ginseng.

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Dissecting the Microbial Community Structure of Internal Organs During the Early Postmortem Period in a Murine Corpse Model

10.21203/rs.3.rs-1099733/v1 ◽

2021 ◽

Author(s):

Ruina Liu ◽

Kai Zhang ◽

Huan Li ◽

Qinru Sun ◽

Xin Wei ◽

...

Keyword(s):

Metabolic Pathways ◽

The Body ◽

Time Since Death ◽

Limited Information ◽

Microbial Composition ◽

Internal Organs ◽

Organ Specific ◽

Forensic Microbiology ◽

The Relationship ◽

Early Postmortem

Abstract Background Microorganisms inhabit and proliferate throughout the body both externally and internally, which are the primary mediators of putrefaction after death. However, limited information is available about the changes in the postmortem microbiota of extraintestinal body sites in the early decomposition stage of mammalian corpses. Results This study applied 16S rRNA barcoding to investigate microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 hours than that at 0.5 or 4 hours. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific. Conclusion The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 hours in internal organs may inform a new direction for organ transplantation.

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In Silico Investigation of Mitragynine and 7-Hydroxymitragynine Metabolism

10.21203/rs.2.10213/v1 ◽

2019 ◽

Author(s):

Taweetham Limpanuparb ◽

Rattha Noorat ◽

Yuthana Tantirungrotechai

Keyword(s):

Gas Phase ◽

In Silico ◽

Metabolic Pathways ◽

Experimental Studies ◽

Medicinal Uses ◽

Detection Techniques ◽

Mass Spectrom ◽

Gibbs Energies ◽

In Silico Study

Abstract Objective: Mitragynine is the main active compound of Mitragyna speciose (Kratom in Thai). The understanding of mitragynine derivative metabolism in human body is required to develop effective detection techniques in case of drug abuse or establish an appropriate dosage in case of medicinal uses. This in silico study is based upon in vivo results in rat and human by Philipp et al. (J. Mass Spectrom., 2009, 44, 1249.) Results: The gas-phase structures of mitragynine, 7-hydroxymitragynine and their metabolites were obtained by quantum chemical method at B3LYP/6-311++G(d,p) level. Results in terms of standard Gibbs energies of reaction for all metabolic pathways are reported with solvation energy from SMD model. We found that 7-hydroxy substitution leads to changes in reactivity in comparison to mitragynine: position 17 is more reactive towards demethylation and conjugation to a glucuronide and position 9 is less reactive towards conjugation to a glucuronide. Despite the changes, position 9 is the most reactive for demethylation and position 17 is the most reactive for conjugation to a glucuronide for both mitragynine and 7-hydroxymitragynine. Our results suggest that 7-hydroxy substitution could lead to different metabolic pathways and raise an important question for further experimental studies of this more potent derivative.

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Discovery of Serum Proteomic Biomarkers for Prediction of Response to Moxibustion Treatment in Rats with Collagen-Induced Arthritis: An Exploratory Analysis

Acupuncture in Medicine ◽

10.1136/acupmed-2015-010909 ◽

2016 ◽

Vol 34 (3) ◽

pp. 184-193 ◽

Cited By ~ 10

Author(s):

Xiao Xu ◽

Miao-Miao Wang ◽

Zhi-ling Sun ◽

Dan-ping Zhou ◽

Ling Wang ◽

...

Keyword(s):

Rat Model ◽

Multiple Testing ◽

Day Treatment ◽

Expression Patterns ◽

Control Group ◽

Sprague Dawley ◽

Collagen Induced Arthritis ◽

Serum Samples ◽

Beneficial Effects ◽

Bovine Collagen

Objective To examine the possible impact of moxibustion on the serum proteome of the collagen-induced arthritis (CIA) rat model. Materials and Methods Thirty-six male Sprague-Dawley rats were included in this experiment. The CIA animal model was prepared by injection of type II bovine collagen in Freund's adjuvant on the first and seventh day. The 36 rats were randomly divided into two groups: the untreated CIA group (control), and the CIA plus treatment with moxibustion (CIA+moxi) group. Moxibustion was administered daily at ST36 and BL23 for 7, 14 or 21 days (n=12 rats each). Arthritis score was used to assess the severity of arthritis. At the end of each 7 day treatment, blood samples from the control group and the CIA+moxi group were collected. After removal of high abundance proteins from serum samples, two-dimensional gel combined with matrix-assisted laser desorption ionisation time-of-flight MS/MS (MALDI-TOF-MS/MS) techniques were performed to examine serum protein expression patterns of the CIA rat model with and without moxibustion treatment. In addition, the relevant proteins were further analysed with the use of bioinformatics analysis. Results Moxibustion significantly decreased arthritis severity in the rats in the CIA+moxi group, when compared with the rats in the CIA group 35 days after the first immunisation (p=0.001). Seventeen protein spots which changed >1.33 or <0.77 at p<0.05 using Bonferonni correction for multiple testing were found to be common to all three comparisons, and these proteins were used for classification of functions using the Gene Ontology method. Consequently, with the use of the Ingenuity Pathway Analysis, the top canonical pathways and a predicted proteomic network related to the moxibustion effect of CIA were established. Conclusions Using the proteomics technique, we have identified novel candidate proteins that may be involved in the mechanisms of action underlying the beneficial effects of moxibustion in rats with CIA. Our findings suggest that immune responses and metabolic processes may be involved in mediating the effects of moxibustion. Moreover, periodxiredoxin I (PRDX1) and inositol 1,4,5-triphosphate receptor (IP3R) may be potential targets.

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Maternal and Post-weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts

International Journal of Molecular Sciences ◽

10.3390/ijms20133229 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3229 ◽

Cited By ~ 4

Author(s):

Moody ◽

Wang ◽

Jung ◽

Chen ◽

Pan

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Metabolic Pathways ◽

Expression Patterns ◽

Sprague Dawley ◽

High Fat ◽

Differentially Methylated Genes ◽

High Fat Diets ◽

Diet Intake ◽

Fat Diets

Calorie-dense high-fat diets (HF) are associated with detrimental health outcomes, including obesity, cardiovascular disease, and diabetes. Both pre- and post-natal HF diets have been hypothesized to negatively impact long-term metabolic health via epigenetic mechanisms. To understand how the timing of HF diet intake impacts DNA methylation and metabolism, male Sprague–Dawley rats were exposed to either maternal HF (MHF) or post-weaning HF diet (PHF). At post-natal week 12, PHF rats had similar body weights but greater hepatic lipid accumulation compared to the MHF rats. Genome-wide DNA methylation was evaluated, and analysis revealed 1744 differentially methylation regions (DMRs) between the groups with the majority of the DMR located outside of gene-coding regions. Within differentially methylated genes (DMGs), intragenic DNA methylation closer to the transcription start site was associated with lower gene expression, whereas DNA methylation further downstream was positively correlated with gene expression. The insulin and phosphatidylinositol (PI) signaling pathways were enriched with 25 DMRs that were associated with 20 DMGs, including PI3 kinase (Pi3k), pyruvate kinase (Pklr), and phosphodiesterase 3 (Pde3). Together, these results suggest that the timing of HF diet intake determines DNA methylation and gene expression patterns in hepatic metabolic pathways that target specific genomic contexts.

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Chronic Inhibition of Mitochondrial Dihydrolipoamide Dehydrogenase (DLDH) as an Approach to Managing Diabetic Oxidative Stress

Antioxidants ◽

10.3390/antiox8020032 ◽

2019 ◽

Vol 8 (2) ◽

pp. 32 ◽

Cited By ~ 5

Author(s):

Xiaojuan Yang ◽

Jing Song ◽

Liang-Jun Yan

Keyword(s):

Oxidative Stress ◽

Type 2 Diabetes ◽

Metabolic Pathways ◽

Reactive Nitrogen Species ◽

Dihydrolipoamide Dehydrogenase ◽

Redox Enzyme ◽

Atp Production ◽

Metabolic Intermediates ◽

Novel Approach

Mitochondrial dihydrolipoamide dehydrogenase (DLDH) is a redox enzyme involved in decarboxylation of pyruvate to form acetyl-CoA during the cascade of glucose metabolism and mitochondrial adenine triphosphate (ATP) production. Depending on physiological or pathophysiological conditions, DLDH can either enhance or attenuate the production of reactive oxygen species (ROS) and reactive nitrogen species. Recent research in our laboratory has demonstrated that inhibition of DLDH induced antioxidative responses and could serve as a protective approach against oxidative stress in stroke injury. In this perspective article, we postulated that chronic inhibition of DLDH could also attenuate oxidative stress in type 2 diabetes. We discussed DLDH-involving mitochondrial metabolic pathways and metabolic intermediates that could accumulate upon DLDH inhibition and their corresponding roles in abrogating oxidative stress in diabetes. We also discussed a couple of DLDH inhibitors that could be tested in animal models of type 2 diabetes. It is our belief that DLDH inhibition could be a novel approach to fighting type 2 diabetes.

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