Transcriptome analysis for identification of indigo biosynthesis pathway genes in Polygonum tinctorium

Biologia ◽  
2015 ◽  
Vol 70 (8) ◽  
Author(s):  
Yoshiko Minami ◽  
Bijaya Ketan Sarangi ◽  
Sanjog Tarachand Thul
Keyword(s):  
De Novo ◽  
Comprehensive Analysis ◽  
Blue Dye ◽  
Biosynthesis Pathway ◽  
Kegg Database ◽  
P450 Monooxygenase ◽  
Blast Search ◽  
Textile Dyeing ◽  
Genes Encoding ◽  
Polygonum Tinctorium

AbstractIndigo is the most important blue dye for textile dyeing and is biosynthesized in Polygonum tinctorium. Some biochemical studies related to biosynthesis are available. However, genomic and transcriptome studies have not received sufficient attention. Here, we report de novo assembly of transcriptome datasets and its comprehensive analysis. A total of 60,395 unigenes were annotated using BLAST search against the different databases. At least 23,721 unigenes mapped onto different pathways using KEGG database. We found that 3,323 genes are involved in biosynthesis of secondary metabolites, 117 phenylalanine, tyrosine and tryptophan biosynthesis and 147 tryptophan metabolisms. Apart from this, indigo biosynthesis pathway genes viz., dioxygenase, monooxygenase, and glucosyltransferase have also been identified. Fourteen genes encoding cytochrome P450 monooxygenase, 26 glucoside dioxygenase, 9 UDP-glucose D-glucosyltransferase and 52 were β-D-glucosidase. These findings provide a foundation for further analysis of this pathway with potential to enhance the synthesis of indican in P. tinctorium

scholarly journals Transcriptomic analyses reveal molecular mechanisms underlying regulation of floral attributes in Lonicera japonica Thunb.

2021 ◽  
Author(s):  
Lei Shi ◽  
Yuan Shen ◽  
Yuhao Chi
Keyword(s):  
Flower Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Floral Scent ◽  
Expression Profiles ◽  
Lonicera Japonica ◽  
Biosynthesis Pathway ◽  
Terpenoid Biosynthesis ◽  
Genes Encoding

Abstract Background Lonicera Japonica Thunb. is a perennial, semi-evergreen and twining vine in the family of Caprifoliaceae, which is widely cultivated in Asia. Thus far, L. japonica is often used to treat some human diseases including COVID-19, H1N1 influenza and hand-foot-and-mouth diseases, however, the regulatory mechanism of intrinsic physiological processes during different floral developmental stages of L. japonica remain largely unknown. Results The complete transcriptome of L. japonica was de novo-assembled and annotated, generating a total of 195850 unigenes, of which 84657 could be functionally annotated. 70 candidate genes involved in flowering transition were identified and the flowering regulatory network of five pathways was constructed in L. japonica. The mRNA transcripts of AGL24 and SOC1 exhibited a downward trend during flowering transition and followed by a gradual increase during the flower development. The transcripts of AP1 was only detected during the floral development, whereas the transcript level of FLC was high during the vegetative stages. The expression profiles of AGL24, SOC1, AP1 and FLC genes indicate that these key integrators might play the essential and evolutionarily conserved roles in control of flowering switch across the plant kingdom. We also identified 54 L. japonica genes encoding enzymes involved in terpenoid biosynthesis pathway. Most highly expressed genes centered on the MEP pathway, suggesting that this plastid pathway might represent the major pathway for terpenoid biosynthesis in L. japonica. In addition, 33 and 31 key genes encoding enzymes involved in the carotenogenesis and anthocyanin biosynthesis pathway were identified, respectively. PSY transcripts gradually increased during the flower development, supporting its role as the first rate-limiting enzyme in carotenoid skeleton production. The expression level of most anthocyanin biosynthetic genes was dramatically decreased during the flower developmental stages, consistent with the decline in the contents of anthocyanin. Conclusion These results identified a large number of potential key regulators controlling flowering time, flower color and floral scent formation in L. japonica, which improves our understanding of the molecular mechanisms underlying the flower traits and flower metabolism, as well as sets the groundwork for quality improvement and molecular breeding of L. japonica.

scholarly journals Phytophthora capsici sterol reductase PcDHCR7 has a role in mycelium development and pathogenicity

2021 ◽  
Author(s):  
Weizhen Wang ◽  
Fan Zhang ◽  
Sicong Zhang ◽  
Zhaolin Xue ◽  
Linfang Xie ◽  
...  
Keyword(s):  
De Novo ◽  
Reductase Activity ◽  
Phytophthora Capsici ◽  
Biosynthesis Pathway ◽  
Wild Type ◽  
Knock Out ◽  
Type Isolate ◽  
De Novo Biosynthesis ◽  
Phytophthora Spp ◽  
Genes Encoding

The de novo biosynthesis of sterols is critical for eukaryotes, however, some organisms lack this pathway including most oomycetes. Phytophthora spp. are sterol auxotroph but remarkably, have retained a few genes encoding enzymes in the sterol biosynthesis pathway. Here we investigated the function of PcDHCR7, a gene in Phytophthora capsici predicted to encode the Δ7-sterol reductase. When expressed in Saccharomyces cerevisiae, PcDHCR7 showed a Δ7-sterol reductase activity. Knocking out PcDHCR7 in P. capsici resulted in loss of the capacity to transform ergosterol into brassicasterol, which means PcDHCR7 has a Δ7-sterol reductase activity in P. capsici itself. This enables P. capsici to transform sterols recruited from the environment for better use. Biological characteristics were compared between wild-type isolate and PcDHCR7 knock-out transformants. The results indicated that PcDHCR7 plays a key role in mycelium development and pathogenicity of zoospores in P. capsici.

scholarly journals Engineering of new-to-nature halogenated indigo precursors in plants

2018 ◽  
Author(s):  
Sabine Frabel ◽  
Bastian Wagner ◽  
Markus Krischke ◽  
Volker Schmidts ◽  
Christina M Thiele ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
De Novo ◽  
Dry Weight ◽  
Cytochrome P450 Monooxygenase ◽  
Blue Dye ◽  
In Planta ◽  
P450 Monooxygenase ◽  
Catalytic Systems ◽  
Modular Assembly ◽  
Human Cytochrome

Plants are versatile chemists producing a tremendous variety of specialized compounds. Here, we describe the engineering of entirely novel metabolic pathways in planta enabling generation of halogenated indigo precursors as non-natural plant products. Indican (indolyl-beta-D-glucopyranoside) is a secondary metabolite characteristic of a number of dyers plants. Its deglucosylation and subsequent oxidative dimerization leads to the blue dye, indigo. Halogenated indican derivatives are commonly used as detection reagents in histochemical and molecular biology applications; their production, however, relies largely on chemical synthesis. To attain the de novo biosynthesis in a plant-based system devoid of indican, we employed a sequence of enzymes from diverse sources, including three microbial tryptophan halogenases substituting the amino acid at either C5, C6, or C7 of the indole moiety. Subsequent processing of the halotryptophan by bacterial tryptophanase TnaA in concert with a mutant of the human cytochrome P450 monooxygenase 2A6 and glycosylation of the resulting indoxyl derivatives by an endogenous tobacco glucosyltransferase yielded corresponding haloindican variants in transiently transformed Nicotiana benthamiana plants. Accumulation levels were highest when the 5-halogenase PyrH was utilized, reaching 0.93 +/-0.089 mg/g dry weight of 5-chloroindican. The identity of the latter was unambiguously confirmed by NMR analysis. Moreover, our combinatorial approach, facilitated by the modular assembly capabilities of the GoldenBraid cloning system and inspired by the unique compartmentation of plant cells, afforded testing a number of alternative subcellular localizations for pathway design. In consequence, chloroplasts were validated as functional biosynthetic venues for haloindican, with the requisite reducing augmentation of the halogenases as well as the cytochrome P450 monooxygenase fulfilled by catalytic systems native to the organelle. Thus, our study puts forward a viable alternative production platform for halogenated fine chemicals, eschewing reliance on fossil fuel resources and toxic chemicals. We further contend that in planta generation of halogenated indigoid precursors previously unknown to nature offers an extended view on and, indeed, pushes forward the established frontiers of biosynthetic capacity of plants.

scholarly journals Exposure to low doses of pesticides induces an immune response and the production of nitric oxide in honeybees

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Merle T. Bartling ◽  
Susanne Thümecke ◽  
José Herrera Russert ◽  
Andreas Vilcinskas ◽  
Kwang-Zin Lee
Keyword(s):  
Nitric Oxide ◽  
Immune Responses ◽  
Bacterial Pathogen ◽  
Wild Plants ◽  
P450 Monooxygenase ◽  
Abiotic Stressors ◽  
Genes Encoding ◽  
Pesticides Exposure ◽  
Colony Survival ◽  
Oxide Synthase

AbstractHoneybees are essential pollinators of many agricultural crops and wild plants. However, the number of managed bee colonies has declined in some regions of the world over the last few decades, probably caused by a combination of factors including parasites, pathogens and pesticides. Exposure to these diverse biotic and abiotic stressors is likely to trigger immune responses and stress pathways that affect the health of individual honeybees and hence their contribution to colony survival. We therefore investigated the effects of an orally administered bacterial pathogen (Pseudomonas entomophila) and low-dose xenobiotic pesticides on honeybee survival and intestinal immune responses. We observed stressor-dependent effects on the mean lifespan, along with the induction of genes encoding the antimicrobial peptide abaecin and the detoxification factor cytochrome P450 monooxygenase CYP9E2. The pesticides also triggered the immediate induction of a nitric oxide synthase gene followed by the delayed upregulation of catalase, which was not observed in response to the pathogen. Honeybees therefore appear to produce nitric oxide as a specific defense response when exposed to xenobiotic stimuli. The immunity-related and stress-response genes we tested may provide useful stressor-dependent markers for ecotoxicological assessment in honeybee colonies.

scholarly journals Dravet syndrome associated mutations in GABRA1, GABRB2 and GABRG2 define the genetic landscape of defects of GABAA receptors

2021 ◽  
Author(s):  
Ciria C Hernandez ◽  
XiaoJuan Tian ◽  
Ningning Hu ◽  
Wangzhen Shen ◽  
Mackenzie A Catron ◽  
...  
Keyword(s):  
Gabaa Receptor ◽  
De Novo ◽  
Epileptic Encephalopathy ◽  
Dravet Syndrome ◽  
First Year ◽  
Genes Encoding ◽  
Genetic Landscape ◽  
Clonic Seizures ◽  
Trafficking Defects ◽  
First Year Of Life

Abstract Dravet syndrome is a rare, catastrophic epileptic encephalopathy that begins in the first year of life, usually with febrile or afebrile hemiclonic or generalized tonic-clonic seizures followed by status epilepticus. De novo variants in genes that mediate synaptic transmission such as SCN1A and PCDH19 are often associated with Dravet syndrome. Recently, GABAA receptor subunit genes (GABRs) encoding α1 (GABRA1), β3 (GABRB3) and γ2 (GABRG2), but not β2 (GABRB2) or β1 (GABRB1), subunits are frequently associated with Dravet syndrome or Dravet syndrome-like phenotype. We performed next generation sequencing on 870 patients with Dravet syndrome and identified nine variants in three different GABRs. Interestingly, the variants were all in genes encoding the most common GABAA receptor, the α1β2γ2 receptor. Mutations in GABRA1 (c.644T>C, p.L215P; c.640C>T, p.R214C; c.859G>A; V287I; c.641G>A, p.R214H) and GABRG2 (c.269C>G, p.T90R; c.1025C>T, p.P342L) presented as de novo cases, while in GABRB2 two variants were de novo (c.992T>C, p.F331S; c.542A>T, p.Y181F) and one was autosomal dominant and inherited from the maternal side (c.990_992del, p.330_331del). We characterized the effects of these GABR variants on GABAA receptor biogenesis and channel function. We found that defects in receptor gating were the common deficiency of GABRA1 and GABRB2 Dravet syndrome variants, while mainly trafficking defects were found with the GABRG2 (c.269C>G, p.T90R) variant. It seems that variants in α1 and β2 subunits are less tolerated than in γ2 subunits, since variant α1 and β2 subunits express well but were functionally deficient. This suggests that all of these GABR variants are all targeting GABR genes that encode the assembled α1β2γ2 receptor, and regardless of which of the three subunits are mutated, variants in genes coding for α1, β2 and γ2 receptor subunits make them candidate causative genes in the pathogenesis of Dravet syndrome.

scholarly journals Lupeol Accumulation Correlates with Auxin in the Epidermis of Castor

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2978
Author(s):  
Donghai Li ◽  
Cheng Pan ◽  
Jianjun Lu ◽  
Wajid Zaman ◽  
Huayan Zhao ◽  
...  
Keyword(s):  
Auxin Transport ◽  
Biosynthesis Pathway ◽  
Comparative Transcriptome ◽  
Hormone Activity ◽  
Promoter Regions ◽  
Pentacyclic Triterpene ◽  
Large Numbers ◽  
Genes Encoding ◽  
Low Levels ◽  
Underlying Mechanisms

Lupeol, a natural lupane-type pentacyclic triterpene, possesses various pharmacological properties, and its production attracts attention. Significant quantities of lupeol are deposited on the castor aerial organ surface and are easily extractable as a predominant wax constituent. Thus, castor might be considered as a potential bioreactor for the production of lupeol. The lupeol biosynthesis pathway is well known, but how it is regulated remains largely unknown. Among large numbers of castor cultivars, we targeted one accession line (337) with high levels of lupeol on its stem surface and low levels thereof on its hypocotyl surface, implicating that lupeol synthesis is differentially regulated in the two organs. To explore the underlying mechanisms, we did comparative transcriptome analysis of the first internode of 337 stem and the upper hypocotyl. Our results show that large amounts of auxin-related genes are differentially expressed in both parts, implying some possible interactions between auxin and lupeol production. We also found that several auxin-responsive cis-elements are present in promoter regions of HMGR and LUS genes encoding two key enzymes involved in lupeol production. Furthermore, auxin treatments apparently induced the expression levels of RcHMGR and RcLUS. Furthermore, we observed that auxin treatment significantly increased lupeol contents, whereas inhibiting auxin transport led to an opposite phenotype. Our study reveals some relationships between hormone activity and lupeol synthesis and might provide a promising way for improving lupeol yields in castor.

D-galactose catabolism in archaea: operation of the DeLey–Doudoroff pathway in Haloferax volcanii

2020 ◽  
Vol 367 (1) ◽  
Author(s):  
Julia-Beate Tästensen ◽  
Ulrike Johnsen ◽  
Andreas Reinhardt ◽  
Marius Ortjohann ◽  
Peter Schönheit
Keyword(s):  
Transcriptional Regulator ◽  
High Specificity ◽  
Comprehensive Analysis ◽  
Haloferax Volcanii ◽  
Knock Out ◽  
Genes Encoding ◽  
Functional Involvement ◽  
Genome Analyses ◽  
Galactose Dehydrogenase ◽  
Substrate Binding Protein

ABSTRACT The haloarchaeon Haloferax volcanii was found to grow on D-galactose as carbon and energy source. Here we report a comprehensive analysis of D-galactose catabolism in H. volcanii. Genome analyses indicated a cluster of genes encoding putative enzymes of the DeLey–Doudoroff pathway for D-galactose degradation including galactose dehydrogenase, galactonate dehydratase, 2-keto-3-deoxygalactonate kinase and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolase. The recombinant galactose dehydrogenase and galactonate dehydratase showed high specificity for D-galactose and galactonate, respectively, whereas KDPGal aldolase was promiscuous in utilizing KDPGal and also the C4 epimer 2-keto-3-deoxy-6-phosphogluconate as substrates. Growth studies with knock-out mutants indicated the functional involvement of galactose dehydrogenase, galactonate dehydratase and KDPGal aldolase in D-galactose degradation. Further, the transcriptional regulator GacR was identified, which was characterized as an activator of genes of the DeLey–Doudoroff pathway. Finally, genes were identified encoding components of an ABC transporter and a knock-out mutant of the substrate binding protein indicated the functional involvement of this transporter in D-galactose uptake. This is the first report of D-galactose degradation via the DeLey–Doudoroff pathway in the domain of archaea.

scholarly journals The Early Transcriptional Response of Human Granulocytes to Infection with Candida albicans Is Not Essential for Killing but Reflects Cellular Communications

2006 ◽  
Vol 75 (3) ◽  
pp. 1493-1501 ◽  
Author(s):  
Chantal Fradin ◽  
Abigail L. Mavor ◽  
Günther Weindl ◽  
Martin Schaller ◽  
Karin Hanke ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Mononuclear Cells ◽  
De Novo ◽  
Transcriptional Response ◽  
Mononuclear Leukocytes ◽  
General Notion ◽  
Genes Encoding ◽  
Global Transcriptional Profile ◽  
Life Threatening ◽  
Systemic Infections

ABSTRACT Candida albicans is a polymorphic opportunistic fungus that can cause life-threatening systemic infections following hematogenous dissemination in patients susceptible to nosocomial infection. Neutrophils form part of the innate immune response, which is the first line of defense against microbes and is particularly important in C. albicans infections. To compare the transcriptional response of leukocytes exposed to C. albicans, we investigated the expression of key cytokine genes in polymorphonuclear and mononuclear leukocytes after incubation with C. albicans for 1 h. Isolated mononuclear cells expressed high levels of genes encoding proinflammatory signaling molecules, whereas neutrophils exhibited much lower levels, similar to those observed in whole blood. The global transcriptional profile of neutrophils was examined by using an immunology-biased human microarray to determine whether different morphological forms or the viability of C. albicans altered the transcriptome. Hyphal cells appeared to have the broadest effect, although the most strongly induced genes were regulated independently of morphology or viability. These genes were involved in proinflammatory cell-cell signaling, cell signal transduction, and cell growth. Generally, genes encoding known components of neutrophil granules showed no upregulation at this time point; however, lactoferrin, a well-known candidacidal peptide, was secreted by neutrophils. Addition to inhibitors of RNA or protein de novo synthesis did not influence the killing activity within 30 min. These results support the general notion that neutrophils do not require gene transcription to mount an immediate and direct attack against microbes. However, neutrophils exposed to C. albicans express genes involved in communication with other immune cells.

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