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Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis

ABSTRACT: Agarwood is an expensive resinous heartwood derived from the wounded Aquilaria plants. To identify the primary genes that maybe related to agarwood formation, we sequenced 2 cDNA libraries generated from healthy and wounded A. sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length of 678.65 bp were obtained, and they were annotated in detail at bioinformatics levels. Of those associated with agarwood formation, 30 putatively encoded enzymes in the sesquiterpene biosynthesis pathway, a handful of transcription factors, and protein kinases related to wound signal transduction. Three full-length cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in Escherichia coli, and enzyme assays revealed that they are active enzymes, with the major products being δ-guaiene. A methyl jasmonate (MJ) induction experiment revealed that the expression of ASS was significantly induced by MJ, and the production of sesquiterpenes was elevated accordingly. The expression of some transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting they maybe positive regulators of ASS. This study provides extensive transcriptome information for Aquilaria spp. and valuable clues for elucidating the mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their regulation.

ORGANISM(S): Aquilaria sinensis

PROVIDER: GSE42246 | GEO | 2013/12/31

SECONDARY ACCESSION(S): PRJNA179445

REPOSITORIES: GEO

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Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis

Project description:Agarwood is an expensive resinous heartwood derived from the wounded Aquilaria plants. To identify the primary genes that maybe related to agarwood formation, we sequenced 2 cDNA libraries generated from healthy and wounded A. sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length of 678.65 bp were obtained, and they were annotated in detail at bioinformatics levels. Of those associated with agarwood formation, 30 putatively encoded enzymes in the sesquiterpene biosynthesis pathway, a handful of transcription factors, and protein kinases related to wound signal transduction. Three full-length cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in Escherichia coli, and enzyme assays revealed that they are active enzymes, with the major products being M-NM-4-guaiene. A methyl jasmonate (MJ) induction experiment revealed that the expression of ASS was significantly induced by MJ, and the production of sesquiterpenes was elevated accordingly. The expression of some transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting they maybe positive regulators of ASS. This study provides extensive transcriptome information for Aquilaria spp. and valuable clues for elucidating the mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their regulation. healthy and wounded stems of three-year-old A. sinensis trees

2013-12-31 | E-GEOD-42246 | biostudies-arrayexpress

Examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis

Project description:Our specific aim is to examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis, as well as Wnt ligands and Wnt signaling mediators during corneal wound healing using a mouse corneal scratch model. The specific structural features of heparan sulfate underlie its role in modulating cellular responses to growth factors such as the Wnts. Heparan sulfate 6-O-endosulfatases (sulf-1 and sulf-2) remove 6-O sulfate group from trisulfated disaccharides present on heparan sulfate chains. Our preliminary results suggest that sulf-1 is upregulated at the protein level in the epithelial cells of wounded mouse corneas, as compared to the undamaged contralateral eye. Modulation of heparan sulfate proteoglycan expression and/or structural modifications of its chains might be an important aspect of the regulation of epithelial cell migration and proliferation during wound healing. RNA preparations from four different conditions, were sent to Microarray Core (E). Gene expression was examined in triplicates at 2 time points (8 and 24 hrs post-wounding: 6 arrays), using the contralateral eye as a control at one time point as a control (3 arrays). To account for a systemic response (i.e. bilateral inflammation) to the corneal wounding, corneas of non-wounded mice (3 arrays) were used. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.

2011-04-29 | E-GEOD-28931 | biostudies-arrayexpress

Hspa8 and ICAM-1 identified as damage-induced mediators of gd T cell activation

Project description:Here we identify a novel members of a gamma delta T cell "wound signature" that are upregulated following wounding and mediate the gamma delta T cell wound response. RNA-seq analysis of wounded and non-wounded epidermis was initially used to identify two new wound signature proteins (ICAM1 and HSPA8)

2021-05-10 | GSE168655 | GEO

Examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis

2011-04-29 | GSE28931 | GEO

Transcriptome of 5-week-old Col-0 and isi1-2 distal leaves 13 in untreated controls or upon wounding leave 8

Project description:In our study, IMPAIRED SUCROSE INDUCTION 1 (ISI1) was identified as a player in long distance wound signaling in Arabidopsis. To further assess the impact of ISI1 on the wound response, we tested the transcriptomes of the wounded isi1-2 mutants in comparison with wounded wild type plants, in order to find genes that were deregulated in isi1 loss-of-function mutants.

2023-09-30 | GSE157938 | GEO

A role for the mitogen-activated protein kinase kinase kinase 1 in epithelial wound healing

Project description:The mitogen-activated protein kinase kinase (MEK) kinase 1 (MEKK1), also known as MAP3K1, mediates activin B (ActB) signals required for eyelid epithelium morphogenesis during mouse fetal development. The present study investigates the role of MEKK1 in epithelial wound healing, another activin-regulated biological process. In a skin wound model, injury markedly stimulates MEKK1 expression and activity, which are in turn required for the expression of genes involved in extracellular matrix (ECM) homeostasis. MEKK1 ablation or down-regulation by interfering RNA significantly delays skin wound closure and impairs activation of Jun NH2-terminal kinases, induction of plasminogen activator inhibitor (PAI)-1, and restoration of cell-cell junctions of the wounded epidermis. Conversely, expression of wild-type MEKK1 accelerates reepithelialization of full-thickness skin and corneal debridement wounds by mechanisms involving epithelial cell migration, a cell function that is partially abolished by neutralizing antibodies for PAI-1 and metalloproteinase III. Our data suggest that MEKK1 transmits wound signals, leading to the transcriptional activation of genes involved in ECM homeostasis, epithelial cell migration, and wound reepithelialization.

2022-07-13 | GSE201823 | GEO

The tissue-engineered human cornea as a model to study expression of matrix metalloproteinases during corneal wound healing

Project description:Corneal injuries remain a major cause of consultation in the ophthalmology clinics worldwide. Repair of corneal wounds is a complex mechanism that involves cell death, migration, proliferation, differentiation, and extracellular matrix (ECM) remodeling. In the present study, we used a tissue-engineered, two-layers (epithelium and stroma) human cornea as a biomaterial to study both the cellular and molecular mechanisms of wound healing. Gene profiling on microarrays revealed important alterations in the pattern of genes expressed by tissue-engineered corneas in response to wound healing. Expression of many MMPs-encoding genes was shown by microarray and qPCR analyses to increase in the migrating epithelium of wounded corneas. Many of these enzymes were converted into their enzymatically active form as wound closure proceeded. In addition, expression of MMPs by human corneal epithelial cells (HCECs) was affected both by the stromal fibroblasts and the collagen-enriched ECM they produce. Most of all, results from mass spectrometry analyses provided evidence that a fully stratified epithelium is required for proper synthesis and organization of the ECM on which the epithelial cells adhere. In conclusion, and because of the many characteristics it shares with the native cornea, this human two layers corneal substitute may prove particularly useful to decipher the mechanistic details of corneal wound healing. Primary cultures of human corneal epithelial cells cultivated on BSA (number of replicates: 7), Collagen type I (number of replicates: 2), Collagen type IV (number of replicates: 2), Fibronectin (number of replicates: 2), Tenascin C (number of replicates: 2) and Laminin (number of replicates: 2) matrix. Central, internal and external ring of wounded Tissue-engineered human cornea.

2015-11-25 | E-GEOD-75336 | biostudies-arrayexpress

Proteomic analysis validates previous findings on wounding-responsive plant hormone signaling and primary metabolism contributing to the biosynthesis of secondary metabolites based on metabolomic analysis in harvested broccoli (Brassica oleracea L. var. italica)

Project description:The plant wound-response is a complex process that generates physiological modiﬁcations for protecting the wounded tissue. In this study, tandem mass tag (TMT)-based quantitative proteomic analysis was performed to clarify the comprehensive molecular mechanism for the wound-response of broccoli subjected to two wounding intensities (0.04 and 1.85 m2 kg−1 for florets and shreds, respectively). Furthermore, integrated proteomic and metabolomic analysis was performed to reveal the interaction among the critical metabolic pathway responses to wounding. The results show that a total of 399 proteins and 266 proteins were identified as differentially expressed proteins (DEPs) in florets and shreds broccoli compared to control, respectively. Bioinformatic analysis indicated that the DEPs were mainly involved in metabolism, genetic information processing, cellular process, environmental information processing and organismal systems. Salicylic acid (SA) and ethylene (ET) biosynthesis were more susceptible to being induced by wounding with lower intensities, whereas, jasmonic acid (JA) biosynthesis was more susceptible to being activated by wounding with higher intensities. Some carbohydrate metabolic pathways and amino acid biosynthesis-related pathways such as phenylalanine, cysteine and methionine metabolic pathways were significantly up-regulated, which promotes the precursor levels for phenolic substances and glucosinolate synthesis. Biosynthesis of secondary metabolites was activated by wounding through regulation of critical proteins involved in the corresponding metabolic pathways.

2021-05-19 | MTBLS2317 | MetaboLights

Transcriptional profiling of macrophages in skin wounds

Project description:Macrophages were isolated from wounded skin 4 and 14 days post wounding. Monocytes were adoptively transferred on days 2 and 12 and traced into the wound.

2021-10-28 | GSE183489 | GEO

Epidermal gene expression in wound healing and after ex vivo injury

Project description:Human in vivo skin wound: Non-wounded skin was obtained by taking punch biopsies from three healthy donors (donor 1,2 and 3). The samples were termed 'skin day 0 in vivo wound'. Skin wound samples were retrieved by making new punch biopsies from the edge of the original biopsies after four days. These samples were termed 'skin day 4 in vivo wound'. As much dermal tissue as possible was removed by dissection to make sure mainly epidermis was present in the samples. The samples were washed in NaCl to possible remove infiltrating inflammatory cells before RNA isolation. Ex vivo skin wounds: Skin was obtained from three healthy donors following reduction surgery (donor 1, 2, and 3). As much dermal tissue as possible was removed dissection. These samples were termed 'skin day 0 ex vivo wound'. Skin was sliced into 1x10 mm slices and incubated in keratinocyte medium for four days with either 1:1000 fold dilution of DMSO or 10 micromolar AG-1478 (dissolved in DMSO). Again as much dermal tissue was removed by dissection as possible before RNA was isolated. These samples were termed 'skin day 4 ex vivo wound' and 'skin day 4 AG-1478 ex vivo wound'. By comparing the gene expression day 4 in ex vivo wound with in vivo wounds it was possible to see which part of the gene expression in wounded skin that was due to the epidermal reaction to injury and how much was due to stimuli from infiltrating inflammatory cells absent in the ex vivo skin wounds. By comparing the data from ex vivo skin wounds day 4 with and without the EGFR-inhibitor AG-1478, it was possible to look at the importance of the EGF-receptor of EGFR for the gene expression in ex vivo wounded skin.

2011-09-13 | E-MEXP-3305 | biostudies-arrayexpress

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