Chitin Oligomer Experiment
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE2538 | GEO | 2005/06/01
SECONDARY ACCESSION(S): PRJNA92695
REPOSITORIES: GEO
Similar Datasets
Project description:Using the ATH1 Affymetrix microarrays consisting of about 23,000 genes, we examined the response of Arabidopsis seedlings to chito-tetramers, chito-octamers and hydrolyzed chitin after 30 min of treatment.
2007-07-12 | E-GEOD-2538 | biostudies-arrayexpress
Project description:Analysis of 14-day-old Columbia-0 seedlings treated with chito-tetramer.Results provide insight into the signaling pathways involved in plant devlopment in response to the four-mer. Chitin is the second biopolymer most abundant at nature, after cellulose, forming part of insect exosqueletons, crustacean shells, krill and fungal spores where is present as a high molecular weight molecule. Previously we showed that Arabidopsis defense related clusters of genes were induced by high molecular weight chitin (CHH) or 8mer oligosaccharides similarly (Ramonell et al., 2005), some of those genes were essential for effective defense against phytopathogenic fungus (Berrocal-Lobo et al., 2010). At this work we show that differentially, a chitin oligosaccharide of lower molecular weight (4mer), induce genes in Arabidopsis related principally to vegetative growth, development and carbon and nitrogen metabolism.
2017-02-17 | GSE83858 | GEO
Project description:Chitin utilization by microbes plays a significant role in cycling of carbon and nitrogen in the biosphere, and the study of the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade this recalcitrant polysaccharide. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and non-redundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics, bacterial genetics, and complex environmental substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in Cellvibrio japonicus. Using RNAseq analysis we found not only the up-regulation of genes that encode CAZymes specific for chitin metabolism but also a coordinated expression of non-chitin specific CAZyme genes. Furthermore, we used mutational analysis to characterize the hex20B gene product, predicted to encode a hexosaminidase, and found that it is required for efficient utilization of chito-oligosaccharides. Surprisingly, two additional gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were essential for shuttling chito-oligosaccharides into the periplasmic space. Here we propose naming these loci cttA (chito-oligosaccharides transporter A) and cttB respectively. This study further develops our model of how C. japonicus can derive nutrients from recalcitrant chitin-containing substrates and may be potentially useful for other environmentally or industrially important bacteria.
2020-04-30 | GSE149593 | GEO
Project description:To explore the transcriptional regulations in pip5k1 pip5k2 mutant and wild type plants before or after inoculation with powdery mildew Erysiphe cichoracearum
2020-03-10 | GSE127919 | GEO
Project description:Strain N16961 grown in M9 + 0.5 % lactate to OD 0.2. Culture was split and one part added 0.6 mM of indicated chitin oligosaccharide. Samples was isolated after 30 and 60 min. cDNA was prepared from 2 ug RNA and labeled with Cy3 (no induction) and Cy5 (induction with chitin oligosaccharide). Samples from at least two independent experiments and a total of four hybridizations for each chitin oligosaccharide and time. A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients. Keywords: growth_condition_design
2005-08-11 | GSE3101 | GEO
Project description:Chitin oligomers, released from fungal cell walls by endochitinase, induce defense and related cellular responses in many plants. However, little is known about chitin responses in the model plant Arabidopsis. We describe here a large scale characterization of gene expression patterns in Arabidopsis in response to chitin treatment using an Arabidopsis microarray consisting of 2,375 EST clones representing putative defense-related and regulatory genes. Transcript levels for 71 ESTs, representing 61 genes, were altered >3-fold in chitin-treated seedlings relative to control seedlings. A number of transcripts exhibited altered accumulation as early as 10 min after exposure to chitin, representing some of the earliest changes in gene expression observed in chitin-treated plants. Included among the 61 genes are those that have been reported to be elicited by various pathogen-related stimuli in other plants. Additional genes, including genes of unknown function, were also identified broadening our understanding of chitin-elicited responses. Among transcripts with enhanced accumulation, one cluster was enriched in genes with both the W-box promoter element and a novel regulatory element. In addition, a number of transcripts had decreased abundance, encoding several proteins involved in cell wall strengthening and wall deposition. The chalcone synthase promoter element was identified in the upstream regions of these genes, suggesting that pathogen signals may suppress expression of some genes. These data indicate that Arabidopsis will be an excellent model to elucidate mechanisms of chitin elicitation in plant defense. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-09-09 | GSE3273 | GEO
Project description:Chitin oligomers, released from fungal cell walls by endochitinase, induce defense and related cellular responses in many plants. However, little is known about chitin responses in the model plant Arabidopsis. We describe here a large scale characterization of gene expression patterns in Arabidopsis in response to chitin treatment using an Arabidopsis microarray consisting of 2,375 EST clones representing putative defense-related and regulatory genes. Transcript levels for 71 ESTs, representing 61 genes, were altered >3-fold in chitin-treated seedlings relative to control seedlings. A number of transcripts exhibited altered accumulation as early as 10 min after exposure to chitin, representing some of the earliest changes in gene expression observed in chitin-treated plants. Included among the 61 genes are those that have been reported to be elicited by various pathogen-related stimuli in other plants. Additional genes, including genes of unknown function, were also identified broadening our understanding of chitin-elicited responses. Among transcripts with enhanced accumulation, one cluster was enriched in genes with both the W-box promoter element and a novel regulatory element. In addition, a number of transcripts had decreased abundance, encoding several proteins involved in cell wall strengthening and wall deposition. The chalcone synthase promoter element was identified in the upstream regions of these genes, suggesting that pathogen signals may suppress expression of some genes. These data indicate that Arabidopsis will be an excellent model to elucidate mechanisms of chitin elicitation in plant defense. Groups of assays that are related as part of a time series. Keywords: time_series_design Computed
2005-09-09 | E-GEOD-3273 | biostudies-arrayexpress
Project description:To see the function of OsCERK1 receptor-like kinase in the chitin elicitor signaling in Rice, we compared the gene expression profiles in the chitin oligosaccharide treated cultured rice cells of vector control and OsCERK1 knock-down mutant (RNAi). Keywords: Defense response 1,Chitin oligosaccharide treatment (vector control), 2,Chitin oligosaccharide treatment (vector control) color swap, 3,Chitin oligosaccharide treatment (OsCERK1 RNAi), 4,Chitin oligosaccharide treatment (OsCERK1 RNAi) color swap
2010-06-24 | E-GEOD-16800 | biostudies-arrayexpress
Project description:To see the function of OsCERK1 receptor-like kinase in the chitin elicitor signaling in Rice, we compared the gene expression profiles in the chitin oligosaccharide treated cultured rice cells of vector control and OsCERK1 knock-down mutant (RNAi). Keywords: Defense response
2010-06-24 | GSE16800 | GEO
Project description:This study evaluates the ability of MpChi, an effector protein from the fungus Moniliophthora perniciosa, in suppressing the transcriptional reprogramming associated with MTI (MAMP-triggered immunity) in Nicotiana tabacum cells exposed to the chitin oligomer NAG6.
2018-09-13 | GSE111980 | GEO