Agrobacterium tumefaciens strain:C58
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ABSTRACT:
PROVIDER: PRJNA270111 | ENA |
REPOSITORIES: ENA
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Project description:This research focuses on the design, manufacturing and validation of a new Agrobacterium tumefaciens C58 whole-genome tiling microarray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The Agrobacterium tumefaciens C58 genome is re-acquired with next-generation sequencing and then used to design the tilinlg microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting Agrobacterium tumefaciens C58 under various growth conditions and then using the tling microarrays to verify expected gene expression patterns.
2014-09-25 | GSE61737 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62750 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes.
2014-10-28 | GSE62749 | GEO
Project description:Purpose: The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence and absence of the two opines nopaline and agrocinopine (more precisely agrocinopine A) to delineated the key-genes associated to opines-response in A. tumefaciens C58.
2018-09-01 | GSE106257 | GEO
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes. 3-week-old A.thaliana Col-0 seedlings were selected for growth in hydroponic systems. A. tumefaciens C58 was inoculated into the hydroponic system and co-cultivation persisted for 8 hours. Leaf tissue was seperated for RNA extraction and hybridization to the ATH1 Affymetrix microarray.
2014-10-28 | E-GEOD-62749 | biostudies-arrayexpress
Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes. 3-week-old A.thaliana Col-0 seedlings were selected for growth in hydroponic systems. A. tumefaciens C58 was inoculated into the hydroponic system and co-cultivation persisted for 8 hours. Root tissue was seperated for RNA extraction and hybridization to the ATH1 Affymetrix microarray.
2014-10-28 | E-GEOD-62750 | biostudies-arrayexpress
Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response.
2015-07-22 | GSE71138 | GEO
Project description:Comparative genomic hybridizations obtained with an original Agrobacterium tumefaciens strain C58 genome-based micro-array were used to detect the presence or absence of genes homologous to those of strain C58 in 25 agrobacterial strains. These strains included six other members of genomovar G8, one to three strains for each of the nine other A. tumefaciens genomovars and one for A. larrymoorei, a sister species of the A. tumefaciens complex. An original probabilistic method was used to segment C58 replicon sequences into regions, that are absent or present in tested strains, allowing us to detect the presence of homologues of C58 coding sequences (CDSs) in tested strains.
2011-09-08 | E-MTAB-558 | biostudies-arrayexpress
Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. We demonstrate that A. tumefaciens biofilm formation is reduced under limiting iron conditions. Treatment of A. tumefaciens cultures with EDDHA, an iron-specific extracellular chelator, inhibited both planktonic growth rate and adherent biomass. These effects were reversed upon addition of exogenous ferrous iron. This reduced biofilm formation effect is independent of the known iron-responsive regulators Irr and RirA. Transcriptome analysis comparing gene expression under iron-replete versus iron-deficient conditions identified hundreds of genes that are differentially regulated. Downregulated genes suggest an iron sparing response. Four biological replicates, independent RNA preparations, one dye swap.
2015-07-22 | E-GEOD-71138 | biostudies-arrayexpress
Project description:The plant pathogen Agrobacterium tumefaciens attaches to and forms biofilms on both biotic and abiotic surfaces. The transition between free-living, planktonic A. tumefaciens and multicellular biofilms is regulated by several well-defined environmental and nutritional inputs, including pH, oxygen tension, and phosphate concentration. In many bacterial species limiting iron levels inhibit attachment and biofilm formation. In several systems intracellular levels of the redox-active manganous (Mn2+) and ferrous (Fe2+) ions are interrelated and have tight corresponding regulation with respect to one another. We show that limiting manganese concentrations elicit similar growth and biofilm phenotypes to those seen under iron-limiting conditions. Microarray analysis comparing gene expression in manganese-replete versus manganese-limiting conditions identified a small number of differentially regulated transcripts. These results indicate that the redox-active manganous and ferrous ions are required for wild-type levels of growth and biofilm formation, and that the manganese-dependent response is primarily post-transcriptional and complementary to, but not redundant with, the iron-dependent response.
2015-07-24 | GSE71266 | GEO