Trancriptome analysis of Agrobacterium tumefaciens C58 cells in the presence of abundant opines
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PROVIDER: PRJNA416011 | ENA |
REPOSITORIES: ENA
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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: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: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: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:Purpose: The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence of GHB and GABA to delineated the key-genes associated to the response of these metabolites in A. tumefaciens C58.
2019-04-29 | GSE121889 | GEO
Project description:Performed RNASeq analysis comparing A. tumefaciens C58 (fabrum) harboring a plasmid driving ectopic expression of mirA regulator gene (ATU_RS08050) from Plac promoter with the isogenic strain haboring the same plasmid with no mirA (Vector control)
2021-12-29 | GSE174467 | GEO
Project description:We investigated the role of the LysR-type transcriptional regulator LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) and several protein-coding genes, such as ampD (atu2113). In our current study we invesigated the role of LsrB in beta-lactam resistance. For this purpose, we constructed a vtlR/lsrB deletion mutant. Total RNA was isolated from this mutant. Sequencing was done on the Illumina NovaSeq 6000 platform. Wild-type samples that derived from the same experiment were published previously (Kraus et al., 2020) (GEO accession: GSE150941). In the vtlR/lsrB mutant around 800 protein coding genes and around 80 sRNA coding genes were downregulated or upregulated at least three-fold (p value ≤ 0.05). Overall, the results demonstrate the huge regulatory effect of LsrB on the transcriptome of A. tumefaciens. Kraus, A., Weskamp, M., Zierles, J., Balzer, M., Busch, R., Eisfeld, J., et al. (2020) Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens. J Bacteriol 202: e00309-20.
2023-08-12 | GSE240243 | GEO