Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1201236 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31799200_1.fastq.gz | Fastqsanger.gz | |||
| SRR31799201_1.fastq.gz | Fastqsanger.gz | |||
| SRR31799202_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:Multipartite bacterial genome organization can confer advantages including coordinated gene regulation and faster genome replication, but is challenging to maintain. Agrobacterium tumefaciens lineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the lab model strain C58, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzed Agrobacterium natural isolates from the French Collection for Plant-Associated Bacteria (CFBP) and identified two strains with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed both replication origins remained active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres were essential. Importantly, the site-specific recombinases XerCD are required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains.
2025-05-05 | GSE285100 | GEO
Project description:Chromosome architecture plays a crucial role in bacterial adaptation, yet its direct impact remains unclear. Different bacterial species, and even strains within the same species, exhibit diverse chromosomal configurations, including a single circular or linear chromosome, two circular chromosomes, or a circular-linear combination. To investigate how these architectures shape bacterial behavior, we generated near-isogenic strains representing each configuration in Agrobacterium tumefaciens C58, an important soil bacterium widely used for plant genetic transformation. Strains with a single-chromosome architecture, whether linear or circular, exhibited faster growth, enhanced stress tolerance, and greater inter-strain competitiveness. In contrast, bipartite chromosome strains showed higher virulence gene expression and enhanced transient plant transformation efficiency, suggesting a pathogenic adaptation. Whole-transcriptome analysis revealed architecture-dependent gene expression patterns, underscoring the profound impact of chromosome organization on Agrobacterium fitness and virulence. These findings highlight how chromosome structure influences bacterial adaptation and shapes evolutionary trajectories.
2025-08-25 | GSE293397 | GEO
Project description:Bacterial species from diverse phyla contain multiple replicons, yet how these multipartite genomes are organized and segregated during the cell cycle remains poorly understood. Agrobacterium tumefaciens has a 2.8 Mb circular chromosome (Ch1), a 2.1 Mb linear chromosome (Ch2), and two large plasmids (pAt and pTi). We used this alpha proteobacterium as a model to investigate the global organization and temporal segregation of a multipartite genome. Using Chromosome Conformation Capture (Hi-C) assays, we demonstrate that both the circular and the linear chromosomes but neither of the plasmids have their left and right arms juxtaposed from their origins to their termini, generating inter-arm interactions that require the broadly conserved structural maintenance of chromosomes (SMC) complex. Moreover, our studies revealed two types of inter-replicon interactions: “ori-ori clustering” in which the replication origins of all four replicons interact, and “Ch1-Ch2 alignment” in which the arms of Ch1 and Ch2 interact linearly along their lengths. We show that the centromeric proteins (ParB1 for Ch1 and RepBCh2 for Ch2) are required for both types of inter-replicon contacts. Finally, using fluorescence microscopy, we validated the clustering of the origins and observed their frequent colocalization during segregation. Altogether, our findings provide a high-resolution view of the conformation of a multipartite genome. We hypothesize that inter-centromeric contacts promote the organization and maintenance of diverse replicons.
2022-01-30 | GSE182881 | GEO
Project description:Linear dicentric bacterial chromosomes in Agrobacterium tumefaciens natural isolates reveal common constraints for replicon fusion
| PRJNA1201172 | ENA
Project description:This study describes physiological changes, morphological adaptations and the regulation of pathogen defense responses in Arabidopsis crown galls. Crown gall development was induced on intact plants under most natural conditions with Agrobacterium tumefaciens. Differential gene expression and the metabolite pattern was determined by comparing crown galls with mock-inoculated inflorescence stalk segments of the same age. Experiment Overall Design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately inoculated with Agrobacterium tumefaciens, strain C58, or mock-inoculated. Plants were cultivated for another 35 days under short day conditions (8 h illumination, 16 h darkness). Gene expression values of four independent experiments of treated material (C58 35dpi 1 to 4) were compared with four non-treated samples of the same age (reference 35dpi 1 to 4). Differential gene expression was analyzed by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).
2009-12-02 | E-GEOD-13927 | biostudies-arrayexpress
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:This study describes physiological changes, morphological adaptations and the regulation of pathogen defense responses in Arabidopsis crown galls. Crown gall development was induced on intact plants under most natural conditions with Agrobacterium tumefaciens. Differential gene expression and the metabolite pattern was determined by comparing crown galls with mock-inoculated inflorescence stalk segments of the same age.
2009-11-19 | GSE13927 | GEO
Project description:In the present study we investigate the role of the LysR-type transcriptional regulators LsrB (Atu2186) and OxyR (Atu4641) in the oxidative stress response of Agrobacterium tumefaciens C58 (alias A. fabrum C58). Therein, we used our existing lsrB-deletion (Kraus et al. 2020*) mutant and constructed two additional mutants: An oxyR and a lsrB/oxyR double deletion mutant. Total RNA was isolated from WT and mutant strains grown in LB medium to mid-exponential phase and withdrawn before or after 15 min, 5 mM H2O2 stress. Residual DNA was removed by RNAse-free Dnase. Sequencing was performed done on the Illumina NovaSeq 6000 platform. Our results reveal a central role for both LysR-type transcriptional regulators in the oxidative stress response of Agrobacterium 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.
2025-03-12 | GSE283062 | GEO
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