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Linear dicentric bacterial chromosomes in Agrobacterium tumefaciens natural isolates reveal common constraints for replicon fusion

ABSTRACT: Linear dicentric bacterial chromosomes in Agrobacterium tumefaciens natural isolates reveal common constraints for replicon fusion

PROVIDER: PRJNA1201172 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31795745_1.fastq.gz	Fastqsanger.gz
	SRR31795745_2.fastq.gz	Fastqsanger.gz
	SRR31795746_1.fastq.gz	Fastqsanger.gz
	SRR31795746_2.fastq.gz	Fastqsanger.gz
	SRR31795747_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Linear dicentric bacterial chromosomes in Agrobacterium tumefaciens natural isolates reveal common constraints for replicon fusion

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

Conformation and dynamic interactions of the multipartite genome in Agrobacterium tumefaciens

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

Chromosome Architecture Impacts Virulence and Competitiveness in Agrobacterium tumefaciens C58

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

Comparative genomic hybridization of Agrobacterium tumefaciens strains on tiling arrays covering the genome of strain C58

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:Two natural isolates of Agrobacterium tumefaciens contain a linear dicentric chromosome

| PRJNA1201236 | ENA

Transcription profiling of fission yeast as telomeres shorten in trt1- strains, and to compare survivors with linear and circular chromosomes

Project description:Time course experiment to watch RNA expression profiles as telomeres shorten in trt1- strains, and to compare survivors with linear and circular chromosomes.

2005-03-01 | E-MEXP-201 | biostudies-arrayexpress

Genome replication and cell division control by the methylation-sensitive GcrA regulator in Agrobacterium tumefaciens

Project description:Bacteria with complex genomes including secondary chromosomes and/or megaplasmids face unique challenges when controlling their cell cycle: they not only need to coordinate genome replication with other cell cycle events such as cell growth and cell division, but also to synchronize the replication of different replicons. In Alphaproteobacteria, replication and maintenance of large extrachromosomal replicons is usually dependent on RepABC modules, as seen for the plant pathogen Agrobacterium tumefaciens. In this study, we demonstrate that the conserved GcrA protein is an essential methylation-dependent transcriptional regulator playing at least two critical roles during the A. tumefaciens cell cycle. First, GcrA is required for the on-time and synchronized firing of the three RepABC-dependent origins of replication of A. tumefaciens that are needed for chromosomal and megaplasmid replication. Second, GcrA triggers the expression of several essential cell division genes for the timely and essential assembly of a functional divisome. These findings highlight how this conserved global regulator can control and then synchronize a variety of essential cell cycle events in Alphaproteobacteria with complex genomes, notably coordinating the maintenance of several RepABC-dependent replicons with cell division.

2026-05-18 | GSE330725 | GEO

RNA-seq gene expression profiling comparing WT and DccrM Ptac-ccrM Agrobacterium tumefaciens C58 cells cultivated in ATGN+/-IPTG.

Project description:The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-type and CcrM-depleted Agrobacterium tumefaciens cells with a dicentric genome with two essential replication origins. We find that DNA methylation has a pleiotropic impact on motility, biofilm formation and viability. Remarkably, CcrM promotes the expression of the repABCCh2 operon, encoding proteins required for replication initiation/partitioning at ori2, and inhibits gcrA, encoding a conserved global cell cycle regulator. Imaging ori1 and ori2 in live cells, we show that replication from ori2 is often delayed in cells with a hypo-methylated genome, while ori2 over-initiates in cells with a hyper-methylated genome. We thus propose that methylation by CcrM stimulates RepABC-dependent chromosomal origins, uncovering a novel and original connection between CcrM-dependent DNA methylation and genome maintenance in an Alphaproteobacterial pathogen.

2024-01-25 | GSE253175 | GEO

Agrobacterium tumefaciens C58 whole-genome tiling microarray design and validation

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

Trancriptome analysis of Agrobacterium tumefaciens C58 cells in the presence of abundant opines

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

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