Project description:Purpose:first,we want to find the genes revelant to curdlan synthesis and oxygen regulation, second, we want to research the function of fnrN gene in Agrobacterium sp. ATCC 31749. Method: samples of cell growth phase, curdlan-producing phase (normoxia) and curdlan-producing phase (micro-oxygen treated) in both Agrobacterium sp. ATCC 31749 wild strain and ΔfnrN strain were collectecd to extract mRNA. Each sample was treated in duplicate. The softwares we used include fastqc, trimmomatic, TopHat2 and Cufflinks. Illumina Hiseq4000 was used to complete the research.
Project description:Agrobacterium deltaense strain CNPSo 3391 was isolated from a soybean nodule in Mozambique. Its genome size was estimated at 4,926,588 bp. This isolate carries several coding sequences for stress tolerance, but no identifiable nodulation or virulence genes. Possible ecological roles of bacteria isolated from legume nodules and closely related to Agrobacterium are discussed.
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.
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.
