Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of pNCF (non-conjugative factor of F plasmid) carrying E.coli biofilm

ABSTRACT: Three E.coli affymetrix antisense arrays were used to examine the global gene expression of pNCF carrying E.coli biofilm. The pNCF is the derivative of only 65 kb non-conjugative factor of F plasmid. It was introduced to E.coli MG1655 strains before prepare the biofilm samples. The biofilms were cultured under the continuous flow cell system using MOP minimal medium supplemented with 0.02% glucose at 37C. The total RNA was extracted directly from the chamber after 48h of incubation for further array procedures according to the manufacture manual.

ORGANISM(S): Escherichia coli

SUBMITTER: Thithiwat May

PROVIDER: E-MEXP-1145 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Escherichia coli harboring a natural IncF conjugative F plasmid develops complex mature biofilms by stimulating synthesis of colanic acid and Curli.

May Thithiwat T Okabe Satoshi S

Journal of bacteriology 20080912 22

It has been shown that Escherichia coli harboring the derepressed IncFI and IncFII conjugative F plasmids form complex mature biofilms by using their F-pilus connections, whereas a plasmid-free strain forms only patchy biofilms. Therefore, in this study we investigated the contribution of a natural IncF conjugative F plasmid to the formation of E. coli biofilms. Unlike the presence of a derepressed F plasmid, the presence of a natural IncF F plasmid promoted biofilm formation by generating the c ...[more]

PMID: 18790864

Similar Datasets

Project description:Purpose: The goal of this study was to use RNA-seq to define the Klebsiella pneumoniae transcriptome recorded under 5 different experimental conditions, and to identify signature genes of each condition by comparing global transcriptional profiles. Methods: mRNA profiles were generated for Klebsiella pneumoniae CH1034 clinical isolate, in triplicate, by deep sequencing. Total RNAs were harvested from bacteria cultured at 37Â°C in M63B1 minimal media under different conditions: (i) planktonic aerobic condition at OD 620nm=0.250 (exponential growth-phase), (ii) overnight planktonic aerobic condition (stationnary growth-phase), (iii) biofilm in a flow-cell chamber after 7 hours of incubation (7-hours old biofilm), (iv) biofilm in a flow-cell chamber after 13 hours of incubation (13-hours old biofilm), (v) bacteria self-dispersed from biofilm recovered in the flow-cell effluent (biofilm-dispersed bacteria). Ribosomal RNAs were removed using the Bacteria Ribo-Zero Magnetic kit (Epicentre Biotechnologies). Libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit (Illumina), and 50bp single-reads were obtained by HiSeq 2000 (Illumina).The sequence reads that passed FastQC quality filters were mapped to the CH1034 genome using BurrowsâWheeler Aligner (BWA) (0.7.12-r1039 version). The transcript levels were determined using HTSeq-count (0.6.1p1 version) with union mode followed by DESeq (1.16.0 version) analysis. qRTâPCR validation was performed using SYBR Green assays. Results: We found that each condition has a specific transcriptional profile, and we identify 4 robust signature genes for each. Conclusion: Our study represents the first detailed analysis of K. pneumoniae transcriptomes under different experimental conditions generated by RNA-seq technology. The data reported here should permit the dissection of complex biologic functions involved in the transition between the sessile and planktonic modes of growth. Determination of the transcriptional profiling of Klebsiella pneumoniae under 5 different experimental conditions. mRNA profiles were generated for bacteria under exponential planktonic growth-phase, stationary planktonic growth-phase, 7 hours-old biofilm, 13 hours-old biofilm and biofilm-dispersed modes, each in three biological replicates, by deep sequencing using Illumina HiSeq

Project description:In α-proteobacteria, strict regulation of cell cycle progression is necessary for the specific cellular differentiation required for adaptation to diverse environmental niches. The symbiotic lifestyle of Sinorhizobium meliloti requires a drastic cellular differentiation that includes genome amplification. To achieve polyploidy, the S. meliloti cell cycle program must be altered to uncouple DNA replication from cell division. In the α-proteobacterium Caulobacter crescentus, cell cycle regulated transcription plays an important role in control of cell cycle progression but this has not been demonstrated in other α-proteobacteria. Here we describe a robust method for synchronizing cell growth that enabled the first global analysis of S. meliloti cell cycle regulated gene expression. The objective of the microarray-based cell cycle gene expression analysis was to determine which genes were transcriptionally regulated as a funciton of a cell cycle in order to understand the contribution of transcriptional regulation to the timing of cell cycle events. The microarray analysis identified 462 genes with cell cycle regulated transcripts, including several key cell cycle regulators, and genes involved in motility, attachment, and cell division. Only 28% of the 462 S. meliloti cell cycle regulated genes were also transcriptionally cell cycle regulated in C. crescentus. Furthermore, CtrA and DnaA binding motif analysis revealed little overlap between the cell cycle-dependent regulons of CtrA and DnaA in S. meliloti and C. crescentus. The predicted S. meliloti cell cycle regulon of CtrA, but not that of DnaA, was strongly conserved in more closely related α-proteobacteria with similar ecological niches as S. meliloti, suggesting that the CtrA cell cycle regulatory network may control functions of central importance to the specific lifestyles of α-proteobacteria. Gene expression levels were quantified in synchronously growing S. meliloti cultures across 8 time points and compared to gene expression levels in unsynchronized culture via a two-color custom agilent array A two-color array format was used with time point from synchronous culture being competed with a sample from unsynchronized culture (control same for all arrays) to determine the cell cycle-phase specific induction or repression of genes relative to batch culture which contains cells in all phases of the cell cycle. For each of the 8 cell cycle time points, four biological replicates were used resulting in 4 arrays per time point and a total of 32 arrays. The arrays also contained duplicates of each probe resulting in two technical replicates per biological replicate per time point.

Dataset Information

Transcription profiling of pNCF (non-conjugative factor of F plasmid) carrying E.coli biofilm

Publications

Escherichia coli harboring a natural IncF conjugative F plasmid develops complex mature biofilms by stimulating synthesis of colanic acid and Curli.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets