Project description:Whole-genome sequencing is an important way to understand the genetic information, gene function, biological characteristics, and living mechanisms of organisms. There is no difficulty to have mega-level genomes sequenced at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. The shotgun sequencing method failed to dissect this genome. After insisting for 10 years and going over 3 generations of sequencing techniques, we successfully dissected the PaP1 genome with 91,715 bp in length. Single-molecule sequencing revealed that this genome contains lots of modified bases, including 51 N6-methyladenines (m6A) and 152 N4-methylcytosines (m4C). At the same time, further investigations revealed a novel immune mechanism of bacteria, by which the host bacteria can recognize and repel the modified bases containing inserts in large scale, and this led to the failure of the shotgun method in PaP1 genome sequencing. Strategy of resolving this problem is use of non-library dependent sequencing techniques or use of the nfi- mutant of E. coli DH5M-NM-1 as the host bacteria to construct the shotgun library. In conclusion, we unlock the mystery of phage PaP1 genome hard to be sequenced, and discover a new mechanism of bacterial immunity in present study. Methylation profiling of Pseudomonas aeruginosa phage PaP1 using kinetic data generated by single-molecule, real-time (SMRT) sequencing on the PacBio RS.
Project description:Oberhardt2008 - Genome-scale metabolic
network of Pseudomonas aeruginosa (iMO1056)
This model is described in the article:
Genome-scale metabolic
network analysis of the opportunistic pathogen Pseudomonas
aeruginosa PAO1.
Oberhardt MA, Puchałka J, Fryer
KE, Martins dos Santos VA, Papin JA.
J. Bacteriol. 2008 Apr; 190(8):
2790-2803
Abstract:
Pseudomonas aeruginosa is a major life-threatening
opportunistic pathogen that commonly infects immunocompromised
patients. This bacterium owes its success as a pathogen largely
to its metabolic versatility and flexibility. A thorough
understanding of P. aeruginosa's metabolism is thus pivotal for
the design of effective intervention strategies. Here we aim to
provide, through systems analysis, a basis for the
characterization of the genome-scale properties of this
pathogen's versatile metabolic network. To this end, we
reconstructed a genome-scale metabolic network of Pseudomonas
aeruginosa PAO1. This reconstruction accounts for 1,056 genes
(19% of the genome), 1,030 proteins, and 883 reactions. Flux
balance analysis was used to identify key features of P.
aeruginosa metabolism, such as growth yield, under defined
conditions and with defined knowledge gaps within the network.
BIOLOG substrate oxidation data were used in model expansion,
and a genome-scale transposon knockout set was compared against
in silico knockout predictions to validate the model.
Ultimately, this genome-scale model provides a basic modeling
framework with which to explore the metabolism of P. aeruginosa
in the context of its environmental and genetic constraints,
thereby contributing to a more thorough understanding of the
genotype-phenotype relationships in this resourceful and
dangerous pathogen.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180020.
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BioModels Database:
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To the extent possible under law, all copyright and related or
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Project description:ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.
Project description:The global transcriptional profile of novel T7-like Pseudomonas aeruginosa phage LUZ100 was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units and gained new insights in the molecular mechanisms of transcriptional regulation of T7-like temperate phages.
Project description:Differential RNA-seq (dRNA-seq) was performed on Pseudomonas aeruginosa alone or shortly after iinfection with the jumbo phage phiKZ
Project description:Genome-scale modeling of Pseudomonas aeruginosa PA14 unveils its broad metabolic capabilities and role of metabolism in drug potentiation
Project description:We previously showed that pre-exposure of the cornea to TLR5 ligand flagellin induces profound mucosal innate protection against pathogenic microbes by reprogramming gene expression. To date, there was no genome-wide cDNA array to detect full scale of flagellin mediated reprogramming of gene expression in mucosal surface epithelial cells. Taking advantage of readily accessible, easily procurable epithelial cell population, this study is the first report to use genome-wide cDNA microarray approach to document genes associated with flagellin-induced protection against Pseudomonas aeruginosa infection in corneal epithelial cells (CECs). Total RNA obtained from isolated mouse corneal epithelial cells of the control (cells scrapped off from the corneas without infection), Pseudomonas aeruginosa infected (6 h post infection) and flagellin pretreated (24 h), followed by Pseudomonas aeruginosa infection (6 h).
Project description:Purpose: The purpose of this study was to investigate the effect of quorum sensing on phage infection. Methods: We constructed the lasR gene knockout strain of Pseudomonas aeruginosa PAO1 and performed transcriptome sequencing.
