Henry2009 - Genome-scale metabolic network of Bacillus subtilis (iBsu1103)
Henry2009 - Genome-scale metabolic network of
Bacillus subtilis (iBsu1103)
This model is described in the article:
iBsu1103: a new genome-scale
metabolic model of Bacillus subtilis based on SEED
Henry CS, Zinner JF, Cohoon MP,
Genome Biol. 2009; 10(6): R69
BACKGROUND: Bacillus subtilis is an organism of interest
because of its extensive industrial applications, its
similarity to pathogenic organisms, and its role as the model
organism for Gram-positive, sporulating bacteria. In this work,
we introduce a new genome-scale metabolic model of B. subtilis
168 called iBsu1103. This new model is based on the annotated
B. subtilis 168 genome generated by the SEED, one of the most
up-to-date and accurate annotations of B. subtilis 168
available. RESULTS: The iBsu1103 model includes 1,437 reactions
associated with 1,103 genes, making it the most complete model
of B. subtilis available. The model also includes Gibbs free
energy change (DeltarG' degrees ) values for 1,403 (97%) of the
model reactions estimated by using the group contribution
method. These data were used with an improved reaction
reversibility prediction method to identify 653 (45%)
irreversible reactions in the model. The model was validated
against an experimental dataset consisting of 1,500 distinct
conditions and was optimized by using an improved model
optimization method to increase model accuracy from 89.7% to
93.1%. CONCLUSIONS: Basing the iBsu1103 model on the
annotations generated by the SEED significantly improved the
model completeness and accuracy compared with the most recent
previously published model. The enhanced accuracy of the
iBsu1103 model also demonstrates the efficacy of the improved
reaction directionality prediction method in accurately
identifying irreversible reactions in the B. subtilis
metabolism. The proposed improved model optimization
methodology was also demonstrated to be effective in minimally
adjusting model content to improve model accuracy.
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Project description:The gene expression of Bacillus subtilis 168 showed 3 major patterns including early expression, transition expression and late expression We monitored Bacillus subtilis gene expression by using microarray at differernt time points Bacillus subtilis 168 was choosed as model for gram-positive to study gene expression at different stages
Project description:Investigation of whole genome gene expression level changes in sporulating Bacillus subtilis 168 delta-prpE mutant, compared to the wild-type strain. The mutation engineered into this strain results in impaired germination of spores. A six chip study using total RNA extracted from three separate wild-type cultures of sporulating Bacillus subtilis 168 and three separate cultures of sporulating mutant strain, Bacillus subtilis 168 delta-prpE, in which prpE (yjbP BSU11630) gene coding for a protein phosphatase is deleted entirely. Each chip consists of four fields able to measure the expression level of 4,104 genes from Bacillus subtilis subsp. subtilis strain 168 NC_000964 with eight 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.
Project description:This SuperSeries is composed of the following subset Series: GSE11873: Bacillus subtilis 168 cells: wild-type vs. ccpN (non polar) GSE11876: Bacillus subtilis 168 cells: wild-type vs. (ccpN-yqfL) double mutant Refer to individual Series
Project description:Transcriptional response of Bacillus subtilis to moenomycin in wild-type 168. Bacillus subtilis 168, WT (-MOE) vs. WT (+MOE). The experiment was conducted in triplicate using three independent total RNA preparations. Untreated samples were labeled with Alexa Fluor 555 and moenomycin treated samples were labeled with Alexa Fluor 647.
Project description:This SuperSeries is composed of the following subset Series: GSE30001: Bacillus subtilis 168 moenomycin stimulon GSE30002: Bacillus subtilis CU1065 ramoplanin stimulon Refer to individual Series
Project description:The transcriptome profiles of a riboflavin-producing recombinant Bacillus subtilis RH33 and wild type Bacillus subtilis 168 were compared using DNA microarrays to identify the target genes for further enhancing riboflavin production. Overall design: Transcriptome profiles of a riboflavin-producing B. subtilis RH33 were compared with those of the wild-type B. subtilis 168 as a control strain during exponentially growing period on LBG medium. These conditions corresponded to the state of high riboflavin production, which was growth related. For each comparison, two independent cultivations on LB medium with 1% glucose were performed, and exponentially growing cells (OD600 3–6) were harvested. The synthesis of cDNA and biotin-labeled cRNA were carried out exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual (2000).
Project description:Transcriptome comparison of Bacillus subtilis 168 grown on solid agar (sample 1-3) or aerated liquid (sample 4-7) 2xSG medium with and without of 0.1 mM manganese. Overall design: B subtilis 168 wild type cells were grown on the top of 2xSG solid medium with 1.5% agar concentration (samples 1-3) with and without manganese in the medium. B subtilis 168 wild type cells were grown in aerated (225rpm) 2xSG liquid medium (samples 4-7) with and without manganese in the medium. In the first experiments 3 biological replicates, while in the second one, 4 biological replicates were used. Dye swaps are included in both experiments.
Project description:The transcriptome profiles of a riboflavin-producing recombinant Bacillus subtilis RH33 and wild type Bacillus subtilis 168 were compared using DNA microarrays to identify the target genes for further enhancing riboflavin production. Transcriptome profiles of a riboflavin-producing B. subtilis RH33 were compared with those of the wild-type B. subtilis 168 as a control strain during exponentially growing period on LBG medium. These conditions corresponded to the state of high riboflavin production, which was growth related. For each comparison, two independent cultivations on LB medium with 1% glucose were performed, and exponentially growing cells (OD600 3–6) were harvested. The synthesis of cDNA and biotin-labeled cRNA were carried out exactly as described in the Affymetrix GeneChip Expression Analysis Technical Manual (2000).
Project description:Gene expression can be highly heterogeneous in clonal cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states, and consequently a population will be composed of cells that are ‘ON’ and cells that are ‘OFF’. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by autostimulatory feedback regulation to obtain the bimodal response. A classical model of bistable differentiation is the development of genetic competence in Bacillus subtilis. Noise in expression of the transcription factor ComK ultimately determines the fraction of cells that enter the competent state. Due to its intrinsic random nature, noise is difficult to investigate. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators, to screen for possible factors that affect noise in the bimodal regulation of ComK. This led to the discovery of Kre, a novel factor that controls the bimodal expression of ComK. Kre appears to affect the stability of comK mRNA. Interestingly, ComK itself represses the expression of kre, adding a new double negative feedback loop to the intricate ComK regulation circuit. Our data emphasize that mRNA stability is an important factor in bimodal regulation. Overall design: Comparing wild type Bacillus subtilis strain 168 (n=2) with Bacillus subtilis PG479 (Δkre, n = 3).
Project description:In this study, we have tried to comprehensively understand the differential expression of genes in B. subtilis when the cells are grown in media with combination of 'C' and 'N' sources compared to a control (in the presence of glucose). Overall design: Organism: Bacillus subtilis str 168, Agilent B.subtilis Gene Expression 8x15k Array AMADID: 020941 designed by Genotypic Technology Private Limited.