Search

The weak organic acid sorbic acid is a commonly used food preservative, as it inhibits the growth of bacteria, yeasts, and molds. We have used genome-wide transcriptional profiling of Bacillus subtilis cells during mild sorbic acid stress to reveal the growth-inhibitory activity of this preservative and to identify potential resistance mechanisms. Our analysis demonstrated that sorbic acid-stressed cells induce responses normally seen upon nutrient limitation. This is indicated by the strong derepression of the CcpA, CodY, and Fur regulon and the induction of tricarboxylic acid cycle genes, SigL- and SigH-mediated genes, and the stringent response. Intriguingly, these conditions did not lead to the activation of sporulation, competence, or the general stress response. The fatty acid biosynthesis (fab) genes and BkdR-regulated genes are upregulated, which may indicate plasma membrane remodeling. This was further supported by the reduced sensitivity toward thefab inhibitor cerulenin upon sorbic acid stress. We are the first to present a comprehensive analysis of the transcriptional response of B. subtilis to sorbic acid stress.

Abstract Background The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cells. The use of prior information, either about the function of the protein encoded by each gene, or about the physical interactions between regulatory factors and the sequences controlling its expression, has emerged as a powerful approach for dissecting complex transcriptional responses. Results We review two different approaches for combining the noisy expression levels of multiple individual genes into robust pathway-level differential expression scores. The first is based on a comparison between the distribution of expression levels of genes within a predefined gene set and those of all other genes in the genome. The second starts from an estimate of the strength of genomewide regulatory network connectivities based on sequence information or direct measurements of protein-DNA interactions, and uses regression analysis to estimate the activity of gene regulatory pathways. The statistical methods used are explained in detail. Conclusion By avoiding the thresholding of individual genes, pathway-level analysis of differential expression based on prior information can be considerably more sensitive to subtle changes in gene expression than gene-level analysis. The methods are technically straightforward and yield results that are easily interpretable, both biologically and statistically.

The gene coding for the secondary transporter called CitM which mediates citrate uptake in Bacillus subtilis was cloned, sequenced and functionally expressed in Escherichia coli. Translation of the base sequence to the primary sequence revealed a transporter that is not homologous to any known secondary transporter. However, CitM shares 60% sequence identity with the gene product of open reading frame N15CR that is on the genome of B. subtilis and which has no known function. Open reading frame N15CR was cloned and expressed in E. coli and discovered to be a citrate transporter too.

Presents a correction to the article "PrlA4 Prevents the Rejection of Signal Sequence Defective Preproteims By Stabilizing the SecA-SecY Interaction During the Initiation of Translocation," by Jeroen P. W. van der Wolk, Peter Fekkes, Andre Boorsma, Janet L. Huie, Thomas J. Silhavy and Arnold J. M. Driessen published in the 1998 issue of "The European Molecular Biology Organization Journal."

The transcriptional responses of yeast cells to a wide variety of stress conditions have been studied extensively. In addition, deletion mutant collections have been widely used to measure the combined effect of gene loss and stress on growth (fitness). Here we present a comparative analysis of 1,095 publicly available transcription and genome-wide fitness profiles in yeast, from different laboratories and experimental platforms. We analyzed these data, using T-profiler, to describe the correlation in behavior of a priori defined functional groups. Two-mode clustering analysis of the fitness T-profiles revealed that functional groups involved in regulating ribosome biogenesis and translation offer general stress resistance. These groups are closely related to growth rate and nutrient availability. General stress sensitivity was found in deletion mutant groups functioning in intracellular vesicular transport, actin cytoskeleton organization, and cell polarity, indicating that they play an key role in maintaining yeast adaptability. Analysis of the phenotypic and transcriptional variability of our a priori defined functional groups showed that the quantitative effect on fitness of both resistant and sensitive groups is highly condition-dependent. Finally, we discuss the implications of our results for combinatorial drug design.