Analysis of Pleiotropic Transcriptional Profiles: a Case Study of DNA Gyrase Inhibition

Abstract

Genetic and environmental perturbations often result in complex transcriptional responses involving multiple genes and regulons. In order to understand the nature of a response, one has to account for the contribution of the downstream effects to the formation of a response. Such analysis can be carried out within a statistical framework in which the individual effects are independently collected and then combined within a linear model. Here, we modeled the contribution of DNA replication, supercoiling, and repair to the transcriptional response of inhibition of the Escherichia coli gyrase. By representing the gyrase inhibition as a true pleiotropic phenomenon, we were able to demonstrate that: (1) DNA replication is required for the formation of spatial transcriptional domains; (2) the transcriptional response to the gyrase inhibition is coordinated between at least two modules involved in DNA maintenance, relaxation and damage response; (3) the genes whose transcriptional response to the gyrase inhibition does not depend on the main relaxation activity of the cell can be classified on the basis of a GC excess in their upstream and coding sequences; and (4) relaxation by topoisomerase I dominates the transcriptional response, followed by the effects of replication and RecA. We functionally tested the effect of the interaction between relaxation and repair activities, and found support for the model derived from the microarray data. We conclude that modeling compound transcriptional profiles as a combination of downstream transcriptional effects allows for a more realistic, accurate, and meaningful representation of the transcriptional activity of a genome.

A novel membrane-bound toxin for cell division, CptA (YgfX), inhibits polymerization of cytoskeleton proteins, FtsZ and MreB, in Escherichia coli

“…We speculate that this TA system may be involved in cell growth regulation under stress conditions, as in other TA systems. For instance, the expression of YgfYX is affected by norfloxacin, an inhibitor of DNA gyrase (Jeong et al ., ). It is interesting to further investigate the importance of YgfYX under such conditions.…”

Thymineless death is associated with loss of essential genetic information from the replication origin

“…Pleiotropic perturbations, genetic and environmental, have been successfully tackled by systemic analysis of genomic activity (e.g. Jeong et al. , 2006; Sangurdekar et al.…”

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

“…Here, we applied a new method, moose 2 , which first identifies such a small subset of invariant genes in silico, and further applies different normalization factors based on the expression strength of each individual gene. In an experiment exposing E. coli to high doses of the DNA damaging agent MMC for an extended period of time, global changes in gene expression can be expected [ 13 , 15 ], and were validated here (Additional file 16 ). Importantly, gene expression changes might not be symmetric, since the log 2 ratio distributions (Fig.…”