Evidence for up and down regulation of 450 genes by rpoB12 (rif) mutation and their implications in complexity of transcription modulation in Escherichia coli

Abstract

Analyses of mutations in rpoB subunit of Escherichia coli that lead to resistance to rifampicin have been invaluable in providing insight into events during transcription continue to be discovered. Earlier we reported that rpoB12 suppresses over-expression of cps genes in Δlon mutant of E. coli, by interfering with the transcription of rcsA. Here we report Microarray based Transcriptome profile of Δlon and Δlon rpoB12 strains. The data analyses clearly reveal that rpoB12 mutation results in the differential expression of ∼450 genes. The transcription profiles of some of the genes namely, rcsA, gadE, csgD, bolA, ypdI, dnaJ, clpP, csrA and hdeA are significantly altered, particularly the genes implicated in virulence. Some of the phenotypic traits namely, biofilm formation, motility, curli synthesis and ability to withstand acidic stress in a lonrpoB12 strain were assessed. The results clearly indicate that rpoB12 up-regulates biofilm formation and curli synthesis while it makes the cells sensitive for growth in acidic medium and inhibits motility almost completely. Furthermore, rpoB12 modulates the expression profile of a significant number of genes involved in stress responses, genes encoding small RNAs. Thus, this study reveals the versatile role of the rpoB12 mutation, especially its impact on the regulation of genes related to virulence and highlights its medical importance.

Convergent genetic adaptation of Escherichia coli in minimal media leads to pleiotropic divergence

“…Since rpoB alleles confer changes to cellular physiology and gene expression in a global sense ( Conrad et al, 2010a ), we tested how the three rpoB alleles change the ability of E. coli to swim in liquid media. Alleles of rpoB have previously been shown to lead to a decrease in the gene expression of genes associated with flagellar biosynthesis, and as a result, reduced motility on plates ( Conrad et al, 2010a ; Meenakshi and Munavar, 2018 ).…”

Improving Furfural Tolerance of Escherichia coli by Integrating Adaptive Laboratory Evolution with CRISPR-Enabled Trackable Genome Engineering (CREATE)

“…Furthermore, microarray-based transcriptome profiling of rpoB12 mutants indicated that certain genes coding for sRNAs were also modulated. For example, the expression of sRNA genes (including ryhB , gadY , glmY , isrB , rydC , ryjA, sokB , csrC , and rye ) was up- or downregulated in the presence of rifampicin . It is possible that mutations in rpoB may cause expression changes of sRNA genes.…”

“…For example, the expression of sRNA genes (including ryhB, gadY, glmY, isrB, rydC, ryjA, sokB, csrC, and rye) was up-or downregulated in the presence of rifampicin. 90 It is possible that mutations in rpoB may cause expression changes of sRNA genes. In this study, the transcriptional level of sRNA SgrS was downregulated, while that of ArrS was upregulated.…”

Microarray based transcriptome profile data of ∆lon and ∆lon rpoB12 strains of Escherichia coli

“…Overnight grown cultures of SG20780 (∆ lon cps-lac ) and MMR6 (∆ lon cps-lac rpoB12 ) were sub-cultured in duplicates and the mid-log phase cultures were used for the microarray experiment. Refer [2] for more details.…”

“… Data source location Tamil Nadu, India. Data accessibility Data are available in this article Related research article “Evidence for Up and Down Regulation of 450 genes by rpoB12 (rif) Mutation and their Implications in Complexity of Transcription Modulation in Escherichia coli” [2] . …”