Effects of DNA Topology on Transcription from rRNA Promoters in Bacillus subtilis

Abstract

The expression of rRNA is one of the most energetically demanding cellular processes and, as such, it must be stringently controlled. Here, we report that DNA topology, i.e., the level of DNA supercoiling, plays a role in the regulation of Bacillus subtilis σA-dependent rRNA promoters in a growth phase-dependent manner. The more negative DNA supercoiling in exponential phase stimulates transcription from rRNA promoters, and DNA relaxation in stationary phase contributes to cessation of their activity. Novobiocin treatment of B. subtilis cells relaxes DNA and decreases rRNA promoter activity despite an increase in the GTP level, a known positive regulator of B. subtilis rRNA promoters. Comparative analyses of steps during transcription initiation then reveal differences between rRNA promoters and a control promoter, Pveg, whose activity is less affected by changes in supercoiling. Additional data then show that DNA relaxation decreases transcription also from promoters dependent on alternative sigma factors σB, σD, σE, σF, and σH with the exception of σN where the trend is the opposite. To summarize, this study identifies DNA topology as a factor important (i) for the expression of rRNA in B. subtilis in response to nutrient availability in the environment, and (ii) for transcription activities of B. subtilis RNAP holoenzymes containing alternative sigma factors.

Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors

“…Activation of this latter is consistent with its role in ppGpp-DksA regulatory subnetwork [40,86] and might counteract the down-regulation of ribosomal RNA promoters under conditions of DNA relaxation [87,88]. The E. coli rpoH gene encoding the heat shock σ 32 (aka σ H ) factor is sensitive to changes of DNA supercoiling, and DNA relaxation induced by novobiocin treatment of B. subtilis, was shown to decrease transcription from both the ribosomal RNA promoters and the promoters dependent on alternative sigma factors including σ H [89,90]. The RNAP σ 70 subunit encoded by rpoD gene confers preference for highly negatively supercoiled templates [91] and its overexpression can increase the global DNA negative superhelicity [39], suggesting a compensatory activation of rpoD expression counteracting the norfloxacin-induced DNA relaxation especially in LZ41 cells lacking the NAPs and hence, their buffering effects due to constraint of negative supercoils.…”

Bacterial transcription during growth arrest

“…For example, decreased negative supercoiling induces the DNA gyrase promoter but represses the topoisomerase I promoter, thus contributing to topological homeostasis in multiple organisms [ 48 , 50 ]. Promoters that are highly active during rapid growth (such as the ribosomal RNA promoters) are repressed by a decrease in negative supercoiling in both E. coli [ 51 ] and Bacillus subtilis [ 52 ]. Trapping of positive supercoils in front of RNAP can also impact transcription elongation, by favoring pausing and backtracking [ 53 ].…”

Isolation, Characterization of B. subtilis from Song River Shore and their Application to Wastewater Treatment

“…Organic persistent particles are contaminants that are soluble in water and has a marked effect on animals, plants and people thriving on it. [14][15] Organizations such as Environment Protection Committee has formulated the guidelines for industries dealing with carcinogenic and toxic effluents for safe disposal of their effluents. [16][17] Other major issue on the cards is management of sewage water in India.…”