Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity

Abstract

Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms: Escherichia coli and Bacillus subtilis. In E. coli, silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the B. subtilis Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in E. coli and B. subtilis, largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of B. subtilis, transcriptional promiscuity must be overcome to silence horizontally acquired DNA in E. coli.

Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits inBacillus subtilis

“…This is consistent with several other studies that tested promoters from Gram-negatives in B. subtilis , including P tac 48 , P lacUV5 49 , the strong synthetic Anderson promoter J23101 31 , and the NarX-NarL two-component system target promoter P dcuS77 33 . This is likely due to differences in the transcription machinery, for example in σ-factor stringency between Gram-negative and Gram-positive species 50 .…”

Pervasive transcription enhances the accessibility of H-NS-silenced promoters and generates bistability in Salmonella virulence gene expression

“…By oligomerizing along the DNA, H-NS silences not only bona fide promoters at the 5' end of genes but also a plethora of spurious intragenic promoters that "infest" A/T-rich horizontally acquired DNA (5)(6)(7). Finding that the inhibition of Rho or NusG causes widespread sense and antisense transcription of H-NS-silenced genes (1, 16) suggests that H-NS-bound DNA is susceptible to transcriptional invasion and that Rho (recruited by NusG) acts to prevent elongation of invading transcription complexes.…”

“…This notion gained momentum with the demonstration that E. coli genes contain a multitude of intragenic promoters in both sense and antisense orientations (3)(4)(5). The phenomenon is particularly dramatic in genomic regions thought to originate from horizontal transfer whose typically higher Adenine and Thymine (AT) content matches the sequence composition of the average bacterial promoter (6). The disproportionally high number of promoter-like sequences in AT-rich DNA can actually be a source of toxicity by causing RNA polymerase titration (7).…”

The LeuO regulator and quiescence: About transcriptional roadblocks, multiple promoters, and crispr‐cas

“…This has led to the difficulty of classifying proteins as transcriptional regulators or NAPs, when possibly such distinction is pointless (Dorman et al, 2020). In this respect, a current view on the role of H‐NS in preventing spurious non‐coding transcription by modulating RNAP binding (Forrest et al, 2022), is based on previous observations of the co‐binding of H‐NS and RNAP (Oshima et al, 2006). This is in congruence with the indirect readout concept; although the direct comparison of an H‐NS nucleation motif and the RNAP promoter‐10 consensus box reveals a potential overlap of DNA sequences that could also have a role (Landick et al, 2015).…”