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RNA polymerase-binding RNA aptamers (RAPs) regulate antisense transcription (AT) in E. coli. These RAPs terminate AT by coordinating Rho activity, impacting both sense and antisense gene expression.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Microbiology

Background:

  • RNA polymerase-binding RNA aptamers (RAPs) are natural cis-acting RNA elements that interact with RNA polymerase.
  • Many RAPs function as transcriptional repressors, particularly in Escherichia coli, by inducing Rho-dependent termination.
  • Antisense transcription (AT) is a regulatory mechanism involving RNA molecules transcribed from the opposite strand of a gene.

Purpose of the Study:

  • To investigate the role of inhibitory RAPs (iRAPs) in the regulation of antisense transcription (AT).
  • To identify RAPs within antisense RNAs and determine their genomic locations and functions.
  • To elucidate the mechanisms by which RAPs modulate AT and influence gene expression.

Main Methods:

  • In silico analysis of antisense transcriptomes in E. coli strains with altered AT regulators (Rho, H-NS, RNaseIII).
  • Identification and characterization of RAPs within antisense RNAs.
  • In vivo validation using reporter systems and analysis in the natural genomic context.

Main Results:

  • RAPs were identified within antisense RNAs at critical genomic positions, mediating termination of AT.
  • Experimental validation confirmed the significant role of RAPs in regulating AT.
  • RAPs were shown to coordinate Rho activity on the antisense strand, leading to transcript termination.
  • In certain contexts, RAPs alleviated transcriptional interference, thereby stimulating sense gene expression.

Conclusions:

  • RNA polymerase-binding RNA aptamers are key regulators of Rho-mediated antisense transcription in E. coli.
  • RAPs play a crucial role in controlling gene expression by terminating antisense transcripts and influencing sense transcription.
  • The findings reveal a novel layer of gene regulation involving RAPs in the bacterial transcriptome.