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The stringent response does not influence ribosome pausing in Bacillus subtilis.

Yaozu Han1,2, Alberto Agnolin1, Frans van der Kloet1

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The stringent response in Bacillus subtilis does not affect ribosome pausing, but impacts enzyme production. Tryptophan codon pausing late in stationary phase suggests nutrient depletion, independent of the stringent response.

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Biochemistry

Background:

  • The stringent response (SR) is a global regulatory mechanism activated by nutrient limitation, typically repressing translation.
  • Bacillus subtilis is industrially significant for enzyme production, primarily during the stationary phase.
  • Translation pausing can negatively impact protein folding and overall production yields.

Purpose of the Study:

  • To investigate the effect of the stringent response on ribosome pausing in Bacillus subtilis.
  • To understand the relationship between the stringent response, translation dynamics, and enzyme production (AmyM).

Main Methods:

  • Genome-wide ribosome profiling was employed in a stringent response mutant strain of B. subtilis.
  • Overexpression of the α-amylase AmyM was used to monitor protein production.
  • Analysis focused on ribosome pausing patterns and overall translation efficiency.

Main Results:

  • Blocking the stringent response increased overall protein synthesis but reduced AmyM production.
  • The stringent response did not significantly alter global ribosome pausing patterns.
  • Increased ribosome pausing at tryptophan codons was observed late in stationary phase, linked to TRAP-controlled gene suppression.
  • Low translation activity in several operons highlighted the role of translation initiation in gene expression regulation.

Conclusions:

  • The stringent response in B. subtilis does not directly cause ribosome pausing, despite affecting protein synthesis and enzyme yield.
  • Tryptophan depletion, indicated by codon-specific pausing, appears to be a stationary phase phenomenon regulated by TRAP, independent of the stringent response.
  • Translation initiation is a critical regulatory point for gene expression in B. subtilis operons.