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Subtle sequence differences between two interacting σ54 -dependent regulators lead to different activation

Daniel Pacheco-Sánchez1, Patricia Marín1, Águeda Molina-Fuentes1

  • 1Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.

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|July 11, 2022
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Summary
This summary is machine-generated.

Two bacterial enhancer-binding proteins, RedR1 and RedR2, control anaerobic 1,3-dihydroxybenzene degradation in Aromatoleum anaerobium. Their distinct regulatory mechanisms and novel assembly modes reveal new insights into gene expression control.

Keywords:
Aromatoleum1,3-dihydroxybenzeneDoxX/D familyanaerobicheterohexamer

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Biochemistry

Background:

  • Aromatoleum anaerobium anaerobically degrades 1,3-dihydroxybenzene (1,3-DHB) using a pathway regulated by two bacterial enhancer-binding proteins (bEBPs), RedR1 and RedR2.
  • These proteins control transcription of σ⁵⁴-dependent promoters, crucial for pathway gene expression.
  • RedR1 and RedR2 share structural similarities but differ in their N-terminal tails, N-terminal domains (NTDs), and C-terminal domains (CTDs), suggesting distinct regulatory functions.

Purpose of the Study:

  • To elucidate the distinct regulatory mechanisms of RedR1 and RedR2 in 1,3-DHB degradation.
  • To investigate the role of protein-protein interactions, specifically between RedR1, RedR2, and BtdS, in pathway regulation.
  • To understand the assembly dynamics of RedR1 and RedR2, including homo- and hetero-oligomerization, and the influence of DNA binding on their activity.

Main Methods:

  • Comparative analysis of RedR1 and RedR2 structures and sequences.
  • Investigating protein-protein interactions using biochemical assays.
  • Studying the effect of effector molecules (1,3-DHB) on regulator activity.
  • Analyzing the role of specific protein domains (NTD, CTD, PAS domain) in regulation and assembly.
  • Assessing promoter activation by different regulator forms and oligomeric states.

Main Results:

  • RedR1 is regulated by classical NTD-mediated negative control released by the effector, while RedR2 is constitutively active and membrane-associated via BtdS.
  • BtdS sequesters RedR2 to the membrane through its NTD, involving specific residues in the PAS domain and N-terminal tail; 1,3-DHB metabolism releases RedR2.
  • Hetero-oligomer formation between RedR1 and RedR2 is favored over homo-oligomers, although truncated RedR1 or full-length RedR2 can activate promoters independently.
  • Promoter DNA acts as an allosteric effector, binding the CTD to modulate ΔNTD-RedR1 multimerization and activity.

Conclusions:

  • A novel mode of bEBP activation and assembly governs the anaerobic 1,3-DHB degradation pathway.
  • The distinct regulatory strategies of RedR1 and RedR2, coupled with their preferential hetero-oligomerization, provide sophisticated control over gene expression.
  • Understanding these mechanisms offers insights into bacterial adaptation and metabolic regulation in anaerobic environments.