International Journal of Molecular Sciences (Aug 2020)

Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl <i>cis/trans</i> Isomerases Identifies Three New PPIase Activities in <i>Escherichia coli</i> That Includes the DksA Transcription Factor

  • Pawel Wojtkiewicz,
  • Daria Biernacka,
  • Patrycja Gorzelak,
  • Anna Stupak,
  • Gracjana Klein,
  • Satish Raina

DOI
https://doi.org/10.3390/ijms21165843
Journal volume & issue
Vol. 21, no. 16
p. 5843

Abstract

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Consistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S), transcriptional factors (DksA and SrrA), replication proteins Hda/DiaA, asparatokinase MetL, Cmk and acid resistance regulator (AriR) overcome some defects of Δ6ppi strains. Interestingly, viability of Δ6ppi bacteria requires the presence of transcriptional factors DksA, SrrA, Cmk or Hda. DksA, MetL and Cmk are for the first time shown to exhibit PPIase activity in chymotrypsin-coupled and RNase T1 refolding assays and their overexpression also restores growth of a Δ(dnaK/J/tig) strain, revealing their mechanism of suppression. Mutagenesis of DksA identified that D74, F82 and L84 amino acid residues are critical for its PPIase activity and their replacement abrogated multicopy suppression ability. Mutational studies revealed that DksA-mediated suppression of either Δ6ppi or ΔdnaK/J is abolished if GroL/S and RpoE are limiting, or in the absence of either major porin regulatory sensory kinase EnvZ or RNase H, transporter TatC or LepA GTPase or Pi-signaling regulator PhoU.

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