Blocking the RecA activity and SOS-response in bacteria with a short α-helical peptide

Abstract

The RecX protein, a very active natural RecA protein inhibitor, can completely disassemble RecA filaments at nanomolar concentrations that are two to three orders of magnitude lower than that of RecA protein. Based on the structure of RecX protein complex with the presynaptic RecA filament, we designed a short first in class α-helical peptide that both inhibits RecA protein activities in vitro and blocks the bacterial SOS-response in vivo. The peptide was designed using SEQOPT, a novel method for global sequence optimization of protein α-helices. SEQOPT produces artificial peptide sequences containing only 20 natural amino acids with the maximum possible conformational stability at a given pH, ionic strength, temperature, peptide solubility. It also accounts for restrictions due to known amino acid residues involved in stabilization of protein complexes under consideration. The results indicate that a few key intermolecular interactions inside the RecA protein presynaptic complex are enough to reproduce the main features of the RecX protein mechanism of action. Since the SOS-response provides a major mechanism of bacterial adaptation to antibiotics, these results open new ways for the development of antibiotic co-therapy that would not cause bacterial resistance.

Inhibition of bacterial stress responses - state of the art

“…Not surprisingly, scientists have developed peptide inhibitors of RecA/LexA, undebatably important targets to inhibit SOS response, which is a principal mechanism of bacterial adaptation to antibiotics. According to the sequence of RecX protein, an active natural RecA inhibitor, 20-amino acid alpha helical peptides were designed showing promising in vitro RecA inhibiting activity and in vivo SOS response blocking activity [89].…”

RecA protein mediates fitness, virulence and DNA damage response (SOS response) in Riemerella anatipestifer

“…As with many other genetic pathways, the SOS response was rst identi ed and then thoroughly studied in Escherichia coli (E. coli) [1]. The SOS response is induced through the activation of the RecA protein [2], RecA is found in all free-living bacteria, and is the most slowly evolving gene involved in DNA metabolism, with an average sequence conservation of 60~70% across the entire bacterial domain of life [3]. E. coli RecA is a 38 KD single subunit protein consisting of 352 amino acid residues, which is the rst protein to be identi ed that involves in recombinant repair of DNA damage [3,4].…”

“…The SOS response is induced through the activation of the RecA protein [2], RecA is found in all free-living bacteria, and is the most slowly evolving gene involved in DNA metabolism, with an average sequence conservation of 60~70% across the entire bacterial domain of life [3]. E. coli RecA is a 38 KD single subunit protein consisting of 352 amino acid residues, which is the rst protein to be identi ed that involves in recombinant repair of DNA damage [3,4]. In uninduced cells, it is present at less than 10,000 monomers per cell [5] and its homologous proteins are widely present in various organisms.…”

Computational elucidation of the binding mechanisms of curcumin analogues as bacterial RecA inhibitors

“…Notably, the bacterial RecA protein plays pivotal roles in several key processes leading to the acquisition of antibiotic resistance, namely, SOS response, horizontal gene transfer, 11 and mutagenesis. 12,13 RecA is a 38 kDa DNA recombinase best known for its regulatory function in bacterial DNA repair. 14 As a DNA-dependent ATPase, it requires ATP to bind ssDNA (single-stranded DNA) in order to form a nucleoprotein lament.…”