Is suramin truly a good inhibitor of the bacterial RecA protein? Inhibition and activation, two sides of the same coin

Bacteria live in a hostile habitat and are continuously exposed to a multitude of environmental stress that can compromise the survival of the cells in the absence of an efficient adaptation system. To survive and adapt to these “hard” conditions, bacteria have developed a global response system that modulates the expression of specific genes and, consequently, the cellular metabolism, allowing the microorganisms to respond to the modification of the environment. This inducible system is termed SOS response, which is mainly triggered by lesion to DNA. The SOS response entails the induction of multiple proteins that promote the integrity of DNA and cell survival. SOS response includes more than 50 genes that carry out diverse functions in response to DNA damage. The role of SOS response is not limited to DNA damage reparation; it also promotes processes that allow the bacteria to resist other stressed abuses. In this manner, microorganism develops tolerance towards the stimuli that triggered the response; this is the mechanism by which bacteria acquire resistance to antibiotics. Many antibiotics trigger the SOS response, either directly through DNA damage or indirectly, e.g., damaging protein or cell wall and membrane or producing toxic intermediates. The resistance and low susceptibility to antimicrobics is a consequence of an overexpression of SOS inducing proteins. The SOS response also contributes to spreading the resistance by promoting horizontal dissemination of antibiotic resistance genes. Stress-induced by antibiotics can promote acquisition and expression of resistance genes by mobile DNA elements, promoting resistance development Only two proteins regulate the SOS expression: a transcriptional repressor LexA and a recombinase enzyme RecA. In a physiological state, LexA inhibits specific gene expression by binding specific SOS-boxes sequences, which are included in the SOS gene promoter region. When cells undergo stress pressure, particularly when lesion on DNA occurred, single-strand DNA (ssDNA) is formed. RecA binds to ssDNA to form a nucleoprotein filament. This complex is a flexible structure and represents the active form of RecA; it can perform three separate functions: homologous recombination, SOS induction and SOS mutagenesis. RecA induces the SOS response by promoting the autocatalytic cleavage of LexA and release from the SOS box, thus inducing the expression of the SOS genes. Our laboratory identified several potential inhibitors for RecA and developed a high throughput assay for screening potential inhibitors of the SOS response. Nautiyal et al. identify the suramin as a potent inhibitor for all biochemical activities for RecA. This work has investigated the mechanism of interaction between RecA and suramin, elucidating the binding site and the inhibition mechanism. Surprisingly the suramin has a dual effect on RecA activity: at high concentration inhibits the ATPase activity of RecA, as previously demonstrated, whereas, at low concentration, it leads to an increase in ATPase activity. Moreover, in the presence of suramin, RecA ATPase activity becomes independent from ssDNA. The activity of suramin has been further investigated in the RecA-LexA interaction. As previously observed, the activity of suramin depends on its concentration; in fact, suramin performs as an activator at low concentrations (<1 µM) even in the absence of ssDNA, while acts as an inhibitor at higher concentrations. To better understand how suramin modulates the RecA activity, molecular docking and molecular dynamic simulations were performed. This study can provide further information regarding a new potential binding site for modulating RecA activity.