A Novel Approach to Overcome Antibiotic Resistance by Targeting ERA, an Essential GTPase That Couples Cell Growth with Cell Division

Authors

• V Kumari
• J Tropea
• G Shi
• D Waugh
• D Court
• X Ji

Abstract

To develop new antibacterial interventions, we are taking an innovative approach by targeting a bacterial protein, ERA. As an essential GTPase, ERA plays an important role in ribosome assembly and cell cycle regulation, and is required for viability in bacteria. The protein has two major conformations, an open form (inactive) and a closed form (active). Crystal structures of apo-ERA and ERA:GDP represent the open conformation, and those of ERA:GTP-analog and ERA:GTP-analog:RNA represent the closed conformation. These four structures outlines the functional cycle of ERA as a chaperone for processing and maturation of 16S rRNA, and a checkpoint for ribosome assembly and final activation of the mature 30S ribosomal subunit. Therefore, ERA is unique among all bacterial functions. We believe that inhibiting the ERA function will inhibit cell growth and cell division. We have identified guanosine tetraphosphate ppGpp [guanosine 3′, 5′-bis(diphosphate)] as a competitive inhibitor. It binds to ERA with higher affinity than GDP or GTP; the equilibrium binding constants (KD) for ppGpp, GDP, and GTP are 0.14, 1.0 and 5.5 µM, respectively. Furthermore, our X-ray crystal structure of Escherichia coli ERA:ppGpp and Aquifex aeolicus ERA:ppGpp complex show that ppGpp binds to ERA in the open (inactive) conformation. Additionally, we have screened small molecules in several databases to an allosteric pocket nearby the GDP-binding pocket of the ERA-GDP complex. Our results of inhibition of GTP hydrolysis of ERA by ppGpp and allosteric inhibitors show the potential of these compounds as novel antibacterial agents against drug-resistant microbes.

Scientific Focus Area: Structural Biology

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