HipBA–promoter structures reveal the basis of heritable multidrug tolerance

Abstract

Multidrug tolerance is largely responsible for chronic infections and caused by a small population of dormant cells called persisters. Selection for survival in the presence of antibiotics produced the first genetic link to multidrug tolerance: a mutant in the Escherichia coli hipA locus. HipA encodes a serine-protein kinase, the multidrug tolerance activity of which is neutralized by binding to the transcriptional regulator HipB and hipBA promoter. The physiological role of HipA in multidrug tolerance, however, has been unclear. Here we show that wild-type HipA contributes to persister formation and that high-persister hipA mutants cause multidrug tolerance in urinary tract infections. Perplexingly, high-persister mutations map to the N-subdomain-1 of HipA far from its active site. Structures of higher-order HipA-HipB-promoter complexes reveal HipA forms dimers in these assemblies via N-subdomain-1 interactions that occlude their active sites. High-persistence mutations, therefore, diminish HipA-HipA dimerization, thereby unleashing HipA to effect multidrug tolerance. Thus, our studies reveal the mechanistic basis of heritable, clinically relevant antibiotic tolerance.

Persistent Persister Misperceptions

“…Therefore, the many persister-related experiments using this variant are not studying an active toxin and conclusions from these studies may be related to persistence but they are not necessarily related to TA systems. For example, hipA7 mutations have been found in antibiotic-tolerant E. coli strains that cause urinary tract infections; yet, activity of the HipA toxin variant after the G22S substitution was not shown (Schumacher et al, 2015). One group has even claimed recently that “Thus, slow growth per se does not induce persistence in the absence of TA-encoded toxins”; yet, their methods include the use of both this non-toxic allele ( hipA7 ) and the flawed delta 10 host (Germain et al, 2015), so their results are unreliable.…”

Wake me when it’s over – Bacterial toxin–antitoxin proteins and induced dormancy

“…76 The HipA-HipA interface blocks the kinase active sites (Figure 2(f)), so persister-associated mutations in the N-subdomain-1 are thought to release HipA from the inactive state. 76 …”

“…75 (e) A multi-molecular complex of E. coli HipA toxin homodimers (red and gold) and HipB antitoxin homodimers (blue and cyan) bound to DNA operator sites O1 and O2 (orange) (PDB ID: 4YG7). 76 (f) The ribbon diagram of a HipA toxin structure is colored as a rainbow from blue (N-terminus) to red (C-terminus) and shows two bound Mg 2+ ions (blue spheres) and ATP (orange sticks) (PDB ID: 3DNT). 77 All cartoon diagrams were generated with the program PYMOL.…”

Biofilms 2015: Multidisciplinary Approaches Shed Light into Microbial Life on Surfaces

“…Dr. Lewis then presented his recent work on the clinical significance of persister enrichment in clinical isolates and the mechanistic basis of heritable, clinically relevant antibiotic tolerance (21). He concluded by presenting his recent work on the discovery of the new antibiotic teixobactin, a cell wall synthesis inhibitor with bactericidal activity against multiple pathogens, including S. aureus and Mycobacterium tuberculosis.…”