Targets for Combating the Evolution of Acquired Antibiotic Resistance

Abstract

Bacteria possess a remarkable ability to rapidly adapt and evolve in response to antibiotics. Acquired antibiotic resistance can arise by multiple mechanisms but commonly involves altering the target site of the drug, enzymatically inactivating the drug, or preventing the drug from accessing its target. These mechanisms involve new genetic changes in the pathogen leading to heritable resistance. This recognition underscores the importance of understanding how such genetic changes can arise. Here, we review recent advances in our understanding of the processes that contribute to the evolution of antibiotic resistance, with a particular focus on hypermutation mediated by the SOS pathway and horizontal gene transfer. We explore the molecular mechanisms involved in acquired resistance and discuss their viability as potential targets. We propose that additional studies into these adaptive mechanisms not only can provide insights into evolution but also can offer a strategy for potentiating our current antibiotic arsenal.

Figure 1

Cycles of drug discovery and antimicrobial resistance. An illustrative schematic is shown presenting several generations of β-lactam antibiotics chronologically coupled to the β-lactamases that have emerged in clinical pathogens to counteract these “next-generation” antibiotics.

Figure 2

Acquisition and spread of antimicrobial resistance. Stress, including treatment with antibiotics, promotes acquired resistance in an initially sensitive strain by driving (A) mutagenesis or (B) horizontal gene transfer. Strains with preexisting resistance can (C) then spread by transmission between people.

Figure 3

The SOS response is a key regulator of transient hypermutation in bacteria. Activation of the stress sensor, RecA (red ovals), promotes self-cleavage of the SOS regulator, LexA (blue ovals). LexA cleavage results in induction of the SOS effectors, which include error-prone DNA polymerases (green circles) that can bypass DNA lesions leading to mutations during error-prone repair.

Figure 4

Targets of the SOS pathway. (A) Structure of the SOS sensor, RecA, shown as a filament (PDB entry 3CMV), with alternating monomers colored dark or light blue. The ssDNA is shown as red spheres. The panel below is a close-up of the ATP binding pocket (PDB entry 1XMS), a site that could be targeted. (B) Shown is dimeric LexA, bound to SOS box DNA (PDB entry 3JSO), with individual monomers colored green and yellow. The C-terminal protease domain (CTD) is connected to the N-terminal DNA binding domain (NTD) by a structurally unresolved linker (dashed line). In the self-cleavage mechanism, LexA undergoes a large conformational change in its C-terminal domain between inactive (red sticks, PDB entry 1JHC) and active states (purple sticks, PDB entry 1JHE) that positions the cleavage loop within the active site, adjacent to the Ser/Lys dyad. The overlaid active and inactive conformations are shown in the bottom panel. (C) Shown is a representative Y-family polymerase, Dpo4, an error-prone polymerase, bound to DNA (PDB entry 1JX4). Unlike high-fidelity T7 polymerase, shown for comparison (PDB entry 1T7P), Dpo4 possesses a more open, exposed catalytic site, which reduces the selectivity for the incoming nucleotide, colored green.

Figure 5

DNA recombination and transport are targets of horizontal gene transfer. Within the donor cell, site-specific recombination and transposition reactions (black arrows) can mobilize antibiotic resistance genes (blue rectangles) to the DNA transport machinery of a bacteriophage (transduction) or a type IV secretion system (conjugation). Environmental naked DNA can be taken up by natural competency (transformation). Once inside the recipient cell, the antibiotic resistance gene may be maintained within a plasmid or recombine with the recipient genome. DNA recombination could be targeted by inhibiting the DDE/integrase family of transposases: a related retroviral integrase is shown in complex with the small molecule raltegravir (PDB entry 3OYA). DNA transport could be targeted by inhibiting relaxase enzymes: the nicking enzyme of S. aureus is shown in complex with oriT DNA (PDB entry 4HT4).