Hibernating ribosomes as drug targets?

Abstract

When ribosome-targeting antibiotics attack actively growing bacteria, they occupy ribosomal active centers, causing the ribosomes to stall or make errors that either halt cellular growth or cause bacterial death. However, emerging research indicates that bacterial ribosomes spend a considerable amount of time in an inactive state known as ribosome hibernation, in which they dissociate from their substrates and bind to specialized proteins called ribosome hibernation factors. Since 60% of microbial biomass exists in a dormant state at any given time, these hibernation factors are likely the most common partners of ribosomes in bacterial cells. Furthermore, some hibernation factors occupy ribosomal drug-binding sites - leading to the question of how ribosome hibernation influences antibiotic efficacy, and vice versa. In this review, we summarize the current state of knowledge on physical and functional interactions between hibernation factors and ribosome-targeting antibiotics and explore the possibility of using antibiotics to target not only active but also hibernating ribosomes. Because ribosome hibernation empowers bacteria to withstand harsh conditions such as starvation, stress, and host immunity, this line of research holds promise for medicine, agriculture, and biotechnology: by learning to regulate ribosome hibernation, we could enhance our capacity to manage the survival of microorganisms in dormancy.

Keywords: antimicrobial resistance; dormancy; hibernation; ribosome; ribosome-targeting drugs.

Figure 1

Can drugs that target active ribosomes in growing cells also target hibernating ribosomes in dormant cells? The schematic illustrates two phases of ribosome activity: active protein synthesis and ribosome hibernation. In actively growing bacteria, ribosomes participate in protein synthesis, and each step of this process—from the initiation of protein synthesis until ribosome recycling—is a known target of ribosome-targeting antibiotics. However, during episodes of cellular stress or nutrient deprivation, ribosomes enter a hibernation state in which they associate with hibernation factors. Despite ribosome hibernation being a widespread phenomenon that is crucial for the ability of pathogenic organisms to endure hostile environments, we know little about the potential ability of ribosome-targeting drugs to interfere with the ribosome’s entry or exit from hibernation. Source: Adapted from “A molecular network of conserved factors keeps ribosomes dormant in the egg” by Leesch et al. (2023) https://doi.org/10.1038/s41586-022-05623-y, with permission from Springer Nature under license no. 5847220809267.

Figure 2

Ribosome hibernation factors can occupy ribosomal drug-binding sites. (A) Schematic illustration compares the ribosomal binding sites for the hibernation factors RMF and HPF, and for tRNAs (labeled as E, P, and A), mRNA, and ribosome-targeting antibiotics that bind to the decoding center (DC-drugs) and the ribosomal mRNA channel. (B) Close-up view illustrating the overlap between the ribosomal binding sites for hibernation factor HPF and several families of ribosome-targeting antibiotics. (C) Schematic illustration of the location of the binding site of Balon relative to the binding sites of ribosome-targeting antibiotics (labeled as PTC-drugs and DC-drugs to indicate their binding to the peptidyl-transferase center and the decoding center of the ribosome, respectively). (D,E) Close-up views illustrating the overlap between the ribosomal binding sites for hibernation factor Balon and several families of ribosome-targeting antibiotics in the small ribosomal subunit (D) and the large ribosomal subunit (E).

Figure 3

Loss of hibernation factors in dormant bacteria potentiates aminoglycoside-mediated toxicity. (A) When cultures of wild-type (WT) and HPF-deficient Listeria monocytogenes are cultured for 72 h in stationary phase and then treated with various antibiotics, they show similar tolerance to the non-ribosome-targeting drugs carbenicillin (CRB), norfloxacin (NOR), and ciprofloxacin (CIP). UN indicates untreated cultures, and CFU stands for colony-forming units. (B) However, when stationary L. monocytogenes cultures are treated with aminoglycoside antibiotics, the HPF-deficient strain shows up to 3 orders of magnitude reduction in CFU compared to WT. Labels indicate the aminoglycoside antibiotics amikacin (AMI), tobramycin (TOB), kanamycin (KAN), and gentamicin (GEN) [this figure is reproduced from Ref (McKay and Portnoy, 2015) with permission from the American Association for Microbiology, license ID 1474012-1].