Antibiotics: Teaching old drugs new tricks
Understanding the mechanism by which streptomycin binds to the small subunit of the mitoribosome may help researchers design less toxic derivatives of this antibiotic.
- Cambridge Institute for Medical Research, University of Cambridge, United Kingdom
- The Department of Haematology, University of Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, United Kingdom
Most of the classes of antibiotics used today were discovered between the 1940s and 1960s. Over the decades, the widespread use of antibiotics and lack of new drugs has led to a rise in antibiotic resistant bacteria, making it increasingly challenging to treat common infections.
Streptomycin was the first discovered aminoglycoside antibiotic, originally derived from the bacterium Streptomyces griseus, and became the primary treatment for tuberculosis and other bacterial infections (Schatz et al., 1944). It eliminates bacteria by irreversibly binding to the small subunit of the machine responsible for producing proteins known as the ribosome, leading to an impaired synthesis of proteins and ultimately the death of the bacterial cell. But streptomycin can also bind to an evolutionarily related ribosome in the mitochondria of humans. This can result in hearing problems known as ototoxicity, which can potentially lead to deafness. Therefore, streptomycin is currently only used as an adjunct treatment if necessary (Waters and Tadi, 2022).
Despite these toxic side effects, the widespread emergence of antibiotic resistance calls for desperate measures and streptomycin is once again in demand to target the bacterium that causes tuberculosis, which has also become resistant to a variety of treatments (Cohen et al., 2020). A better knowledge of the molecular mechanism that enables streptomycin to bind to the human mitochondrial ribosome may help researchers find ways to reduce the ototoxic effects caused by the drug.
Now, in eLife, Alexey Amunts and colleagues from the University of Sweden – including Yuzuru Itoh, Vivek Singh, Anas Khawaja as joint first authors – report new insights into the structure and function of the small ribosomal subunit in human mitochondria that binds to streptomycin (Itoh et al., 2022a). Itoh et al. used a method called single particle electron cryo-microscopy (cryo-EM) to analyse the structure of the mitochondrial ribosome in humans, also known as the mitoribosome. This technique generated a much higher resolution structure of streptomycin bound to the bacterial ribosome than previous X-ray crystallography or previous cryo-EM studies.
The experiments revealed that several physiologically important molecules and clusters of iron and sulphur are integrated into the small subunit of the mitoribosome. This suggests that as the mitoribosome is assembled, these clusters may stabilise interactions between proteins in regions where ribosomal RNA has been deleted over the course of evolution.
The study also indicates a potential regulatory link between the three main metabolic pathways in mitochondria: mitoribosome biogenesis, iron-sulfur assembly, and fatty-acid synthesis. Dysfunctional mitochondria are linked to many diseases, including muscular diseases and Friedreich’s ataxia, and the chemical-level detail provided by Itoh et al. lays the foundation for future efforts to better understand the role of mitochondria in human health and disease (Pirinen et al., 2020; Gomes et al., 2013; Marmolino, 2011).
A highlight of the study by Itoh et al. is the elucidation of the detailed interactions between streptomycin and the mitoribosome (Figure 1). The team showed that the aldehyde group found on the streptose sugar moiety of streptomycin is hydrated to a geminal diol (an organic compound with two hydroxyl groups bound to the same carbon) prior to binding to the ribosome. This hydration enables multiple hydrogen bonding interactions between streptomycin and the phosphate backbone of the ribosomal RNA.
Figure 1
Illustration of how the aminoglycoside antibiotic streptomycin causes ototoxicity.
Ototoxicity is a condition where drugs, such as streptomycin, can cause hearing problems and even deafness. It has previously been shown that patients, who are more likely to get ototoxicity, have mutations in the nucleotides located in the mitochondrial ribosome, or mitoribosome. These mutations introduce new RNA base pairings that harden the structure of the small unit of the ribosome (grey). Itoh et al. have shown that streptomycin (red and blue sticks, experimental cryo-EM map is shown as mesh) binds directly to the nucleotides A1555 and C1556 (orange) of the small subunit of the mitoribosome via hydrogen bonds (dashed grey lines), making it even more rigid. This impairs the ribosome’s ability to translate mRNA into proteins (pink ladder mRNA cartoon has been superimposed from the E. coli ribosome structure PDB: 7K00 to show where the mRNA is likely positioned in relation to the streptomycin).
The work by Itoh et al. also provides new insights into how streptomycin can cause ototoxicity (Figure 1). Sequencing the mitochondrial DNA of patients suffering from hearing loss has previously revealed frequent mutations in specific nucleotides, which introduce new RNA base pairings that locally rigidify the structure of the mitoribosome (Gao et al., 2017). The researchers found that streptomycin adds to this rigidification by directly binding to one of these nucleotides, which in turn impairs the ribosome’s ability to translate messenger RNA into protein. These important new structural insights explain how hearing loss may be induced or aggravated by streptomycin and may facilitate the design of less toxic aminoglycoside antibiotic derivatives in the future.
Moreover, previous studies have suggested that antibiotics that induce mitochondrial dysfunction could be modified to treat some cancers (Karp and Lyakhovich, 2022). Cancer stem cells depend on oxidative phosphorylation, which can be blocked with certain antibiotics. For example, the antibiotic drug tigecycline can inhibit the translation of mitochondrial proteins and has been proposed as a therapeutic strategy for acute myeloid leukaemia (Skrtić et al., 2011). The exciting study from Itoh et al. may allow other ‘off-target’ antibiotics to be repurposed as cancer therapeutics by harnessing the three-dimensional structure of the drug bound to its biomolecular target for rational drug design. Unravelling the molecular mechanisms that drive the assembly of the mitoribosome is also a fertile area of research that promises to yield additional new targets for cancer therapy beyond the mature mitoribosome (Itoh et al., 2022b).
References
-
Evidence for expanding the role of streptomycin in the management of drug-resistant Mycobacterium tuberculosisAntimicrobial Agents and Chemotherapy 64:e00860-20.https://doi.org/10.1128/AAC.00860-20
-
Friedreich’s ataxia: past, present and futureBrain Research Reviews 67:311–330.https://doi.org/10.1016/j.brainresrev.2011.04.001
-
Streptomycin, a substance exhibiting antibiotic activity against gram-positive and gram-negative bacteriaExperimental Biology and Medicine 55:66–69.https://doi.org/10.3181/00379727-55-14461
Article and author information
Author details
Publication history
Copyright
© 2022, Faille and Warren
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 914
- views
-
- 92
- downloads
-
- 0
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Antibiotics: Teaching old drugs new tricks
eLife 11:e84702.
https://doi.org/10.7554/eLife.84702
Further reading
-
- Immunology and Inflammation
- Structural Biology and Molecular Biophysics
Antibodies are a major component of adaptive immunity against invading pathogens. Here, we explore possibilities for an analytical approach to characterize the antigen-specific antibody repertoire directly from the secreted proteins in convalescent serum. This approach aims to perform simultaneous antibody sequencing and epitope mapping using a combination of single particle cryo-electron microscopy (cryoEM) and bottom-up proteomics techniques based on mass spectrometry (LC-MS/MS). We evaluate the performance of the deep-learning tool ModelAngelo in determining de novo antibody sequences directly from reconstructed 3D volumes of antibody-antigen complexes. We demonstrate that while map quality is a critical bottleneck, it is possible to sequence antibody variable domains from cryoEM reconstructions with accuracies of up to 80–90%. While the rate of errors exceeds the typical levels of somatic hypermutation, we show that the ModelAngelo-derived sequences can be used to assign the used V-genes. This provides a functional guide to assemble de novo peptides from LC-MS/MS data more accurately and improves the tolerance to a background of polyclonal antibody sequences. Following this proof-of-principle, we discuss the feasibility and future directions of this approach to characterize antigen-specific antibody repertoires.
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
The two identical motor domains (heads) of dimeric kinesin-1 move in a hand-over-hand process along a microtubule, coordinating their ATPase cycles such that each ATP hydrolysis is tightly coupled to a step and enabling the motor to take many steps without dissociating. The neck linker, a structural element that connects the two heads, has been shown to be essential for head–head coordination; however, which kinetic step(s) in the chemomechanical cycle is ‘gated’ by the neck linker remains unresolved. Here, we employed pre-steady-state kinetics and single-molecule assays to investigate how the neck-linker conformation affects kinesin’s motility cycle. We show that the backward-pointing configuration of the neck linker in the front kinesin head confers higher affinity for microtubule, but does not change ATP binding and dissociation rates. In contrast, the forward-pointing configuration of the neck linker in the rear kinesin head decreases the ATP dissociation rate but has little effect on microtubule dissociation. In combination, these conformation-specific effects of the neck linker favor ATP hydrolysis and dissociation of the rear head prior to microtubule detachment of the front head, thereby providing a kinetic explanation for the coordinated walking mechanism of dimeric kinesin.
