Vigneshwari Sivakumar ’29
Antibiotic resistance poses one of the most urgent challenges in modern medicine. However, recent work indicates that lasso peptides may hold promise for inhibiting multidrug-resistant bacterial pathogens. Maksimov et al. define lasso peptides as “a class of ribosomally synthesized posttranslationally modified natural products found in bacteria” (2012). The ‘lasso’ refers to their knot-like structure, which gives these peptides remarkable stability–even under immense heat or protease exposure (Shihoya et al., 2025). Many bacteria, including E. coli, secrete lasso peptides in response to environmental stress and competition (Braffman et al., 2019). For example, bacteria in nutrient-limited environments may secrete lasso peptides to inhibit competing strains and gain a survival advantage through increased resource access. Given lasso peptides’ potential to naturally inhibit competing bacterial strains, they are now being explored as therapeutic agents for targeting highly antibiotic-resistant bacteria.
In their 2019 study, Braffman et al. investigated the lasso peptides microcin J25 and capistruin, focusing on their inhibition of RNA polymerase. This essential enzyme transcribes DNA into RNA, enabling bacteria to produce the proteins necessary for survival (Hsieh & Borger, Biochemistry). Mechanistically, microcin J25 and capistruin prevent the folding of the RNA polymerase trigger loop (TL). When this critical structure cannot form, the enzyme cannot properly catalyze transcriptional elongation, effectively halting RNA synthesis (Braffman et al., 2019). Because these peptides disrupt such a fundamental cellular process, they may suppress bacterial growth, including strains highly resistant to antibiotic treatment.
Despite lasso peptides’ promising potential, translating them into practical therapeutics remains a challenge. A major limitation of lasso peptides’ therapeutic efficacy is their limited ability to penetrate bacterial cells. This challenge is magnified in gram-negative bacteria, whose complex outer membrane exhibits highly selective permeability, preventing many antibiotics and foreign molecules from entering the cell (May & Grabowicz, 2018). To explore this issue, a study was conducted by Carson et al., where they saw how a particular peptide, cloacaenodin, could or could not pass through E. coli’s protective membrane. For some context, E. coli is a common gram-negative bacteria that cause sickness related to the gut, like diarrhea and vomiting (Cleveland Clinic, 2023). The study had manipulated E. coli’s outer membrane by causing a mutation in the lptD gene, which made the membrane more permeable. The results showed that the regular E. coli strain was not inhibited, while the mutated strain (with a weaker membrane) was more susceptible to the peptide and experienced more inhibition, thus proving that the membrane is the main reason for the bacteria to resist the peptide (Carson et al., 2024).
Next, the study tried to use engineering to find ways to allow the peptide to enter the bacterial cell. The researchers found that the peptide is allowed to inhibit E. coli when it is entered with the help of some sort of TonB-Dependent Transporter (Carson et al., 2024). A TonB-Dependent Transporter is a transporter found on the membrane of a cell that can bind to a ferric chelate, which is a compound containing iron, and helps transport it into the cell (Noinaj et al., 2010). However, the study had found that the lasso peptide cloacaenodin did not contain any iron. So, the focus was shifted to explore the particular gene coding for the TonB-Dependent Transporter, and it was found that the PPJIDHOO_03000 gene was responsible. The researchers had then tested cloacaenodin against six strains that had the PPJIDHOO_03000 gene, and found that four of the six had been inhibited (Carson et al., 2024). While there were more technical reasons as to why the other two strains showed low inhibition, the main takeaway was that the three main components for a successful bacterial inhibition was first the presence of the cloacaenodin lasso peptide, which can only function and potentially kill the bacterial cell by damaging the RNA polymerase if it is transported by a TonB-Dependent Transporter, which can only be present if it is coded by the PPJIDHOO_03000 gene.
When looking at the potential of cloacaenodin from a broad perspective, we can say that it could be quite dangerous if not administered properly. This is because it can shut down the RNA Polymerase regardless of the bacteria, and so, it can potentially inhibit “good” bacteria (e.g., probiotics in our guts). For this reason, there are many ongoing studies on how the lasso peptide itself could be manipulated and engineered such that it will only target the bacteria it needs to. Furthermore, bacterial resistance will always be an enduring issue. Any small mutation in the bacteria’s DNA can lead to the production of a protein that may disable cloacaenodin or any other lasso peptide. However, this is still a new field, and there are current studies exploring how this possible issue could be prevented, and even understanding the peptides themselves. As of now, we do have a promising antibiotic option that can target any infectious bacteria, as long as the lasso peptide can reach its proper destination.
Vigneshwari Sivakumar is a staff writer at The Princeton Medical Review. She can be reached at vs7850@princeton.edu.
References
Braffman, N. R., Piscotta, F. J., Hauver, J., Campbell, E. A., Link, A. J., & Darst, S. A. (2019). Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proceedings of the National Academy of Sciences, 116(4), 1273-1278.
Cleveland Clinic. (2023, November 22). E. coli infection. Cleveland Clinic. https://my.clevelandclinic.org/health/diseases/16638-e-coli-infection
Hsieh, M.-L., & Borger, J. (2023, July 17). Biochemistry, RNA Polymerase. In StatPearls [Internet]. StatPearls Publishing.
Maksimov, M. O., Pelczer, I., & Link, A. J. (2012). Precursor-centric genome-mining approach for lasso peptide discovery. Proceedings of the National Academy of Sciences, 109(38), 15223-15228.
May, K. L., & Grabowicz, M. (2018). The bacterial outer membrane is an evolving antibiotic barrier. Proceedings of the National Academy of Sciences, 115(36), 8852-8854.
Noinaj N, Guillier M, Barnard TJ, Buchanan SK. TonB-dependent transporters: regulation, structure, and function. Annu Rev Microbiol. 2010;64:43-60. doi: 10.1146/annurev.micro.112408.134247. PMID: 20420522; PMCID: PMC3108441.
Shihoya, W., Akasaka, H., Jordan, P.A. et al. Structure of a lasso peptide bound ETB receptor provides insights into the mechanism of GPCR inverse agonism. Nat Commun 16, 3446 (2025). https://doi.org/10.1038/s41467-025-57960-x
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