Protein Balance Influences Gene Changes in Bacteria Resistant to Antibiotics

Jenn Hoskins
14th March, 2025

Protein Balance Influences Gene Changes in Bacteria Resistant to Antibiotics

Lon protease deficiency in Escherichia coli increases the frequency of large IS-element-flanked genomic duplications encompassing folA during early adaptation to trimethoprim, revealing that proteostasis modulates the mutational landscape of antibiotic resistance evolution.

Image adapted from: Jena et al. / CC BY (Source)

Key Findings

  • *Researchers at IISER Pune found that E. coli bacteria can duplicate specific genes to produce more of a protective enzyme, helping them resist the antibiotic trimethoprim.*
  • *When the Lon gene is disabled, E. coli more frequently duplicates these resistance genes, enhancing their survival during antibiotic treatment.*
  • *Over time, duplicated genes are often replaced by mutations, but some bacteria maintain multiple gene copies alongside mutations to sustain high levels of resistance.*
Antibiotic resistance remains a significant challenge in treating bacterial infections. Understanding the mechanisms behind how bacteria evolve resistance is crucial for developing effective therapies. Recent research from the Indian Institute of Science Education and Research (IISER) Pune sheds light on how gene duplication contributes to antibiotic resistance in Escherichia coli. In their study, the researchers focused on the enzyme dihydrofolate reductase (DHFR), which is targeted by the antibiotic trimethoprim. They previously discovered that mutations in the mgrB gene led to increased production of DHFR, helping the bacteria survive trimethoprim exposure[1]. Building on this, the new study revealed that E. coli can further enhance DHFR levels through the spontaneous duplication of a large genomic segment that includes the folA gene, responsible for encoding DHFR. Although such duplications are rare in wild-type E. coli, their occurrence becomes more frequent in strains where the lon gene is knocked out. The lon gene encodes a protease involved in protein degradation, and its absence alters the mutational landscape, promoting gene duplication events early during antibiotic adaptation. Gene duplication-amplification (GDA) plays a critical role in generating genetic variation that can be acted upon by natural selection[2]. In the context of antibiotic resistance, GDA allows bacteria to temporarily increase the number of copies of resistance genes, thereby boosting the production of protective enzymes like DHFR. This mechanism not only provides immediate resistance but also sets the stage for further genetic changes that can solidify and enhance resistance over time. The study employed long-term evolution experiments to observe how E. coli populations adapt to sustained trimethoprim pressure. The researchers found that while folA duplications frequently occurred to confer resistance, these duplications were often reversed when the antibiotic pressure was removed. However, under continuous antibiotic exposure, the reversal of gene duplications was slower. This persistence was partly due to the acquisition of point mutations in the DHFR enzyme or its promoter region, which helped maintain sufficient levels of the enzyme even as the number of gene copies decreased. Interestingly, some bacterial populations maintained both folA duplications and resistance-conferring point mutations when under high trimethoprim pressure. This dual strategy ensured that even if some DHFR mutants were degraded due to proteolysis, the overall levels of functional DHFR remained high enough to confer resistance. This finding highlights the complex interplay between gene dosage and protein quality control mechanisms in bacterial adaptation[3]. Proteostasis, the regulation of protein synthesis, folding, and degradation, emerged as a crucial factor in the evolution of gene dosage. The study demonstrated that the degradation of mutated DHFR proteins by the Lon protease imposed a selective pressure to maintain multiple copies of the folA gene. This ensures that enough functional enzyme is available despite the loss of some protein variants. Consequently, proteostasis acts as a determinant of copy number evolution, influencing how bacteria balance gene expression demands with protein quality control[4]. The researchers also explored the dynamics of gene duplication and reversal using mathematical models. These models corroborated the experimental findings, showing that gene duplication provides a flexible and reversible means for bacteria to respond to fluctuating antibiotic pressures. This adaptability is particularly important in environments where antibiotic levels may vary, allowing bacteria to swiftly increase or decrease resistance as needed. Previous studies have shown that antibiotic heteroresistance, where a bacterial population contains subpopulations with varying levels of resistance, can lead to treatment failures[3]. The current study builds on this concept by demonstrating that gene duplication-amplification contributes to heteroresistance by creating transiently resistant subpopulations. These subpopulations can survive antibiotic exposure and potentially give rise to fully resistant strains through further genetic mutations. Moreover, the research aligns with findings that gene duplication can accelerate adaptive evolution by increasing the likelihood of beneficial mutations[2]. By providing extra copies of resistance genes, GDAs not only offer immediate protection but also facilitate the accumulation of additional mutations that enhance resistance, making the bacterial population more robust against antibiotics. Overall, this study from IISER Pune provides valuable insights into the genetic strategies bacteria use to develop antibiotic resistance. By elucidating the role of gene duplication and proteostasis in maintaining resistance, the research highlights potential targets for new therapeutic approaches. For instance, disrupting gene duplication mechanisms or enhancing proteolysis of resistance proteins could undermine the bacteria's ability to sustain high levels of resistance, thereby restoring the efficacy of existing antibiotics. In conclusion, the evolution of antibiotic resistance in E. coli involves a delicate balance between gene duplication, mutation, and protein regulation. The findings underscore the importance of considering both genetic and proteomic factors in understanding and combating antibiotic resistance. As antibiotic resistance continues to pose a global health threat, studies like this one are essential for developing strategies to outpace bacterial adaptation and ensure the continued effectiveness of antimicrobial therapies.

GeneticsBiochemEvolution

References

Main Study

1) Proteostasis modulates gene dosage evolution in antibiotic-resistant bacteria

Published 12th March, 2025

https://doi.org/10.7554/eLife.99785

Related Studies

2) Gene amplification and adaptive evolution in bacteria.

https://doi.org/10.1146/annurev-genet-102108-134805

3) Mechanisms and clinical relevance of bacterial heteroresistance.

https://doi.org/10.1038/s41579-019-0218-1

4) Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria.

https://doi.org/10.1371/journal.pgen.1005612


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