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通过功能鉴定 TolC 受体噬菌体 U136B 的实验进化,确定了一种与吸附作用相关的尾丝蛋白,这是通过强烈的平行适应实现的。

Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation.

机构信息

Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.

BEACON Center for the Study of Evolution in Action, East Lansing, Michigan, USA.

出版信息

Appl Environ Microbiol. 2023 Jun 28;89(6):e0007923. doi: 10.1128/aem.00079-23. Epub 2023 May 16.


DOI:10.1128/aem.00079-23
PMID:37191555
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10304864/
Abstract

Bacteriophages have received recent attention for their therapeutic potential to treat antibiotic-resistant bacterial infections. One particular idea in phage therapy is to use phages that not only directly kill their bacterial hosts but also rely on particular bacterial receptors, such as proteins involved in virulence or antibiotic resistance. In such cases, the evolution of phage resistance would correspond to the loss of those receptors, an approach termed evolutionary steering. We previously found that during experimental evolution, phage U136B can exert selection pressure on Escherichia coli to lose or modify its receptor, the antibiotic efflux protein TolC, often resulting in reduced antibiotic resistance. However, for TolC-reliant phages like U136B to be used therapeutically, we also need to study their own evolutionary potential. Understanding phage evolution is critical for the development of improved phage therapies as well as the tracking of phage populations during infection. Here, we characterized phage U136B evolution in 10 replicate experimental populations. We quantified phage dynamics that resulted in five surviving phage populations at the end of the 10-day experiment. We found that phages from all five surviving populations had evolved higher rates of adsorption on either ancestral or coevolved E. coli hosts. Using whole-genome and whole-population sequencing, we established that these higher rates of adsorption were associated with parallel molecular evolution in phage tail protein genes. These findings will be useful in future studies to predict how key phage genotypes and phenotypes influence phage efficacy and survival despite the evolution of host resistance. Antibiotic resistance is a persistent problem in health care and a factor that may help maintain bacterial diversity in natural environments. Bacteriophages ("phages") are viruses that specifically infect bacteria. We previously discovered and characterized a phage called U136B, which infects bacteria through TolC. TolC is an antibiotic resistance protein that helps bacteria pump antibiotics out of the cell. Over short timescales, phage U136B can be used to evolutionarily "steer" bacterial populations to lose or modify the TolC protein, sometimes reducing antibiotic resistance. In this study, we investigate whether U136B itself evolves to better infect bacterial cells. We discovered that the phage can readily evolve specific mutations that increase its infection rate. This work will be useful for understanding how phages can be used to treat bacterial infections.

摘要

噬菌体能治疗对抗生素有抗药性的细菌感染,最近受到关注。噬菌疗法的一个想法是使用不仅直接杀死细菌宿主,还依赖特定细菌受体的噬菌体,例如参与毒力或抗生素抗性的蛋白质。在这种情况下,噬菌体的抗药性进化将对应于这些受体的丧失,这种方法称为进化引导。我们之前发现,在实验进化过程中,噬菌体 U136B 可以对大肠杆菌施加选择压力,使其失去或改变其受体,即抗生素外排蛋白 TolC,这通常会导致抗生素耐药性降低。然而,为了使像 U136B 这样依赖 TolC 的噬菌体能够在治疗中使用,我们还需要研究它们自身的进化潜力。了解噬菌体的进化对于开发改良的噬菌体疗法以及在感染过程中跟踪噬菌体种群都至关重要。在这里,我们对 10 个重复实验种群中的噬菌体 U136B 进化进行了表征。我们量化了导致 10 天实验结束时 5 个存活噬菌体种群的噬菌体动力学。我们发现,所有 5 个存活种群的噬菌体在原始或共同进化的大肠杆菌宿主上的吸附率都有所提高。使用全基因组和全种群测序,我们确定这些更高的吸附率与噬菌体尾部蛋白基因中的平行分子进化有关。这些发现对于未来的研究将是有用的,这些研究可以预测关键噬菌体基因型和表型如何影响噬菌体的功效和存活,尽管宿主的抗药性在进化。抗生素耐药性是医疗保健中的一个持续问题,也是可能有助于维持自然环境中细菌多样性的一个因素。噬菌体(“噬菌体”)是专门感染细菌的病毒。我们之前发现并表征了一种称为 U136B 的噬菌体,它通过 TolC 感染细菌。TolC 是一种抗生素耐药蛋白,有助于细菌将抗生素泵出细胞。在短时间内,噬菌体 U136B 可用于进化地“引导”细菌种群失去或修饰 TolC 蛋白,有时会降低抗生素耐药性。在这项研究中,我们研究了 U136B 本身是否会进化以更好地感染细菌细胞。我们发现噬菌体很容易进化出特定的突变,从而提高其感染率。这项工作对于了解如何利用噬菌体治疗细菌感染将是有用的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/242edd25bd33/aem.00079-23-f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/0ac06795aa36/aem.00079-23-f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/abb5d14ff90a/aem.00079-23-f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/5b252523c519/aem.00079-23-f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/a525a66060a1/aem.00079-23-f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/242edd25bd33/aem.00079-23-f005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/0ac06795aa36/aem.00079-23-f001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/abb5d14ff90a/aem.00079-23-f002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/5b252523c519/aem.00079-23-f003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/a525a66060a1/aem.00079-23-f004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5704/10304864/242edd25bd33/aem.00079-23-f005.jpg

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[1]
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引用本文的文献

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Phage Therapy for Urinary Tract Infections: Progress and Challenges Ahead.

Int Urogynecol J. 2025-5-13

[2]
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Emerg Microbes Infect. 2025-12

[3]
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Proc Natl Acad Sci U S A. 2024-12-24

[4]
The rise, fall, and resurgence of phage therapy for urinary tract infection.

EcoSal Plus. 2024-12-12

[5]
The TolC and Lipopolysaccharide-Specific Bacteriophage TLS-the Archetype Virus.

Phage (New Rochelle). 2024-9-16

[6]
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Front Cell Infect Microbiol. 2024-8-26

[7]
Structural and functional diversity of Resistance-Nodulation-Division (RND) efflux pump transporters with implications for antimicrobial resistance.

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[8]
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[9]
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本文引用的文献

[1]
Host Range Expansion of Phage Sf6 Evolves through Point Mutations in the Tailspike.

J Virol. 2022-8-24

[2]
Host-parasite coevolution promotes innovation through deformations in fitness landscapes.

Elife. 2022-7-6

[3]
Phage-antibiotic combination is a superior treatment against Acinetobacter baumannii in a preclinical study.

EBioMedicine. 2022-6

[4]
Essential Topics for the Regulatory Consideration of Phages as Clinically Valuable Therapeutic Agents: A Perspective from Spain.

Microorganisms. 2022-3-26

[5]
Selection for Phage Resistance Reduces Virulence of Shigella flexneri.

Appl Environ Microbiol. 2022-1-25

[6]
Phage Therapy for Antibiotic-Resistant Bacterial Infections.

Annu Rev Med. 2022-1-27

[7]
The Antibiotic Efflux Protein TolC Is a Highly Evolvable Target under Colicin E1 or TLS Phage Selection.

Mol Biol Evol. 2021-9-27

[8]
Coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance.

Proc Natl Acad Sci U S A. 2021-6-8

[9]
Sustained coevolution of phage Lambda and involves inner- as well as outer-membrane defences and counter-defences.

Microbiology (Reading). 2021-5

[10]
Complete Genome Sequence of Escherichia coli Bacteriophage U136B.

Microbiol Resour Announc. 2021-4-1

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