Science｜The rapid evolution of mobile genetic elements helps bacteria resist bacteriophages

Written | 617 Responsible Editor | The relationship between Enzyme Beauty bacteriophages and bacteria love and kill each other has promoted the evolution of the two
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In recent years, we have initially revealed a variety of methods for bacteria to resist phages, such as the CRISPR system and several innate immune mechanisms
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However, we still know very little about the innate immune mechanism of bacteria, and it is not clear how bacteria use the innate immune mechanism to gain resistance to bacteriophages, and how they lose this resistance
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Since bacteriophages use certain surface structures (such as membrane receptors) as their target receptors to infect, it has been suggested that receptor mutations may be a major strategy for bacteria to resist bacteriophages, but the receptor mutations may adapt to the bacteria themselves.
The environment has a greater impact, so this hypothesis remains to be explored
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Recently, the Martin F.
Polz team from the Massachusetts Institute of Technology (MIT) and the Frédérique Le Roux team from the French Ocean Development Institute jointly published an article titled Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages in Science.
, Provides some answers to the above questions
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This article uses Vibrio bacteria in the ocean to reveal that this type of bacteria does not use receptor mutations, but uses rapid turnover of genetic mobile elements to obtain phage resistance
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Previously, the author collected 93 consecutive days of seawater in Canoe Bay in Nahant, USA, and obtained more than 1,300 strains of Vibrio, and selected 3 days of Vibrio as a "bait" to isolate and obtain phage
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Exploring the infection relationship between bacteriophages and Vibrio, the authors found that even if there are only a few SNP differences between the core genomes of two bacteria, they still cause different resistances to different phages
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Therefore, the author further selected 23 strains of Brachy Vibrio isolated from a near clonal for follow-up research
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Among them, 22 strains of slow Vibrio can be infected by two different types of long-tailed phages.
The first type of phage (orange) contains 4 strains, and the second type of phage (purple) contains 18 strains
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Under different MOI conditions, infecting Vibrio slow with bacteriophages will cause two phenomena: (1) Vibrio slows lysis and phage proliferation; (2) The host is lysed under high concentration of phage, but the phage cannot proliferate , That is, the phenomenon of lysis from without
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Through a series of infection experiments, the author found that the host range that these phages can adsorb is much larger than the host range that they can kill
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Since the above two types of phage infect through different receptors, and all of the slow Vibrio bacteria have genes encoding related receptors, the author believes that the receptors cannot explain the observed phenomenon, that is, different slow Vibrio bacteria have Different phage resistance, and further explored other potential mechanisms
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Through the comparative analysis of the genomes of the slow Vibrio bacterium, the authors finally identified 28 flexible genomic regions larger than 5kb, of which 26 regions have obvious mobile genetic element (MGE) characteristics and contain at least one gene related to phage defense
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The author defines 26 MGEs as phage defense elements (PDE)
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Statistics found that one strain contains 6-12 PDEs
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Next, the author explored the effect of PDE on phage resistance
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The author found that Vibrio (PDE1, PDE2, PDE3) resistant to phages in the orange group and Vibrio resistant to phages in the purple group (PDE4, PDE5) have different PDEs
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Among them, PDE1, PDE4, and PDE5 contain a type 1 restricted modification (RM) system, and PDE2 and PDE3 contain several possible defense genes
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And the author also found that the insertion of PDE does not destroy the function of the host
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Moreover, these 5 PDEs also exist in the genomes of other Vibrio species, suggesting that these PDEs can undergo horizontal gene transfer
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In order to further explore the contribution of different PDEs to phage resistance, the authors performed single knockout and combined knockout of PDE1, PDE2 and PDE3, and carried out infection experiments under different concentrations of phage
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The results showed that when PDE2 or PDE3 was knocked out alone, the phenotype was similar to that of the wild type; but when PDE2 and PDE3 were knocked out at the same time, the phage resistance of the knockout strain was significantly weaker
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When PDE1 and PDE2 are knocked out at the same time, the phenotype is similar to that of PDE1 alone; but when PDE1 and PDE3 are knocked out at the same time, the resistance is significantly weakened, indicating that PDE3 provides stronger resistance than PDE2
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However, there is no phage reproduction in the above cases, and only when 3 PDEs are knocked out at the same time, the strain becomes sensitive to phage
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The author also explored the genes that are not explicitly annotated in the PDE
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It was discovered that 2 of the 3 PDEs carried unidentified phage defense genes
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Interestingly, the author explored the diversity of receptors at the population level and found that in the same population, the receptors are highly similar, which means that if the phage resistance is mainly determined by the PDE carried, then The flow rate of PDE will be very fast, and the related resistance genes are mobile
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The author’s follow-up analysis of Brachy Vibrio confirmed this: First, there may be a difference of at least 1 PDE between Brachy Vibrio without any SNP difference; the two groups of slow Vibrio which are resistant to the orange or purple group of phages There are at least 5 PDE differences in Vibrio, but only 14 SNP differences; in about 90 days, the author has observed differences in the abundance of different PDEs-PDE3 has always maintained a higher rate of possession, while PDE2 only increased in the last time
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Finally, the author analyzed Listeria, Salmonella, and Clostridium using public databases and found that similar to Vibrio chronicus, the flexible genome regions of these bacteria are highly related to the phage defense regions
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In summary, the study proved that the innate immune mechanism can be rapidly transferred at the population level.
This conclusion has three important implications: (1) Due to the high coexistence diversity of many natural bacterial populations, resistance at the clonal level can be Effectively reduce the concentration of phage and reduce the frequency of phage-host encounters; (2) The movable element with resistance genes makes phage resistance a rapidly changing phenotype, independent of the core genome; (3) In When long-term or repeated use of phage therapy for treatment, the ability of bacteria to quickly acquire phage resistance should be considered
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It is worth mentioning that in the same period, Science magazine also published comments on the research by Sean Meaden and Professor Peter C.
Fineran
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