CRISPR-Cas accelerates phage evolution

AbstractAdaptive immune systems face a control challenge: they should react with enough strength to clear an infection while avoiding to harm their organism. CRISPR-Cas systems are adaptive immune systems of prokaryotes that defend against fast evolving viruses. Here, we explore the CRISPR-Cas control challenge and look how its reactivity, i.e. its probability to acquire a new resistance, impacts the epidemiological outcome of a phage outbreak and the prokaryote’s fitness. We show that in the absence of phage evolution, phage extinction is driven by the probability to acquire at least one resistance. However, when phage evolution is fast, phage extinction is driven by an epidemiological critical threshold: any reactivity below this critical threshold leads to phage survival whereas any reactivity above it leads to phage extinction. We also show that in the absence of autoimmunity, high levels of reactivity evolve. However, when CRISPR-Cas systems are prone to autoimmune reactions, intermediate levels of reactivity are evolutionarily optimal. These results help explaining why natural CRISPR-Cas systems do not show high levels of reactivity.

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Genome Sequence and Analysis of a Propionibacterium acnes Bacteriophage

Journal of Bacteriology ◽

10.1128/jb.00106-07 ◽

2007 ◽

Vol 189 (11) ◽

pp. 4161-4167 ◽

Cited By ~ 23

Author(s):

Mark D. Farrar ◽

Karen M. Howson ◽

Richard A. Bojar ◽

David West ◽

James C. Towler ◽

...

Keyword(s):

Host Range ◽

Human Skin ◽

Genome Organization ◽

Propionibacterium Acnes ◽

Opportunistic Infections ◽

Acne Vulgaris ◽

Phage Evolution ◽

Wide Range ◽

High Degree ◽

Degree Of Similarity

ABSTRACT Cutaneous propionibacteria are important commensals of human skin and are implicated in a wide range of opportunistic infections. Propionibacterium acnes is also associated with inflammatory acne vulgaris. Bacteriophage PA6 is the first phage of P. acnes to be sequenced and demonstrates a high degree of similarity to many mycobacteriophages both morphologically and genetically. PA6 possesses an icosahedreal head and long noncontractile tail characteristic of the Siphoviridae. The overall genome organization of PA6 resembled that of the temperate mycobacteriophages, although the genome was much smaller, 29,739 bp (48 predicted genes), compared to, for example, 50,550 bp (86 predicted genes) for the Bxb1 genome. PA6 infected only P. acnes and produced clear plaques with turbid centers, but it lacked any obvious genes for lysogeny. The host range of PA6 was restricted to P. acnes, but the phage was able to infect and lyse all P. acnes isolates tested. Sequencing of the PA6 genome makes an important contribution to the study of phage evolution and propionibacterial genetics.

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The complete nucleotide sequence of phiCTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages

Molecular Microbiology ◽

10.1046/j.1365-2958.1999.01158.x ◽

1999 ◽

Vol 31 (2) ◽

pp. 399-419 ◽

Cited By ~ 109

Author(s):

Keisuke Nakayama ◽

Shigehiko Kanaya ◽

Makoto Ohnishi ◽

Yoshiro Terawaki ◽

Tetsuya Hayashi

Keyword(s):

Pseudomonas Aeruginosa ◽

Gene Transfer ◽

Nucleotide Sequence ◽

Horizontal Gene Transfer ◽

Complete Nucleotide Sequence ◽

Phage Evolution

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T4 phage evolution data in terms of a time-dependent Topal-Fresco mechanism

Biochemical Genetics ◽

10.1007/bf00566059 ◽

1994 ◽

Vol 32 (11-12) ◽

pp. 383-395 ◽

Cited By ~ 9

Author(s):

W. Grant Cooper

Keyword(s):

Time Dependent ◽

Phage Evolution ◽

T4 Phage

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Resolving the structure of phage-bacteria interactions in the context of natural diversity

10.1101/2021.06.27.449121 ◽

2021 ◽

Author(s):

Kathryn M Kauffman ◽

William K Chang ◽

Julia M Brown ◽

Fatima Aysha Hussain ◽

Joy Y Yang ◽

...

Keyword(s):

Microbial Communities ◽

Host Range ◽

Large Scale ◽

Genomic Diversity ◽

Interaction Networks ◽

Bacterial Strains ◽

Quantitative Estimates ◽

Phage Evolution ◽

Marine Vibrio ◽

In The Wild

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in "the wild" remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain quantitative estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that killing in environmental interaction networks is sparse - with phage predator loads low for most bacterial strains and phages host-strain-specific in their killing. Paradoxically, we also find that although overlap in killing is generally rare between phages, recombination is common. Together, these results indicate that the number of hosts that phages infect is often larger than the number that they kill and suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it will be important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on killing host range.

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Genome sequence and characterization of five bacteriophages infecting Streptomyces coelicolor and Streptomyces venezuelae: Alderaan, Coruscant, Dagobah, Endor1 and Endor2

10.1101/2020.09.02.279620 ◽

2020 ◽

Author(s):

Aël Hardy ◽

Vikas Sharma ◽

Larissa Kever ◽

Julia Frunzke

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Streptomyces Coelicolor ◽

Morphological Differentiation ◽

Viral Diversity ◽

Isolation And Characterization ◽

Phage Evolution ◽

Transmission Electron ◽

Family Based

AbstractStreptomyces are well-known antibiotic producers, and are also characterized by a complex morphological differentiation. Streptomyces, like all bacteria, are confronted with the constant threat of phage predation, which in turn shapes bacterial evolution. However, despite significant sequencing efforts recently, relatively few phages infecting Streptomyces have been characterized compared to other genera. Here, we present the isolation and characterization of five novel Streptomyces phages. All five phages belong to the Siphoviridae family, based on their morphology as determined by transmission electron microscopy. Genome sequencing revealed that four of them were temperate phages, while one had a lytic lifestyle. Moreover, one of the newly sequenced phages shows very little homology to already described phages, highlighting the still largely untapped viral diversity. Altogether, this study expands the number of characterized phages of Streptomyces and sheds light on phage evolution and phage-host dynamics in Streptomyces.

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Plasmid Transfer via Transduction from Streptococcus thermophilus to Lactococcus lactis

Journal of Bacteriology ◽

10.1128/jb.01448-07 ◽

2008 ◽

Vol 190 (8) ◽

pp. 3083-3087 ◽

Cited By ~ 20

Author(s):

Andreas Ammann ◽

Horst Neve ◽

Arnold Geis ◽

Knut J. Heller

Keyword(s):

Lactococcus Lactis ◽

Streptococcus Thermophilus ◽

Plasmid Transfer ◽

Direct Transfer ◽

Phage Evolution ◽

Plasmid Transduction

ABSTRACT Using Streptococcus thermophilus phages, plasmid transduction in Lactococcus lactis was demonstrated. The transduction frequencies were 4 orders of magnitude lower in L. lactis than in S. thermophilus. These results are the first evidence that there is phage-mediated direct transfer of DNA from S. thermophilus to L. lactis. The implications of these results for phage evolution are discussed.

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