Bacterial Retrons Function In Anti-Phage Defense

Millman, Adi; Bernheim, Aude; Stokar-Avihail, Avigail; Fedorenko, Taya; Voichek, Maya; Leavitt, Azita; Oppenheimer-Shaanan, Yaara; Sorek, Rotem

doi:10.1016/j.cell.2020.09.065

Cited by 282 publications

(267 citation statements)

References 64 publications

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“…1B, Table S2). They can be broadly grouped into three categories : (i) known defense systems such as a type-III restriction enzyme, the type-II EcoO109I RM system (39), retrons (7,8,18,37), Gabija (17) or Septu (17); (ii) uncharacterized systems with protein domains that were previously associated with bacterial immunity such as SIR2 (17,41), TIR (17) and HEPN (18,42); (iii) systems encoding proteins with no annotated domain or whose domain is currently not associated with anti-phage defense, such as NACHT and various domains of unknown function (DUFs). Based on these observations, we hypothesized that the P4-encoded locus between psu and int may constitute a reservoir of bacterial immune systems that likely participate in interviral competition.…”

Section: P4-like Satellite Phages Encode a Hotspot For Bacterial Immumentioning

confidence: 99%

Prophage-encoded hotspots of bacterial immune systems

Rousset

Dowding

Bernheim

et al. 2021

Preprint

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The arms race between bacteria and phages led to the emergence of a variety of genetic systems used by bacteria to defend against viral infection, some of which were repurposed as powerful biotechnological tools. While numerous defense systems have been identified in genomic regions termed defense islands, it is believed that many more remain to be discovered. Here, we show that P2- like prophages and their P4-like satellites have genomic hotspots that represent a significant source of novel anti-phage systems. We validate the defense activity of 14 systems spanning various protein domains and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Immunity hotspots are present across prophages of distant bacterial species, highlighting their biological importance in the competition between bacteria and phages.

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Section: P4-like Satellite Phages Encode a Hotspot For Bacterial Immumentioning

confidence: 99%

Prophage-encoded hotspots of bacterial immune systems

Rousset

Dowding

Bernheim

et al. 2021

Preprint

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“…5). Anti phage activity was demonstrated for multiple retrons and mutations that affect the ncRNA secondary structure and branching site or RTase catalytic motif eliminated the defense [146,149]. About 2000 retron systems were found within the defense islands with RTases that could be fused to or accompanied by ATPases, ribosyltransferases, and endonucleases as effector proteins [146,149].…”

Section: Induced Cell Dormancy or Suicide -Abortive Infection (Abi) And Toxin-antitoxin (Ta) Systemsmentioning

confidence: 99%

Microbial Arsenal of Antiviral Defenses. Part II

Musharova

Severinov

2021

Biochemistry Moscow

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Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). The constant threat of phage infection is a major force that shapes evolution of microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering had been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection. In the first part defense associated with cell surface, roles of small molecules, and innate immunity systems relying on DNA modification were discussed. The second part focuses on adaptive immunity systems, abortive infection mechanisms, defenses associated with mobile genetic elements, and novel systems discovered in recent years through metagenomic mining.

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“…In the absence of this native operon, the ncRNA and RT can be expressed from a plasmid lacking the accessory protein. Since the accessory protein is a core component of the phage-defense conferred by retrons [10][11][12] , this reduced system would phage defense capacity, yet continues to produce abundant RT-DNA. We quantified this RT-DNA using a relative qPCR, comparing amplification by primers against the msd region, which can use both the RT-DNA and plasmid as a template, to amplification by primers that only amplify the plasmid (Fig 1c,d).…”

Section: Modifications To the Retron Ncrna That Affect Rt-dna Productionmentioning

confidence: 99%

“…This reverse transcribed DNA (RT-DNA) is produced in cells from a universally delivered cassette in high abundance such that it overcomes inefficiencies and increases rates of genome editing. One retroelement class that has been useful in this regard are bacterial retrons 6,8,9 , which are elements involved in phage defense [10][11][12][13] . Retrons are attractive as a biotechnology due to their compact size, tightly defined sites of RT initiation and termination, lack of known host factor requirements, and lack of transposable elements.…”

Section: Introductionmentioning

confidence: 99%

Improved architectures for flexible DNA production using retrons across kingdoms of life

Sc¹,

Kd²,

Bhattarai-Kline

et al. 2021

Preprint

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Exogenous DNA is a critical molecular tool for biology. This is particularly true for gene editing, where exogenous DNA can be used as a template to introduce precise changes to the sequence of a cell's genome. This DNA is typically synthesized or assembled in vitro and then delivered to target cells. However, delivery can be inefficient, and low abundance of template DNA may be one reason that precise editing typically occurs at a low rate. It has recently been shown that producing DNA inside cells can using reverse transcriptases can increase the efficiency of genome editing. One tool to produce that DNA is a retron, a bacterial retroelement that has an endogenous role in phage defense. However, little effort has been directed at optimizing the retron for production of designed sequences when used as a component of biotechnology. Here, we identify modifications to the retron non-coding RNA that result in more abundant reverse transcribed DNA. We also test architectures of the retron operon that enable efficient reverse transcription across kingdoms of life from bacteria, to yeast, to cultured human cells. We find that gains in DNA production using modified retrons are portable from prokaryotic to eukaryotic cells. Finally, we demonstrate that increased production of RT-DNA results in more efficient genome editing in both prokaryotic and eukaryotic cells. These experiments provide a general framework for production of DNA using a retron for biotechnological applications.

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Bacterial Retrons Function In Anti-Phage Defense

Abstract: Highlightsd Retrons are preferentially located in defense islands d Retrons, together with their effector genes, protect bacteria from phages d Protection from phage is mediated by abortive infection

Cited by 282 publications

References 64 publications

Prophage-encoded hotspots of bacterial immune systems

Prophage-encoded hotspots of bacterial immune systems

Microbial Arsenal of Antiviral Defenses. Part II

Improved architectures for flexible DNA production using retrons across kingdoms of life

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