AbpA and AbpB provide anti-phage activity in &lt;i&gt;Escherichia coli&lt;/i&gt;

Yasui, Ryota; Washizaki, Ayaka; Furihata, Yuko; Yonesaki, Tetsuro; Otsuka, Yuichi

doi:10.1266/ggs.89.51

Cited by 12 publications

(13 citation statements)

References 53 publications

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“…Such mutations allowed phages to escape the systems Lamassu, Hachiman, ietAS , Retron-Eco8, ShosTA, Borvo, and some AVAST systems (Figure 3, Figure 6). Previous studies on the anti-phage defense systems AbiK (Bouchard and Moineau, 2004; Wang et al, 2011), AbiQ (Samson et al, 2013b), ApbA/B (Yasui et al, 2014), DarTG (LeRoux et al, 2022), Tin (Mosig et al, 1997), and Nhi (Bari et al, 2022) have also reported phage escape via mutation in one of these core replication proteins. Thus, diverse defense systems have evolved to sense or target the core determinants of phage replication.…”

Section: Resultsmentioning

confidence: 99%

“…Although our understanding of bacterial immunity has substantially expanded by these recent discoveries, for the vast majority of the defense systems it is still unknown how they recognize invading phages, and this remains a major unanswered question in the field. Previous studies on individual defense systems, have addressed this question by examining phage mutants that escape defense (Bari et al, 2022;Depardieu et al, 2016;Huiting et al, 2022;Millman et al, 2020;Samson et al, 2013a;Tal et al, 2021Tal et al, , 2022Yasui et al, 2014). Such phages sometimes evade bacterial immunity by mutations in phage components that activate the bacterial defense system; thus escape mutants can generate valuable insights into the mechanism of defense activation (Samson et al, 2013a).…”

Section: Introductionmentioning

confidence: 99%

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Discovery of phage determinants that confer sensitivity to bacterial immune systems

Stokar-Avihail

Fedorenko

Garb

et al. 2022

Preprint

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Over the past few years, numerous anti-phage defense systems have been discovered in bacteria. While the mechanism of defense for some of these systems is understood, a major unanswered question is how these systems sense phage infection. To systematically address this question, we isolated 192 phage mutants that escape 19 different defense systems. In many cases, these escaper phages were mutated in the gene sensed by the defense system, enabling us to map the phage determinants that confer sensitivity to bacterial immunity. Our data identify specificity determinants of diverse retron systems and reveal phage-encoded triggers for multiple abortive infection systems. We find general themes in phage sensing and demonstrate that mechanistically diverse systems have converged to sense either the core replication machinery of the phage, phage structural components, or host takeover mechanisms. Combining our data with previous findings, we formulate key principles on how bacterial immune systems sense phage invaders.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Discovery of phage determinants that confer sensitivity to bacterial immune systems

Stokar-Avihail

Fedorenko

Garb

et al. 2022

Preprint

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“…1A ). AbpA and AbpB (AbpAB) coexpression suppresses the growth of many lytic phages harboring double-stranded DNA (dsDNA) genomes ( 14 ). AbpA and AbpB physically interact for phage defense.…”

Section: Introductionmentioning

confidence: 99%

“…AbpAB is activated after the middle stage of infection and inhibits DNA replication in T2, T4, and T7 phages. However, the T4 phage can evade the AbpAB defense system through a mutation in gene 41, which encodes a replicative DNA helicase ( 14 , 15 ). However, the function of Gp41 in this system, the AbpAB activation mechanism after phage infection, and how AbpAB inhibits phage propagation remain unclear.…”

Section: Introductionmentioning

confidence: 99%

Phage single-stranded DNA-binding protein or host DNA damage triggers the activation of the AbpAB phage defense system

Sasaki,

Takita,

Fujishiro

et al. 2023

mSphere

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Bacteria have developed various defense mechanisms against phages. Abortive infection (Abi), a bacterial defense mechanism, can be achieved through various means, including toxin-antitoxin systems, cyclic oligonucleotide-based antiphage signaling systems, and retrons. AbpA and AbpB (AbpAB) defend against many lytic phages harboring double-stranded DNA genomes in Escherichia coli ; however, how AbpAB senses phage infection and inhibits its propagation remains unclear. Here, we demonstrated that AbpAB inhibited the growth of the φX174 lytic phage with single-stranded DNA (ssDNA) as well as the lysogenization and induction of the Sakai prophage 5 lysogenic phage. The AbpAB defense system limits T4 and φX174 phage propagation via Abi. AbpA contains a nuclease domain at its N-terminus, and AbpB has an ATP-dependent RNA helicase domain; both domains are required for phage defense. This system is activated by phage Gp32 binding to ssDNA and inhibits E. coli growth. Without phage infection, DNA replication inhibitors or defects in the DNA repair factors RecB and RecC activate this system. Therefore, the E. coli AbpAB defense system may sense DNA-protein complexes, including the phage-encoded ssDNA-binding protein or those formed by interrupting host DNA replication or repair. IMPORTANCE Although numerous phage defense systems have recently been discovered in bacteria, how these systems defend against phage propagation or sense phage infections remains unclear. The Escherichia coli AbpAB defense system targets several lytic and lysogenic phages harboring DNA genomes. A phage-encoded single-stranded DNA-binding protein, Gp32, activates this system similar to other phage defense systems such as Retron-Eco8, Hachiman, ShosTA, Nhi, and Hna. DNA replication inhibitors or defects in DNA repair factors activate the AbpAB system, even without phage infection. This is one of the few examples of activating phage defense systems without phage infection or proteins. The AbpAB defense system may be activated by sensing specific DNA-protein complexes.

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“…The AbpAB antiphage defense system was described before the identification of Hachiman 62 . AbpAB encodes a nuclease (AbpA) and a Ski2-like helicase (AbpB) with combined activity against DNA.…”

Section: Discussionmentioning

confidence: 99%

Hachiman is a genome integrity sensor

Tuck,

Adler,

Armbruster

et al. 2024

Preprint

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Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman comprises a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact dsDNA. When the HamAB complex detects DNA damage, HamB helicase activity liberates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating ‘phantom’ cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and eukaryotic enzymes suggest this bacterial immune system has been repurposed for diverse functions across all domains of life.

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AbpA and AbpB provide anti-phage activity in <i>Escherichia coli</i>

Cited by 12 publications

References 53 publications

Discovery of phage determinants that confer sensitivity to bacterial immune systems

Discovery of phage determinants that confer sensitivity to bacterial immune systems

Phage single-stranded DNA-binding protein or host DNA damage triggers the activation of the AbpAB phage defense system

Hachiman is a genome integrity sensor

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