A nucleotide-sensing endonuclease from the Gabija bacterial defense system

ABSTRACTThe arms race between bacteria and phages has led to the development of exquisite bacterial defense systems including a number of uncharacterized systems distinct from the well-known Restriction-Modification and CRISPR/Cas systems. Here, we report functional analyses of the GajA protein from the newly predicted Gabija system. The GajA protein is revealed as an endonuclease unique in that: 1. It may function as a restriction enzyme or a site-specific nicking enzyme, depending on the arrangement of the recognition sequences; 2. Its activity is strictly regulated by nucleotides concentration. NTP and dNTP at physiological concentrations can fully inhibited the robust DNA cleavage activity of GajA. Interestingly, the nucleotide inhibition is mediated by an ATPase-like domain, which usually hydrolyzes ATP to stimulate the DNA cleavage when associated with other nucleases. These features suggested the mechanism of the Gabija defense in which an endonuclease activity was suppressed at normal condition, while activated by the depletion of NTP and dNTP upon the replication and transcription by invaded phages. This work highlights a concise strategy to utilize a single protein for phage resistance via nucleotide regulatory.

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A nucleotide-sensing endonuclease from the Gabija bacterial defense system

Nucleic Acids Research ◽

10.1093/nar/gkab277 ◽

2021 ◽

Author(s):

Rui Cheng ◽

Fengtao Huang ◽

Hui Wu ◽

Xuelin Lu ◽

Yan Yan ◽

...

Keyword(s):

Dna Cleavage ◽

Nicking Endonuclease ◽

Defense Systems ◽

Cleavage Activity ◽

Dna Cleavage Activity ◽

Dna Nicking ◽

Nucleotide Regulation ◽

Nucleotide Inhibition ◽

Functional Analyses ◽

Restriction Modification

Abstract The arms race between bacteria and phages has led to the development of exquisite bacterial defense systems including a number of uncharacterized systems distinct from the well-known restriction-modification and CRISPR/Cas systems. Here, we report functional analyses of the GajA protein from the newly predicted Gabija system. The GajA protein is revealed as a sequence-specific DNA nicking endonuclease unique in that its activity is strictly regulated by nucleotide concentration. NTP and dNTP at physiological concentrations can fully inhibit the robust DNA cleavage activity of GajA. Interestingly, the nucleotide inhibition is mediated by an ATPase-like domain, which usually hydrolyzes ATP to stimulate the DNA cleavage when associated with other nucleases. These features suggest a mechanism of the Gabija defense in which an endonuclease activity is suppressed under normal conditions, while it is activated by the depletion of NTP and dNTP upon the replication and transcription of invading phages. This work highlights a concise strategy to utilize a DNA nicking endonuclease for phage resistance via nucleotide regulation.

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DNA-cleavage activity of the iron(II) complex with optically active ligands, meta- and para-xylyl-linked N’,N’-dipyridylmethyl-cyclohexane-1,2-diamine

Bioorganic & Medicinal Chemistry Letters ◽

10.1016/j.bmcl.2021.127834 ◽

2021 ◽

Vol 36 ◽

pp. 127834

Author(s):

Koichi Kato ◽

Yoshimi Ichimaru ◽

Yoshinori Okuno ◽

Yoshihiro Yamaguchi ◽

Wanchun Jin ◽

...

Keyword(s):

Dna Cleavage ◽

Optically Active ◽

Cleavage Activity ◽

Dna Cleavage Activity

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A YoeB toxin cleaves both RNA and DNA

Scientific Reports ◽

10.1038/s41598-021-82950-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Julia McGillick ◽

Jessica R. Ames ◽

Tamiko Murphy ◽

Christina R. Bourne

Keyword(s):

Dna Cleavage ◽

Divalent Cations ◽

Nuclease Activity ◽

Dose Dependence ◽

Cleavage Activity ◽

Double Stranded Dna ◽

Dna Cleavage Activity ◽

Evolutionarily Conserved ◽

Toxin Protein ◽

Rna And Dna

AbstractType II toxin-antitoxin systems contain a toxin protein, which mediates diverse interactions within the bacterial cell when it is not bound by its cognate antitoxin protein. These toxins provide a rich source of evolutionarily-conserved tertiary folds that mediate diverse catalytic reactions. These properties make toxins of interest in biotechnology applications, and studies of the catalytic mechanisms continue to provide surprises. In the current work, our studies on a YoeB family toxin from Agrobacterium tumefaciens have revealed a conserved ribosome-independent non-specific nuclease activity. We have quantified the RNA and DNA cleavage activity, revealing they have essentially equivalent dose-dependence while differing in requirements for divalent cations and pH sensitivity. The DNA cleavage activity is as a nickase for any topology of double-stranded DNA, as well as cleaving single-stranded DNA. AtYoeB is able to bind to double-stranded DNA with mid-micromolar affinity. Comparison of the ribosome-dependent and -independent reactions demonstrates an approximate tenfold efficiency imparted by the ribosome. This demonstrates YoeB toxins can act as non-specific nucleases, cleaving both RNA and DNA, in the absence of being bound within the ribosome.

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