Antiviral Type III CRISPR signalling via conjugation of ATP and AdoMet

Chi, Haotian; Hoikkala, Ville; Grüschow, Sabine; Graham, Shirley A.; Shirran, Sally L.; White, Malcolm F.

doi:10.1101/2023.06.26.546636

Cited by 2 publications

(1 citation statement)

References 51 publications

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“…However, it is possible that the largest subunits of Type III-A and III-B effectors produce not fully identical sets of oligonucleotides, which results in activation of distinct CARF-domain nucleases. Consistently, a great variety of cOA-activated effectors specifically associated with Type III-B loci was recently discovered [31,40,63,64]. Another plausible explanation for the observed discrepancies between the immunity responses maintained by Type III-A and III-B systems relies on the different kinetics of the reactions catalyzed by the effectors.…”

Section: Discussionmentioning

confidence: 82%

Interference Requirements of Type III CRISPR-Cas Systems fromThermus thermophilus

Karneyeva,

Kolesnik,

Livenskyi

et al. 2023

Preprint

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Among the diverse prokaryotic adaptive immunity mechanisms, the Type III CRISPR-Cas systems are the most complex. The multisubunit Type III effectors recognize RNA targets complementary to CRISPR RNAs (crRNAs). Target recognition causes synthesis of cyclic oligoadenylates that activate downstream auxiliary effectors, which affect cell physiology in complex and poorly understood ways. Here, we studied the ability of III-A and III-B CRISPR-Cas subtypes fromThermus thermophilusto interfere with plasmid transformation. We find that for both systems, requirements for crRNA-target complementarity sufficient for interference depend on the target transcript abundance, with more abundant targets requiring shorter complementarity segments. This result and thermodynamic calculations indicate that Type III effectors bind their targets in a simple bimolecular reaction with more extensive crRNA-target base pairing compensating for lower target abundance. Since the targeted RNA used in our work is non-essential for either the host or the plasmid, the results also establish that a certain number of target-bound effector complexes must be present in the cell to interfere with plasmid establishment. For the more active III-A system, we determine the minimal length of RNA-duplex sufficient for interference and show that the position of this minimal duplex can vary within the effector. Finally, we show that the III-A immunity is dependent on the HD nuclease domain of the Cas10 subunit. Since this domain is absent from the III-B system the result implies that theT. thermophilusIII-B system must elicit a more efficient cyclic oligoadenylate dependent response to provide the immunity.

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Section: Discussionmentioning

confidence: 82%

Interference Requirements of Type III CRISPR-Cas Systems fromThermus thermophilus

Karneyeva,

Kolesnik,

Livenskyi

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems

Nicastro,

Burroughs,

Iyer

et al. 2023

Nucleic Acids Research

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While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency—free nucleotides. Through comparative genomics and sequence-structure analysis, we identified several distinct effector domains, which we named Calcineurin-CE, HD-CE, and PRTase-CE. These domains, along with specific versions of the ParB and MazG domains, are widely present in diverse prokaryotic immune systems and are predicted to degrade nucleotides by targeting phosphate or glycosidic linkages. Our findings unveil multiple potential immune systems associated with at least 17 different functional themes featuring these effectors. Some of these systems sense modified DNA/nucleotides from phages or operate downstream of novel enzymes generating signaling nucleotides. We also uncovered a class of systems utilizing HSP90- and HSP70-related modules as analogs of STAND and GTPase domains that are coupled to these nucleotide-targeting- or proteolysis-induced complex-forming effectors. While widespread in bacteria, only a limited subset of nucleotide-targeting effectors was integrated into eukaryotic immune systems, suggesting barriers to interoperability across subcellular contexts. This work establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.

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Antiviral Type III CRISPR signalling via conjugation of ATP and AdoMet

Cited by 2 publications

References 51 publications

Interference Requirements of Type III CRISPR-Cas Systems fromThermus thermophilus

Interference Requirements of Type III CRISPR-Cas Systems fromThermus thermophilus

Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems

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