An RNA Repair Operon Regulated by Damaged tRNAs

Hughes, Kevin J.; Chen, Xinguo; Burroughs, A. Maxwell; Aravind, L.; Wolin, Sandra L.

doi:10.1016/j.celrep.2020.108527

Cited by 44 publications

(83 citation statements)

References 91 publications

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“…Based on these data, we propose the following model for Csx28 activation and activity (Fig. 4 signaling within Type III CRISPR-Cas systems [41], or damaged tRNA halves as specific signaling activators of RNA repair systems [42]; or (b) a direct binding interaction between Csx28 and Cas13:crRNA:target-RNA that can only be formed when Cas13 is in this ternary conformation. This protein-protein interaction between Csx28 and activated Cas13 could be similar to what is observed within Type I CRISPR-Cas systems when the target-bound Cascade complex recruits the effector DNase, Cas3 [43][44][45].…”

Section: Discussionmentioning

confidence: 99%

CRISPR-Csx28 forms a Cas13b-activated membrane pore required for robust CRISPR-Cas adaptive immunity

VanderWal

Park

Polevoda

et al. 2021

Preprint

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Type VI CRISPR-Cas systems use the RNA-guided RNase Cas13 to defend bacteria against viruses, and some of these systems encode putative membrane proteins that have unclear roles in Cas13-mediated defense. Here we show that Csx28, of Type VI-B2 systems, forms membrane pore structures to slow cellular metabolism upon viral infection, and this activity drastically increases anti-viral defense. High- resolution cryo-EM reveals that Csx28 exists unexpectedly as a detergent-encapsulated octameric pore, and we then show these Csx28 pores are membrane localized in vivo. Activation of Csx28 in vivo strictly requires sequence-specific recognition of viral mRNAs by Cas13b, and this activation results in Csx28-mediated membrane depolarization, slowed metabolism, and inhibition of sustained viral infection. Together, our work reveals an unprecedented mechanism by which Csx28 acts as a downstream, Cas13b-activated, effector protein that uses membrane perturbation as an anti-viral defense strategy.

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Section: Discussionmentioning

confidence: 99%

CRISPR-Csx28 forms a Cas13b-activated membrane pore required for robust CRISPR-Cas adaptive immunity

VanderWal

Park

Polevoda

et al. 2021

Preprint

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“…Bacteriophage RNA ligases that rejoin tRNA halves produced by anticodon nucleases, rendering phages resistant to this defense mechanism 24,25 , as well as bacterial tRNA ligases whose expression is activated by tRNA fragments 26 are known. Such RNA ligases could function as anti-CRISPR mechanisms against type VI, in which case the activation of RNase toxins would become the primary defense line.…”

Section: Discussionmentioning

confidence: 99%

tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

Semenova

Jain

Kolesnik

et al. 2021

Preprint

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Type VI CRISPR-Cas systems are the only CRISPR variety that cleaves exclusively RNA1,2. In addition to the CRISPR RNA (crRNA)-guided, sequence-specific binding and cleavage of target RNAs, such as phage transcripts, the type VI effector, Cas13, causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from phage spread3,4. We show here that the principal form of collateral RNA degradation elicited by Cas13a protein from Leptotrichia shahii upon target RNA recognition is the cleavage of anticodons of multiple tRNA species, primarily those with anticodons containing uridines. This tRNA cleavage is necessary and sufficient for bacterial dormancy induction by Cas13a. In addition, Cas13a activates the RNases of bacterial toxin-antitoxin modules, thus indirectly causing mRNA and rRNA cleavage, which could provide a back-up defense mechanism. The identified mode of action of Cas13a resembles that of bacterial anticodon nucleases involved in antiphage defense5, which is compatible with the hypothesis that type VI effectors evolved from an abortive infection module6,7 encompassing an anticodon nuclease.

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“…Noteworthy, in some bacteria including S. Typhimurium, rsr and Y RNA genes are located within an "RNA repair" operon including rtcA-rtcB encoding RNA cyclase and RNA ligase, respectively [193]. The transcription of the whole operon is activated by tRNA fragments resulting from the SOS response to DNA damage [200]. tRNA fragments also accumulate when tRNAs are hypomodified, such as in ∆truA strain missing Ψ at positions 38, 39, and 40 in the anticodon arm of some tRNAs [201].…”

Section: Srna Modificationsmentioning

confidence: 99%

“…tRNA fragments also accumulate when tRNAs are hypomodified, such as in ∆truA strain missing Ψ at positions 38, 39, and 40 in the anticodon arm of some tRNAs [201]. Since tRNA fragments are both natural substrates of PNPase and of RtcB religation, it is possible that assembly of RYPER protects them from degradation and that the expression of RtcB could restore tRNAs from halves and translation [200]. Interestingly, E. coli RtcB re-ligates a 16S rRNA 3 fragment containing the anti-Shine-Dalgarno sequence cleaved by the MazF toxin [202].…”

Section: Srna Modificationsmentioning

confidence: 99%

RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence

Antoine

Bahena-Ceron

Bunwaree

et al. 2021

Genes

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RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.

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An RNA Repair Operon Regulated by Damaged tRNAs

Cited by 44 publications

References 91 publications

CRISPR-Csx28 forms a Cas13b-activated membrane pore required for robust CRISPR-Cas adaptive immunity

CRISPR-Csx28 forms a Cas13b-activated membrane pore required for robust CRISPR-Cas adaptive immunity

tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence

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