Cryptic Prophage (phage 🧬🪤 in 🦠)

academic.oup.com/nar/article/53… We discovered a new, wide-spread phage defense system based on serine recombinase PinQ in E. coli cryptic prophage Qin that inverts 1,797 bp in another cryptic prophage, e14, to encode two chimeric proteins that block adsorption of T2 phage. @NAR_Open

biorxiv.org/content/10.648… p 8: VBNCs? VBNCs = persisters (doi:10.1111/1462-2920.14075) & phages induce persistence (DOI: 10.1111/1751-7915.14543) & TAs work in conjunction with restriction systems (DOI: 10.1128/spectrum.03388-23) to make persisters during phage infection.

nature.com/articles/s4156…, @alexjmeeske Fits well with our previous report (2022) that E. coli CRISPR-Cas prevents expression of cryptic prophage lysis protein YdfD (Qin) and lysis protein RzoD (DLP-12) thru RNA-RNA interactions (doi 10.3390/ijms232416195).

science.org/doi/10.1126/sc… Usual conceptional plagiarism by Balaban group by failing to cite translation-inhibiting methods (doi 10.1128/AAC.02135-12, 2013), prior hibernation model (doi 10.1016/j.bbrc.2020.01.102), and results related to starvation (doi 10.1111/1462-2920.14075).

@ugobananas_uuu @NobregaFL @ZhiyingZ_960228 @garushyants Is it related to persister cell formation in E. coli upon starvation (doi:10.1111/1462-2920.14075)?

This is the first time we observed bacteria use plasmolysis to defence against phages! biorxiv.org/content/10.648… Thanks all the authors to discover this together! @NobregaFL @ZhiyingZ_960228 @garushyants Dinshaw and Eugene

@Jiaxing_Tan_ Abortive infection as defined by Sorek means death. It does not exist. Term has no meaning now that it is being redefined to include growth inhibition. Abi should not be used then since it has no clear meaning. Yes, celebrate the diversity, but death makes no sense.

@crypticprophage Thanks, I think it depends on how you define abortive infection. It's becoming increasingly clear that the mechanisms of immune systems of bacteria are extremely diverse. I also agree with the point that abortive infection doesn't mean killing itself.

doi.org/10.64898/2026.… More, excellent proof that there is no such thing as abortive infection, this time for CBASS.

Yes, been saying this for years...by analogy with toxin/antitoxin systems and by showing Abi does not occur as published for MqsR/MqsA/MqsC (doi 10.1128/spectrum.03388-23) as well this review: doi.org/10.3390/v15091…

@Jiaxing_Tan_ Yes, been saying this for years...by analogy with toxin/antitoxin systems and by showing Abi does not occur as published for MqsR/MqsA/MqsC (doi 10.1128/spectrum.03388-23) as well this review: doi.org/10.3390/v15091…

@crypticprophage Can you put more information on this claim?

@IngaTrails For Eco2: "The mechanism of Eco2 appears to be akin to that of the HEPN–MNT toxin–antitoxin system, ..." but you fail to cite the 1st ref for the mechanism for this TAs. You also fail to cite the 1stTAs that inhibited phage. For ApeA, you were forced to cite the prior lit.

@crypticprophage what do you mean? Eco2 has nothing to do on AMPylation. We cited your paper on ApeA HEPN study, our study complements your findings in NAR and adds extra info about tRNA cleavage that was relevant to Eco2 paper.

Toprim is different domain than HEPN. MNT can fit in here. tRNA cleavage expriments from our MNT-HEPN study really helped for Eco2. The study: pubmed.ncbi.nlm.nih.gov/33290744/

doi.org/10.1093/ismeco… More evidence that E. coli CRISPR-Cas is both (i) active (not inactive as originally published) and (ii) primarily for prophages as we found in 2022 (doi: 10.3390/ijms232416195).

nature.com/articles/s4159… Retron Eco2, another derivative of TA system HEPN-MntA (doi: 10.1093/nar/gkaa855), works as a trimeric complex that is activated by T2 phage endonuclease DenB, which cleaves msDNA & leads to RNA degradation.

biorxiv.org/content/10.648… Reminiscent of 1st report of one anti-phage defense controlling another: TA cascade in which RNase (type II) toxin MqsR controls type V toxin GhoT (pore former, ATP-depleting) by cleaving antitoxin GhoS mRNA during stress (doi:10.1111/1462-2920.12063).

nature.com/articles/s4159… Exciting anti-persister work using Lactobacilli-derived compounds (indole-related tryptamine + itaconic anhydride + terpinen-4-ol) in a vaginal wash to treat UPEC infections. Excellent persister time-kill graphs (i.e., with plateaus!).

Factual errors: (1) Hobby, not Bigger, discovered persisters in 1942. (2) Hobby and Bigger used 6 experiments to prove dormancy in the 1940s. (3) Crux: authors confuse metabolic state of cells prior to persistence with dormant persisters.

nature.com/articles/s4425… Reviewed? Ab itself induces UPEC persistence (like all lethal stresses) so of course most persisters come from cells that were growing prior to Ab treatment, as shown 2013 (doi:10.1128/AAC.02135-12), so no spontaneous persisters, just elegant regulation.

@DaanFvdBerg Possible, since NucC leads to cDNA degradation, but non-physiological conditions since pBAD used to turn on protospacer production; i.e., to induce CRISPR-CAS, so probably not cell death as claimed.

@crypticprophage Wondering about your opinion on the NucC phage defense effector, whether you think that one counts as true abortive infection (doi.org/10.1016/j.molc…)

nature.com/articles/s4157… Two prominent 'merchants of death' finally recognize pervasiveness of TA systems but grossly undercount them (but up to #2 now!). Beyond drinking the KoolAid: Little evidence Abi or programmed cell death in procaryotes.

journals.asm.org/doi/10.1128/mb… More evidence for the ppGpp ribosome dimerization persister model (PRDP) using Legionella. "...it is likely...hibernation takes place in only a subset of cells, and, ribosome hibernation drives phenotypic heterogeneity and contributes to persistence."