Our new publication is alive! Viruses don't release genome randomly. Using a NGS method, we show that Flock House virus releases its RNAs in a programmed sequence, overcoming distinct energy barriers. This is guided by RNA-capsid interactions. journals.asm.org/doi/10.1128/...
Ordered release of genomic RNA during icosahedral virus disassembly | Journal of Virology
Viruses need to strike a balance between structural rigidity and flexibility to achieve both sufficient protection and rapid release of packaged genome into host cells. During the process of genome de...
journals.asm.org
![Text reading - Broader principle of multimeric polymerase structures dictating possible recombination mechanisms
- 'Engineering' demands for greater control over transcription
- [[@Viral Genome Principles]]
- [[@Segmentation in viruses may allow for more precise gene regulation]]
- [[Evolution and Emergence of RNA Viruses]] by [[Edward C. Holmes]]
- [[Genome Modularity]]
- Demarcation by or acquisition of TRS allows for viral reassortment or new gene formation in a relatively modularized fashion
- High fidelity of replication needed to be evolutionarily acquired first before expansion of the genome/elaboration of the TRS subgenomic recombination gene regulation system(?)
- How does this work in that bisegmented coronavirus?
- [[@Identification and genomic characterization of a novel bisegmented coronavirus in the lesser panda]]
- Categorizing everything as the copy choice model is imprecise as there can be many distinct routes to this outcome
- [[Viral Recombination Mechanisms]]
- Polymerase processivity, fidelity, and speed all relate to backtracking probability
- [[Polymerase Backtracking]], [[RdRp Backtracking]]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ev7x7v5gslxqemrth5svomcm/bafkreihsso3sfcpyb5mnzwbyb3phl6lzioqcjalkfq3ugbpid6biuo3hpu)
![Text reading - What is the trigger for TRS sequences? Backtracking related?
- Maybe
- No direct demonstration that they are related that I've noted
- Most definitely secondary structure dependent in my mind
- arteriviruses and coronaviruses both employ TRS
- Many different TRS sequences, so not strictly sequence dependent
- Engineerability with non-natural TRS in recombination-deficient viruses
- Doesn't even need to be a linear piece of nucleic acid, can be circular with TRS and still work
- [[@Discontinuous template switching generates coronavirus subgenomic RNAs from the 3ʹ viral genome end by 5ʹ to 3ʹ transcription]]
- [[@An atomistic model of the coronavirus replication-transcription complex as a hexamer assembled around nsp15]]
-
> Finally, the original template would need to unwind from the nascent strand for polymerization to continue on the new template. As with proofreading, we propose the shift in the dsRNA position upon base pairing of the nascent strand to the TRS-L triggers activation of nsp13 and backtracking of the template. This would unwind the original template from the nascent strand, while leaving it base paired with the new template (Fig. 7E). Once unwinding is complete, the dsRNA formed at the TRS-L juncture with the new template could shift back into the polymerase active site and finish synthesis on the remaining nucleotides of the 5′ leader (Fig. 7F)
-
> We should note that binding of the N protein to the nsp13 dimer appears to block access to the nsp13.1 RNA-binding groove, suggesting that nsp13.2 may govern backtracking in this situation. While the template has so far been seen by cryo-EM only engaging with nsp13.1, modeling of the relevant states indicates that nsp13.2 could perform this backtracking function as well. Thus, it may be that nsp13.1 governs backtracking for proofreading during positive-strand synthesis, but nsp13.2 governs backtracking for proofreading and transcription during negative-strand s…](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ev7x7v5gslxqemrth5svomcm/bafkreibe4ne6h3yyqfz6xa75hnmsfe3vpvsrf5wknu2gojcoeqlfgz5zwe)
![Text reading - nucleoside/nucleotide analogs influence backtracking probability because they are incorporated on the growing strand, what about nucleic acid modifications on the template strand?
- I think it's unlikely but recombination probabilities could be correlated with modification maps across coronavirus genomes
- m6a or 5mc not a sequence dependent minimal trigger for programmed backtracking
- can still replicate virus in KO cell lines for writer proteins so presumably does not eliminate sgmRNA production
- Other proteins besides core RTC complex involved?
- Exo and endonucleases
- [[@Commentary on Routh Menachery nsp15 paper]]
- [[@SARS-CoV-2 EndoU-ribonuclease regulates RNA recombination and impacts viral fitness]]
- [[Coronavirus nsp14]]
- [[@The coronavirus proofreading exoribonuclease mediates extensive viral recombination]]
collapsed:: true
-
> significant preference for a UUG motif
-
> MHV-ExoN(-) mutants showed decreased recombination junction frequency and altered populations of sgmRNAs and DVGs
-
> whether nsp14 ExoN alleviates backtracking as proposed
- quote from [[@Template switching by coronavirus polymerase requires helicase activity and is stimulated by remdesivir and molnupiravir]]
- This prediction does not align with what was observed in [[@The coronavirus proofreading exoribonuclease mediates extensive viral recombination]]
collapsed:: true
- If ExoN increases recombination, shouldn't it promote backtracking in certain contexts if that is what mediates all non-homologous recombination (including sgmRNA formation)?
- Sequence specificity and preference for recombination at poly U tracts perhaps due to polymerase slipping and subsequent backtracking
- A bit surprised to see copyback events [[Copy-Back RNAs]] detected given no(?) reports of these being generated based on sequencing data
- [[@Defective viral genome detection review]]
-](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ev7x7v5gslxqemrth5svomcm/bafkreihser2hyfjfpaooupuflqipmmh5kokqnnl72domomu3bc37oj6qea)
