6 ms·
The top answer at the link explains it best: Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including
by FormerBandmate 4y ago
The top answer at the link explains it best:
Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses.
For coronaviruses in particular, we know that the poly(A) tail is required for replication, functioning in conjunction with the 3' untranslated region (UTR) as a cis-acting signal for negative strand synthesis and attachment to the ribosome during translation. Mutants lacking the poly(A) tail are severely compromised in replication.
- subroutine 4y agoAdding a poly(A) tail when engineering rna plasmids is so common that it's part of the standard feature library of most plasmid editors. Here I have a screenshot of the ApE editor displaying one plasmid I made for a neurobio experiment involving the overexpression of two chimeric proteins (actin and profilin, respectively linked to green and red fluorophores; note the editor has autotagged the polyA tail feature): https://ibb.co/XSCSKC9 https://ibb.co/XSCSKC9
- x-shadowban 4y agoCan you add any number of A's, or just 1, or shorten it by 1, and it still is functional?
- subroutine 4y agoThe number of adenine repeats that confer functional properties is quite variable but it definitely needs to be more than "just 1". I've seen anywhere from 25-250 used in designed plasmids. The exact number people use in their engineered sequence is based on a number of factors, not all of them scientific in nature (e.g. companies charge per basepair synthesize a bespoke polypeptide; e.g. you copied the sequence from a previous clone into ApE and that sequence used 30 repeats and worked fine).
- deleted 4y ago[deleted]
- kevviiinn 4y agoIirc there's a protein that adds 12-15 slowly then another protein comes in and adds another 200+ when it detects the start of the tail. Not sure about the details about how or why it stops tho. At least when considering mRNA getting prepped for nuclear export
- subroutine 4y agoYou are probably right, I'm not an expert on this process. But there's likely a difference between the innate eukaryotic cell polyadenylation process vs. how coronavirus accomplishes polyadenylation because coronavirus rna never enters the nucleus.
- kolinko 4y agoIn this case it probably works most reliably with around this number of As, and less/more would decrease reliability, butnitmwould still be functional. Most of genetics is like that.
- kevviiinn 4y agoWith more As you risk running into the upper limit on sequence length for the virus shell and with less you run the risk of quicker degradation and not enough expression
- subroutine 4y agoThe first point being only a concern if you are a virus. If instead you are engineering say, an rna vaccine, you could package your transcript into lipofectamine instead of a coronavirus envelope ;) but point taken, there's always an upper limit.
- kevviiinn 4y agoAlso a concern when engineering viruses for research or other treatments such as the AAVs
- subroutine 4y agoTrue. I should have said "if you are using a virus"
- koeng 4y agoApE is one of those tools that is so old-school but just works. I used to hate using it but it's really grown on me - Snapgene is just too darn expensive and benchling isn't very power user friendly
- userbinator 4y agoLooks almost like a hex editor.
- sleepydog 4y agoIt reminds me of Wireshark
- samus 4y agoIt kind of is. We are not quite advanced enough to have the equivalent of true programming languages for genetics.
- digitaltrees 4y agoBut we will. GitHub for genetics would be awesome
- ramesh31 4y agoThe biological equivalent of an endline
- qclibre22 4y agoThe stop codon is more like the '\n' or '\0' in computing. Polya tails protect against degradation and is used for nuclear export of RNA.
- subroutine 4y agoThis is true, but perhaps worth noting the nuclear transport function of polyA tails don't come into play for coronavirus. The payload of coronavirus is a positive-sense single-stranded RNA. Which means it does not need to enter the nucleus for preprocessing and can basically just start replicating shortly after entering a cell. See diagram... https://upload.wikimedia.org/wikipedia/commons/f/f4/Coronavirus_replication.png https://upload.wikimedia.org/wikipedia/commons/f/f4/Coronavi... There might be a software analog to another polyA tail feature: the provision of a 'shelf-life'. Each replication cycle removes a few adenosines, and at a certain point the tail sequence is too short to recruit protection and the RNA is ushered into the degradation pathway.
- NobleLie 4y agoI don't think the genome has a specific length of the tail (33 is a consensus length) During genomic assays, the poly a tail will not be a specific length, but a single consensus sequence is still provided. This was also posted in the first comment: > Similar to eukaryotic mRNA, the positive-strand coronavirus genome of ~30 kilobases is 5’-capped and 3’-polyadenylated. It has been demonstrated that the length of the coronaviral poly(A) tail is not static but regulated during infection; however, little is known regarding the factors involved in coronaviral polyadenylation and its regulation. Here, we show that during infection, the level of coronavirus poly(A) tail lengthening depends on the initial length upon infection and that the minimum length to initiate lengthening may lie between 5 and 9 nucleotides. By mutagenesis analysis, it was found that (i) the hexamer AGUAAA and poly(A) tail are two important elements responsible for synthesis of the coronavirus poly(A) tail and may function in concert to accomplish polyadenylation and (ii) the function of the hexamer AGUAAA in coronaviral polyadenylation is position dependent. Based on these findings, we propose a process for how the coronaviral poly(A) tail is synthesized and undergoes variation. Our results provide the first genetic evidence to gain insight into coronaviral polyadenylation. Peng Y-H, Lin C-H, Lin C-N, Lo C-Y, Tsai T-L, Wu H-Y (2016) Characterization of the Role of Hexamer AGUAAA and Poly(A) Tail in Coronavirus Polyadenylation. PLoS ONE 11(10): e0165077
- koheripbal 4y agoInterestingly, vaccines also have a long repeating sequence at the end. It provides molecular stability.
- lambdasquirrel 4y agoFound a wikipedia article describing it: https://en.wikipedia.org/wiki/Polyadenylation https://en.wikipedia.org/wiki/Polyadenylation
- amelius 4y agoCan a drug target that sequence specifically?
- lsternlicht 4y agoNo
- eyelidlessness 4y agoIs it that simple? From a lay perspective (and granted I’m a little foggy because I actually have covid right now), I’d expect the answer is yes but with huge unintended consequences.
- tomohelix 4y agoOk yes, theoretically you can make something targeting the polyA tail. But everything else you body make will also get targeted because this is basically a marker of all RNA for translation. Now making a drug that targets only viruses and not your body RNA? Possible but it is so hard not much progress has been made.
- dimisdas 4y agoIs regex a drug feature we are building towards?
- kps 4y agoYou can't parse DNA with regex.
- WirelessGigabit 4y agoNot with that attitude.
- amstan 4y agoIf stackoverflow taught me anything, you will only summon Zalgo by trying.
- userbinator 4y agoattachment to the ribosome during translation There's been a lot of analogies with NOP slides in the comments here and there, but if you look at how the process of reading the genome works, this section is more like the leader/trailer on a tape: https://en.wiktionary.org/wiki/leader#Noun https://en.wiktionary.org/wiki/leader#Noun "A piece of material at the beginning or end of a reel or roll to allow the material to be threaded or fed onto something, as a reel of film onto a projector or a roll of paper onto a rotary printing press." https://en.wiktionary.org/wiki/trailer#Noun https://en.wiktionary.org/wiki/trailer#Noun "A short blank segment of film at the end of a reel, for convenient insertion of the film in a projector."
- worewood 4y agoAnd this fits nicely because the genome replication really looks like a roll of film being played
- kevviiinn 4y agoOnly if the film gets bent and twisted around itself, binding on itself to activate or deactivate sequences and with the read film actively getting spliced to create slightly different versions of the scenes Honestly it's fuckin wild, there's a lot going on rather than just linear read->express
- xg15 4y agoAs a coder, I find it a bit frustrating how often explanations in biology contain fuzzy phrases like "plays a role in" or "is required for" or "works together with" or "modulates the activity of" - without ever expected what role it plays, why it is required or how it works together. So props to them for going a bit more into detail here - and also highlighting that the reason for the fuzzy phrases can often be that we literally don't know the details: The empirical basis may be "if this thing is removed then this other thing won't work", without us necessarily knowing why this is the case.
- kevviiinn 4y agoIt isn't unknown its just complicated. There are numerous proteins involved, such as a protein that detects the poly A tail and if not present will degrade the RNA by cleavage.
- sublinear 4y agoI think you'll find similar bullshittery in the details of every topic that isn't math. Think of it like finding "TODO" comments in old code.
- eropple 4y agoI mean, historically mathematics have had areas full of "HACK:" comments, too--ones retroactively applied to the whole of Newtonian physics, even, but it's still useful enough that we keep it around!
- af3d 4y agoNewtonian physics is not "a hack". It yields very precise results for simple gravitational interactions, at least up to the point where relativistic effects begin to dominate. Even Einstein's equations are not 100% "perfect". All mathematical models have their limitations. (Although some do produce better approximations than others.)
- eropple 4y ago