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Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

bioinformatics.stackexchange.com

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Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#101

Post by sublinear »

xg15 wrote: post #99
FormerBandmate wrote: post #15

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…

As 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…

I 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.

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#102

Post by kevviiinn »

subroutine wrote: post #70
x-shadowban wrote: post #67

Earlier quoted context omitted.

Can you add any number of A's, or just 1, or shorten it by 1, and it still is functional?

The 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…

Iirc 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

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#103

Post by kevviiinn »

kolinko wrote: post #96
x-shadowban wrote: post #67

Earlier quoted context omitted.

Can you add any number of A's, or just 1, or shorten it by 1, and it still is functional?

In 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.

With 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

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#104

Post by IshKebab »

jboy55 wrote: post #84

It amazes me that the genome is only 29k long. If you were to write a computer virus now, it probably wouldn't be that short, let alone something that can infect and kill millions of people.

A computer virus that just replicates and causes damage can be a lot smaller than that.

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#105

Post by doctor_eval »

jkingsman wrote: post #48

If this sort of question fascinates you, you might like "Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine"[0], an article written with a tone that I've found to resonate with engineers and like-minded folk. [0] https://berthub.eu/articles/posts/reverse-engineering-source...

Fantastic article!

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#106

Post by sleepydog »

userbinator wrote: post #91
subroutine wrote: post #24

Earlier quoted context omitted.

Adding 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): ht…

Looks almost like a hex editor.

It reminds me of Wireshark

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#107

Post by kevviiinn »

worewood wrote: post #66
userbinator wrote: post #64

Earlier quoted context omitted.

attachment 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 "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 ree…

And this fits nicely because the genome replication really looks like a roll of film being played

Only 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

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#108

Post by kevviiinn »

cornel_io wrote: post #75
kps wrote: post #57

Earlier quoted context omitted.

You can't parse DNA with regex.

They used to say that about email addresses. But hold my beer and I'll be back in like a month with some buggy half-assed crap that kinda does the job and only occasionally crashes the system!

In my experience genetics is a bit more complicated than an email address

Yes, that is an understatement

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