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  • ELIZABETH NOLAN: Where we left off yesterday

  • was beginning to discuss methods for unnatural amino acid

  • incorporation into proteins using the ribosome.

  • And the methodology that was introduced

  • and where we need to continue today

  • is the Schultz method of using the native ribosome

  • to play some tricks and get unnatural amino acids

  • into proteins.

  • So we'll work through this further to show

  • how the rest of the machinery was generated

  • and then we'll consider some of the limitations

  • and some of that came up in questions last time.

  • And then we'll close with a discussion

  • of one strategy that's a different strategy that

  • uses actually an orthogonal ribosome, which

  • is really, really neat here.

  • So where we left off last time in terms of the Schultz Method

  • was that we needed a unique codon

  • for the unnatural amino acid, right?

  • And a stop codon was reassigned.

  • So TAG or Amber stop.

  • And the other thing that we need that we'll discuss now

  • involves the requirement of an orthogonal tRNA

  • and aminoacyl-tRNA synthetase pair that

  • can be used in this method.

  • So the question is, where does this come from?

  • So where do we get a tRNA and an aaRS

  • that can be used for this unnatural amino acid

  • of interest.

  • And one way to think about this in terms of a search

  • is to think about different tRNAs and aaRS

  • from different organisms.

  • And so what's found if tRNAs are compared

  • between bacteria, eukaryotes, [INAUDIBLE],,

  • there's evolutionary divergence.

  • And so can that evolutionary divergence

  • be taken advantage of?

  • And effectively, is it possible to find

  • some tRNA and its aminoacyl-tRNA synthetase

  • from one organism that's orthogonal to the corresponding

  • tRNA and aminoacyl-tRNA synthetase

  • in the organism of interest.

  • So effectively, if we want to use E. coli,

  • we want to find a pair from another organism that's

  • completely independent of the endogenous E. coli machinery.

  • So what does this mean?

  • A lot of trial and error was done

  • to identify a pair from another organism.

  • And where they ended up finding one is from a methanogen.

  • So methanococcus jannaschii here.

  • OK, and this initial pair was for tyrosine.

  • And so, there's some features of this pair that

  • are noteworthy to bring up.

  • So first if we think about the aminoacyl-tRNA synthetase here.

  • This one has an unusual feature.

  • So when we discuss these aaRS, remember

  • we discussed the mechanism and we also

  • discussed what happens if a wrong amino acid is selected.

  • And we learned that they have editing function

  • and that there's editing domains.

  • What also came up in those discussions

  • is that we need to take every one of these enzymes

  • as a case-by-case basis.

  • And as it turns out, this particular enzyme

  • does not have an editing domain.

  • So then the thing to think about is,

  • why would that be useful from the standpoint of incorporating

  • an unnatural amino acid?

  • So what's the benefit there?

  • So what does this editing domain do?

  • AUDIENCE: It's one less thing to have

  • to fix if you're assuming that the editing domain would

  • recognize and hydrolyze an unnatural amino acid

  • that you put in even if you got the binding site to recognize

  • it, or the first binding site to recognize it.

  • ELIZABETH NOLAN: Exactly right.

  • There's no deacylation happening, so no hydrolosis.

  • So it's just more likely this unnatural amino acid can

  • be a successful substrate and there's

  • less engineering that has to be done in terms

  • of modifying the enzyme here.

  • So, another point in terms of--

  • they found that it does not acylate E. coli tRNA.

  • OK, and that's important for trying to use this in E. coli

  • here.

  • What's the potential problem?

  • So is this going to be specific for the unnatural amino acid

  • of interest?

  • No way, right?

  • Unlikely at least, and depending on what type

  • of a natural amino acid you're thinking about,

  • it may definitely be a no way.

  • So there's some experimental work

  • to do to make this specific for the unnatural amino acid

  • of interest, which means there has to be some mutagenesis

  • and selection, which we're not going

  • to talk about in detail here.

  • So what about the tRNA?

  • So we need to think about the tRNA structure right

  • and how tRNAs interact with aaRS, right?

  • And recall, we had in an earlier lecture one

  • example of a crystal structure of this complex.

  • And we saw there's many positions where they interact.

  • What was known in this system here is that they figured--

  • OK, and also keep in mind, just backing up a minute,

  • this tRNA, as we know, based on this nomenclature

  • has an anticodon for tyrosine.

  • So that's going to have to be mutated

  • to be the anticodon on the Amber stop

  • in order to use in this method.

  • Right?

  • So this is going to have to be mutated

  • to give us tRNA(CUA) where this is indicating

  • the anticodon here.

  • So that mutation, we don't want that mutation

  • to disrupt the interaction between the tRNA

  • and aminoacyl-tRNA synthetase, right?

  • And it turns out there were minimal interactions

  • in that area for the native system.

  • So the thinking was that these mutations

  • could be tolerated here.

  • So with that said, what is the potential problem

  • with this tRNA?

  • So if we want to put this tRNA into E. coli,

  • it can't be recognized by any of the E. coli aaRS.

  • So all of these recognition issues come up.

  • So, here again with another example,

  • where there needed to be some mutagenesis and selection

  • to prevent interactions between this tRNA

  • from the methanogen and the aaRS of E. coli.

  • And effectively what they did is to pick 11 positions

  • on the tRNA, which I'll just chart out.

  • OK, so here's our tRNA.

  • Here's our CUA anticodon here.

  • And effectively these ends are positions where they randomized

  • and did mutagenesis here.

  • So they identified these 11 positions.

  • OK?

  • And these 11 positions do not interact

  • with the aaRS here of the pair.

  • So the idea is to maintain this interaction,

  • but prevent any interaction of this tRNA with E. coli

  • machinery here.

  • So effectively, they used a method

  • called directed evolution to do selection.

  • And what might happen out of that,

  • imagine you have some large pool of mutant tRNA,

  • what might happen?

  • So here OK, so the end result is that the tRNA

  • might be non-functional.

  • Right?

  • So the mutation was not helpful.

  • OK?

  • It might be non-orthogonal, meaning

  • that it's recognized by the endogenous E. coli machinery

  • or it may be orthogonal here.

  • OK, so recognized only OK?

  • And so this is what needs to be selected for here.

  • And so assays need to be done that allows these

  • to be differentiated here.

  • So the end result is an orthogonal pair.

  • But the point is, you can't just take this pair

  • from the other organism.

  • It needs to be further modified.

  • So where does that put us in terms

  • of the cartoon we saw yesterday without some of these details?

  • So here we have the tRNA that has this amber anticodon.

  • So that's our orthogonal tRNA.

  • We have an unnatural amino acid that's

  • able to get into the organism of interest.

  • And we have the orthogonal tRNA synthetase.

  • So these give us this aminoacyl-tRNA

  • with the unnatural amino acid.

  • And then that can be incorporated into the A

  • site of the ribosome.

  • Right so this is a case where we have a plasma DNA.

  • Here's the gene of interest in red.

  • And somewhere in that gene, a stop codon

  • has been placed to allow for incorporation

  • of this unnatural amino acid somewhere

  • within the polypeptide chain as shown here.

  • So if we think about the scope of this methodology,

  • where does this take us?

  • So, it's quite broad.

  • This type of work has been applied beyond E. coli,

  • so in yeast and mammalian cells.

  • At present, there is many, many different unnatural amino acids

  • that can be incorporated and it's used by many labs.

  • So that's something to keep in mind.

  • If you're developing a new method,

  • you'd really like other folks in other labs

  • to be able to use your method.

  • There's a lot of troubleshooting to do experimentally

  • to get it up and running.

  • And Joanne's a wonderful person to talk about that

  • if you're curious for details.

  • Just some amino acid scope, and you

  • know what maybe we could do.

  • So these are some earlier examples

  • of unnatural amino acids that can be incorporated.

  • And what are some of the neat things?

  • If we look just here for example, there's an azide.

  • Why might we want an azide?

  • AUDIENCE: Click chemistry.

  • ELIZABETH NOLAN: Yeah, click chemistry, right.

  • Some chemistry that could be done after protein expression

  • or maybe in a cell.

  • Here we have a benzophenone.

  • So they're useful for cross linking experiments

  • and we'll likely talk about benzophenone cross linking

  • in recitation five in detail.

  • We see some sugars here.

  • This is the damsel group.

  • That's a fluorophore.

  • So there's many possibilities here.

  • Just looking at these molecules, what's something

  • similar about all of them?

  • We think about them compared to a native amino acid.

  • AUDIENCE: I was just that they're small.

  • ELIZABETH NOLAN: OK, they're quite small.

  • AUDIENCE: It's a kind of modified tyrosine.

  • It will have some sort of benzo group that's modified.

  • ELIZABETH NOLAN: So they're sort of

  • phenylalinine or tyrosine like, right?

  • And does that make sense from the standpoint

  • of using this machinery initially?

  • Yes, and you can imagine looking for other pairs

  • to put in other types of unnatural amino acids.

  • So that's reflective there.

  • Just as some further examples, So this

  • is another example of using an unnatural amino acid that can

  • be useful for click chemistry.

  • And I picked this in part, for one, this unnatural amino acid

  • looks very different than the ones we saw on the prior slide.

  • But there's aminoacyl-tRNA synthetase

  • and the tRNA for this alkyne.

  • And so you can imagine expressing a protein with this

  • at a specific location.

  • And then after the fact, clicking on a molecule

  • like this fluorophore here.

  • So just thinking about this process,

  • why maybe was this put on later rather than in the cell?

  • AUDIENCE: Do you mean clicking it on or synthesizing--

  • or putting that whole thing on?

  • ELIZABETH NOLAN: Yeah, as you can imagine someone

  • could have thought, rather than clicking this

  • on after the fact, why not just use this whole moiety here

  • as the unnatural amino acid?

  • So this fluorophore.

  • AUDIENCE: It would be hard to find a synthetase

  • to accommodate that fluorophore.

  • ELIZABETH NOLAN: It might be hard to find a synthetase.

  • AUDIENCE: Might just be too much [INAUDIBLE]..

  • It might not fit physically within the ribosome machinery.

  • ELIZABETH NOLAN: That could be.

  • AUDIENCE: Are you asking why we would not put it in?

  • ELIZABETH NOLAN: Yeah, I'm just asking

  • you to think about this, right?

  • So you know, what needs to be thought about, right?

  • So here, there's still a chemical step

  • after this unnatural amino acid was put in.

  • And in this case, why might that be?

  • Maybe it's a permeability issue.

  • We don't know if that molecule readily taken up

  • by the organism.

  • Is it a size issue, that it's hard to get machinery

  • to accommodate this type of molecule here.

  • AUDIENCE: Is it folding?

  • ELIZABETH NOLAN: Folding of--

  • AUDIENCE: If you had it, is the question like,

  • you put it on the floor, which is after

  • like it's been processed--

  • ELIZABETH NOLAN: Yeah, maybe it messed up.

  • AUDIENCE: If it's a floppy thing,

  • it might interfere with folding, or folding might

  • interfere with its, like--

  • ELIZABETH NOLAN: Right, so can the the polypeptide

  • breach its native confirmation with this perturbation.

  • Just to think about.

  • And here are just some examples of unnatural amino acids

  • that can be used for fluorine NMR as was mentioned last time.

  • OK.

  • So this is all really exciting, but what is the limitation?

  • And there is a major limitation of this methodology

  • as it was first described.

  • So the major limitation is that the efficiency is low.

  • OK?

  • And if we consider wanting to incorporate

  • one unnatural amino acid into a polypeptide,

  • so there is one amber stop codon put in, what was found

  • is that about 20% to 30% efficiency for incorporation

  • of one unnatural amino acid.

  • OK?

  • And then this value plummeted to less than 1%

  • for incorporation of two unnatural amino acids.

  • So imagine there's two amber stop

  • codons put within the gene.

  • So why is this?

  • This is because what's observed is

  • that only a small amount of the protein or polypeptide

  • synthesized reaches completion.

  • And so, how can we think about this?

  • Imagine here, I'm just going to draw some polypeptide chain

  • going from end to C terminus.

  • Let's imagine this is 20 kilodaltons in size.

  • And maybe this unnatural amino acid

  • is being placed right in the middle.

  • OK?

  • So we want to put an unnatural amino acid here.

  • OK?

  • So, imagine you make your plasma DNA to do this.

  • You have the tRNA and aaRS and the unnatural amino acid,

  • and you do your expression, and then

  • you take a look by SDS page, so gel electrophoresis,

  • what you see?

  • So imagine here we have 20, 10, five, so kilodaltons here.

  • Right?

  • So we have some molecular weight markers let's just say here.

  • If you do this, say for the native sequence.

  • So you haven't put in the stop codon.

  • Imagine there's your protein.

  • If we have the unnatural amino acid, what do we see?

  • Something like this.

  • So what does this tell you?

  • First of all, why do you look at the native one?

  • Effectively, you want some positive control

  • because if you can't express your polypeptide

  • with the native sequence, you're not

  • going to want to go try to stick in an unnatural amino acid,

  • right?

  • There's a problem.

  • So that's your positive control.

  • So we see in this make believe gel,

  • there's one band at 20 kilodaltons, which

  • is the size of that.

  • If that ever happens to you, you've

  • had an instant gratification protein trap.

  • So, what about this lane with the unnatural amino acid?

  • What do we see and what does this data tell us?

  • Lindsey.

  • AUDIENCE: It's like early truncation.

  • ELIZABETH NOLAN: Yeah, something happened.

  • So early truncation, and why are you saying that?

  • We see two bands.

  • There's one band with the expected migration

  • to about 20 kilodaltons.

  • And then there's the second band that's coming up

  • around 10 kilodaltons.

  • And based on what I sketched out here,

  • that unnatural amino acid is roughly

  • around the 10 kilodalton mark.

  • OK?

  • What about the relative intensity of these bands?

  • What do we see more of?

  • AUDIENCE: The truncated one.

  • ELIZABETH NOLAN: We see more of the truncated form.

  • So what's going on?

  • we?

  • Need to think about our ribosome.

  • And there's some polypeptide being made.

  • And then what's coming here?

  • We either have our tRNA with the unnatural amino acid

  • or the release factor, right?

  • So there's going to be competition

  • for binding in the A site between the tRNA

  • and the release factor.

  • And so this is getting back to, I

  • believe, Max's question from last time about using the stop

  • codon, right?

  • There's fundamentally a problem here.

  • So, yeah.

  • AUDIENCE: How does the release time test different

  • for different stop codons?

  • ELIZABETH NOLAN: Yes, so we discussed

  • that I think in lecture four.

  • So there's a release factor one and release factor two,

  • and there's three different stop codons.

  • So they both recognize one of the same and two different.

  • And in this case release factor one recognizes the amber stop

  • codon here.

  • So we're not worrying about release factor two

  • competing with this stop codon because it doesn't

  • recognize this stop codon here.

  • Right?

  • So if release factor one goes in,

  • we get premature termination.

  • And that results in truncated protein.

  • So is this a problem?

  • And how much of a problem is it?

  • AUDIENCE: So you're saying that the release factors comes in

  • because it's recognizing the codon that's trying to--

  • or that originally was a stop codon?

  • ELIZABETH NOLAN: Yeah, because the codon is still

  • a stop codon.

  • AUDIENCE: So in the wild type, it

  • wasn't that we replaced-- sorry.

  • So we replaced it with a stop.

  • But the stop wasn't there originally.

  • And so that's why you get the full 20 length, right?

  • ELIZABETH NOLAN: Yes.

  • So you have--

  • AUDIENCE: Yeah,

  • ELIZABETH NOLAN: OK, continue.

  • AUDIENCE: There was no stop before.

  • Now there's a stop, but it's not supposed to act like a stop,

  • right?

  • ELIZABETH NOLAN: Right.

  • AUDIENCE: So here it is acting like a stop kind of?

  • ELIZABETH NOLAN: It depends what enters the A-site.

  • So a stop codon is a stop codon.

  • But the idea is that this tRNA has

  • been tweaked to allow a tRNA to recognize the stop.

  • But there's going to be competition

  • because you have the tRNA that's going to deliver

  • the unnatural amino acid.

  • But you also have release factor around.

  • So this release factor one is in the endogenous pool.

  • So the question is, which one gets there and does the job?

  • Right?

  • And so what that gel is telling you is that there's a mixture.

  • Right?

  • Sometimes the tRNA will get there

  • and translation continues until you get to the desired stop

  • where you want translation to stop, in terms of stopping.

  • Or if the release factor gets there, you get termination.

  • So you get some truncated protein.

  • AUDIENCE: How do you know, though,

  • that you've got in the end-- that you actually

  • got the unnatural amino acid in the 20 [INAUDIBLE]

  • and not just the original?

  • Is that fluorescing?

  • ELIZABETH NOLAN: No.

  • I mean, just imagine we're just looking at protein here--

  • I mean, where this came from.

  • AUDIENCE: So it would look the same?

  • ELIZABETH NOLAN: If you had a fluorescent amino acid,

  • you'd see something-- no.

  • Because if you didn't have the unnatural amino acid there,

  • what else could be there?

  • AUDIENCE: Just like the native.

  • ELIZABETH NOLAN: But what native amino acid can be incorporated

  • if there is a stop?

  • AUDIENCE: Oh, because you also put in the mRNA.

  • ELIZABETH NOLAN: Yeah.

  • Right.

  • So there has to be a stop.

  • Now, that's also backtracking why

  • you need to make sure everything's orthogonal.

  • Because you don't want one of the endogenous amino

  • aminoacyl-tRNA synthetases to put some endogenous amino acid

  • on this tRNA.

  • OK?

  • So either full length with the unnatural amino acid

  • or truncated because RF1 came along here.

  • Right?

  • So in terms of how much of a problem this is,

  • in some respects, it depends on what you need

  • and what you want to do.

  • If you're over expressing protein

  • and you can deal with this mixture

  • and get enough full length, maybe that's OK.

  • If you're doing an experiment in cells,

  • you have to ask, what is the consequence of also having

  • some truncated protein around?

  • What does that mean for the cell?

  • What does that mean for your measurement there for that?

  • So how can we get around this problem of RF1?

  • So effectively, we want to diminish RF1 mediated chain

  • termination.

  • What are some possibilities?

  • Is that feasible?

  • So we could do that and we could get a better yield.

  • That would be great for protein overexpression.

  • If we could minimize truncated phenotypes,

  • that would be great for an experiment in cells.

  • You don't need to worry about what this truncated protein

  • might do.

  • So what are possibilities?

  • So can we knock down or knock out our RF1?

  • AUDIENCE: [INAUDIBLE]

  • ELIZABETH NOLAN: So this is a wonderful little story.

  • I'll just tell a little bit about,

  • we're not going to go into huge detail.

  • But for quite some time, it was thought that RF1

  • was essential in E. coli.

  • So a lot of experiments were done with E. coli K12

  • and even if you go look on a website about all

  • the genes in E. coli K12, it will tell you RF1 is essential.

  • But then in 2012, a paper came out

  • in ACS Chemical Biology, where they

  • were doing some work in a different strain of E. coli.

  • So there's many different E. coli's.

  • And K12 is a laboratory workhorse.

  • And there's also strains, E. coli B.

  • And they're also laboratory workhorses.

  • So maybe many of you have used BL 21DE3 cells

  • for protein expression.

  • So this lab was working in E. coli B strain,

  • and found that RF1 could be knocked out;

  • that it's not essential.

  • So then the question is, what's going on?

  • And as it turns out, the essentiality of RF1 in E. coli

  • turned out to be due to an issue with RF2.

  • And in the K12 release factor 2 has a single point mutation

  • that makes it less able to stop at certain stop codons.

  • So when you had both of those together, it was deleterious.

  • So RF1 can be knocked out.

  • Would you want to do that?

  • AUDIENCE: So, RF1 can be knocked out without RF2 or RF3,

  • I don't remember.

  • ELIZABETH NOLAN: Yeah, there are three release factors.

  • RF3 is a GTPase.

  • It's a little different.

  • AUDIENCE: There's redundant kind of behavior.

  • ELIZABETH NOLAN: There's some redundancy.

  • And I mean, something too just to ask

  • is, if you can knock it out and the cell is viable,

  • viability is different than normal healthy cell.

  • So those E. coli B, without RF1 will grow,

  • but are they growing and replicating

  • as well as the wild type?

  • No.

  • No.

  • But is it good enough?

  • And I think again, it comes down to asking what is it

  • that you want to do?

  • So maybe if you're over expressing protein

  • and you're going to purify that, it's not such a big deal.

  • But again, if you're looking at some cellular process,

  • you're going to need to think about what's

  • happening if RF1 can't terminate translation for, you know,

  • its repertoire of proteins and genes there.

  • There will be some consequence of that perturbation

  • just to keep in mind.

  • But there's certainly work going on with that now that it

  • was found not to be essential.

  • So in vitro translation, just something to think about.

  • If you're going to work in a test tube,

  • could you just do this outside of the cell?

  • And then, the possibility we're going to discuss in closing

  • is this one of a new ribosome, which I think is pretty cool.

  • So, is it possible to have an orthogonal ribosome here

  • to get around this problem?

  • So effectively, can we make a new ribosome

  • that only translates the message encoded in a plasmid that

  • has the gene of interest where you want

  • the unnatural amino acid to go?

  • And so thinking about this in cartoon form,

  • imagine we have E. Coli or some organism,

  • and there's the native ribosome, and this native ribosome

  • translates all of the native wild type

  • mRNAs and gives synthesis of the proteome.

  • But then imagine we can put in an orthogonal ribosome

  • into this organism.

  • And this orthogonal ribosome only

  • recognizes an orthogonal mRNA, which

  • means it only translates off of this orthogonal mRNA

  • and only gives you synthesis of the protein

  • you want with the unnatural amino acid.

  • So how to think about doing this?

  • Need to think back about the initiation process,

  • and that mRNAs have a ribosome binding site.

  • So effectively, it's necessary to engineer an mRNA that

  • contains a ribosome binding site that will not

  • direct translation by the endogenous ribosome,

  • so some new ribosome binding site.

  • OK?

  • And then this orthogonal ribosome

  • needs to be engineered such that it's specifically

  • binding to the orthogonal mRNA.

  • And it doesn't bind to the wild type mRNAs there.

  • So no translation of the cellular message

  • because this ribosome binding site and orthogonal ribosome

  • are a match.

  • OK?

  • So a unique binding site.

  • So in thinking about how to do this,

  • you want to think about the ribosome structure.

  • And we know that the 16S rRNA is involved

  • in binding to the mRNA at the beginning of the initiation

  • step.

  • So what was done was to mutate the 16S

  • and come up with an orthogonal ribosome.

  • So this has been done.

  • That's not a solution to the problem of RF1

  • terminating translation on its own.

  • So then the next question is, if we

  • can have just this orthogonal ribosome and orthogonal mRNA,

  • can we improve that system to minimize RF1 mediated chain

  • termination?

  • So effectively what we want to do

  • is prevent RF1 from binding to the A-site

  • of the orthogonal ribosome.

  • But it's still going to do its job for the endogenous ribosome

  • here.

  • So what needs to happen?

  • And we'll go through the steps.

  • This is just the schematic in cartoon form.

  • So imagine we're starting with native ribosomes

  • and orthogonal ribosomes.

  • And we have tRNAs and RF1.

  • And nothing has been done to this orthogonal ribosome

  • so RF1 can still bind there.

  • And so we want to have some evolution.

  • So mutagenesis and selection of the orthogonal ribosome

  • such that only the tRNA goes to the A-site.

  • And RF1 only goes to the wild type ribosome.

  • So there's other possibilities.

  • One possibility I'll just throw out there

  • is using rather than a triplet, a quadruplet codon there,

  • which we won't talk about.

  • There's more than one solution to the problem.

  • But where we're going to focus on is work done to minimize RF1

  • and how to think about doing that

  • from the standpoint of what we know

  • of ribosome structure and the interactions.

  • OK?

  • So the name of this new O ribosome

  • is Ribo-X and so what did they do?

  • They started with the orthogonal ribosome.

  • OK?

  • And so, the first is that there needs

  • to be some mutation to the ribosome,

  • so libraries of mutants.

  • There needs to be some selection process.

  • So effectively, there is a requirement for of activity

  • from the ribosome.

  • and.

  • When there's this, there needs to be some sequencing.

  • Or identity determination, so where is the mutation?

  • Here.

  • And then with some mutant in hand,

  • that looks like it's a good option,

  • there needs to be assays to study it.

  • And we're pretty much going to focus on step four.

  • I'll briefly say something about steps one, two, and three here.

  • So the first thing is, if we want to mutate this O ribosome,

  • how do we think about designing a mutant library?

  • And so, what we need to think about in this case

  • because the goal is to minimize RF1 mediated chain termination

  • and enhance tRNA getting into this A-site,

  • we want to look at how the ribosome interacts

  • with RF1, how it interacts with the tRNA,

  • and also think about the mRNA there.

  • And so, there's crystal structures available.

  • There might be biochemical information available.

  • But really to ask, where does that

  • make sense to make mutations?

  • And so if we think about the stop codon being recognized

  • by the tRNA and RF1 in the A-site,

  • somehow we want to mutate the ribosomal RNA in that region

  • to give us the desired outcome.

  • So what they did is mutate 16S rRNA

  • to favor suppression of the amber stop codon by the tRNA.

  • And crystal structures guided the library design.

  • And so they looked at crystal structures

  • where tRNAs are bound to the A-site

  • or where RF1 is bound to the A-site.

  • And from these, they selected seven different positions

  • of the RNA and randomly mutated them.

  • So that gives you some new mutants to study.

  • Then there needs to be a selection process.

  • So the mutant needs to be active.

  • Some of these mutations might cause the ribosome

  • to be inactive and that won't be very helpful.

  • And so they developed an assay based on antibiotic resistance

  • to select.

  • And effectively, an enzyme that provides resistance

  • to chloranfenicol, which is an antibiotic that

  • blocks translation and was put under the control

  • of the O ribosome.

  • So you can imagine using antibiotic resistance

  • as a selection there.

  • And then the sequencing, once we've

  • selected first some mutants, we have

  • to ask where is the mutation?

  • And so what they found after going through this work

  • is that for Ribo-X it's only a double mutant in the 16 S rRNA.

  • So two positions, U3531G and U534A.

  • So these mutations in proved suppression of the amber stop

  • codon, and I also point out these mutations

  • are very unusual.

  • So, at least at the time of this work,

  • no sequenced natural ribosome had these two mutations here.

  • And they're found in very few examples of sequenced RNase

  • here.

  • So, I mean, just to think about the ribosome's so huge

  • and just two point mutations can make this change here.

  • So what's seen in terms of some characterization.

  • What do we need to ask in terms of characterization.

  • Bless you.

  • So something we want to ask about is fidelity here.

  • So if we think about fidelity, one, we can ask,

  • if we're using this to express some protein,

  • what is the protein yield and how does that

  • compare to the native ribosome?

  • We want it to incorporate amino acids correctly

  • with high fidelity and incorporation

  • of the unnatural amino acid.

  • So doesn't this incorporate amino acids?

  • So that's the question we need to ask.

  • OK?

  • And then of course, we need to ask about amber stop codon

  • suppression efficiency.

  • And so, in thinking about this what

  • is the point of comparison?

  • So we can imagine in all of these comparing

  • this new orthogonal ribosome Ribo-X

  • to the starting orthogonal ribosome.

  • Right?

  • Here.

  • So what are the experiments?

  • So first let's think about protein yield.

  • And I'll just say, I have a pet peeve

  • when people don't report their protein yields in experimental.

  • So if you're doing biochemistry, always

  • think about doing that there.

  • So what they did is an experiment

  • where they made a plasmid.

  • So we have an orthogonal DNA that will give orthogonal mRNA.

  • So this gets transcribed...

  • to give the orthogonal mRNA and then it gets translated

  • by either the O ribosome...

  • or Ribo-X. And the result of this

  • is a fusion protein where we have a protein called

  • GST, glutathione S-transferase, and then MBP, which

  • is maltose-binding protein.

  • And as we move forward, it will become clearer

  • why they use this fusion.

  • OK so just the first question is, how does

  • the yield of protein compare?

  • Are they doing a similar job or were these two mutations

  • detrimental?

  • So here's the result from this experiment

  • one looking at protein yield.

  • OK, so again we're looking at an SDS page gel that's

  • being stained for the protein.

  • And we see that this GST and BP fusion has a molecular weight

  • of 71 kilodaltons, right?

  • And what we see up here are the components

  • that were in each of the experiments for each

  • of the lanes.

  • So here in this lane, we have no O ribosome,

  • no Ribo-X but the plasmid was included.

  • Here, we have the orthogonal ribosome in the plasmed,

  • here Ribo-X in the plasmid.

  • So what do we see?

  • Pardon?

  • AUDIENCE: Are they all the same yield?

  • ELIZABETH NOLAN: Are they all the same yield?

  • There's three lanes.

  • AUDIENCE: [INAUDIBLE]

  • ELIZABETH NOLAN: Yeah, so no orthogonal ribosome,

  • no translation.

  • And that's a good thing to see, right?

  • That tells you that this orthogonal mRNA is not

  • being translated by the endogenous ribosome.

  • That's an important observation.

  • And then I think what you meant to say,

  • is that in these two lanes where we

  • have either the starting orthogonal

  • ribosome or Ribo-X, what we see is

  • what appears to be a very similar amount of protein.

  • So here, you know you assume and you look at the experimental,

  • the same volumes were loaded, all of these things.

  • We're getting the same amount of protein yield.

  • So that's a great result here.

  • So that's good news.

  • What's the next experiment?

  • And we'll close, I think on this experiment.

  • So the next experiment is amino acid misincorporation.

  • So again, what they did is they used this GST MBP fusion

  • protein.

  • And there's a linker region here.

  • And in this linker region, they engineered a protease cleavage

  • site here.

  • So for thrombin here.

  • And why did they do this to look at amino acid misincorporation,

  • whether that's happening.

  • Effectively, they took advantage of the fact

  • that GST contains cystine, whereas maltose binding protein

  • has no cystine.

  • So their idea was let's use radio

  • labeled cystine as a probe and monitor for radioactive cystine

  • incorporation.

  • So effectively, what can be done is

  • that this can be expressed and purified

  • in the presence of the radio labeled cystine.

  • Thrombin can be used to cleave.

  • And then you can look and ask is there radioactivity

  • associated with GST?

  • And we hope the answer is yes.

  • And is there radioactive activity

  • associated with maltose binding protein.

  • And so where we'll begin on Friday is looking at the data

  • from this assay.

  • But until then, what I'd like you to think about

  • is in terms of amino acid misincorporation,

  • kind of strengths and limitations of this assay.

  • Right so the choice of using one amino acid

  • to take a look there.

  • OK?

  • So I'll see you Friday.

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