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  • JOANNE STUBBE: OK, so what I want to do today

  • is hopefully finish up or get pretty close to finishing up

  • module 6, where we've been focused on bacterial uptake

  • of iron into cells.

  • In the last lecture, I briefly introduced you

  • to gram-positive and gram-negative

  • big peptidoglycan, small peptidoglycan,

  • outer-cell membrane.

  • They both have the same goals.

  • They've got to get--

  • They take up iron the same way from a siderophore, which

  • is what we talked about last time, or by a heme.

  • And we'll talk a little bit about that.

  • And that's what you focused on in your problem set.

  • But they have different apparati to do

  • that, because of the differences between the outer--

  • because of the cell walls' distinctions

  • between gram-negative and gram-positive.

  • So we were talking, at the end of the class,

  • about, this was for the siderophores

  • which we talked about.

  • We need to take them up.

  • These are common to all uptake systems.

  • You have some kind of ATPase system and ABC ATPase.

  • We're not going to talk about that in detail,

  • but it uses ATP to bring these molecules

  • and also heme molecules across the plasma membrane.

  • And then, in all cases, you have this issue

  • of how do you get the iron out of whatever the carrier is,

  • be it a siderophore where the carriers can bind very tightly

  • or heme where you also have to do something

  • to get the iron out of the heme so that it can be used.

  • And so what I want to just say, very briefly--

  • and this you all should know now.

  • So now we're looking at heme uptake.

  • I'm not going to spend a lot of time drawing the pictures out,

  • but, if you look at the PowerPoint cartoon, what

  • you will see is there is a protein like this, which

  • hopefully you now have been introduced to from your problem

  • set.

  • So this could be IsdB or IsdH.

  • And we'll come back to that, subsequently.

  • And it sits on the outside of the peptidoglycan.

  • So this is the protein.

  • The key thing that is present in all these Isd proteins

  • is-- let me draw this differently-- is a NEAT domain.

  • OK?

  • And we'll come back to that later on.

  • But this domain--

  • So you have a big protein, and there's

  • one little domain that's going to suck the heme out.

  • And so what happens is we'll see in Staph. aureus, which

  • is what we're going to be focused on,

  • you have hemoglobin.

  • And somehow-- and I'm going to indicate heme

  • as a ball of orange, with a little planar

  • thing as the protoporphyrin IX.

  • OK, are you all with me?

  • And then somehow this gets sucked out

  • into the NEAT domain, where--

  • And again, all of these gram-positive and gram-negative

  • systems are slightly different, but in the Staph. aureus system

  • we'll be talking about today and you

  • had to think about in the problem set you basically

  • have a cascade of proteins which have additional NEAT

  • domains from which, because this is such a large peptidoglycan,

  • you need to transfer the heme to the plasma-membrane

  • transporter.

  • And what's interesting about these systems

  • and is distinct is that they end up,

  • they're covalently bound to the peptidoglycan.

  • And I'm going to indicate peptidoglycan as "PG."

  • And we'll talk about that reaction today--

  • the enzyme that catalyzes those reactions.

  • And all of these guys end up covalently bound

  • to the peptidoglycan-- which is distinct from all

  • of the experiments you looked at in your problem set.

  • Nobody can figure out how to make the peptidoglycan

  • with these things covalently bound.

  • So what you're looking at is a model for the actual process.

  • OK, so, also-- so that's the gram-positive.

  • And in the gram-negative, one has two ways of doing this.

  • And again, these parallel the ways with siderophore uptake.

  • So you have an outer membrane--

  • So this is the outer membrane.

  • And you have a beta barrel, with a little plug in it.

  • And so these beta barrels, they're at, like, 20 or 30

  • of these things in the outer membranes.

  • And they can take up siderophores,

  • as we talked about last time, but they can also

  • take up hemes.

  • OK?

  • So each one of these is distinct,

  • although the structures are all pretty much the same.

  • And so what you see in this case is,

  • there are actually two ways that you can take heme up.

  • So you can take up heme directly.

  • And we'll see that what we'll be looking at

  • is hemoglobin, which has four alpha 2 beta 2.

  • So this could be hemoglobin.

  • That's one of the major sources, and it is the major source

  • for Staph. aureus.

  • And so this can bind directly to the beta barrel--

  • gets extracted.

  • The heme gets extracted.

  • The protein doesn't get through.

  • And so the heme is transferred through this beta barrel.

  • OK.

  • So that's one mechanism.

  • And then there's a second mechanism.

  • And the second mechanism involves a hemophore.

  • And the hemophore is going to pick up the heme.

  • And so every organism is distinct.

  • There are many kinds of hemophores.

  • And I have a definition of all of these--

  • the nomenclature involved.

  • And so, after class today, I'll update these notes,

  • because that's not in the original--

  • the definitions aren't in the original PowerPoint.

  • OK?

  • So what you have, over here, is the hemophore

  • that somehow extracts the heme out

  • of hemoglobin or haptoglobin.

  • We'll see that's another thing.

  • So this gets extracted and then gets

  • transferred, in that fashion.

  • And so these hemophores come in all flavors and shapes.

  • They're different-- for example, in Pseudomonas or M.

  • tuberculosis.

  • And we're not going to talk about them further,

  • but the idea is they all use these beta-barrel proteins

  • to be able to somehow transfer the heme across.

  • And what happens, just as in the case-- if you go back

  • and you look at your notes from last time,

  • there's a periplasmic binding protein

  • that takes the heme and shuttles it, again,

  • to these ABC transporters.

  • OK?

  • So, in this system, again, you have

  • a periplasmic binding protein.

  • And this goes to the ABC transporter,

  • which uses ATP and the energy of hydrolysis of ATP,

  • to transfer this into the cytosol.

  • OK, so this is the same.

  • That remains the same.

  • And the transporters are distinct.

  • And then, again, once you get inside the cell,

  • what do you have to do?

  • You've got to get the iron out of the heme.

  • So the problems that you're facing

  • are very similar to the siderophores.

  • So, in all cases--

  • So the last step is, in the cytosol,

  • you need to extract the iron.

  • And you can extract--

  • usually, this is in a plus-3 oxidation state.

  • So you extract the iron.

  • And this can be done by a heme oxygenase, which

  • degrades the heme.

  • OK.

  • In some cases, people have reported

  • that you can reduce the iron 3 to iron 2, when the heme can

  • come out, but that still probably is not an easy task

  • because you've got four--

  • you've got four nitrogens, chelating to the heme,

  • and the exchange, the ligand exchange, rates

  • are probably really slow.

  • So I would say the major way of getting

  • the iron out of the heme is by degradation of the heme.

  • And we're not going to talk about that in detail at all,

  • either.

  • OK.

  • So that's the introductory part.

  • And here's the nomenclature, which

  • I've already gone through.

  • I've got all these terms defined.

  • And if you don't remember that, or you don't remember it

  • from the reading, you have a page with all the names--

  • which are confusing.

  • And so the final thing I wanted to say,

  • before we go on and actually start looking at peptidoglycans

  • and gram-positive bacteria and heme uptake

  • in Staph. aureus, which is what I was going to focus on

  • in this little module, is to just show you,

  • bacteria desperately need iron.

  • So what do they do?

  • This is what they do.

  • OK, so, here you can see-- and some bacteria

  • make three or four kinds of siderophores.

  • Others only make one or two kinds of siderophores,

  • but what they've done is they've figured out

  • how to scavenge the genes that are required

  • for these beta barrels.

  • So they can take up a siderophore

  • that some other bacteria makes.

  • OK?

  • And that's also true of yeast.

  • Yeast don't make siderophores, but most yeast have,

  • in their outer membranes, ways of picking up

  • siderophores and bringing it into the cell, since--

  • and remember we talked about the fact

  • there were 500 different kinds of siderophores.

  • But you can see that the strategy is exactly the same.

  • You have a beta barrel.

  • You have-- these are all periplasmic binding proteins.

  • This picture is screwed up, in that they forgot the TonB.

  • Remember, there's a three-component machine,

  • TonB, ExbB and D, which is connected to a proton motive

  • force across a plasma membrane, which

  • is key for getting either the heme or the iron

  • into the periplasm.

  • And you use a periplasmic binding protein,

  • which then goes through these ATPase transp--

  • ABC-ATPase transporters.

  • So what I showed you was heme uptake, iron uptake, but in all

  • of these cases, like Staph. aureus we'll be talking about,

  • we can also get iron out of transferrin.

  • We've talked about that.

  • That's the major carrier in humans.

  • The siderophores can actually extract the iron

  • from the transferrin.

  • And remember the KD was 10 to the minus 3,

  • so somehow, again, you've got to get iron transferred

  • under those conditions.

  • And that's how these guys survive.

  • So they're pretty desperate to get iron.

  • And inside, once they get inside the cell,

  • you have all variations of the theme to get the iron out.

  • But they're all sort of similar.

  • Somehow, you've got to get rid of whatever is tightly binding

  • it.

  • And if you're creative, you can reuse

  • whatever is tightly binding it, to go pick up some more metal.

  • OK.

  • So that just summarizes what I just said.

  • And so, in two seconds, I'm going to show you,

  • now-- we've spent one whole lecture,

  • a little more than a lecture, talking

  • about iron uptake in humans via DMT1,

  • the iron-2 transporter, and the transferrin transfer receptor.

  • So, in the plus-two and plus-three states,

  • we just started looking at the strategies by bacteria

  • and saw how widespread they are.

  • And then the question is, how do you win?

  • OK, bacteria need iron.

  • We need iron.

  • And the question is, how do you reach--

  • and we have a lot of bacteria growing in us, [LAUGH]

  • so we've reached some kind of homeostasis.

  • But with the pathogenic ones, of course,

  • we really want to get rid of them.

  • And so that's what the issue is.

  • And there have been a bunch of articles.

  • You can read about this in a lot of detail,

  • if you're interested in the more medical aspects of this.

  • But this war between bacteria and humans.

  • And really it's sort of fight for nutrients.

  • And, in this case, the nutrient is iron.

  • Has received a lot of attention, because we're

  • desperate for new kinds of targets

  • for antibiotics, because of the resistance problems.

  • And so nutrient limitation and iron sequestration

  • from a pathogenic organism might represent a new target.

  • Of course, what are the issues?

  • The issues are, we also need iron.

  • And so, if you lower the amount of iron,

  • then you might be in trouble, as well.

  • So what we know is, bacteria, viruses--

  • bacteria have been extensively studied;

  • viruses, less so, also protozoa, such as the malaria system--

  • all are known to depend on iron for growth.

  • And so, again, if you want to read about this,

  • you can read about some of the strategies

  • these organisms [LAUGH] use to get iron away

  • from the human systems.

  • And it's sort of amazing, when you

  • look at the details of how things have evolved,

  • back and forth, back and forth, [LAUGH] in terms of survival.

  • And so really what it's all about is homeostasis.

  • OK?

  • And that's what was all about in cholesterol.

  • And we'll see, with reactive oxygen species,

  • that's what it's all about.

  • So, somehow, using hepcidin--

  • which is the human master regulator,

  • the peptide hormone--

  • we need to figure out how to keep ourselves alive

  • while killing off these bacteria, in some way,

  • by sequestering the iron from the bacteria.

  • OK.

  • So this is an important problem that has

  • received a lot of attention.

  • And most of you know that the Nolan Lab is doing

  • beautiful studies in this area.

  • OK.

  • So what I want to do now, for the rest of the lecture,

  • is focus on Staph. aureus.

  • OK?

  • And Staph. aureus is--

  • methicillin-resistant Staph. aureus is a major problem,

  • throughout the world.

  • We don't have any ways to kill this guy.

  • And so that's why I decided to pick this target,

  • but there are many other [LAUGH] of these pathogens around that

  • have problems--

  • have also resistance problems, Staph. aureus

  • being the one that's been most extensively studied

  • in the last decade or so.

  • But bacteria has come back in vogue.

  • For years, nobody on campus cared anything about [LAUGH]

  • microorganisms or bacteria.

  • The microbiome has brought it back in vogue,

  • because people think they're going to be

  • able to figure that all out.

  • OK.

  • But anyhow, bacteria have always been extremely important,

  • not only in terms of human health

  • but in terms of how the whole world functions.

  • There are so many of them, and they

  • do so much interesting stuff.

  • And we have to live with them, side by side.

  • So anyhow, we're going to look at Staph. aureus.

  • That's what we're going to focus on, because of this problem.

  • And I think Staph. aureus, which many people don't realize,

  • is that 30% of all people have Staph. aureus on your skin

  • or in regions that are not breaching into the bloodstream.

  • So we all have Staph. aureus.

  • So 30% of us have this bacteria.

  • If you get-- if wherever it's localized is breached,

  • and it gets into our bloodstream,

  • then it's all over, because Staph. aureus

  • can colonize almost anywhere.

  • That's different from other organisms.

  • Some organisms can only colonize in the lungs.

  • Some colonize in the heart.

  • So these can colonize almost all tissues.

  • And what you know is, if you start

  • thinking about physiology-- and again, I'm not an MD--

  • but different tissues have different environments.

  • OK?

  • And so a lot of organisms find siderophore an environment

  • where they can best live and then take up--

  • make their home there.

  • But Staph. aureus is one of these guys

  • that can go anywhere.

  • And so this makes it specifically very insidious.

  • And you can get septicemia, or you can get endocarditis,

  • or you can get all kinds of horrible diseases associated

  • with Staph. aureus, once it breaches the barrier.

  • OK.

  • So what we need to do, as you've already seen from your problem

  • set, to understand how Staph. aureus can get heme

  • into its cytosol to be able to function,

  • to be able to grow effectively, is,

  • we need to look at the outer cell wall or the peptidoglycan.

  • So what I'm going to do is spend a few minutes

  • talking about the structure of the peptidoglycan.

  • And then we'll go back in and we'll

  • talk about how these proteins that you worked on

  • in the problem set covalently bind to the peptidoglycan

  • and allow you to take up iron to the cell.

  • And why is heme a major target?

  • Heme is a major target for Staph. aureus.

  • They've evolved.

  • The major source of iron, we all know,

  • is hemoglobin now, in red blood cells.

  • And so Staph. aureus has developed proteins--

  • endotoxins, really-- that can go in

  • and-- there's proteins that can insert into red blood cell

  • membranes, make a pore.

  • The blood cells lyse, and now the bacteria

  • are extremely happy because they have huge amounts of heme.

  • And then they want to take that heme into--

  • to help them survive.

  • So Staph. aureus are amazingly creative,

  • in terms of getting the heme that they need for survival.

  • OK.

  • So, peptidoglycan.

  • Most of you have probably seen peptidoglycan before.

  • I'm just going to say a few things about peptidoglycan.

  • So let's look at--

  • let's see.

  • Where do I want to do this?

  • All right.

  • So I'm going to erase this.

  • We're going to look at the cell wall.

  • OK.

  • And what you can see, here, I'm going to draw just a few things

  • on the board.

  • But what you can see here, in this cartoon,

  • is you have two kinds of sugars--

  • N-acetylglucosamine and N-acetylmuramic acid.

  • N-acetylglucosamine is a precursor

  • to N-acetylmuramic acid.

  • And what you see, attached to N-acetylmuramic acid,

  • are little blue balls.

  • And that's the peptide that turns out

  • it starts out with a pentapeptide

  • and goes to a tetrapeptide.

  • And what you see here, in the purple balls--

  • and this is unique to Staph. aureus--

  • is, other amino acids, they're all the same,

  • and this is glycine.

  • So, if you look down here, here are the disaccharides, shown up

  • here.

  • Here is-- yeah, one, two, three, four, five.

  • Here is the pentapeptide.

  • And what do you notice unusual about the pentapeptide?

  • You have a D glutamine.

  • OK?

  • And I was just reading a whole bunch of papers

  • on somebody's thesis--

  • tomorrow, actually.

  • And you're trying to make this guy,

  • nobody can study this stuff.

  • Why?

  • Because you have to make a peptidoglycan.

  • And I'll show you.

  • It's complicated.

  • You have to stick on a pentapeptide.

  • You have to stick on the glycines.

  • And how do you get the substrates

  • for your enzymatic reactions?

  • So we've known this pathway for decades,

  • but it's taken really good chemists

  • to be able to figure out how to look at these individual steps.

  • And so what's unusual, here, is, if you replace glutamine

  • with a glutamate, it doesn't work very well at all.

  • OK, so it's that subtle.

  • Here you've got this huge macromolecule,

  • and you're replacing an NH2 with an OH,

  • and you alter the resistance to different bacteria.

  • And again, you have this unusual pentaglycine.

  • And you'll see in the cartoon, in a few minutes,

  • where do you think this glycine, pentaglycine comes from?

  • Well, it actually comes from a tRNA that binds glycine.

  • OK, you've seen that before.

  • But, instead of using the ribosome

  • to make this little peptide, it uses nonribosomal peptide

  • synthetases.

  • And this all happens in the cytosol of the cell.

  • So, what do we know about the structure?

  • I'm just going to draw N-acetylglucosamine.

  • And what I'm going to do is put some R groups on here.

  • So I'm going to put OX.

  • And then here we have N-acetyl.

  • So that's an acetate group.

  • Here I'm going to put another OR group.

  • OK, so the two things I want to focus on,

  • the two things I'm going to focus on, is this X

  • and this R. So is N-acetylglucosamine.

  • And then the second one is N-acetylmuramic acid.

  • And, in both of these cases, X is equal to UDP.

  • So we're going to come back to this

  • in the last module on nucleotides.

  • So nucleotides play a central role in RNA and DNA,

  • but they also play a central role

  • in moving around all sugars inside the cell.

  • So what you have here, actually, is a pyrophosphate linkage

  • to UDP.

  • OK?

  • And if we look at N-acetylglucosamine,

  • R is equal to H. OK?

  • But if we look at muramic acid, what we're going to see

  • is that nature has put on a lactic acid in this position.

  • OK, so here's your methyl group, from your lactic acid.

  • And here's the carboxylate.

  • So this is the R group in N-acetylmuramic acid.

  • OK.

  • Now, what we're going to see is, while most sugars--

  • and this is true in humans, and it's also true in bacteria--

  • are carried around and transported within the cell

  • as linked nucleotides, what we'll also see in the cell

  • wall-- which has made them extremely challenging to study,

  • made the whole pathway extremely challenging to study--

  • in addition to X equal to UDP, X can also

  • be equal to sort of an amazing structure.

  • And the structure is slightly different

  • in different bacteria, but this strategy

  • is also used in humans, where you have a lipid

  • and you have a lipid that acts as--

  • is made from-- hopefully you now know--

  • is isopentenyl pyrophosphate.

  • OK?

  • And there are seven of these, where you

  • have the trans configuration.

  • There are now three of these, which

  • have the cis configuration.

  • Just make sure I get my--

  • is that right?

  • Yeah, that's right.

  • OK, so you have three of these that

  • have the cis configuration.

  • And then you have a terminal dimethyl L configuration.

  • And this is C55.

  • So, if you're a synthetic chemist,

  • and you're trying to stick on a couple of these sugars

  • with hydrocarbon on the tail, with C55,

  • you can imagine you would have one heck of a trouble, number

  • one, synthesizing it but, number two, dealing with it.

  • And so this goes to the question which

  • I think is really interesting is,

  • many people think about polymerization reactions.

  • We're going to see this polymer is non-template-dependent,

  • in contrast to polymers of DNA RA, where you have a template.

  • And furthermore, DNA and RNA are pretty soluble.

  • These things become insoluble.

  • So you're making a phase transition from soluble state

  • to an insoluble state, around the bacteria.

  • And I think it's really sort of a tribute to Strominger, who

  • worked on this many years ago, that he figured out

  • sort of the pathway.

  • But now it's only with recent studies, and really

  • some very hard work synthetically,

  • and also in terms of the microbiology and biochemistry,

  • that it's really allowed us to elucidate this.

  • So X, in this case, can also be this lipid.

  • So I'm just pointing out what the issues are.

  • And if you look at the cell wall, biosynthetic pathway--

  • so this is inside--

  • you're not going to be responsible for the details

  • of this.

  • But this is outside.

  • OK.

  • So you start out with a couple of sugars.

  • These are the sugars we just talked about.

  • OK.

  • So now what you do is add on these five amino acids.

  • So, over here, we ultimately need

  • to add on five amino acids.

  • And what do we see about the amino acids?

  • They're unusual, because they can have the D-- they are not

  • necessarily L-amino acids.

  • They can be D-amino acids.

  • And these things unfortunately are

  • unique to different organisms.

  • So, if you worked out a synthetic method for one,

  • you're still faced with the problem that every one of them

  • has different pentapeptides stuck on the end of it.

  • Now, how would you attach--

  • you've now had a lot of biochemistry,

  • where you've dealt with amino acids,

  • in the first half of this course.

  • How would you attach amino acids--

  • form and the linkages--

  • to this lactic acid?

  • Can anybody tell me?

  • What would you do, to make that attachment?

  • AUDIENCE: You activate the carboxylate.

  • JOANNE STUBBE: Yeah, so we have to activate the carboxylate.

  • How do you activate the carboxylate?

  • AUDIENCE: Make an AMP.

  • JOANNE STUBBE: Yeah.

  • So you make an AMP, just like you've seen with nonribosomal--

  • the adenlyating enzyme of nonribosomal polypeptide

  • synthases, and you've seen with tRNAs.

  • OK.

  • So you see the same thing, over and over and over again.

  • So you add these things on.

  • The difference is that, again, these things, which

  • are all soluble, down here, these are all

  • soluble with the nucleotides.

  • Now, because ultimately this needs

  • to go from the inside of the cell

  • to the outside of the cell, what you do,

  • presumably, is take this lipid-- so you have the C55 lipid,

  • with one phosphate on it.

  • And then you attach it to one sugar.

  • So here it's attached to the muramic acid,

  • and that's called "lipid 1."

  • You add N-acetylglucosamine with a glycosyltransferase.

  • That's lipid 2.

  • And that's the substrate for the polymerization reaction.

  • What is the issue?

  • The issue is, it's in the cytosol

  • and all the chemistry happens on the outside of the cell.

  • But, of course, if you move it from the inside to the outside,

  • you don't want your substrates to float away.

  • You've got to keep them there.

  • OK?

  • And that's especially [LAUGH] true

  • in gram-positives, where we have no outer membrane.

  • So the question is, how does this species get from this side

  • to this side?

  • OK.

  • In the last couple years, people have proposed--

  • and so this has taken a long time.

  • People have been looking for these proteins for decades.

  • These are called "flipases."

  • So you still have this issue-- again,

  • this big, huge thing that needs to be transferred.

  • And I think what's even more amazing,

  • in the case of Staph. aureus, is that you

  • put on the pentaglycine in the cytosol.

  • So, here, what you'll see--

  • I think this is E. coli.

  • I can't remember one from the other.

  • But, instead of having DAP, which is diaminopimelate,

  • you actually have lysine.

  • So, here, what you have in Staph. aureus is a lysine,

  • and the lysine has an amino group.

  • And attached to this amino group is the pentaglycine.

  • And this all occurs in the cytosol.

  • So this is quite remarkable.

  • So then, not only do you have to get the disaccharide

  • with the pentapeptide on it, you need to have,

  • here, the pentaglycine on it, as well.

  • And this becomes really important in thinking

  • about trying to study what's going on in the polymerization

  • reaction, which is the target of natural products

  • that are currently used, clinically.

  • OK.

  • So this thing's got to flip.

  • And then what you have is a substrate.

  • You have a growing chain.

  • OK, and then what you need to do is extend this chain,

  • so you have a glycosyltransferase.

  • So you have two things.

  • You have phosphoglycosyltransferase.

  • And then the other thing you have is a TP, which

  • is a transpeptidase.

  • OK.

  • And so the transpeptidase-- we're going to come back

  • to this in a second, but--

  • is ultimately responsible for making a cross link.

  • Which is what gives the bacteria cell wall rigidity.

  • Now, in many organisms, the glycosyltransferase

  • and the transpeptidase are on the same protein.

  • They're two domains.

  • But, in many organisms, they're not.

  • OK, so you have two separate proteins.

  • And furthermore, in Staph. aureus

  • there are now five of these kinds of proteins.

  • So the question is, what are all five

  • of these glycosyltransferase doing?

  • Which ones are involved in which?

  • Which ones are involved in antibiotic resistance?

  • And I think, when you start looking at it like this,

  • you know, it's very complex.

  • You realize what a hard problem this actually is.

  • But we now have the tools, I think,

  • because of beautiful studies that

  • have been done in the last few years,

  • to start investigating this.

  • So this just shows, here, again, we have our lipid 2.

  • We have our growing chain.

  • And here we have our pentaglycine.

  • So this is Staph. aureus.

  • And we take D-alinine D-alinine, and form a cross-link

  • and kick out D-alinine.

  • And many of you have probably seen this before.

  • I used to teach this in high school.

  • [LAUGH] So that D-alinine D-alinine

  • looks like penicillin.

  • And we understand that this works--

  • it looks amazing, like a serine protease, which

  • you're all very familiar with.

  • We've seen this hundreds of times, now,

  • in the earlier part--

  • to form this cross-link.

  • And that cross-link is essential for the viability

  • of the organism, in different ways.

  • And you can imagine, if a bacteria is dividing,

  • that you might have different peptidoglycal structure

  • at the site, where the two dividing bacteria are

  • going to split apart.

  • So that might be why you want to have

  • multiple glycosyltransferases in this overall process.

  • OK.

  • So this is just a cartoon that shows you targets.

  • These are all natural products.

  • Here's penicillin.

  • It targets--

  • It looks-- not in this picture, but you

  • can use your imagination.

  • It looks just like D-alinine D-alinine.

  • Binds in the active site, and covalently

  • modifies a serine involved in that reaction.

  • Moenomycin.

  • What does this look like?

  • This is sort of amazing.

  • It's got this lipid thing, hanging off the end.

  • That's a natural product.

  • It binds, also, to the glycosyltransferase.

  • And people are actively investigating this.

  • You can imagine, this is not so easy to make

  • as a new antibiotic.

  • And then we have vancomycin, and vancomycin

  • is able to bind D-alinine D-alinine.

  • So these are all natural products that target cell wall.

  • And, by far and away, the penicillins

  • are the ones that are used much more prevalently.

  • We have hundreds of variations of the theme.

  • And, again, it's the war between the bacteria and the human,

  • to figure out how to keep themselves growing.

  • And so we have many variations on the beta-lactams.

  • And you can take this even a step further, if you go--

  • in addition to the peptidoglycan,

  • you have polymers of teichoic acid--

  • which I'm not [LAUGH] going to go into.

  • But now people, for the first time, this year,

  • have been able to reconstitute this polymer biosynthetic

  • pathway.

  • And this is a new target for design of the antibacterial.

  • So I think it's exciting times, and we have really smart people

  • working on this problem.

  • And they now, for the first time, can set up the assays,

  • so they can screen for small molecules that

  • hopefully can target cell wall, which is unique to bacteria.

  • OK.

  • So what I want to do is talk about,

  • in the last few minutes, as we're now

  • moving into Staph. aureus.

  • OK?

  • And we're going to focus in on heme uptake rather

  • than siderophore uptake.

  • But if you look at this, what do we know about Staph. aureus?

  • We know what a bit, because everybody and his brother

  • has been studying it because of the problems with resistance.

  • So, here, again, Staph. aureus actually

  • has two biosynthetic pathways encoded in its genome.

  • And what these pathways code for are these two siderophores.

  • OK?

  • And if you look at this, what's unusual?

  • Does anybody see anything unusual

  • about the siderophore structure, if you look at it carefully?

  • I don't want to spend a lot of time on this,

  • but what do you see in the structure?

  • Can you read it?

  • Or, if you brought your handout, you can probably read it.

  • Since I insist on having the windows open,

  • it's harder to read this.

  • But what do we see, in siderophore,

  • in this siderophore, Staphyloferrin A?

  • See anything you recognize?

  • Yeah.

  • AUDIENCE: Some citrates?

  • JOANNE STUBBE: Yeah, citrates.

  • So, again, we're using citrate.

  • We saw polycitrate can bind iron as a siderophore in itself.

  • And, in fact, most gram-negative bacteria

  • have iron-siderophore uptake system.

  • Here, actually, all of these--

  • if you look at this carefully, the biosynthetic pathway,

  • you know, is made out of basic metabolites.

  • OK?

  • That you see out of normal, central metabolic pathways.

  • And what happens is, there's an ABC transporter and an ATPase--

  • FhuC is an ATPase--

  • all of this is written down in your notes--

  • that allow the siderophore to bring iron into the cell.

  • And I think what's interesting here,

  • and I've already pointed this out,

  • in addition to the siderophores that the organism makes it also

  • has a generic transporter that allows siderophores

  • made by other organisms to bring iron into the cell.

  • And so, again, that's a strategy that's

  • used over and over again.

  • So here's a xenosiderophore transport system,

  • desperately trying to get iron.

  • OK.

  • So the ones we're going to be talking about and focusing on

  • specifically are the heme uptake systems.

  • And these are the ones you've already

  • hopefully thought about, now, from your problem set.

  • We have to extract--

  • I just told you that red blood cells have most of the iron.

  • So Staph.

  • has been incredibly creative in generating endotoxins

  • that lyse red blood cells, allowing the heme--

  • hemoglobin, OK?

  • So we have endotoxins from the organism

  • that lyse red blood cells.

  • And so what you get out, then, is hemoglobin.

  • Which, again, has four hemes and iron.

  • And you want to get--

  • the key thing is to get the iron out of the heme.

  • So you want to be able to extract the iron out

  • of the heme.

  • And also-- and I have this down in your nomenclature--

  • it turns out red blood cells have another protein, called

  • "haptoglobin," that binds to hemoglobin.

  • And that's another place that these organisms have

  • evolved to extract the heme--

  • to extract the heme.

  • So, in all of these cases, you're

  • extracting the heme out of the protein.

  • And so, over here, you see the two different ways to do that.

  • And we have different proteins that are able to do this.

  • And then, eventually, the heme that's extracted

  • is passed through this peptidoglycan,

  • eventually to the plasma membrane, where

  • the heme goes into the cytosol.

  • And in this organism, to get it out,

  • you have to break down the heme.

  • You have to cleave it into pieces by the enzyme called

  • "heme oxygenases."

  • OK.

  • So I don't want to really say very much

  • about the siderophores, except to say--

  • let me comment on iron sensing.

  • And you saw-- and this would be Staph. aureus,

  • but it's in true iron-sensing for most bacteria.

  • You saw iron-sensing predominantly

  • at the translational level.

  • Which was unusual.

  • That's why we talked about it, in humans.

  • Here, iron-sensing is predominantly

  • at the transcriptional level.

  • So this sensing occurs transcriptionally.

  • And so you have a transcription factor, which is called "Fur."

  • And Fur is a transcription factor.

  • That name is used for almost all organisms.

  • And I'm not going to say much about this,

  • but we're going to look at the operon in a minute.

  • But here's Fur.

  • And if Fur has iron bound, what it does is a repressor.

  • And it shuts down transcription of all the proteins

  • that you might think it would shut down.

  • They can no longer take up iron into the cell,

  • because you have excess iron and you don't need anymore.

  • Again, you want to control iron, because you

  • have problems if you have too much iron

  • with oxidative stress.

  • OK.

  • So, if you look at the operon--

  • let's see.

  • So look at the operon, here.

  • So here's the operon.

  • And we're going to see that the key proteins involved

  • in heme uptake are called the "Isd" proteins.

  • And so, if you look at all of these Isd proteins, this Isd

  • protein and that one, they all have these little Fur boxes.

  • [LAUGH] So we have a Fur box ahead,

  • which regulates whether you're going to make a siderophore

  • or whether you're going to make all this equipment required

  • to take up heme.

  • So all of that makes sense, and people

  • have studied this extensively, in many of these organisms.

  • OK.

  • So what I want to do now is, I'm going to show you this cartoon

  • overview.

  • And then we'll look at a few experiments

  • that people have done to try to look at what basis in reality

  • this cartoon model has to what actually happens

  • inside the cell.

  • So let's look at--

  • I can never remember the names of these things.

  • I'm just going to call it the "Isd proteins."

  • And so there are two proteins, we're going to see,

  • that are closest to the surface, that directly interact with

  • hemoglobin-- or haptoglobin and hemoglobin--

  • the other ones that are going to somehow get

  • the heme out of the proteins.

  • And then these each have little NEAT domains.

  • So N1 is a NEAT domain.

  • So they have a name for that, which I've also written down.

  • It's, like, 120 amino acids.

  • And each one of these proteins sometimes has two,

  • sometimes has three, sometimes has one,

  • and they're structurally all the same.

  • But it turns out that you can't just pick up one and replace it

  • with another.

  • There's something about the spinach

  • on each side of these NEAT domains

  • that is key, you can imagine, for the directionality

  • of the transfer.

  • So you want something that the heme is going to get down here.

  • You don't want something where the equilibrium

  • is going to stay up there.

  • So this is not an easy problem.

  • And this is a problem that we discussed in the beginning--

  • the importance of exchange ligands.

  • Because somehow we're going to have a heme in a little NEAT

  • domain, but it's going to move into the next domain.

  • It just doesn't hop.

  • It's covalently bound.

  • So how do you transfer one heme to the next heme?

  • And we have a lot of structural information,

  • but I would say we still don't understand how

  • these transfers actually occur.

  • OK.

  • So there's a couple other things that I want to point out, here.

  • So IsB and IsH extract from heme and hemoglobin.

  • This gives you a feeling, which you also

  • saw from the problem set, that these little domains--

  • N1 domains, N2 domains--

  • are all NEAT domains.

  • So we have multiple domains.

  • And what we're going to see, and this

  • is key to the way these organisms function,

  • is that these Isd proteins are covalently

  • attached to the peptidoglycan.

  • So the issue is, we need to covalently attach the Isd

  • proteins to the peptidoglycans.

  • And the protein--

  • There are two different proteins that do this.

  • So the Isd proteins have ZIP codes.

  • Where have we seen this?

  • We see this over and over and over again.

  • We have little sequences of peptides that are

  • recognized by another protein.

  • OK?

  • So we have ZIP codes.

  • And the ZIP codes, I'll just say "see PowerPoint"

  • for the sequence.

  • And it turns out, if you look over here,

  • all of these proteins with a yellow anchor

  • have little ZIP codes in them.

  • OK?

  • [LAUGH] And they're recognized by a protein

  • called "sortase A."

  • OK.

  • So we'll see that, in addition to the Ist proteins,

  • we have sortases.

  • And we have sortase A and B, and they

  • recognize the ZIP codes, distinct ZIP codes,

  • and are required to attach the Isd proteins covalently

  • to the peptidoglycan.

  • And in the peptidoglycan of any gram-positive, a lot of things

  • are covalently attached to the peptidoglycan.

  • So, I mean, can you imagine-- how

  • dense do you need these proteins, to be

  • able to do these switches?

  • I mean, this is a cartoon overview

  • that really doesn't tell you anything

  • about the complexity of all that--

  • what does a peptidoglycan look like?

  • Well, it's got a lot of water and a lot of space

  • in between these N-acetylglucosamine,

  • N-acetylmuramic acids.

  • So this is involved in the covalent attachment.

  • And it, in fact, involves what you've seen over

  • and over again-- involves covalent catalysis

  • with a cystine in its active site.

  • OK?

  • So what I want to do is briefly look at what

  • these sortases actually do.

  • I'm not going to write it on the board.

  • I'll walk you through it and then, next time--

  • hopefully, you've already thought

  • about this in some form, but I'll walk you through it

  • and go through it next time.

  • And then what we're going to do is simply

  • look at a few experiments with Isd proteins,

  • to look at this movement of heme across the membrane,

  • similar to the kinds of experiments

  • that you had on the problem set that was due this week.

  • OK.

  • So, because I don't have much time

  • and I can't write that fast and you can't write that fast,

  • either, [LAUGH] I'm going to walk you

  • through sort of what's going on in this reaction.

  • OK.

  • So, remember, all of these things

  • are anchored to the plasma membrane.

  • OK, so that's the other thing.

  • Sometimes they have single, transmembrane-spanning regions.

  • Sometimes they have lipids that are actually bound.

  • I wanted to say one other thing, here.

  • So these yellow things are anchored

  • by sortase A. The blue thing is anchored by sortase B.

  • And IsdE is anchored by a lipid, covalently bound.

  • OK, so we have three different strategies, to anchor.

  • OK?

  • And every organism is distinct.

  • Whoops, I'm going the wrong way.

  • OK, so what happens in this reaction?

  • So here's our ZIP code.

  • OK, and what we know about this-- and here's sortase A.

  • Sortase A is anchored to the plasma membrane.

  • In a further cartoon, they don't have it anchored,

  • but I tell you it's anchored.

  • And we know we get cleavage between threonine and glycine.

  • And we know we have a sulfhydryl on the active site.

  • So, this chemistry, we've seen over and over and over and over

  • again, whether it's with serine or with a cystine,

  • you have to have the right equipment

  • to acylate the enzyme.

  • So what happens here is you acylate the enzyme.

  • And so this is the part of the protein that's

  • going to get transferred, ultimately, to-- this

  • is lipid 2, with the pentaglycine.

  • And at the end of the pentaglycine

  • you have an amino group.

  • That's-- you're going to attach this protein,

  • IsdA or IsdB to this lyse--

  • the end-terminal amino group of glycine in the pentaglycine.

  • So you form.

  • Again, you cleave this peptide bond.

  • And you have this piece left over from your Isd protein.

  • You now have this covalently attached to the sortase.

  • And again, what you're doing is going

  • to regenerate the sortase, so you

  • can do more of these reactions.

  • And here you're forming your linkage to the Isd protein.

  • OK?

  • Does everybody see what's going on in that reaction?

  • So another cartoon version of this, and then I'll stop here.

  • This is a more chemical version.

  • Again, this is the sortase.

  • Here is your amino-acid sequence.

  • You go through a tetrahedral intermediate.

  • This is all a figment of our imaginations,

  • [LAUGH] based on what we think-- what we do understand,

  • in the test tube of peptide bond hydrolysis--

  • not so much in the enzymes.

  • But you generate an acylated attached protein.

  • And then we have our pentaglycine,

  • the terminal amino group that goes through,

  • again, a tetrahedral intermediate to form

  • this linkage.

  • So what's happening-- I think this is, like, so, again,

  • amazing--

  • what's happening is, you're transferring--

  • you've got your lipid 2, and you've

  • transferred it across this membrane

  • into the outside of your bacteria.

  • So you've gotta hang it there.

  • That's why you need these big, huge lipids.

  • And what you're going to do is attach to this pentaglycine.

  • You're going to attach each of these Isd proteins, covalently.

  • And then what you do--

  • So you make this guy.

  • Then you attach this whole thing onto the growing polypeptide

  • chain.

  • I mean, this is, like, an amazing machine

  • that they've unraveled, I think, from studies

  • that have been done in the last five years or so.

  • So, next time, we'll come back and talk a little bit

  • about the Isd proteins, but I think

  • you should be fine, looking.

  • You've looked at-- all you're doing is transferring heme,

  • and we don't understand the detailed mechanism

  • of how that happens.

  • That's something hopefully some of you will figure out.

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