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Why don't mitochondria have plasmids?

Why don't mitochondria have plasmids?


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According to the endosymbiotic theory, mitochondria are descended from specialised bacteria (probably purple nonsulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm [ref].

And plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes [ref].

I was however taught that mitochondria have no plasmid and only have circular DNA. If the endosymbiotic theory is true, then how come mitochondria have no plasmid?


The mitochondrial genome is highly reduced; many mitochondrial genes have been transferred to the nuclear genome (see endosymbiotic gene transfer) and therefore the mitochondria are fully dependent on the nucleus to function.

Bacteria need not necessarily have a plasmid. Usually, all the important genes are present in the chromosomal DNA. Since the mitochondria have lost most of their genes and retain only a few genes that are highly essential for their function, the likelihood of retention of any plasmid DNA is very low. However, there are some reports of plasmid-like DNA in mitochondria (mostly in plants).

  1. Handa (2008): in Brassica
  2. Robison et al., (2005): in carrots
  3. Collins et al., (1981): in Neurospora (a fungus)

Likewise, chloroplasts also harbour plasmid-like DNA (google-scholar hits).


Mitochondria

00:00:06.20 Hi. My name is Jodi Nunnari. I'm a professor at the University of California at Davis,
00:00:12.29 in the department of Molecular and Cellular biology.
00:00:16.04 And in fact, I am a cell biologist and as such, I am dedicated to understanding how the insides of cells,
00:00:24.00 especially our cells, which are eukaryotic cells, are organized
00:00:27.28 and how the internal structures in those cells, help our eukaryotes, help our bodies function
00:00:34.14 and exist and be healthy.
00:00:37.01 So, in particular, I'm interested in a sub-cellular organelle called mitochondria
00:00:43.03 and that is the reason the title of my talk is "I Breathe for Mitochondria".
00:00:48.09 I'm very passionate about this organelle, I have studied it my entire career
00:00:54.10 and my fascination with the organelle began by thinking about how we came into being,
00:01:00.22 in other words, how we evolved, as eukaryotes, as such complex organisms.
00:01:06.19 So, I'm going to tell you a story
00:01:08.15 and I hope by the end of the talk that you will be as fascinated as I am about mitochondria.
00:01:14.10 So, once upon a time, about 4 billion years ago,
00:01:19.10 the first cell was born.
00:01:21.24 And that cell was really simple and a lot of scientists think that that simple cell,
00:01:27.14 and what do I mean by cell? A cell is a compartment enclosed by a membrane
00:01:33.10 which is a lipid based structure that by its very nature is impermeable to water and other ions.
00:01:40.27 So, it creates a barrier, or a protected environment.
00:01:44.10 That cell, a lot of scientists think, gave rise to the three major kingdoms of life
00:01:51.14 that exist on earth now: bacteria, archaea and eukaryotes.
00:01:56.29 Of course, we're eukaryotes.
00:01:59.03 Now, bacteria and archaea are also known as prokaryotes.
00:02:04.01 And they represent an amazing diversity of life on this planet and we wouldn't exist without them.
00:02:11.01 They're simple cells in comparison to our eukaryotic cells,
00:02:15.06 but they can actually exist, they can talk to one another,
00:02:18.03 they can aggregate and function in communities, but if you look inside them,
00:02:23.09 they're relatively more simple than us eukaryotic cells.
00:02:27.25 Eukaryotic cells, the hallmark of a eukaryotic cell is that inside of it,
00:02:33.19 it contains a compartment that encloses our genetic material,
00:02:38.15 or one of our major components of our genetic material, our nuclear chromosomes.
00:02:43.19 It's called the nucleus, I'm sure you guys are all familiar with that.
00:02:47.20 That's the hallmark of a eukaryotic cell, but the eukaryotic cell has many more compartments than just that
00:02:53.17 and these have all become specialized in a way that has enabled these cells
00:03:00.00 to build complex multi-cellular organisms, like, for example, me.
00:03:05.18 Who can talk and breathe and walk and so on.
00:03:09.22 Now, as a, how did that happen? How can a eukaryotic cell do that
00:03:14.09 and prokaryotes can't?
00:03:16.16 Well, one of the answers lies in the fact that eukaryotic cells have expanded by almost 20,000 fold:
00:03:24.14 for example, their genetic material.
00:03:26.09 And genetic material encodes the building blocks, or the map, of the cell.
00:03:31.29 The proteins, all the regulatory mechanisms that allow us to respond to the environment.
00:03:38.14 It expanded eukaryotes over prokaryotes, its genome, by that much.
00:03:43.04 Now, as a consequence, they happen to be much larger cells,
00:03:46.28 and if you look down here, to this image, this simple bright field image,
00:03:53.07 you can see in white, the white circle, is a eukaryotic cell
00:03:57.03 and in the blue circle, and so is the red, two different types,
00:04:00.05 a white blood cell and a red blood cell and in blue, that little itty bitty thing is a bacterium,
00:04:09.09 so that's in the other kingdom. So, as a result of expanding the genetic material,
00:04:14.23 these cells, our cells, are very much bigger and much more complex in size.
00:04:20.01 So, how come bacteria, prokaryotes, haven't done that?
00:04:24.22 In other words, what happened here, at this branch point in evolution,
00:04:29.05 that enabled us to become as complex as we are?
00:04:32.28 Well, enter of course, my passion, which is mitochondria.
00:04:37.20 And mitochondria are very unique in terms of eukaryotic organelles
00:04:43.22 because they're derived from bacteria.
00:04:46.25 Of course, the other organelle that's derived from bacteria, a bacterium,
00:04:51.02 is the chloroplast, which defines the plant cell.
00:04:53.26 But, in every single eukaryotic cell, has mitochondria or has had them and lost them along the way.
00:05:01.05 So, how did they come into being?
00:05:03.00 Well, the thought is, evolutionary biologists think that an archaic type prokaryote
00:05:10.15 engulfed a bacterium and they formed a symbiotic relationship
00:05:15.14 that evolved during evolution to give rise to the modern day eukaryotic cell.
00:05:22.26 Now, why do we think that?
00:05:24.04 Well, mitochondria have a lot of features that are in common with bacteria
00:05:29.04 and they're very, the genetic signature is there to indicate that.
00:05:33.18 They have two membranes, as you can see here,
00:05:36.24 they have an outer membrane and an inner membrane, just like bacteria,
00:05:41.02 and that inner membrane, those two membranes encapsulate two separate compartments,
00:05:47.00 termed the intermembrane space and the matrix.
00:05:49.24 Now, all four of these compartments are highly specialized
00:05:53.18 in terms of their composition and their function, yet they all work together to work for us in the cell
00:06:00.09 and that is to make energy through aerobic oxygen dependent production of energy
00:06:07.15 and of course, that's very advantageous, because we are on earth in a very oxygen-rich environment.
00:06:14.05 And as a consequence of being derived from bacteria,
00:06:17.29 they have their own genome, they have maintained their own genome,
00:06:21.12 although it’s been modified in a very advantageous way for us.
00:06:28.01 So, you can see from this image here of this electron micrograph
00:06:33.13 that's been 3-dimensionally reconstructed, that the inner membrane, in contrast to what you'd see in bacteria,
00:06:40.27 is highly proliferated and differentiated to form these deep invaginations
00:06:45.16 and this is exactly where energy is produced in this organelle.
00:06:50.06 Highly specialized for energy production.
00:06:54.04 So, as a consequence, maybe you weren't aware of this, but you actually have two genomes.
00:07:00.07 You have your nuclear genomes,
00:07:02.01 this happens to be the complement of chromosomes in the nucleus of a female,
00:07:07.05 and you know, its 23andme, but you also have your mitochondrial genome.
00:07:14.14 And it is significantly smaller. So, the smallest chromosome is about 47 million base pairs
00:07:22.02 that happens to be chromosome 21.
00:07:25.00 And in contrast 3,000 fold smaller is the mitochondrial genome,
00:07:30.22 which encodes only 13 proteins in addition to some regulatory RNAs,
00:07:36.04 and those 13 proteins have been maintained and specialized for energy production.
00:07:42.18 And they work together with the nuclear chromosomes to create energy for us
00:07:47.18 in a very coordinated way. Even though that genome is small,
00:07:52.24 it's very mighty and in fact, in comparison to your nuclear chromosomes,
00:07:58.24 which come from your mother and father,
00:08:00.28 it only comes from your mother and it's present inside of us, in each cell,
00:08:05.09 in many, many, many, many more copies than your nuclear chromosomes.
00:08:09.22 And I hope you appreciate that each little circle is a mitochondrial chromosome,
00:08:15.23 and that's how many of those are in a given cell in your body, in the background.
00:08:22.10 And of course, they're maternally inherited.
00:08:25.00 So, the fact that that genome has been so reduced over the course of evolution
00:08:33.25 makes it relatively energetically cost-efficient to maintain.
00:08:39.11 It's still connected to the membrane that actually drives,
00:08:43.15 is responsible, that inner membrane, for the synthesis of ATP
00:08:48.09 and still encodes part of the key complexes in that membrane
00:08:52.25 that give rise to energy. So, that small nature, the low energetic cost,
00:08:58.25 yet, being still there so it can be coordinated with the nuclear genome,
00:09:05.08 makes it, makes mitochondria turn into an extremely highly efficient machine
00:09:12.06 dedicated to energy production in a eukaryotic cell.
00:09:16.08 And so back to evolution here, it's very tempting to speculate that the acquisition of mitochondria
00:09:26.11 occurred at exactly the same time point that we branched off and become eukaryotes.
00:09:32.14 And that the reason for that is that they allowed the energy that the cell required
00:09:39.11 for the eukaryotic nucleus, the nuclear genome, to expand, as I mentioned before,
00:09:46.10 and that expansion allowed for the complexity, many more proteins to be synthesized,
00:09:51.17 many more regulatory mechanisms exist, to exist for us, which allowed us to become multicellular,
00:09:58.28 as you see here, so, I'd like to talk a little bit about how mitochondria makes energy for us
00:10:06.08 because it is an amazing process.
00:10:08.10 So, every day, we eat food, we are what we eat, literally,
00:10:12.27 and that food in the form of protein, carbohydrates and lipids
00:10:17.23 are taken up by our body and metabolized by a complex network of intermediary metabolic pathways.
00:10:25.13 And the background of this slide is a circuitry, the chemical reactions that occur inside our cells,
00:10:31.21 that link all the possible metabolism, not only breaking them down,
00:10:37.03 but building up building blocks that we need for life,
00:10:40.16 like, for example, lipids, that get put into our membranes, that make us impermeable to water
00:10:49.19 and protected. So, all those food sources break down in a way
00:10:55.02 that allows the production of simple carbon sources
00:10:59.03 that flow through what is known as the Krebs, or TCA, cycle
00:11:03.24 to produce reducing equivalents and these reducing equivalents
00:11:08.22 that are captured from the TCA cycle and other pathways in the cell,
00:11:13.05 funnel into a respiratory complex, a chain of macromolecular complexes in the inner membrane
00:11:22.18 that shuttle electrons in exchange for transporting protons to generate chemical energy
00:11:30.25 that, in a process that's dependent on molecular oxygen,
00:11:34.07 gets, that allows us to synthesize ATP.
00:11:38.21 Now, ATP is the energy that our cells use and that energy is stored in the chemical bond in that molecule.
00:11:47.14 And it fires all, a lot of these pathways that you see in the background here.
00:11:52.16 And allows us to make building blocks, again, to create cells for our bodies
00:11:57.25 and develop and exist.
00:12:01.21 So, this seems a little daunting, this network in the background
00:12:07.01 but it's fascinating in the sense that it really is who we are,
00:12:11.11 all our metabolism and in fact, exploring the relevance of these metabolic pathways
00:12:17.24 is undergoing a renaissance in biological research
00:12:21.26 as many investigators are beginning to realize that really understanding how these networks get changed,
00:12:29.14 in pathogenesis, in states such as cancer, are key to curing these diseases.
00:12:35.01 So, please don't be afraid of this network, it is life itself.
00:12:41.06 So, let's take a closer look at what's happening inside mitochondria
00:12:45.03 to produce energy. Here you see a schematic depiction of mitochondria,
00:12:51.11 the outer membrane, and the inner membrane, and here's the TCA cycle,
00:12:56.08 and carbon sources are coming in, they're producing reducing agents,
00:13:01.10 and those electrons are getting transported down an electron transport chain.
00:13:07.25 And by that I mean, these are huge macromolecular complexes that are embedded in the membrane
00:13:12.22 that move electrons and in doing so, can pump protons outside,
00:13:19.17 from the inside of mitochondria, to the outside.
00:13:22.26 And that generates what we call a proton motive force,
00:13:27.06 and this proton motive force is essential for producing ATP
00:13:32.06 and drives many other processes that are essential in the mitochondrion and our eukaryotic cells.
00:13:39.29 So, this proton motive force is harnessed by an ATP synthase complex,
00:13:45.13 another large complex in the inner membrane
00:13:48.00 to create ATP from ADP and phosphate.
00:13:53.07 And a lot, in a fascinating way, many of these complexes have been looked at at the atomic scale
00:14:00.26 and actual, we can see what they look like at the atomic scale,
00:14:04.18 and amazingly, they're fantastic machines.
00:14:08.05 The first one is actually a piston driven machine, that pumps protons,
00:14:15.09 and this one here, is especially elegant, it's a rotary machine,
00:14:20.29 and you can see that when protons flow down the gradient,
00:14:25.26 it drives the rotation of the head groups and produces conformational changes in those groups
00:14:34.16 that are harnessed for the production of ATP.
00:14:38.21 And if you think about it, in the context of the fact that we consume and produce our body weight,
00:14:46.03 every day, in ATP, you can imagine these engines running in our cells
00:14:51.25 going full-bore, thank goodness.
00:14:54.28 So, back to the fact that we have these two genomes,
00:15:02.03 both the nuclear genome and the mitochondrial genome.
00:15:04.26 And I've just hopefully convinced you how absolutely critical mitochondria are,
00:15:09.12 not only for us to exist, that's why we breathe, for energy production,
00:15:15.13 and I think that's, that importance is underscored by the fact that mutations
00:15:20.10 in both the nuclear genes and in the mitochondrial genome cause pretty severe and significant diseases.
00:15:27.22 There's a spectrum, they can present in very young people,
00:15:31.26 they can come to very old people, some of them are mild, some of them are extremely severe and fatal,
00:15:38.06 and very unfortunate, but you can have mutations in both that cause these diseases.
00:15:43.27 Both the nuclear and the mitochondrial genome.
00:15:46.10 And of course, if you have a mutation in your mitochondrial genome,
00:15:49.21 you may not, it may not be present in every single copy of the genome in your cells
00:15:54.17 and I've highlighted here, in blue and red, for example,
00:15:58.08 just so you can think about it, those might be the copies in your cell that are mutated.
00:16:04.29 Given that you inherit your mitochondrial DNA from your mother,
00:16:10.06 the percentage of mutated forms she has and how that gets segregated
00:16:14.14 into your various tissues often determines the severity of the mitochondrial disease that you have.
00:16:21.12 And often, mutations have different threshold levels in different tissues.
00:16:27.13 And in fact, the next slide depicts kind of the array of disorders that present in mitochondrial diseases
00:16:34.26 and you can see that you have effects from the very top of your head to the bottom of your body
00:16:41.21 and most of the major organ systems are affected in mitochondrial diseases.
00:16:46.27 But of course, especially the ones, for example, like skeletal muscle,
00:16:50.25 that rely quite a bit on the production of ATP.
00:16:54.00 As I said, these diseases are often devastating, and unfortunately, there is no cure for these diseases,
00:17:02.12 but I am hopeful that with the advent of new tools and genomics
00:17:07.29 and large scale analysis, that we will begin, with these tools, to unravel what happens in these diseases,
00:17:15.13 and to develop therapeutics, within the next 10 or 20 years or so,
00:17:20.14 that will hopefully be able to treat these diseases.
00:17:24.29 In addition to mitochondrial specific diseases, mitochondrial disorders,
00:17:29.26 mitochondrial dysfunction in many ways, is thought to contribute into many other diseases,
00:17:37.00 such as cancer and even to how we age, how our bodies age over time.
00:17:41.29 So, this is a fundamental organelle that's part of almost every cell that we have,
00:17:48.16 that's absolutely critical to understand, which is why I'm devoted to the research that I am.
00:17:55.13 So, what I've told you so far, and hope to convince you of the importance of mitochondria,
00:18:02.04 and why to be passionate about studying them,
00:18:04.28 is that they're unique in that they're derived from bacteria,
00:18:08.05 via an endosymbiotic event and that they're probably pivotal in the evolution
00:18:13.24 of who we are today, specifically of eukaryotic cells.
00:18:18.09 As a consequence of their origins, they have their own genome,
00:18:22.28 and they're able to create a proton motive force in a very efficient manner because of their small genome
00:18:29.22 and their large inner-membrane surface area to synthesize ATP
00:18:36.14 and to generate that for many other things that are important for our cells
00:18:41.06 to exist. And they're also essential, of course, for human health.
00:18:48.17 Now, even though they have been derived from bacteria,
00:18:53.05 as I mentioned, their genomes are now much smaller,
00:18:55.20 and as a consequence, they can't survive alone.
00:18:59.09 If you took them outside of a cell, they can't exist, you can't build one, however,
00:19:06.12 from scratch, you need to maintain them inside cells.
00:19:10.11 So, they're semi-autonomous, we refer to that as semi-autonomous.
00:19:15.00 And this just really is a schematic depicting how different they are from their ancestors,
00:19:22.23 which started with anywhere around 4,000 genes and now,
00:19:28.05 present day mitochondria only have 12, so they've lost a lot of their genetic material,
00:19:34.19 a lot of it is just gone, a lot of it has gone to the nucleus,
00:19:38.14 and then, there are new innovations for mitochondria,
00:19:42.03 many new, different, and different from their bacterial origins, functions that they have,
00:19:47.25 and in fact, one of those, of course, is the ability to import proteins
00:19:52.28 that are synthesized in the cytosol as a consequence of genes being in the nucleus.
00:19:57.29 And being able to import them inside the organelle, and actually properly sort them
00:20:03.13 to all the various different compartments that they have.
00:20:06.28 They also have evolved ways of importing lipids so that they can grow,
00:20:11.13 they self-template and grow inside cells.
00:20:14.13 And they've also acquired dynamic behaviors,
00:20:18.12 which is really, which are really important for them to integrate into the functions required in eukaryotic cells.
00:20:26.17 And this just really makes the point in a visual way,
00:20:30.26 of how different they are from their ancestors.
00:20:35.15 So, on the bottom here, you see a bacterium, and it's a very solitary thing in this instance,
00:20:41.10 very rod-like shaped, bean-like shape, and it's, this one is in the process of division,
00:20:46.14 in the bottom on the top here is mitochondria in a eukaryotic cell.
00:20:51.09 This eukaryotic cell is a single celled organism, the budding yeast Saccharomyces cerevisiae,
00:20:57.24 which many of us use as a tool inside the labs,
00:21:02.01 an excellent genetic tool to dissect the function and the biogenesis of the mitochondrial compartment,
00:21:09.11 and other things. And what you see here is that in contrast to the bacterium,
00:21:15.00 the mitochondria in this cell are very connected.
00:21:19.20 And the genome inside of them is distributed throughout this network
00:21:24.25 that they have formed and in fact, you can see that really nicely on the next slide
00:21:30.12 in this instance in time, in this eukaryote, this is a stereo pair,
00:21:34.11 if you can cross your eyes, you can see it in three dimensions,
00:21:39.00 and you can see that in this instant of time, the mitochondria's present in a single copy,
00:21:45.24 but it's highly differentiated, it's branched,
00:21:48.23 it's distributed very nicely all over the cell.
00:21:52.25 But if you look at the behavior of this organelle over time,
00:21:56.19 and that's shown here, you can see events corresponding to mitochondrial fusion,
00:22:02.01 in other words, coming together, and mitochondria dividing,
00:22:06.04 and it turns out the machines, the molecular machines that mediate these processes
00:22:10.18 are new inventions inside the cell.
00:22:13.18 These organelles don't divide like their ancestors did.
00:22:17.01 Now, why have they evolved these kinds of properties to be dynamic?
00:22:21.04 Well, first off, if you connect up mitochondria like this,
00:22:25.15 you make a real efficient energy conductor and it's able to distribute ATP, for example,
00:22:34.02 very efficiently through this cell.
00:22:36.04 Secondly, this dynamic behavior, this fusing and dividing,
00:22:41.04 allows both the organelle, in other words the lipid part of it,
00:22:45.23 and the genome, to be nicely distributed also, which is key because you can't make these de novo.
00:22:52.27 And then there's also content mixing, when two mitochondria fuse,
00:22:59.24 to become a single one, they can mix their compartments together,
00:23:05.12 and so, for example, if you have a certain load of mutation in that organelle,
00:23:11.19 because you have a mutated form of mitochondrial DNA,
00:23:14.12 in a certain percentage, you can kind of buffer the effects of that with the rest,
00:23:19.06 which is normal and wild-type.
00:23:21.14 And then finally, this dynamic behavior, this constant changing,
00:23:26.24 allows them to be a responsive system, responsive to the needs of the cell.
00:23:33.01 And in that context, you can see that this is harnessed nicely
00:23:37.08 because if you look at mitochondria,
00:23:40.14 where it is, what it looks like, inside diverse cell types,
00:23:44.16 for example, skin cells, or skeletal muscle cells, these images are taken from a live zebra fish,
00:23:51.13 which is a really great model, again, vertebrate model, for cell biologists,
00:23:57.15 you can see that what the mitochondria look like, where they are,
00:24:01.29 are very different in these two cell types.
00:24:04.20 Completely responding to the needs of those cell types for energy and other things.
00:24:09.12 So, they're adaptable because of their dynamic behavior.
00:24:13.15 And then, finally, dynamic behavior has been harnessed
00:24:17.07 to kind of facilitate the communication of mitochondria with other compartments inside cells.
00:24:23.16 So, let's go back to thinking about how we arose,
00:24:27.06 the eukaryotic cells arose, and the other major endomembrane system inside the cell,
00:24:35.07 which is the endoplasmic reticulum. The endoplasmic reticulum is the compartment
00:24:40.20 that encloses the chromosomes, the nuclear chromosomes,
00:24:44.06 hallmarks of eukaryotic cells, the nucleus, and proliferates from there
00:24:49.23 and spreads out throughout the cell to form a network that almost acts also as a structural component,
00:24:55.25 as well as an entryway for the secretion of proteins outside the cells for communication.
00:25:02.17 These two ancient endomembrane systems came together and have evolved ways to communicate
00:25:09.27 and that is shown here, in this movie, again, this is the simple eukaryote, budding yeast.
00:25:15.19 And you can see in red are mitochondria and in green are endoplasmic reticulum
00:25:21.06 and you can see how dynamic the behavior of both is,
00:25:24.11 but you can also see, I hope, that in many places they're connecting and contacting
00:25:29.22 and these are extremely important functional hubs where these two organelles are communicating
00:25:36.09 and the endoplasmic reticulum is even aiding in how mitochondria divide and distribute,
00:25:42.12 so these two ancient endomembrane systems have evolved together
00:25:46.21 and have evolved ways to communicate that are really important for the health of eukaryotic cells.
00:25:52.16 So, in the second part of the talk, I wanted to point out that even though mitochondria are bacterial in origin,
00:26:00.18 they have evolved many additional behaviors
00:26:03.03 that make them amenable for our eukaryotic cells.
00:26:08.01 They're dynamic behaviors that enable them to communicate with other cellular structures,
00:26:13.04 and most importantly, these dynamic behaviors,
00:26:16.17 the mechanisms actually, that cause these dynamic behaviors,
00:26:21.26 are all wired into to other signaling pathways that monitor the health status of cells.
00:26:29.04 And so, this has allowed mitochondria to become integrated with cellular needs
00:26:35.07 in a very nice way. So, I hope that I have convinced you
00:26:41.18 that mitochondria are an absolutely fascinating organelle
00:26:45.26 and I think the best is yet to come in terms of studying them.
00:26:50.26 As I said before, it's an exciting time in biology, where advances in proteomics,
00:26:57.00 in other words, sequencing proteins, sequencing genomes, is now available,
00:27:02.24 and we can take a system wide view of how this organelle functions
00:27:07.12 within a cellular and organismal context
00:27:11.11 to hopefully unravel its role in normal situations and also in disease situations.
00:27:19.08 So, if I've tantalized you to delve further,
00:27:23.00 here's three possible places where you could start.
00:27:26.13 These are three very accessible papers, go to the library and get them,
00:27:31.19 and I encourage you, at some point in your life, to study mitochondria.
00:27:36.04 Thank you.

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Prokaryotes are single-celled organisms that are composed of the bacteria. Unlike eukaryotic cells, they are less structured, contain no nucleus, and lack membrane-bound organelles. And being single-celled as they are, prokaryotes too don’t have mitochondria.

In fact, in a loose sense, they serve as the “mitochondria” of themselves. To put it another way, mitochondria are part of eukaryotic cells, which according to scientific studies evolved from ancestral bacteria.

Endosymbiosis Theory (Source: Wikimedia) Lynn Margulis (Source: Wikimedia) The mitochondria and chloroplasts (photosynthetic organelle) in eukaryotes are the known descendants of aerobic prokaryotes. In 1967, scientist Lynn Margulis published her Endosymbiosis theory about the formation of eukaryotic cells as well as the origin of the organelles contained inside them.

To explain the origin of the mitochondria and chloroplasts, she suggested that they were once free-living prokaryotes that were engulfed by a larger eukaryotic cell.

  • Through time, the organelles became one with those cells, yet remained to be genetically distinct from their host. One important evidence for this claim is the presence of unique genetic material in the eukaryotes’ mitochondria and chloroplasts.
  • Margulis added that life itself, therefore, prevailed over the world not by combat, but rather by networking.


Why Do We Inherit Mitochondrial DNA Only From Our Mothers?

For a long time, biologists thought our DNA resided only in the control center of our cells, the nucleus.

Then, in 1963, a couple at Stockholm University discovered DNA outside the nucleus. Looking through an electron microscope, Margit and Sylvan Nass noticed DNA fibers in structures called mitochondria, the energy centers of our cells.

Our mitochondrial DNA accounts for a small portion of our total DNA. It contains just 37 of the 20,000 to 25,000 protein-coding genes in our body. But it is notably distinct from DNA in the nucleus. Unlike nuclear DNA, which comes from both parents, mitochondrial DNA comes only from the mother.

Nobody fully understands why or how fathers’ mitochondrial DNA gets wiped from cells. An international team of scientists recently studied mitochondria in the sperm of a roundworm called C. elegans to find answers.

Their results, published this week in the journal Science, show that paternal mitochondria in this type of roundworm have an internal self-destruct mechanism that gets activated when a sperm fuses with an egg. Delaying this mechanism, the scientists found, led to lower rates of embryo survival. Down the road, this information could help scientists better understand certain diseases and possibly improve in vitro fertilization techniques.

This work “comes closest to elucidating a key development process that has perplexed us for a long time,” said Justin St. John, a professor at the Hudson Institute of Medical Research in Australia, who was not involved in the research.

It’s well known that the transfer of mitochondrial DNA from mother to offspring, often called maternal inheritance, occurs in humans and most multicellular organisms. Maternal inheritance is what allows genetic testing services like 23andMe to trace our maternal ancestries. You inherited your mitochondrial DNA from your mother, who inherited hers from her mother and so forth.

Maternal inheritance also gave rise to the idea that there exists a “Mitochondrial Eve,” a woman from whom all living humans inherited their mitochondrial DNA.

Before this research, it had been thought that maternal inheritance was orchestrated by processes in the mother’s egg cells, said Ding Xue, a professor at the University of Colorado Boulder and one of the authors of the paper. Large structures called autophagosomes, for instance, are known to engulf paternal mitochondria shortly after a sperm penetrates an egg.

Dr. Xue and his colleagues found, however, that the paternal mitochondria in the roundworms actually started to break down before any autophagosomes reached them. “It’s like a suicide mechanism,” said Byung-Ho Kang, a professor at the Chinese University of Hong Kong and another author of the paper.

The researchers identified a gene, called cps-6, that seemed to initiate the breakdown process within paternal mitochondria. They found that deleting cps-6 caused paternal mitochondria to linger longer in the embryo. It also led to higher rates of embryonic death.

“This paper provides the first experimental data suggesting that it’s not good to keep sperm mitochondrial DNA,” said Vincent Galy, a researcher at Pierre and Marie Curie University in Paris, who was not involved in the study.

It’s unclear whether having some paternal mitochondrial DNA in our cells leads to health problems. To date, there’s been one reported possible case, detailed in 2002 by researchers in Denmark. In a man with mitochondrial myopathy, a neuromuscular disease, the scientists discovered a mutation on mitochondrial DNA that came from his father. It’s possible, however, that the mutation occurred spontaneously after conception, rather than being inherited directly from his father.

Further research could shed light on diseases caused by mitochondrial DNA, which can lead to blindness, nerve damage and dementia, Dr. Xue said. Because it’s a somewhat lengthy screening process, doctors don’t generally check patients for the inheritance of paternal mitochondria. But “as we do more studies, we might actually find that it’s closely related to some human diseases,” Dr. Xue said.

More studies could also expand understanding of an in vitro fertilization technique that involves injecting a single sperm directly into an egg. Some researchers have studied whether this technique leads to the presence of sperm mitochondrial DNA in the embryo, but “there are contradictory results,” Dr. Galy said.

The big mystery that remains is why maternal inheritance occurs so consistently across organisms, Dr. Xue said. One theory has to do with the fact that sperm must generate a lot of energy when competing to fertilize an egg. During this time, sperm mitochondria are overworked, which could possibly damage their DNA and lead to mutations.

But this theory, and all others, are still speculative, Dr. Xue said. “This is a longstanding biological question,” he said. “There must be a fundamental, important reason why most species actually adopt the same style of mitochondrial inheritance.”


Part 2: Mitochondrial Metabolism and Cell Decisions

00:00:08.09 Hi.
00:00:09.22 My name is Jared Rutter,
00:00:11.00 and I'm a Professor in the Department of Biochemistry
00:00:13.06 and an Investigator of the Howard Hughes Medical Institute
00:00:16.17 at the University of Utah.
00:00:18.03 And I'm gonna tell you in this second part of my series
00:00:20.28 about what I believe to be a very important role of mitochondria,
00:00:25.14 and their metabolism,
00:00:27.15 in controlling how cells make decisions.
00:00:30.27 And in this talk, I'm going to allude to some data
00:00:34.25 generated by Vettore Therapeutics,
00:00:36.17 which is a company that I co-founded
00:00:39.03 and I'm quite involved in.
00:00:41.07 So, as I alluded to in my first part,
00:00:45.02 the first part of this series,
00:00:47.27 my laboratory made it a goal to understand some of the
00:00:52.24 uncharacterized mitochondrial proteins
00:00:55.10 that are conserved across evolution.
00:00:57.02 And that has led us into thinking about a lot of different mitochondrial processes
00:01:02.06 and making what we believe are some interesting discoveries
00:01:04.27 about how mitochondria work
00:01:08.06 and how they communicate with the rest of the cell.
00:01:10.16 And what I'm going to tell you about today is a story
00:01:13.22 about metabolite transport.
00:01:16.14 So, when glucose is brought into the cell,
00:01:19.03 it's converted through the actions of glycolysis
00:01:21.27 to pyruvate.
00:01:23.21 And that pyruvate, in most differentiated cells in our body,
00:01:27.06 is taken into the mitochondria,
00:01:29.04 where it's converted to acetyl-CoA,
00:01:31.02 which then donates its carbons to the TCA cycle.
00:01:35.27 And through this process,
00:01:38.14 this enables highly efficient ATP production,
00:01:41.01 as I alluded to in detail in the first part of my talk.
00:01:47.12 So, some cells in our body, however,
00:01:50.10 don't do this quite so efficiently,
00:01:52.27 and instead convert pyruvate and other glycolytic intermediates
00:01:56.24 into building blocks that help to fuel
00:02:01.07 cell growth and proliferation.
00:02:02.22 And this is most famous in the context of cancer,
00:02:05.02 where this is known as the Warburg effect.
00:02:07.23 And again, this is thought to enable
00:02:10.20 building blocks to be produced from carbon that's brought into the cell,
00:02:14.15 rather than just the production of ATP.
00:02:18.16 So, I want to also point out that in this context
00:02:22.01 some of that pyruvate can be converted to lactate,
00:02:27.07 and that lactate be exported.
00:02:28.06 And that will be very important
00:02:30.22 toward the end of this talk.
00:02:34.10 So, this is, arguably, the most well known,
00:02:38.23 well studied metabolic pathway in all of biology.
00:02:42.03 But surprisingly, one obligate component of this pathway
00:02:46.27 was not molecularly identified until a few years ago,
00:02:49.11 and that is the process by which
00:02:52.21 pyruvate enters the mitochondria.
00:02:54.25 Pyruvate is a charged molecule
00:02:56.26 and doesn't pass through membranes efficiently on its own.
00:02:59.01 It needs a protein to enable that to happen.
00:03:01.15 And that protein was, again,
00:03:03.24 not molecularly identified until a few years ago,
00:03:06.15 when it turns out that two of the proteins
00:03:09.16 that we had been studying
00:03:11.23 as being highly conserved but uncharacterized mitochondrial proteins
00:03:15.24 turned out to form a dimeric complex
00:03:19.18 known as the mitochondrial pyruvate carrier, or MPC.
00:03:23.15 The MPC is an obligate heterodimer.
00:03:25.26 There's an MPC1 protein and an MPC2 protein.
00:03:29.00 Those two proteins come together.
00:03:31.14 Both of them are absolutely required
00:03:34.04 for the function of this complex.
00:03:35.28 And in the absence of one or the other,
00:03:38.08 the other one just gets degraded.
00:03:40.12 And I will allude to that later, when we talk about studies in mice.
00:03:45.17 A graduate student, John Schell,
00:03:48.19 was heavily involved in the discovery of the MPC
00:03:51.07 and the early work at thinking about the roles of this complex,
00:03:54.26 and he gives a great introduction to the discovery
00:03:58.18 and the importance of this protein
00:04:01.16 in mediating some of the metabolic effects
00:04:04.01 that we see in cancer.
00:04:05.25 And it would be great to watch.
00:04:08.25 But I just want to summarize that and tell you
00:04:11.20 that one thing that John found, not surprisingly perhaps,
00:04:15.06 is that many of those cells that do this so-called Warburg effect,
00:04:19.00 where pyruvate is maintained in the cytosol,
00:04:21.20 not imported into the mitochondria and oxidized.
00:04:26.02 many of those cells actually have
00:04:30.02 low expression of the MPC.
00:04:32.03 Or, in the case of some cancers,
00:04:34.08 mutations or deletions that impair the activity of the MPC.
00:04:38.06 And frequently, that is coupled with high expression
00:04:41.28 of this MCT4 lactate exporter
00:04:44.24 that removes lactate from the cytosol.
00:04:48.22 But the question really is, does that matter?
00:04:52.13 Does it matter that those cells
00:04:55.23 have this MPC-low/MCT4-high situation,
00:05:00.28 and as a result have a metabolic program
00:05:04.27 that's characterized by aerobic glycolysis, so to sp.
00:05:08.24 which is how it's known,
00:05:11.14 as opposed to carbohydrate oxidation in the mitochondria?
00:05:14.17 Does that metabolism actually matter
00:05:17.07 for the behavior of those cells?
00:05:19.10 And the system in which we've studied that in greatest detail
00:05:22.28 is depicted here, and this is the intestinal epithelium shown here.
00:05:27.11 And the key feature of this is that these intestinal stem cells.
00:05:31.05 those intestinal stem cells sit here
00:05:35.03 at the base of the crypt,
00:05:37.08 in a protected compartment,
00:05:39.06 and proliferate and then differentiate
00:05:41.29 as they move up the crypt and into the villus,
00:05:44.06 eventually forming all the mature cell types
00:05:46.20 of the intestinal epithelium
00:05:49.28 that perform the barrier function and all the other essential functions
00:05:54.02 that this epithelium performs.
00:05:57.04 There's also another great thing about studying the intestinal epithelium,
00:06:01.05 and that is that it's very highly organized.
00:06:03.13 Again, with the stem cells sitting at the base of this crypt,
00:06:07.13 you know where they are, you know what they look like.
00:06:10.08 And also, there are great ex-vivo systems for studying this system.
00:06:15.09 And another great feature of the intestinal stem cell system
00:06:19.19 is the abil. the ability we have to make
00:06:22.26 these so-called intestinal organoids, as shown here,
00:06:25.23 and these are two examples shown.
00:06:27.25 So, these organoids are essentially an intestinal epithelium
00:06:31.23 that is folded back on itself to create
00:06:34.28 an enclosed structure that is complete with intestinal crypts,
00:06:39.04 as shown here,
00:06:41.01 where the stem cells, again,
00:06:42.25 sit at the base of this crypt,
00:06:45.07 and as they proliferate and differentiate
00:06:47.01 cause the extrusion of this crypt
00:06:50.01 from what would otherwise be a spherical organoid.
00:06:53.03 So, one of the things that John wanted to do
00:06:56.15 is ask the question of whether these stem cells,
00:07:00.10 which normally have low expression of the MPC,
00:07:03.14 actually require that low expression of the MPC
00:07:05.29 to act like stem cells.
00:07:07.27 So, what he did was rather simple:
00:07:10.12 force those stem cells to express the MPC at a higher level
00:07:14.27 and ask, what is the consequence of that?
00:07:16.21 And what he found is that that essentially causes these stem cells
00:07:20.03 to stop acting like stem cells.
00:07:22.02 They lose the ability to make new crypts, as shown here.
00:07:26.06 Those cells don't die,
00:07:28.21 but they stop acting like stem cells
00:07:30.24 and even stop expressing many of the molecular markers of stem cells.
00:07:33.26 And interestingly, one thing that he found
00:07:36.14 is that this phenotype of MPC overexpression
00:07:39.22 was completely reversed
00:07:42.14 when he treated these organoids with an inhibitor of the MPC
00:07:45.17 that had been. had been discovered almost 50 years ago now,
00:07:48.22 and we now know to be a quite specific
00:07:52.23 and very useful inhibitor of the mitochondrial pyruvate carrier.
00:07:57.16 And moreover, John did another experiment,
00:08:00.17 which was to isolate stem cells from these wild type organoids,
00:08:04.21 plate them again,
00:08:07.08 and ask for their ability to make a new organoid.
00:08:10.07 And what he found is that treatment with this MPC inhibitor
00:08:14.07 in that experiment
00:08:16.13 caused a rather dramatic increase
00:08:18.29 in the ability of these stem cells to make a new organoid,
00:08:21.18 to a similar or even greater level
00:08:25.00 than the effects caused by very canonical, well known drugs
00:08:29.10 that are used to promote stemness:
00:08:31.10 valproic acid and an inhibitor of the GSK3-beta protein,
00:08:35.06 which causes activation of the Wnt/beta-catenin system.
00:08:40.15 And I won't show you the data for this, but loss.
00:08:44.12 genetic loss of the MPC in intestinal stem cells,
00:08:46.27 in vivo in mice,
00:08:49.06 not surprisingly leads to an expanded and hyperproliferative stem cell compartment
00:08:54.20 in vivo.
00:08:56.15 And I'll allude later to some of the consequences of that, we think.
00:08:59.14 So, the MPC sits here at this very critical juncture,
00:09:04.20 between the metabolic programs operated by many stem cells and cancer cells,
00:09:10.25 which require pyruvate metabolism in the cytosol,
00:09:15.26 and those characterized by pyruvate oxidation in the mitochondria.
00:09:20.08 It sits in this critical juncture.
00:09:22.02 And we believe that this MPC activity
00:09:24.16 -- the activity of this complex to promote mitochondrial pyruvate import --
00:09:28.22 has an active role in promoting differentiation
00:09:31.27 and limiting stemness.
00:09:35.15 And I want to make one critical point.
00:09:37.15 We've often thought about this,
00:09:40.00 and people ask us all the time,
00:09:41.22 well, does this mean these stem cells just don't have mitochondria?
00:09:44.18 It turns out, as pointed to in.
00:09:47.25 with yellow arrows here,
00:09:50.07 these stem cells are chock full of mitochondria.
00:09:53.08 They have more mitochondria
00:09:56.18 than the differentiated cells around them,
00:09:58.09 but it's just those mitochondria appear not to be focused
00:10:02.08 on doing mitochondrial pyruvate oxidation. It's really fascinating to think what they might be doing
00:10:08.17 and how that mitochondrial function is controlled.
00:10:13.13 So, the question is how this relates
00:10:17.09 to the signaling that goes on in stem cells,
00:10:19.22 because we all know about the signaling
00:10:22.12 that tells a stem cell to be maintained a stem cell.
00:10:26.01 And how does this metabolic program interface with that?
00:10:30.09 And I want to just point to a couple of experiments
00:10:33.14 done by colleagues of mine,
00:10:35.09 Roo Wisidagama, who was a graduate student in the lab of Carl Thummel
00:10:38.11 in the Department of Human Genetics at the University of Utah.
00:10:42.21 And they used the Drosophila system
00:10:45.16 and have done really elegant work studying the impacts of the MPC there.
00:10:52.04 And the system that they have employed is a system
00:10:54.21 that enables the generation of clones in the Drosophila intestinal epithelium
00:10:58.10 that, simultaneously to a genetic manipulation,
00:11:01.15 also turn on the expression of GFP.
00:11:05.06 So, you can see a clone, here, that. in the control animals,
00:11:09.19 that generates a clone of a certain number of cells.
00:11:13.02 And when the APC gene.
00:11:15.03 two genes in Drosophila.
00:11:17.17 are deleted, that clone becomes much larger.
00:11:19.28 And the APC gene is a tumor suppressor,
00:11:23.04 the most commonly mutated gene in colon cancer,
00:11:25.29 which causes hyperproliferation through constitutive activation
00:11:29.18 of the Wnt/beta-catenin pathway.
00:11:31.25 The same thing happens in flies,
00:11:34.08 and as a result, you get hyperproliferation
00:11:36.14 of those stem cells and a large clone.
00:11:40.13 And the experiment that they did, among many others,
00:11:43.26 is now to force those stem cells to express the MPC,
00:11:48.24 and ask, what is the effect of that?
00:11:50.24 And the effect of that is that those stem cells
00:11:54.04 essentially stop proliferating.
00:11:56.16 And very interestingly, these stem cells don't die.
00:11:59.14 They just stop proliferating, and this is quantified here.
00:12:02.28 They just stop proliferating.
00:12:05.25 So, even though the signaling is presumably
00:12:10.06 telling these stem cells to proliferate.
00:12:12.17 APC is mutated, the. the.
00:12:16.02 presumably the transcriptional program is driving proliferation.
00:12:19.08 But when the metabolism doesn't cooperate,
00:12:22.03 these stem cells don't proliferate.
00:12:26.00 I think that puts this effect of
00:12:29.11 the MPC controlling stemness and differentiation
00:12:32.10 into a very interesting light.
00:12:35.24 So, I alluded to data in mammals and in flies.
00:12:40.03 There's data that I won't show you in fish,
00:12:43.00 which shows, similarly,
00:12:45.18 a very important role of the MPC.
00:12:47.13 Others have shown this effect in other stem cell types.
00:12:50.13 So, does this actually have an impact on tumor formation?
00:12:54.09 Does this effect of the MPC control oncogenesis, in vivo,
00:13:00.03 in the intestine?
00:13:02.01 So, Claire Bensard, a current MD-PhD student in the lab,
00:13:05.02 did an experiment where she eliminated the MPC.
00:13:09.02 again, specifically in intestinal stem cells,
00:13:11.28 eliminated MPC1.
00:13:14.01 It's interesting. This is a hetero. heterodimeric protein.
00:13:17.27 So, we're deleting the MPC1 gene,
00:13:20.10 and the mRNA for MPC1 is lost.
00:13:22.13 MPC2 is not.
00:13:24.21 But interestingly, this is an obligate heterodimer,
00:13:27.04 and as a result of that even though MPC2
00:13:31.10 presumably continues to be expressed,
00:13:33.18 it's completely eliminated from the intestinal epithelium,
00:13:36.18 presumably due to degradation because its partner, MPC1,
00:13:40.29 is no longer being expressed.
00:13:42.22 So, we end up in a situation where the MPC
00:13:45.11 is absent from the intestinal epithelium.
00:13:47.28 So, what effect does this have on tumorigenesis?
00:13:51.03 So, Claire did a really nice experiment
00:13:54.09 where she subjected these mice to an environmental,
00:13:58.01 oncological stress in the intestine
00:14:00.25 and asked for their ability, or their propensity,
00:14:03.13 to generate tumors in the intestine.
00:14:05.11 And what she observed is a dose-dependent increase
00:14:08.05 in tumorigenesis from the wild type to the heterozygote
00:14:12.00 to the genetic loss animals,
00:14:14.15 as shown by the height of these bars --
00:14:19.06 it's the number of lesions per animal.
00:14:21.15 And the red colors indicate.
00:14:23.23 indicate more aggressive tumors,
00:14:25.28 again being generated in the. in those animals
00:14:28.25 where in the stem cells lacked MP. the MPC.
00:14:31.25 So, more tumors, and those tumors were more aggressive.
00:14:35.02 And again, all that's happening here is loss of
00:14:38.10 this mitochondrial pyruvate carrier specifically in the stem cells.
00:14:42.12 I think that's a very important consequence
00:14:46.16 of loss of the MPC.
00:14:48.05 So, not only does the MPC
00:14:50.13 appear to limit stemness, directly,
00:14:53.05 but also oncogenesis.
00:14:54.24 Most likely an indirect effect of affecting stemness.
00:14:58.13 And I haven't told you about this,
00:15:01.11 but it's becoming clear from others in the field
00:15:04.22 that this process also plays a very important role
00:15:07.25 in inflammation and fibrosis.
00:15:10.27 So, based on this,
00:15:13.00 we thought this would be a great idea for a way
00:15:15.24 to maybe deal with some of the pathologies
00:15:18.12 associated with these processes:
00:15:21.18 oncogenesis, hyperinflammatory disease, fibrotic disease.
00:15:26.18 And so, we decided to start a company
00:15:29.04 along with my uncle, Bill Rutter,
00:15:30.29 and decided to.
00:15:33.18 can we find a way to activate the MPC?
00:15:36.07 That seems to be what we need to do,
00:15:38.03 to activate this process, prevent oncogenesis or reverse it,
00:15:41.28 and potentially also prevent inflammation and fibrosis.
00:15:47.17 So, it. we started a company and hired a fantastic scientist
00:15:50.27 to lead the scientific operations,
00:15:53.01 Mark Parnell.
00:15:54.27 And we figured out very quickly that activating the MPC
00:15:58.23 was not going to be an easy task.
00:16:00.14 And to date, we've completely failed.
00:16:02.11 But what Mark did instead
00:16:05.19 was to come upon a way to perform a related metabolic manipulation
00:16:10.11 that seems to have many of the same consequences.
00:16:13.26 And that is through inhibition of this MCT4 protein.
00:16:18.07 So, again, this is a lactate exporter
00:16:20.25 that takes the lactate that's made from cytosolic pyruvate
00:16:25.22 and exports it.
00:16:28.10 And what appears to be the case.
00:16:30.13 when MCT4 is inhibited,
00:16:32.19 presumably cytosolic lactate accumulates,
00:16:34.27 cytosolic pyruvate accumulates,
00:16:36.19 and that perhaps just drives, by mass action,
00:16:39.15 mitochondrial pyruvate uptake and metabolism.
00:16:42.04 And the net effect is similar to as if.
00:16:44.20 to what we've seen when we overexpress the MPC genetically.
00:16:50.04 So, that's what we tried to do:
00:16:53.18 inhibit the MCT4 protein.
00:16:55.15 And Mark was able to develop
00:16:58.22 some very potent and specific inhibitors of the M. of MCT4,
00:17:02.22 and their statistics are shown here.
00:17:04.18 The key features of this is that the MCT4 inhibitor that he found,
00:17:09.01 this VB253 compound,
00:17:11.04 is very potent for MCT4
00:17:13.25 and selective over the related MCT1 protein,
00:17:17.19 inhibition of which seems to cause some toxicity.
00:17:21.00 So, this protein. this VB253 molecule is also.
00:17:25.09 has quite good pharmacological properties
00:17:27.24 and seems to be quite safe.
00:17:29.21 So, I'm gonna show you some of the data
00:17:32.09 that's been generated with this compound,
00:17:34.11 again, with the idea that by manipulating these metabolic pathways
00:17:37.16 we might be able to rewire metabolism,
00:17:41.15 change cell behaviors in a way that would be beneficial therapeutically.
00:17:47.25 One of the indications that we've been most interested
00:17:51.22 in trying to treat with this VB253 compound
00:17:55.28 is idiopathic pulmonary fibrosis.
00:17:58.29 And there's still a lot to be understood
00:18:01.22 about the disease pathogenesis of IPF,
00:18:06.26 but a few things that we do know.
00:18:10.06 it's clear that fibroblasts. fibroblasts become activated
00:18:14.09 and form this so-called myofibroblast cell type.
00:18:18.09 And myofibroblasts, like cancer cells and like stem cells
00:18:22.11 that we talked about previously,
00:18:24.20 exhibit this highly glycolytic phenotype,
00:18:26.20 characterized by low MPC expression, high MCT4 expression.
00:18:32.11 again, characteristic of that metabolic phenotype.
00:18:36.05 And this disease process is also contributed to
00:18:40.00 by pro-fibrotic macrophages,
00:18:42.14 which also exhibit that same metabolic profile.
00:18:46.16 So, this might be a scenario
00:18:49.12 where, if we could inhibit this MCT4 protein in this context,
00:18:53.02 this might reverse the pathogenic behaviors of these cells,
00:18:58.11 limit the deposition of extracellular matrix
00:19:01.07 and lung fibrosis.
00:19:03.10 So, that's what we set out to test.
00:19:05.18 So, just to show you some of the data behind what I just said.
00:19:08.23 so, it turns out these pro-fibrotic myofibroblasts
00:19:12.18 do express a large amount of this MCT4 protein,
00:19:17.05 as shown by staining here,
00:19:19.13 as well as these activated macrophages.
00:19:21.17 Both of them show this high MCT4 staining.
00:19:25.06 And again, this is the target of this VB253 molecule.
00:19:29.03 So, if this mol. if this protein is inhibited,
00:19:31.26 does it have an effect?
00:19:33.18 And it turns out that it does.
00:19:35.11 So, what you're looking at here is pathological scoring,
00:19:38.03 on the left,
00:19:40.21 of a mouse model of idiopathic pulmonary fibrosis,
00:19:45.02 where mice are given bleomycin to induce lung fibrosis,
00:19:48.09 and then the fibrosis is scored
00:19:51.25 as a function of time.
00:19:53.23 And interestingly, what was done here is to actually give bleomycin first,
00:19:57.06 create injury,
00:19:59.10 and then treat with this MCT4 inhibitor.
00:20:02.14 And in spite of doing it in that order,
00:20:05.05 which is a more challenging experimental paradigm,
00:20:07.26 this VB253 molecule actually decreases the fibrosis score,
00:20:10.29 a little bit better than what's the standard of care now in patients,
00:20:15.12 which is a molecule called pirfenidone.
00:20:18.11 And on the right, you see that smooth muscle actin,
00:20:20.23 which again is a marker of fibrosis,
00:20:22.24 which is almost normalized by VB253.
00:20:29.11 This are just examples of smooth muscle actin staining.
00:20:32.02 Again, from. compared to the control,
00:20:35.04 bleomycin causes a dramatic increase
00:20:39.00 in staining with smooth muscle actin,
00:20:41.06 coincident with fibrosis.
00:20:44.10 This is partially reversed by pirfenidone,
00:20:47.06 but seems to be almost completely reversed
00:20:50.00 by inhibition of MCT4.
00:20:52.09 And this seems to be cell autonomous.
00:20:55.04 And this was a very important result for us.
00:20:57.07 What's being done here is to take fibroblasts from IPF patients,
00:21:01.16 culture them in vitro, where they're the only cell type in the dish,
00:21:04.25 and in that context inhibition of MCT4
00:21:08.18 leads to a decrease in the production of smooth muscle actin.
00:21:12.20 So, that tells us that this effect on decreased smooth muscle actin
00:21:17.17 at least can be partially explained
00:21:20.11 by actions directly on these fibroblasts.
00:21:22.22 It's not something complex going through the brain or the liver
00:21:26.21 or the skeletal muscle.
00:21:28.18 This seems to be happening locally in the lung.
00:21:31.21 Finally, the last data slide I want to show you
00:21:36.06 is that this has an effect on the ability of the lung
00:21:39.14 to contract in breathing.
00:21:41.10 And this whole body plethysmography
00:21:43.19 is a measure of bronchial obstruction.
00:21:46.25 And you'll notice that when. upon bleomycin treatment,
00:21:49.13 there is more bronchial obstruction,
00:21:51.15 less breathing capacity.
00:21:53.11 That is maybe decreased a little bit by these two molecules,
00:21:56.10 which are, again, the standard of care
00:21:59.07 approved for treatment in humans.
00:22:00.25 But inhibition of MCT4 works a little bit better, even,
00:22:03.11 to decrease this bronchial obstruction
00:22:05.14 and promote healthy lung function.
00:22:08.03 So, we're really excited about the idea that rewiring metabolism in this way,
00:22:13.25 by inhibition of MCT4,
00:22:16.16 might change the behavior of these cells.
00:22:19.14 Again, we have no evidence that these fibroblasts die
00:22:23.10 or that these macrophages die.
00:22:26.08 They just change their behavior.
00:22:28.09 And that altered behavior decreases the production
00:22:32.18 of the extracellular matrix that promotes fibrosis
00:22:35.24 and leads to a decrease in fibrosis itself.
00:22:39.18 And we're really interested to try and understand
00:22:43.12 not only the applications of this in human disease
00:22:45.15 but also really fundamentally understand,
00:22:47.21 how is it that by just altering the metabolism of these cells
00:22:52.02 does that change their behavior?
00:22:54.29 And again, this just reminds me to tell you that
00:22:59.24 we think that this might be going on
00:23:02.23 through the actions of the mitochondrial pyruvate carrier.
00:23:04.29 Pyruvate that enters the mitochondria ends up being converted into
00:23:08.26 very important signaling molecules,
00:23:10.24 like acetyl-CoA and other TCA cycle intermediates,
00:23:14.13 that are known to have important signaling roles in the cytosol and the nucleus.
00:23:18.19 And perhaps, one of those molecules
00:23:21.13 plays an important role in changing cell behavior.
00:23:23.21 There are also very important redox effects.
00:23:26.04 So, I think it's critical for us to understand,
00:23:28.23 how do our cells sense their metabolic state?
00:23:32.25 And it's something that I believe we're just beginning to understand.
00:23:36.22 How do they know what metabolites they have?
00:23:39.10 And I think if we could understand that,
00:23:42.16 we might better understand
00:23:46.06 how manipulations like inhibition of MCT4
00:23:49.03 change their behavior.
00:23:50.24 And maybe we'd be able to make even better manipulations,
00:23:53.03 build better drugs that would treat people better.
00:23:56.01 So, I also think it's. you know, the MPC is not unique
00:24:00.23 in being an important metabolic control point
00:24:02.18 there are many others.
00:24:04.12 And if we can identify those metabolic control points and manipulate them,
00:24:06.13 we might be able to make even better manipulations
00:24:08.25 to better change the behavior of cells
00:24:13.21 to improve human health.
00:24:18.12 And I told you a little bit about IPF.
00:24:20.20 We think there are many manifestations
00:24:23.13 -- cancer being one that's perhaps the most obvious --
00:24:26.12 where modulation of this metabolic program,
00:24:29.22 the disposition of pyruvate,
00:24:32.00 might have important consequences.
00:24:34.05 And we're really anxious trying to understand
00:24:37.00 the different ways that this can be used.
00:24:40.00 So, I just want to thank the people that did the work.
00:24:42.16 I alluded to many of them as we went through.
00:24:44.29 They've been fantastic collaborators,
00:24:47.07 and thanks to those that paid for this work to be conducted,
00:24:50.19 and thanks to you for listening.


B1 Cell Biology Flashcards Preview

Where are Eukaryotic cells found?

Eukaryotic cells are found in plants, animals, fungi and protists (single-celled organisms that don’t fit other categories)

How large are Eukaryotic cells?

They are 10 - 100 micrometres in size

What is a Eukaryote?

A eukaryote is an organism made up of eukaryotic cells

What is a prokaryote?

A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle

How large are prokaryotic cells?

Prokaryotic cells are 0.1 - 5.0 micrometres in size

What are the key features of a Prokaryotic cell?


  • Plasmids - small ring/s of DNA
  • No Mitochondria
  • No chloroplasts
  • Single DNA loop floating in Cytoplasm

What are the organelles found in an Animal Cell?


  • Cell membrane
  • Nucleus
  • Ribosomes
  • Mitochondria
  • Cytoplasm

What is the role of the Cell Membrane?

The cell membrane separates the interior (inside) of the cell from the environment outside
It is selectively permeable (it can control substances moving in and out of the cell)

What is the role of the nucleus in the cell?

The nucleus is the "control centre" of the cell It contains chromosomes (which contains the cells genetic material)

What is the role of Ribosomes in the cell?

Ribosomes perform protein synthesis (making proteins)

What is the role of Mitochondria in the cell?

Mitochondria is where aerobic respiration takes place which supplies energy to the cell

What is the role of Cytoplasm in the cell?

Cytoplasm is a jelly-like fluid that fills the cell It is where most of the cell's chemical reactions take place

What organelles do a plant cell have that an animal doesn't?

What is a vacuole?

A vacuole is a fluid-filled sac that stores water

It is enclosed in a membrane

It can make up as much as 90% of a plant cell’s volume

What do chloroplasts contain?

Chloroplasts contain Chlorophyll

What is chlorophyll needed for?

Chlorophyll are needed for photosynthesis

What is the cell wall made of?

The cell wall are made up of Cellulose

What is the role of the cell wall?

The Cell wall makes the cell rigid and increases the structural strength of the cell

What type of cells are Bacteria?

What are the sub-cellular structures in a Bacterial cell?

What are Flagella?

Flagella are whip-like structures used for movement

What are Plasmids?

Plasmids are small rings of DNA

What is Cell Differentiation?

Cell Differentiation is the process where a cell develops new sub-cellular structures (structures inside a cell) to let it perform a specific function

This makes a cell Specialised

When does Cell Differentiation in animals mainly occur?

Cell differentiation in animals mainly happens in Embryos

The cells divide to form embryos that differentiate (specialise) to produce cells that can perform all of the body's functions

How are Sperm Cells specialised?


  • Sperm cells have flagellum which helps it move towards the egg cell
  • The middle section is filled with Mitochondria to provide the sperm with the energy it needs to travel to the egg cell
  • The Acresome at the the tip of the cell contains enzymes to penetrate the egg
  • The Nucleus contains half of an organisms genetic material. This combines with the egg's half to fertilise the egg cell

What are the key features of a Neurone (Nerve Cell)?

What is the Axon in a Neurone and how is it specialised?

The Axon is the part of the Neurone that electric signals travel along

It is long to increase the distance the electrical signal can travel

What is the Myelin Sheath in a Neurone and how is it specialised?

It is a sheath made of myelin that surrounds the Axon of the Neurone

This stops the electric nerve signals from leaking out the nerve cell. This increases the speed of transmission of electrical signals

What are Dendrites in a neurone and how is it specialised?

Dendrites are branches of the Nerve cell

Multiple Dendrites spread outwards from the cell to transfer the electrical messages to other neurones


Types of plasmids

Plasmids can be classified into various categories, but the most commonly known classification is based on their functions. According to this, they are divided into 5 different types &ndash fertility plasmids, resistance plasmids, col plasmids, virulence plasmids and metabolic or degradative plasmids.

Bacterial cells don&rsquot have genders, but cells that have fertility plasmids, or F plasmids, can form pili, which are tiny tube-like structures, and connect to a neighboring cell. This allows the transfer of genetic material from the cell to its neighbor. Therefore, it confers the status of &ldquomale&rdquo to that bacterial cell in a process called conjugation.

Resistance plasmids contain genes that endow that cell with resistance to antibiotics, or other growth-inhibiting substances. Cells with R plasmids usually produce substances that can destroy the inhibiting factor, thus increasing their survival rate. At times, these plasmids can spread widely in a generation. As expected, these R plasmids are not favorable to humans or other animals to which these cells can be pathogenic.

Col plasmids are an interesting category of plasmids. These confer upon their host the ability to kill other organisms of its own kind. Col plasmids code for substances that can destroy other bacteria by increasing the permeability of their cell membrane, affecting their DNA or RNA, etc. However, these skills can only be used by a bacterium against similar species. For instance, E. coli has col plasmids that produce colicins. These can only be used to kill other strains of E. coli. Some of the plasmids also produce bacteriocins, which can be used to used kill organisms belonging to the Enterobacter species.

Conjugation (Photo Credit : Wikimedia Commons)

The next type of plasmids are the virulence plasmids. As you can likely deduce from the name, these plasmids provide or increase the virulence factor of bacteria. Virulence is a measure of how harmful an organism is. For instance, not all strains of E. coli are dangerous and disease causing, but there are some species that possess virulence plasmids and can cause diseases like diarrhea.

The final type of plasmids are the metabolic or degradative plasmids. These give cells the ability to break down substances like sugars, or toluene, etc. These plasmids can come in very handy for the cell. For instance, the cell may be able to break down a complex substance into simpler molecules, which can be a source of usable energy for the cell.


Answers and Replies

As I understand it, plasmids, like mitochondria, have their own genetic material and are capable of self-replication.

According to Wikipedia: Plasmids are considered replicons, units of DNA capable of replicating autonomously within a suitable host. However, like viruses, they are not classified as life. Plasmids are transmitted from one bacterium to another through conjugation. Unlike viruses, plasmids are "naked" DNA. However, some classes of plasmids encode the conjugative "sex" pilus necessary for their own transfer.

My understanding of that is that a bacteria gets their plasmids not because of the replication of their circular chromosome, nor because that chromosome have genes to code for the plasmid (I don't really know if that's possible), but because of the self-replication of their own plasmids.

So, my question is how the first plasmid got into the first bacteria, if they are not in their chromosomes? Were they a virus other prokaryotic cell that had circular DNA, and got phagocytosed by that bacteria ?

As I understand it, plasmids, like mitochondria, have their own genetic material and are capable of self-replication.

According to Wikipedia: Plasmids are considered replicons, units of DNA capable of replicating autonomously within a suitable host. However, like viruses, they are not classified as life. Plasmids are transmitted from one bacterium to another through conjugation. Unlike viruses, plasmids are "naked" DNA. However, some classes of plasmids encode the conjugative "sex" pilus necessary for their own transfer.

My understanding of that is that a bacteria gets their plasmids not because of the replication of their circular chromosome, nor because that chromosome have genes to code for the plasmid (I don't really know if that's possible), but because of the self-replication of their own plasmids.

So, my question is how the first plasmid got into the first bacteria, if they are not in their chromosomes? Were they a virus other prokaryotic cell that had circular DNA, and got phagocytosed by that bacteria ?

IMHO, the recent discovery of mega-viruses, including some with size and/or genetics bigger than small bacteria, suggests 'Life' definition needs to be loosened.

Is pollen alive ? Not without a female flower. So, akin to a virus or phage.
Spores ? Yes, as self contained.

Tricky.
Looks like the origins of 'life as we know it' were even more of a 'free for all' orgy than 'tis yet comfortable to admit.

Modern parallel may be 'lichen', which is, wiki-quote, 'a composite organism that emerges from algae or cyanobacteria living among the filaments (hyphae) of the fungi in a mutually beneficial symbiotic relationship.'

IIRC, recent research suggests many lichens have a third, previously unsuspected team-member, yeast. This is also a fungi, but has evolved a rather different life-style.

Whatever, IIRC, several lichens' components seem well along to losing their independence, discarding 'surplus' genetic function, perhaps evolving towards what far future might consider akin to 'plasmids'.
-)


What Would Happen If a Cell Didn't Have Mitochondria?

Cells that have no mitochondria are unable to convert oxygen into energy, found in the form of adenosine triphosphate (ATP). All multicellular eukaryotic organisms, including plants and animals, have mitochondria in some cells, but prokaryotes and some single-cell eukaryotes do not have mitochondria.

Although all multicellular eukaryotes have mitochondria, mitochondria do not exist in all cells. For instance, human red blood cells don't contain mitochondria, which prevents them from using the oxygen they carry. If these cells had mitochondria, they would use the oxygen instead of transporting it to other cells. Most unicellular eukaryotes that do not have mitochondria are parasitic, as they are unable to make energy for themselves and therefore must live off a host organism.

In addition to producing ATP, mitochondria serve a number of other functions. Mitochondria play a role in the construction of blood and certain hormones, while also helping to regulate the concentration of calcium ions within the cell. They also play a determining role in programmed cell death by releasing a certain chemical that signals the cell to die. Mitochondrial disorders can affect this function, causing the premature death of a large number of cells, which could damage organs. Most of these disorders are related to mutations within the mitochondrial DNA.


Contents

Although prokaryotic organisms do not possess a membrane bound nucleus like the eukaryotes, they do contain a nucleoid region in which the main chromosome is found. Extrachromosomal DNA exists in prokaryotes outside the nucleoid region as circular or linear plasmids. Bacterial plasmids are typically short sequences, consisting of 1 kilobase (kb) to a few hundred kb segments, and contain an origin of replication which allows the plasmid to replicate independently of the bacterial chromosome. [9] The total number of a particular plasmid within a cell is referred to as the copy number and can range from as few as two copies per cell to as many as several hundred copies per cell. [10] Circular bacterial plasmids are classified according to the special functions that the genes encoded on the plasmid provide. Fertility plasmids, or f plasmids, allow for conjugation to occur whereas resistance plasmids, or r plasmids, contain genes that convey resistance to a variety of different antibiotics such as ampicillin and tetracycline. There also exist virulence plasmids that contain the genetic elements necessary for bacteria to become pathogenic as well as degradative plasmids that harbor the genes that allow bacteria to degrade a variety of substances such as aromatic compounds and xenobiotics. [11] Bacterial plasmids can also function in pigment production, nitrogen fixation and the resistance to heavy metals in those bacteria that possess them. [12]

Naturally occurring circular plasmids can be modified to contain multiple resistance genes and several unique restriction sites, making them valuable tools as cloning vectors in biotechnology applications. [9] Circular bacterial plasmids are also the basis for the production of DNA vaccines. Plasmid DNA vaccines are genetically engineered to contain a gene which encodes for an antigen or a protein produced by a pathogenic virus, bacterium or other parasites. [13] Once delivered into the host, the products of the plasmid genes will then stimulate both the innate immune response and the adaptive immune response of the host. The plasmids are often coated with some type of adjuvant prior to delivery to enhance the immune response from the host. [14]

Linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia (to which the pathogen responsible for Lyme disease belongs), several species of the gram positive soil bacteria of the genus Streptomyces, and in the gram negative species Thiobacillus versutus, a bacterium that oxidizes sulfur. The linear plasmids of prokaryotes are found either containing a hairpin loop or a covalently bonded protein attached to the telomeric ends of the DNA molecule. The adenine-thymine rich hairpin loops of the Borrelia bacteria range in size from 5 kilobase pairs (kb) to over 200 kb [15] and contain the genes responsible for producing a group of major surface proteins, or antigens, on the bacteria that allow it to evade the immune response of its infected host. [16] The linear plasmids which contain a protein that has been covalently attached to the 5’ end of the DNA strands are known as invertrons and can range in size from 9 kb to over 600 kb consisting of inverted terminal repeats. [15] The linear plasmids with a covalently attached protein may assist with bacterial conjugation and integration of the plasmids into the genome. These types of linear plasmids represent the largest class of extrachromosomal DNA as they are not only present in certain bacterial cells, but all linear extrachromosomal DNA molecules found in eukaryotic cells also take on this invertron structure with a protein attached to the 5’ end. [15] [16]

Mitochondrial Edit

The mitochondria present in eukaryotic cells contain multiple copies of mitochondrial DNA referred to as mtDNA which is housed within the mitochondrial matrix. [17] In multicellular animals, including humans, the circular mtDNA chromosome contains 13 genes that encode proteins that are part of the electron transport chain and 24 genes that produce RNA necessary for the production of mitochondrial proteins these genes are broken down into 2 rRNA genes and 22 tRNA genes. [18] The size of an animal mtDNA plasmid is roughly 16.6 kb and although it contains genes for tRNA and mRNA synthesis, proteins produced as a result of nuclear genes are still required in order for the mtDNA to replicate or for mitochondrial proteins to be translated. [19] There is only one region of the mitochondrial chromosome that does not contain a coding sequence and that is the 1 kb region known as the D-loop to which nuclear regulatory proteins bind. [18] The number of mtDNA molecules per mitochondria varies from species to species as well as between cells with different energy demands. For example, muscle and liver cells contain more copies of mtDNA per mitochondrion than blood and skin cells do. [19] Due to the proximity of the electron transport chain within the mitochondrial inner membrane and the production of reactive oxygen species (ROS), and due to the fact that the mtDNA molecule is not bound by or protected by histones, the mtDNA is more susceptible to DNA damage than nuclear DNA. [20] In cases where mtDNA damage does occur, the DNA can either be repaired via base excision repair pathways, or the damaged mtDNA molecule is destroyed (without causing damage to the mitochondrion since there are multiple copies of mtDNA per mitochondrion). [21]

The standard genetic code by which nuclear genes are translated is universal, meaning that each 3-base sequence of DNA codes for the same amino acid regardless of what species from which the DNA comes. However, this universal nature of the code is not the case with mitochondrial DNA found in fungi, animals, protists and plants. [17] While most of the 3-base sequences in the mtDNA of these organisms do code for the same amino acids as those of the nuclear genetic code, there are some mtDNA sequences that code for amino acids different from those of their nuclear DNA counterparts.

Coding differences found in the mtDNA sequences of various organisms
Genetic code Translation table DNA codon involved RNA codon involved Translation with this code Comparison with the universal code
Vertebrate mitochondrial 2 AGA AGA Ter (*) Arg (R)
AGG AGG Ter (*) Arg (R)
ATA AUA Met (M) Ile (I)
TGA UGA Trp (W) Ter (*)
Yeast mitochondrial 3 ATA AUA Met (M) Ile (I)
CTT CUU Thr (T) Leu (L)
CTC CUC Thr (T) Leu (L)
CTA CUA Thr (T) Leu (L)
CTG CUG Thr (T) Leu (L)
TGA UGA Trp (W) Ter (*)
CGA CGA absent Arg (R)
CGC CGC absent Arg (R)
Mold, protozoan, and coelenterate mitochondrial 4 and 7 TGA UGA Trp (W) Ter (*)
Invertebrate mitochondrial 5 AGA AGA Ser (S) Arg (R)
AGG AGG Ser (S) Arg (R)
ATA AUA Met (M) Ile (I)
TGA UGA Trp (W) Ter (*)
Echinoderm and flatworm mitochondrial 9 AAA AAA Asn (N) Lys (K)
AGA AGA Ser (S) Arg (R)
AGG AGG Ser (S) Arg (R)
TGA UGA Trp (W) Ter (*)
Ascidian mitochondrial 13 AGA AGA Gly (G) Arg (R)
AGG AGG Gly (G) Arg (R)
ATA AUA Met (M) Ile (I)
TGA UGA Trp (W) Ter (*)
Alternative flatworm mitochondrial 14 AAA AAA Asn (N) Lys (K)
AGA AGA Ser (S) Arg (R)
AGG AGG Ser (S) Arg (R)
TAA UAA Tyr (Y) Ter (*)
TGA UGA Trp (W) Ter (*)
Chlorophycean mitochondrial 16 TAG UAG Leu (L) Ter (*)
Trematode mitochondrial 21 TGA UGA Trp (W) Ter (*)
ATA AUA Met (M) Ile (I)
AGA AGA Ser (S) Arg (R)
AGG AGG Ser (S) Arg (R)
AAA AAA Asn (N) Lys (K)
Scenedesmus obliquus mitochondrial 22 TCA UCA Ter (*) Ser (S)
TAG UAG Leu (L) Ter (*)
Thraustochytrium mitochondrial 23 TTA UUA Ter (*) Leu (L)
Pterobranchia mitochondrial 24 AGA AGA Ser (S) Arg (R)
AGG AGG Lys (K) Arg (R)
TGA UGA Trp (W) Ter (*)
Amino acids biochemical properties nonpolar polar basic acidic Termination: stop codon

The coding differences are thought to be a result of chemical modifications in the transfer RNAs that interact with the messenger RNAs produced as a result of transcribing the mtDNA sequences. [22]

Chloroplast Edit

Eukaryotic chloroplasts, as well as the other plant plastids, also contain extrachromosomal DNA molecules. Most chloroplasts house all of their genetic material in a single ringed chromosome, however in some species there is evidence of multiple smaller ringed plasmids. [23] [24] [25] A recent theory that questions the current standard model of ring shaped chloroplast DNA (cpDNA), suggests that cpDNA may more commonly take a linear shape. [26] A single molecule of cpDNA can contain anywhere from 100-200 genes [27] and varies in size from species to species. The size of cpDNA in higher plants is around 120–160 kb. [17] The genes found on the cpDNA code for mRNAs that are responsible for producing necessary components of the photosynthetic pathway as well as coding for tRNAs, rRNAs, RNA polymerase subunits, and ribosomal protein subunits. [28] Like mtDNA, cpDNA is not fully autonomous and relies upon nuclear gene products for replication and production of chloroplast proteins. Chloroplasts contain multiple copies of cpDNA and the number can vary not only from species to species or cell type to cell type, but also within a single cell depending upon the age and stage of development of the cell. For example, cpDNA content in the chloroplasts of young cells, during the early stages of development where the chloroplasts are in the form of indistinct proplastids, are much higher than those present when that cell matures and expands, containing fully mature plastids. [29]

Circular Edit

Extrachromosomal circular DNA (eccDNA) are present in all eukaryotic cells, are usually derived from genomic DNA, and consist of repetitive sequences of DNA found in both coding and non-coding regions of chromosomes. EccDNA can vary in size from less than 2000 base pairs to more than 20,000 base pairs. [30] In plants, eccDNA contain repeated sequences similar to those that are found in the centromeric regions of the chromosomes and in repetitive satellite DNA. [31] In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA, 5S ribosomal DNA and telomere DNA. [30] Certain organisms, such as yeast, rely on chromosomal DNA replication to produce eccDNA [31] whereas eccDNA formation can occur in other organisms, such as mammals, independently of the replication process. [32] The function of eccDNA have not been widely studied, but it has been proposed that the production of eccDNA elements from genomic DNA sequences add to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes. [33]

A distinct type of extrachromosomal DNA, denoted as ecDNA, is commonly observed in human cancer cells. [2] [7] ecDNA found in cancer cells contain one or more genes that confer a selective advantage. ecDNA are much larger than eccDNA, and are visible by light microscopy. ecDNA in cancers generally range in size from 1-3 MB and beyond. [2] Large ecDNA molecules have been found in the nuclei of human cancer cells and are shown to carry many copies of driver oncogenes, which are transcribed in tumor cells. Based on this evidence it is thought that ecDNA contributes to cancer growth.

Viral DNA are an example of extrachromosomal DNA. Understanding viral genomes is very important for understanding the evolution and mutation of the virus. [34] Some viruses, such as HIV and oncogenetic viruses, incorporate their own DNA into the genome of the host cell. [35] Viral genomes can be made up of single stranded DNA (ssDNA), double stranded DNA (dsDNA) and can be found in both linear and circular form. [36]

One example of infection of a virus constituting as extrachromosomal DNA is the human papillomavirus (HPV). The HPV DNA genome undergoes three distinct stages of replication: establishment, maintenance and amplification. HPV infects epithelial cells in the anogenital tract and oral cavity. Normally, HPV is detected and cleared by the immune system. The recognition of viral DNA is an important part of immune responses. For this virus to persist, the circular genome must be replicated and inherited during cell division. [37]

Recognition by host cell Edit

Cells can recognize foreign cytoplasmic DNA. Understanding the recognition pathways has implications towards prevention and treatment of diseases. [38] Cells have sensors that can specifically recognize viral DNA such as the Toll-like receptor (TLR) pathway. [39]

The Toll Pathway was recognized, first in insects, as a pathway that allows certain cell types to act as sensors capable of detecting a variety of bacterial or viral genomes and PAMPS (pathogen-associated molecular patterns). PAMPs are known to be potent activators of innate immune signaling. There are approximately 10 human Toll-Like Receptors (TLRs). Different TLRs in human detect different PAMPS: lipopolysaccharides by TLR4, viral dsRNA by TLR3, viral ssRNA by TLR7/TLR8, viral or bacterial unmethylated DNA by TLR9. TLR9 has evolved to detect CpG DNA commonly found in bacteria and viruses and to initiate the production of IFN (type I interferons ) and other cytokines. [39]

Inheritance of extrachromosomal DNA differs from the inheritance of nuclear DNA found in chromosomes. Unlike chromosomes, ecDNA does not contain centromeres and therefore exhibits a non-Mendelian inheritance pattern that gives rise to heterogeneous cell populations. In humans, virtually all of the cytoplasm is inherited from the egg of the mother. [40] For this reason, organelle DNA, including mtDNA, is inherited from the mother. Mutations in mtDNA or other cytoplasmic DNA will also be inherited from the mother. This uniparental inheritance is an example of non-Mendelian inheritance. Plants also show uniparental mtDNA inheritance. Most plants inherit mtDNA maternally with one noted exception being the redwood Sequoia sempervirens that inherit mtDNA paternally. [41]

There are two theories why the paternal mtDNA is rarely transmitted to the offspring. One is simply the fact that paternal mtDNA is at such a lower concentration than the maternal mtDNA and thus it is not detectable in the offspring. A second, more complex theory, involves the digestion of the paternal mtDNA to prevent its inheritance. It is theorized that the uniparental inheritance of mtDNA, which has a high mutation rate, might be a mechanism to maintain the homoplasmy of cytoplasmic DNA. [41]

Sometimes called EEs, extrachromosomal elements, have been associated with genomic instability in eukaryotes. Small polydispersed DNAs (spcDNAs), a type of eccDNA, are commonly found in conjunction with genome instability. SpcDNAs are derived from repetitive sequences such as satellite DNA, retrovirus-like DNA elements, and transposable elements in the genome. They are thought to be the products of gene rearrangements.

Extrachromosomal DNA (ecDNA) found in cancer have historically been referred to as Double minute chromosomes (DMs), which present as paired chromatin bodies under light microscopy. Double minute chromosomes represent

30% of the cancer-containing spectrum of ecDNA, including single bodies and have been found to contain identical gene content as single bodies. [7] The ecDNA notation encompasses all forms of the large, oncogene-containing, extrachromosomal DNA found in cancer cells. This type of ecDNA is commonly seen in cancer cells of various histologies, but virtually never in normal cells. [7] ecDNA are thought to be produced through double-strand breaks in chromosomes or over-replication of DNA in an organism. Studies show that in cases of cancer and other genomic instability, higher levels of EEs can be observed. [3]

Mitochondrial DNA can play a role in the onset of disease in a variety of ways. Point mutations in or alternative gene arrangements of mtDNA have been linked to several diseases that affect the heart, central nervous system, endocrine system, gastrointestinal tract, eye, and kidney. [18] Loss of the amount of mtDNA present in the mitochondria can lead to a whole subset of diseases known as mitochondrial depletion syndromes (MDDs) which affect the liver, central and peripheral nervous systems, smooth muscle and hearing in humans. [19] There have been mixed, and sometimes conflicting, results in studies that attempt to link mtDNA copy number to the risk of developing certain cancers. Studies have been conducted that show an association between both increased and decreased mtDNA levels and the increased risk of developing breast cancer. A positive association between increased mtDNA levels and an increased risk for developing kidney tumors has been observed but there does not appear to be a link between mtDNA levels and the development of stomach cancer. [42]

Extrachromosomal DNA is found in Apicomplexa, which is a group of protozoa. The malaria parasite (genus Plasmodium), the AIDS-related pathogen (Taxoplasma and Cryptosporidium) are both members of the Apicomplexa group. Mitochondrial DNA (mtDNA) was found in the malaria parasite. [43] There are two forms of extrachromosomal DNA found in the malaria parasites. One of these is 6-kb linear DNA and the second is 35-kb circular DNA. These DNA molecules have been researched as potential nucleotide target sites for antibiotics. [44]

Gene amplification is among the most common mechanisms of oncogene activation. Gene amplifications in cancer are often on extrachromosomal, circular elements. [45] One of the primary functions of ecDNA in cancer is to enable the tumor to rapidly reach high copy numbers, while also promoting rapid, massive cell-to-cell genetic heterogeneity. [7] [6] The most commonly amplified oncogenes in cancer are found on ecDNA and have been shown to be highly dynamic, re-integrating into non-native chromosomes as homogeneous staining regions (HSRs) [46] [7] and altering copy numbers and composition in response to various drug treatments. [47] [5] [48]

The circular shape of ecDNA differs from the linear structure of chromosomal DNA in meaningful ways that influence cancer pathogenesis. [49] Oncogenes encoded on ecDNA have massive transcriptional output, ranking in the top 1% of genes in the entire transcriptome. In contrast to bacterial plasmids or mitochondrial DNA, ecDNA are chromatinized, containing high levels of active histone marks, but a paucity of repressive histone marks. The ecDNA chromatin architecture lacks the higher-order compaction that is present on chromosomal DNA and is among the most accessible DNA in the entire cancer genome.


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