Saturday, 10 June 2017

Mitochondrial heterogeneity, metabolic scaling and cell death


Juvid Aryaman, Hanne Hoitzing, Joerg P. Burgstaller, Iain G. Johnston and Nick S. Jones


Cells need energy to produce functional machinery, deal with challenges, and continue to grow and divide -- these activities and others are collectively referred to as "cell physiology". Mitochondria are the dominant energy sources in most of our cells, so we'd expect a strong link between how well mitochondria perform and cell physiology. Indeed, when mitochondrial energy production is compromised, deadly diseases can result -- as we've written about before.

The details of this link -- how cells with different mitochondrial populations may differ physiologically -- is not well understood. A recent article shed new light on this link by looking at a measure of mitochondrial functionality in cells of different sizes. They found what we'll call the "mitopeak" -- mitochondrial functionality peaks at intermediate cell sizes, with larger and smaller cells having less functional mitochondria. The subsequent interpretation was that there is an “optimal”, intermediate, size for cells. Above this size, it was suggested that a proposed universal relationship between the energy demands of organisms (from microorganisms to elephants) and their size predicts the reduction in the function of mitochondria. Smaller cells, which result from a large cell having divided, were suggested to have inherited their parent's low mitochondrial functionality. Cells were predicted to “reset” their mitochondrial activity as they initially grow and reach an “optimal” size.

We were interested in the mitopeak, and wondered if scientifically simpler hypotheses could account for it. Using mathematical modelling, our idea was to use the observation that as a cell becomes larger in volume, the size of its mitochondrial population (and hence power supply) increases in concert. We considered that a cell has power demands which also track its volume, as well as demands which are proportional to surface area and power demands which do not depend on cell size at all (such as the energetic cost of replicating the genome at cell division, since the size of a cell's genome does not depend on how big the cell is). Assuming that power supply = demand in a cell, then bigger cells may more easily satisfy e.g. the constant power demands. This is because the number of mitochondria increases with cell volume yet the constant demands remain the same regardless of cell size. In other words, if a cell has more mitochondria as it gets larger, then each mitochondrion has to work less hard to satisfy power demand.

To explain why the smallest cells also have mitochondria which do not appear to work hard, we suggested that some smaller cells could be in the process of dying. If smaller cells are more likely to die, and if dying cells have low mitochondrial functionality (both of these ideas are biologically supported), then, by combining this with the power supply/demand picture above, the observed mitopeak naturally emerges from our mathematical model.

As an alternative model, we also suggested that the mitopeak could come entirely from a nonlinear relationship between cell size and cell death, with mitochondrial functionality as a passive indicator of how healthy a cell is. This indicates the existence of multiple hypotheses which could explain this new dataset.




Interestingly, we also found that the mitopeak could be an alternative to one aspect of a model we used some time ago to explain a different dataset, looking at the physiological influence of mitochondrial variability. Then, we modelled the activity of mitochondria as a quantity that is inherited identically by each daughter cell from its parent, plus some noise -- noting that this was a guess at the true behaviour because we didn't have the data to make a firm statement. We needed this relationship because observed functionality varied comparatively little between sister cells but substantially across a population. The mitopeak induces this variability without needing random inheritance of functionality, and may thus be the refined picture we've been looking for. These ideas, and suggestions for future strategies to explore the link between mitochondria and cell physiology in more detail, are in our new BioEssays article here. Juvid, Nick, and Iain.

Mirrored from here

Monday, 27 March 2017

Dynamin-Related Protein 1-Dependent Mitochondrial Fission Changes in the Dorsal Vagal Complex Regulate Insulin Action

http://www.cell.com/cell-reports/fulltext/S2211-1247(17)30216-4

Beatrice M. Filippi, Mona A. Abraham, Pamuditha N. Silva, Mozhgan Rasti, Mary P. LaPierre, Paige V. Bauer, Jonathan V. Rocheleau, Tony K.T. Lam
Type 2 diabetes is a condition where the body does not produce enough, or is resistant to, insulin. In this study, the authors investigated the role mitochondrial dynamics plays in insulin resistance and glucose regulation. As well as its clinical consequences, this study offers to shed light on the relationship between glucose homeostasis and mitochondrial functionality.
In healthy rodents, the hypothalamus and dorsal vagal complex (DVC) regulate glucose homeostasis in the liver (which is where excess glucose is stored). However, after a high fat diet (HFD) as short as 3 days, this regulation is disrupted. This link between the DVC and high-fat feeding has been poorly understood. 
The authors found that, after a HFD, DVC neuronal cells in rats had a higher density of mitochondria, and these mitochondria were less elongated, shorter and less branched. 
The authors tested the effect of providing the 3-day HFD rats with an infusion of  MDIVI-1, which is an inhibitor of the mitochondrial fission factor Drp-1 (by blocking its translocation from the cytosol into the mitochondria). The authors found that, upon infusion, mitochondrial morphology was restored to wild-type levels, the glucose infusion rate increased to normal levels, as well as the glucose production rate decreasing to normal levels. This was confirmed through molecular inhibition of Drp-1 via adenoviral-mediated inhibition. Furthermore, inducing overexpression of Drp-1 in the DVC of rats which were fed normally induced insulin resistance and recapitulated the effects of HFD.

The authors found that endoplasmic reticulum (ER) stress was necessary and sufficient  to induce DVC-mediated insulin resistance, and that ER stress was a consequence of mitochondrial fission.


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Thoughts: Are these associations still observed on a long-term high-fat diet, rather than a 3-day alteration to diet?

Tissue-Specific Mitochondrial Decoding of Cytoplasmic Ca2+ Signals Is Controlled by the Stoichiometry of MICU1/2 and MCU

http://www.cell.com/cell-reports/pdf/S2211-1247(17)30213-9.pdf

Paillard M, Csordás G, Szanda G, Golenár T, Debattisti V, Bartok A, Wang N, Moffat C, Seifert EL, Spät A, Hajnóczky G

Mitochondrial respiration is sensitive to the concentration of calcium in the cytoplasm, acting as an important control mechanism of respiration rate. It is known that different tissues have different responses to the presence of calcium. For instance, in the liver, calcium oscillations in the cytoplasm tend to be low frequency and are effectively propagated to intra-mitochondrial calcium concentrations. However, in the heart, oscillations are high frequency and are integrated into a more continuous intra-mitochondrial calcium signal.

Here, the authors investigated the difference in mitochondrial response to calcium concentration in different tissues by measuring the relative stoichiometry of two protein components of the mitochondrial calcium uniporter: MCU (a calcium pore unit) and MICU1 (a Calcium-sensing regulator). The authors found that, in heart tissue, a low MICU1 to MCU ratio is present, which results in a low cytoplasmic calcium threshold for mitochondrial accumulation of calcium, relative to liver tissue. Furthermore, heart tissue displayed a more shallow response curve to cytoplasmic calcium, suggesting lower cooperativity in cardiac tissue, relative to liver tissue. Therefore, the ratio of MICU1:MCU controls the tissue-specific response to cytoplasmic calcium.



Monday, 30 January 2017

Tunneling nanotubes promote intercellular mitochondria transfer followed by increased invasiveness in bladder cancer cells

https://www.ncbi.nlm.nih.gov/pubmed/28107184

Jinjin Lu, Xiufen Zheng, Fan Li, Yang Yu, Zhong Chen, Zheng Liu, Zhihua Wang, Hua Xu, Weimin Yang

In cell culture, cells have been observed to create long, thin, protrusions to connect to other cells and transfer material, including entire organelles such as mitochondria. These protrusions are called tunneling nanotubes (TNTs). In this study, the authors co-culture two kinds of urothelial bladder cancer cells: T24 (highly invasive) and RT4 (less invasive) cells. The authors observed the formation of TNTs between the two cell types and mitochondrial exchange between the cell types.

The authors found that the RT4 cells became more motile after intercellular mitochondria trafficking from T24 cells (RT4-Mito-T24) by around a factor of 2 relative to RT4 cells. Xenograft tumours from RT4-Mito-T24 cells were also around twice as large as T24 cells after ~30 days of growth.

This shows that transfer of material from a highly invasive cell type to a less invasive cell type results in increased invasive ability. It suggests that mitochondrial content may be the causal variable in determining invasive ability in this system.


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Thoughts: This study adds to a growing body of evidence that mitochondrial content contributes to determining metastatic potential of cancer cells. What is it about these mitochondria that causes the increase in invasiveness? Are there other factors which are transferred through the TNTs? Is mitochondrial transfer necessary, or indeed sufficient, to see these effects? Interesting to note that the nuclear background of these cell types are presumably not the same -- to what extent can the nuclei be different between these cell types to observe the increase in invasiveness?

Wednesday, 7 December 2016

Selective removal of deletion-bearing mitochondrial DNA in heteroplasmic Drosophila

http://www.nature.com/articles/ncomms13100

Nikolay P. Kandul, Ting Zhang, Bruce A. Hay & Ming Guo

Mitophagy is the process by which mitochondria are engulfed and degraded within the cell. It has long been thought that mitophagy has a role to play in quality control in the mitochondrial population, however it has remained unclear whether the effect can selectively degrade faulty organelles, or instead is an unbiased process, in vivo. A potential confounding effect is cell division where, simply by dividing, mutants can be driven to fixation through stochastic effects.

To address this question, the authors developed a Drosophila model which can inducibly generate a mitochondrial mutation which would otherwise be lethal if present at birth in the whole-body. This is done through the inducible expression of a mitochondrially-targetted restriction enzyme which cleaves mtDNA in Drosophila in two places, creating a 2584 bp deletion which disrupts or removes several important mitochondrial genes. The authors were able to induce expression of this restriction enzyme in a non-essential, energy-intense, post-mitotic tissue, namely the indirect flight muscle. This is an ideal tissue to study mitophagy, since its energy requirements imply the need for a healthy mitochondrial population, and is non-dividing so does not suffer from confounding effects from the stochastic nature of mtDNA dynamics.

Flies tended to accumulate ~76% heteroplasmy in the mitochondrial deletion by day 10 after hatching, stabilizing thereafter, with no large difference in mtDNA copy number. The flies had similar flight performances to wild-type animals, suggesting that the tissue may withstand high levels of heteroplasmy without phenotypic consequences.

The authors probed the effects of modulating the expression of genes which have been thought to play a role in mitophagy, and measured the resultant heteroplasmy. They investigated Atg1, Atg8a, Pink1 and Parkin, which all had the expected effects on heteroplasmy. Parkin overexpression caused ~71% reduction in heteroplasmy, and Atg1 caused ~72% reduction, these genes having the largest effect sizes. The authors found that inhibition of mitochondrial fusion through MFN silencing had a modest effect on heteroplasmy reduction (37%), which is expected if defective mitochondria are not allowed to re-enter the mitochondrial network. Interestingly, inhibiting ATP synthase from hydrolysing ATP and therefore maintaining mitochondrial membrane potential, through expression of ATPIF1, had a synergistic effect with MFN silencing, resulting in a 64% effect size.  This suggests that mitochondria with mutated mtDNAs may attempt to cheat the mitophagic system by consuming ATP to maintain their membrane potential and avoid detection.



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Thoughts:

These results show that mitophagy can be a selective process, and may be induced to have greater effect sizes. The key question is, if mitophagy is able to clear mitochondrial mutants, why do we see them at all in the wild-type case? What is the tradeoff that keeps mitophagy low? It would be interesting to see the lifespan of these flies upon induction of mitophagy. Are they more susceptible to other pathologies e.g. cancer or aging?

Tuesday, 1 November 2016

Evolution of Cell-to-Cell Variability in Stochastic, Controlled, Heteroplasmic mtDNA Populations

http://www.cell.com/ajhg/fulltext/S0002-9297(16)30397-4

Iain G. Johnston and Nick S. Jones
 
Mitochondrial DNA (mtDNA) contains instructions for building important cellular machines. We have populations of mtDNA inside each of our cells -- almost like a population of animals in an ecosystem. Indeed, mitochondria were originally independent organisms, that billions of years ago were engulfed by our ancestor's cells and survived -- so the picture of mtDNA as a population of critters living inside our cells has evolutionary precedent! MtDNA molecules replicate and degrade in our cells in response to signals passed back and forth between mitochondria and the nucleus (the cell's "control tower"). Describing the behaviour of these population given the random, noisy environment of the cell, the fact that cells divide, and the complicated nuclear signals governing mtDNA populations, is challenging. At the same time, experiments looking in detail at mtDNA inside cells are difficult -- so predictive theoretical descriptions of these populations are highly valuable.

Why should we care about these cellular populations? MtDNA can become mutated, wrecking the instructions for building machines. If a high enough proportion of mtDNAs in a cell are mutated, our cells struggle and we get diseases. It only takes a few cells exceeding this "threshold" to cause problems -- so understanding the cell-to-cell distribution of mtDNA is medically important (as well as biologically fascinating). Simple mathematical approaches typically describe only average behaviours -- we need to describe the variability in mtDNA populations too. And for that, we need to account for the random effects that influence them.
 
​In our cells, signals from the "control tower" nucleus lead to the replication (orange) and degradation (purple) of mtDNA. These processes affect mtDNA populations that may contain normal (blue) and mutant (red) molecules. Our mathematical approach -- extending work addressing a similar but simpler system -- describes how the total number of machines, and the proportion of mutants, is likely to behave and change with time and as cells divide.
 
In the past, we have used a branch of maths called stochastic processes to answer questions about the random behaviour of mtDNA populations. But these previous approaches cannot account for the "control tower" -- the nucleus' control of mtDNA. To address this, we've developed a mathematical tradeoff -- we make a particular assumption (which we show not to be unreasonable) and in exchange are able to derive a wealth of results about mtDNA behaviour under all sorts of different nuclear control signals. Technically, we use a rather magical-sounding tool called "Van Kampen's system size expansion" to approximate mtDNA behaviour, then explore how the resulting equations behave as time progresses and cells divide.

Our approach shows that the cell-to-cell variability in heteroplasmy (the potentially damaging proportion of mutants in a cell) generally increases with time, and surprisingly does so in the same way regardless of how the control tower signals the population. We're able to update a decades-old and commonly-used expression (often called the Wright formula) for describing heteroplasmy variance, so that the formula, instead of being rather abstract and hard to interpret, is directly linked to real biological quantities. We also show that control tower attempts to decrease mutant mtDNA can induce more variability in the remaining "normal" mtDNA population. We link these and other results to biological applications, and show that our approach unifies and generalises many previous models and treatments of mtDNA -- providing a consistent and powerful theoretical platform with which to understand cellular mtDNA populations. The article is in the American Journal of Human Genetics here and a preprint version can be viewed here. (crossed from Evolution, Energetics & Noise)

Sunday, 23 October 2016

Cellular Allometry of Mitochondrial Functionality Establishes the Optimal Cell Size

http://www.sciencedirect.com/science/article/pii/S1534580716306268

Teemu P. Miettinen and Mikael Björklund

Cells in a population, despite having the same genetic content, are often very different from each other due to the stochastic nature of biological processes. An example is cellular size: some cells are big, some are small and some have an intermediate size. How does the size of a cell affect its functionality? Is there an optimal cell size? This paper focusses on how mitochondrial functionality changes with cell size.

It is known that if a cell is twice as big, it will approximately have twice as many mitochondria, keeping the mitochondrial density roughly constant. However, the expression of mitochondrial genes becomes less than twice as high, meaning that bigger cells express relatively less mitochondrial genes. This may mean that there is a particular cell size corresponding to optimal mitochondrial functionality.

In the paper, they use single cell flow cytometry to measure the size of about 10^5-10^6 cells. Additionally, the mitochondrial membrane potential per unit cell size (ΔΨ) is measured. The relationship between cell size and ΔΨ can then be investigated.

Some of the findings are:
  • Consistent with previous studied, mitochondrial mass increases linearly with cell size
  • ΔΨ first increases as cells get larger, but then decreases again as cells get very large.
  • Mitochondrial respiration is highest in intermediate-sized cells
  • Intermediate-sized cells show the lowest variation in mitochondrial membrane potential
  • A higher ΔΨ variation is correlated with a higher rate of apoptosis (cell death)
  • Intermediate-sized cells showed (on average) the fastest growth

These results strongly indicate that mitochondrial functionality is largest in intermediate-sized cells in a population. Cells also seem to try to maintain the size at which mitochondrial functionality is largest, meaning that this is probably an optimal cell size.




Tuesday, 18 October 2016

Mitochondrial Dysfunction Prevents Repolarization of Inflammatory Macrophages

http://www.cell.com/cell-reports/supplemental/S2211-1247(16)31213-X

Jan Van den Bossche, Jeroen Baardman, Natasja A. Otto, Saskia van der Velden, Annette E. Neele, Susan M. van den Berg, Rosario Luque-Martin, Hung-Jen Chen, Marieke C.S. Boshuizen, Mohamed Ahmed, Marten A. Hoeksema, Alex F. de Vos, Menno P.J. de Winther

Macrophages are types of white blood cell. They engulf and digest bodies which do not possess the correct protein markers which mark healthy cells. Whilst these cells play a crucial role in immunity, their dysfunction is associated with a number of auto-immune diseases such as asthma and rheumatoid arthritis. Macrophages exist in a spectrum of states, ranging from pro-inflammatory (M1) to anti-inflammatory (M2). In this study, the authors wished to investigate the mechanisms which prevent the transition from M1 to M2, so that we may better understand the mechanisms of inflammation.

Previous studies have shown that M1 cells are reliant upon glycolysis whereas M2 cells use mitochondrial oxidative phosphorylation (OXPHOS). These modes of energy production have also been associated with promoting the activation of these macrophage states. The authors find here that when macrophages are induced (using LPS + IFN-γ) to become M1 (pro-inflammatory) cells, this process inhibits OXPHOS. The signal (IL-4) which induces M2 (anti-inflammatory) cells cannot reverse this suppression of OXPHOS, and so they remain trapped in the pro-inflammatory state. The authors found that nitric oxide production by M1 cells, which is used as an antimicrobial mechanism and inhibits mitochondrial function, prevents the ability of M1 macrophages to be reprogrammed as non-inflammatory M2 cells.

Tuesday, 11 October 2016

Loss of Dendritic Complexity Precedes Neurodegeneration in a Mouse Model with Disrupted Mitochondrial Distribution in Mature Dendrites

López-Doménech G, Higgs NF, Vaccaro V, Roš H, Arancibia-Cárcamo IL, MacAskill AF, Kittler JT

http://www.cell.com/cell-reports/abstract/S2211-1247(16)31208-6

Miro proteins link mitochondria to motor proteins, allowing them to be trafficked through neurons. In this study, the authors disrupted the expression of Miro proteins in neurons to understand the role of mitochondrial trafficking in neurodegeneration. The authors found that Miro1-KO caused the distribution of mitochondria in dendrites (the branched extensions of nerve cells which receive electrochemical signals from other neurons) to become more accumulated around the soma, and more sparse along dendrites. Miro1-KO cells also appeared smaller and less developed than wild-type neurons; this was also shown to be the case in an inducible Miro1-KO system in mature neurons of the forebrain of mice. The deletion of this gene was associated with neurodegeneration 12 months after induction of Miro1-KO.



Tuesday, 20 September 2016

Prediction of multidimensional drug dose responses based on measurements of drug pairs

Anat Zimmer, Itay Katzir, Erez Dekel, Avraham E. Mayo, and Uri Alon

http://www.pnas.org/content/113/37/10442.full

*Not mitochondrial, but very cool

Cocktail therapies are common to treatments of a diverse array of diseases, in order to combat effects such as: antibiotic resistance in bacterial infections; persister cells in tuberculosis; and chemotheraputic resistance in cancer. It is, however, incredibly difficult to optimize the dose of multiple theraputic agents because of combinatorial explosions. For instance, if we have 10 possible doses for 3 different drugs, then we must test 10x10x10 = 1000 different dose combinations to find the optimal treatment. This becomes 10,000 if we wish to use 4 drugs. What makes this problem even more difficult is that drugs often show antagonism: it is not simply the case that using higher and higher doses of each drug is more effective, the optimum is often found at intermediate doses.

Here, the authors use mathematics to try and approximate the optimal dose of a cocktail of three or more drugs (N in general) whilst avoiding the problem of combinatorial explosion. They model the survival of cells (g) versus drug concentration (Di), for each drug (i), using Hill curves. They approximate g(D1, ... ,DN) using information only from single-drug dose response curves g(Di) and two-drug data g(Di, Dj) for all pairs of drugs. Their computation therefore only scales quadratically with the number of drugs N, rather than exponentially if we were to brute-force compute the global optimum. The authors show that their method is able to well-describe dose-response curves for a case study of six triplet and two quadruplet combination therapies, with 0.85 < R^2 < 0.93 for all of the examples tested.

These methods not only allow us to find the most effective doses, but also has the potential to minimize side effects by optimizing with the assumption that side-effects increase with higher dose. More realistic predictions could be made with more accurate models for side-effects.


Friday, 16 September 2016

Lactate metabolism is associated with mammalian mitochondria

Ying-Jr Chen, Nathaniel G Mahieu, Xiaojing Huang, Manmilan Singh, Peter A Crawford, Stephen L Johnson, Richard W Gross, Jacob Schaefer, Gary J Patti

http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.2172.html

Lactate is sometimes referred to as "metabolic waste" but this has been established as a misnomer for quite some time, with it being shown as early as the 1920s that lactate can be transformed back into glucose via gluconeogenesis in the liver. There are multiple other examples where shuttling of lactate between tissues allows it to be metabolised. However,  it remains controversial whether individual cells are able to metabolise this apparent metabolic by-product.

Here, the authors show that lactate is able to enter mitochondria and participate in mitochondrial energy metabolism. By culturing cells in radiolabelled lactate, the authors show that carbon from lactate can be found in intermediate metabolites of the TCA. They show that mitochondria are able to metabolize lactate, suggesting that they are able to import the metabolite, and that mitochondria possess the necessary enzyme (lactate dehydrogenase B) to convert lactate into the better-known mitochondrial substrate, pyruvate. The authors suggest this may be particularly relevant in cancer cells, which have particularly high glycolysis and lactate production.


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Thoughts: It seems like a pretty important follow-up question to ask how much lactate is used by mitochondria relative to secretion in vivo. If the effect is big, doesn't this mean extracellular acidification rate is not a good metric of glycolysis levels?

Tuesday, 13 September 2016

The repopulating cancer cells in melanoma are characterized by increased mitochondrial membrane potential

http://www.sciencedirect.com/science/article/pii/S0304383516305122

Don G. Lee, Beom K. Choi, Young H. Kim, Ho S. Oh, Sang H. Park, Young Soo Bae, Byoung S. Kwon

In this study, the authors investigate whether mitochondrial membrane potential (ΔΨ) serves as a biomarker of higher proliferative potential in melanoma cells. The authors found that tumour cells which survived stressors such as serum starvation and cisplatin treatment had substantially higher ΔΨ. Furthermore, upon sorting cells into categories of low and high ΔΨ, the authors found that high-ΔΨ cells tended to induce tumour growth whereas low-ΔΨ could not, for doses of 10^5 cells/mouse: this was demonstrated for cells grown in vitro as well as sorted tumour cells grown in vivo.


Thursday, 8 September 2016

Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans

Bryan L. Gitschlag, Cait S. Kirby, David C. Samuels, Rama D. Gangula, Simon A. Mallal, Maulik R. Patel


Why haven't deleterious mutations in mitochondrial DNA gone extinct? Naively, if a mutation has a negative impact on the fitness of an organism, then that organism may be less likely to reproduce and, in time, we expect to see fewer organisms with the mutation in nature. And yet deleterious mutations in mtDNA are still seen and passed down from generation to generation (albeit that this is often through carriers who bear such mutations at lower loads). 

The authors of this study explore this simple, but fundamental, question by establishing a slightly deleterious mtDNA variant in C. elegans, called uaDF5. This is a deletion mutation which removes four protein-coding genes and seven tRNAs. The authors show that worms are still viable with a mutant load as high as 80% (but lethal at 100%), and that mtDNA copy number tended to increase in individuals with large mutant load (suggesting expansion of the total mtDNA population so that there are enough wild-type mtDNA molecules to fulfil the metabolic needs of the animal). The authors also determined that it is unlikely that the mutation has a proliferative advantage by virtue of its smaller size, through comparison with another deletion mutant which was much smaller.

In addition to mtDNA copy number control, the authors suggest an additional mechanism whereby mutant mtDNAs may proliferate. The authors find that silencing of the mitochondrial unfolded protein response (mt-UPR) causes a substantial reduction in mutant load. The mt-UPR is thought to provide a protective role against adverse conditions for mitochondria; the authors suggest here that the process inadvertently allows mutants to proliferate as it suppresses mitophagy: the mechanism by which faulty mitochondria are recycled by the cell. They show this by blocking mt-UPR and parkin-mediated mitophagy to show a recovery in mutant load.



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Thoughts: A natural question to ask is, given that these heteroplasmic animals are less fit, why do cells not have a larger mitophagy rate if this allows quality control? Is there some tradeoff where wild-type mtDNAs are also consumed? Perhaps with a lower probability?




Thursday, 10 March 2016

Selective Vulnerability of Cancer Cells by Inhibition of Ca2+ Transfer from Endoplasmic Reticulum to Mitochondria

http://www.sciencedirect.com/science/article/pii/S2211124716301334

César Cárdenas, Marioly Müller, Andrew McNeal, Alenka Lovy, Fabian Jaňa, Galdo Bustos, Felix Urra, Natalia Smith, Jordi Molgó, J. Alan Diehl, Todd W. Ridky, J. Kevin Foskett

Mitochondria are often found to be tethered to another organelle of the cell, called the endoplasmic reticulum (ER). The ER releases calcium into the mitochondria, which stimulates energy metabolism by increasing the rate of several catalysts in the metabolic network. A basal level of calcium release is necessary for mitochondrial ATP production in many cell types. Without this, cells tend to start recycling themselves through autophagy, as a survival mechanism.

In this study, the authors probe the difference in response to normal and cancer cells, to blocking calcium release (using the drug XeB, as well as genetic knockdown of the gene InsP3R) from the ER to mitochondria. The authors compared the cell death response of non-tumourigenic MCF10A cells to three tumorigenic cell lines (MCF7, T47D and HS578T). At 5uM XeB, the authors find that breast tumour cell lines experienced significant cell death (43, 53 and 22%) whereas normal cells were less sensitive to the drug (5% cell death). Similar effect sizes were seen in prostate cancer cells, at the same drug concentration. It was also the case that XeB did not induce large cell death in primary human fibroblasts, when compared to transformed cells.

The authors found that providing the tumour cells with additional pyruvate rescued their proliferation rate. Calcium stimulates the enzyme pyruvate dehydrogenase, which takes pyruvate from glycolysis and converts it into acetyl-coa, for use in mitochondrial metabolism. Therefore it is reasonable to conclude that providing additional pyruvate pushes flux through the network, to compensate for lower enzymatic activity (by mass-action kinetics).

The authors hypothesized that nucleoside supplementation may also rescue the effect of calcium import inhibition, since mitochondrial metabolism is intertwined with nucleoside synthesis (a necessity for DNA synthesis). Indeed, the authors found that nucleoside supplementation ameliorated cytotoxicity by ~50%. This indicates that nucleoside production of mitochondria is more important than their energy production, in this model. The authors show mechanistically that, when cancer cells are blocked in calcium uptake, they progress through the cell cycle normally, but their progression into mitosis results in necrotic cell death. In contrast, normal cells halt their cell cycle at G1 phase.



Thursday, 4 February 2016

Segregation of naturally occurring mitochondrial DNA variants in a mini-pig model

 
Gael Cagnone, Te-Sha Tsai, Kanokwan Srirattana, Fernando Rossello, David R. Powell, Gary Rohrer, Lynsey Cree, Ian A. Trounce, Justin St. John
 
Recent work in mice has shown that different mitochondrial sequences (haplotypes) will tend to accumulate in different tissues, and this segregation depends on the sequence in question.

In this study, the authors study four mtDNA mutations, over three generations of mini-pigs. These mutations were: Del A376 affecting 12 rRNA; Del A1302 affecting 16s rRNA; Del A1394 affecting 16s rRNA; and Del A9725 affecting NADH3 (a protein of the electron transport chain). The authors investigated which tissues had variable mutant load, and found that mutant load is significantly reduced in diaphragm (4/4 mutants), muscle (3/4 mutants), brain (2/4 mutants) and fat (2/4 mutants). 
 
They then go on to correlate the variation with mtDNA copy number, across all tissues, and all generations. In one of the four cases, no correlation was observed. However, in Del A376 and Del 1302, variant load had a fairly strong negative correlation with mtDNA copy number; in Del 1394, the correlation was weaker and also negative.
 
The authors therefore suggest that mutant load is lowered in high-respiratory tissue, such as brain, diaphragm, muscle, liver, heart and fat.


 
 
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Thoughts: Are these mutants deleterious to respiratory activity? I imagine so, since they are all deletion mutations, so cause frameshifts. If that is the case, I wonder if the mutations could be ranked by how much they inhibit OXPHOS? I wonder whether the strongest inhibitors either have i) the strongest gradient with mtDNA copy number or ii) lowest overall abundance in all tissues?

I also find it pretty surprising that frameshift mutations can be found in healthy pig tissues, even 2-15%. I wonder whether there is a complementation effect happening here: several different mutants producing transcription products that the others cannot?

Tuesday, 19 January 2016

Accurate concentration control of mitochondria and nucleoids

 Rishi Jajoo, Yoonseok Jung, Dann Huh, Matheus P. Viana, Susanne M. Rafelski, Michael Springer, Johan Paulsson

http://classic.sciencemag.org/content/351/6269/169.long

When a cell divides, all components in the cell need to go into either one of the daughter cells. The cell has developed mechanisms to make sure that some components, for example chromosomes, are correctly segregated. How does this work for mitochondria? Does the cell have active mechanisms to push equal amounts of mitochondria in each daughter cell, or do the mitochondria randomly move into one of the daughters?

In this paper, they try to answer these questions in fission yeast S. Pombe.
It was shown before that mitochondria are pushed to both of the cell poles before cell division, which would suggest that this is a mechanism of segregating the mitochondria.

However, in this paper they show that in the last 15% of the cell cycle, mitochondria spatially re-equilibrate themselves throughout the cell. When the cell divides, the mitochondrial volume in a daughter cell tracks the cytoplasmic volume of that daughter cell. For example, if the two daughters get 60% and 40% of the cytoplasmic volume, they will on average also get 60% and 40% of the mitochondrial volume.
The same is true of mitochondrial nucleoids, which contain the mitochondrial DNA; they too segregate in proportion to the cytoplasmic volume.

However, the errors made in nucleoid segregation are smaller than you would expect from passive mechanisms. Using the example from above, passively one would expect that each nucleoid has a probability of 0.6 of ending up in the larger daughter (the one with 60% of the cytoplasm) and a probability of 0.4 of ending up in the other daughter. This is called binomial partitioning and has a certain error size associated with it. The actual errors that are made in S. Pombe (i.e. the deviations from perfect partitioning) are smaller than binomial errors.

A model that would explain these sub-binomial nucleoid segregation errors is to assume that the nucleoids are regularly spaced out within the mitochondria. It is not known how this regular spacing is accomplished by the cell.

The authors also find that the number of nucleoids that are produced from beginning to end of the cell cycle does not depend on the initial amount that was present. This suggests that S. Pombe does not not use feedback control to produce its nucleoids (or other mitochondrial proteins). Feedback control is energetically expensive. Rather, nucleoids are randomly added throughout the cell cycle, following a Poisson distribution.



Wednesday, 13 January 2016

TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions

http://www.sciencedirect.com/science/article/pii/S1097276515009363

Inmaculada Martínez-Reyes, Lauren P. Diebold, Hyewon Kong, Michael Schieber, He Huang, Christopher T. Hensley, Manan M. Mehta, Tianyuan Wang, Janine H. Santos, Richard Woychik, Eric Dufour, Johannes N. Spelbrink, Samuel E. Weinberg, Yingming Zhao, Ralph J. DeBerardinis, Navdeep S. Chandel

In this study, the authors investigate the effect of eliminating mtDNA from cells, on metabolism. This is often achieved by incubation with the chemical ethidium bromide, which prevents the protein responsible for mtDNA replication (POLG) from working. However, ethidium bromide is toxic and has potentially off-target effects. The authors engineered cells which, upon exposure to an antibiotic, express a dominant-negative form of POLG (DN-POLG), thereby removing potential off-target effects. Within 6 days of induction of DN-POLG, mtDNA transcription had ceased.

Cells had a greatly reduced proliferation rate (although still viable), despite having access to glucose and pyruvate: metabolites required to drive glycolysis and the TCA cycle respectively. As discussed in [1] (see here) mitochondria oxidise NADH to NAD+, the substrate of glycolysis. The authors introduced two non-mammalian proteins (NDl1 and AOX), which together carry electrons in a similar manner to the electron transport chain, but do not pump protons across the inner mitochondrial membrane. In this way, NAD+ can be restored, without generating mitochondrial ATP from oxidative phosphorylation. The authors show that these proteins are sufficient to drive flux through the TCA cycle, and increase the NAD+/NADH ratio. However, the authors find that these cells still have an impaired proliferation rate (at odds with the findings in [1]?)

The authors investigated an alternative reason for the impaired proliferation of these cells: mitochondrial membrane potential (ΔΨm). Cells without mtDNA cannot pump protons to maintain ΔΨm, but ATP synthase is still able to hydrolyse ATP from glycolysis, to maintain ΔΨm. An endogenous inhibitor of this function is the protein ATPIF1. The authors knocked out this gene, and showed that cells without mtDNA are able to maintain their ΔΨm at wild-type levels. These ATPIF1-KO cells had a, statistically significant, partial recovery in proliferation rate.

Interestingly, treating the ATPIF1-KO cells with an antioxidant, which mops up ROS (canonically considered to be the bad-guy of mitochondrial physiology, see here), reduced the proliferation rate. This shows that ROS, as well as ΔΨm, are necessary for cells to proliferate.



[1] Wiley, Christopher D., et al. "Mitochondrial Dysfunction Induces Senescence with a Distinct Secretory Phenotype." Cell metabolism (2015).




Thursday, 7 January 2016

Mitochondrial Dysfunction Induces Senescence with a Distinct Secretory Phenotype

http://www.sciencedirect.com/science/article/pii/S1550413115005781

Wiley CD, Velarde MC, Lecot P, Liu S, Sarnoski EA, Freund A, Shirakawa K, Lim HW, Davis SS, Ramanathan A, Gerencser AA, Verdin E, Campisi J

Cellular senescence is the process by which dividing cells permanently lose their ability to replicate. This phenotype can inhibit the growth of cancerous cells, but it is also thought to occur in normal tissues during aging. It is known that mitochondrial dysfunction can induce senescence, however the mechanisms of this are unclear.

The authors show that several different kinds of mitochondrial dysfunction can induce senescence in the IMR-90 cell line: mtDNA depletion; drugs which inhibit the electron transport chain (rotenone and antimycin A); and inhibition of a particular mitochondrial chaperone (HSPA9) which aids in import of proteins into mitochondria.

Mitochondria oxidise NADH to NAD+ in a number of metabolic reactions involved in generating energy. NAD+ is a substrate of glycolysis, whereas NADH is a product, which can inhibit the pathway if it is not removed. As glycolysis provides pyruvate, the substrate of oxidative phosphorylation, a reduced NAD+/NADH ratio may be expected to slow down glycolysis and therefore oxidative phosphorylation.

The authors provide evidence that the mechanism of mitochondrially-induced senescence is lowered NAD+/NADH ratios, suggesting energetic collapse. This is supported by an increased ADP/ATP ratio in these cells. They find that supplementation of pyruvate to cells can partially rescue the senescent phenotype.

The authors further show the relevance of mitochondrially-induced senescence, by investigating the effect in POLG mutator mice (mice which accumulate mtDNA mutations in time and have a progerioid phenotype). The authors found that the progerioid mice had many more senescent cells in affected tissues, with lowered NAD+/NADH ratios compared to wild-type mice.


Tuesday, 5 January 2016

Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy

http://www.sciencedirect.com/science/article/pii/S1550413115005690

Sukumar M, Liu J, Mehta GU, Patel SJ, Roychoudhuri R, Crompton JG, Klebanoff CA, Ji Y, Li P, Yu Z, Whitehill GD, Clever D, Eil RL, Palmer DC, Mitra S, Rao M, Keyvanfar K, Schrump DS, Wang E, Marincola FM, Gattinoni L, Leonard WJ, Muranski P, Finkel T, Restifo NP

Cancer immunotherapy involves using the immune system to target and eradicate tumours. One method is to isolate and transfer immune cells into the patient. There are a number of different kinds of immune cell, one of which is called the T cell. T cells themselves divide into a number of subtypes, two of which are: effector memory (EM) and stem-cell memory (SCM) T cells. It is known that SCM cells are able to persist for longer periods of time, and are more effective in attacking tumour cells than EM cells. It is therefore desirable to be able to enrich for SCM cells, in a mixed population of T cells, to deliver a more potent immunotherapy.

In this study, the authors stain a mixed population of T cells with a chemical which causes cells with a large mitochondrial membrane potential (ΔΨm) to fluoresce more strongly (using TMRM). They find that fractions with low membrane potential are enriched for SCM cells, whereas fractions with high membrane potential are enriched for EM cells. Indeed, the authors show in a variety of cell lines that low ΔΨm is associated with stem-like properties.

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Thoughts:
Curiously, low ΔΨm cells had a lower glycolysis rate, and higher spare respiratory capacity, and lower baseline respiratory rate, compared to high ΔΨm cells. Low ΔΨm cells tend to favour fatty acid oxidation, which provides an alternative substrate to glucose for energy production. However, fatty acid oxidation drives the Krebs cycle, which in turn can drive oxidative phosphorylation. So, given that these cells are not undergoing glycolysis, one might expect ΔΨm low cells to have a higher resting oxygen consumption rate? It would be interesting to know the ATP concentration of the ΔΨm low cells: my guess would be that they have a lower ATP concentration?

Monday, 16 November 2015

Single Nucleotides in the mtDNA Sequence Modify Mitochondrial Molecular Function and Are Associated with Sex-Specific Effects on Fertility and Aging


M. Florencia Camus, Jochen B.W. Wolf, Edward H. Morrow, Damian K. Dowling 

In this study, the authors bred flies containing the same nuclear genome, but different mitochondrial genomes, corresponding to different mitochondrial haplotypes from across the world. In doing this, the authors were able to demonstrate how the mitochondrial genotype can affect the phenotype of the fly, without considering the effect of nuclear DNA.

In 7 of the 13 haplotypes considered, the authors found that mtDNA copy number was increased in females above males, with the effect becoming stronger with age. Conversely (and strikingly), across 9 of the 13 mitochondrial genes tested, mitochondrial gene expression was higher in males, in all 9 genes, across all 13 haplotypes.

The authors found that mean longevity was higher in female flies. This intriguing finding, although only correlative, suggests that differences in the expression of the mitochondrial genome between males and females, may result in increased female longevity, as this may provide a selective advantage for such haplotypes (as mtDNA is maternally inherited). As an additional curiosity, the authors found that the Brownsville haplotype in this nuclear background induces cytoplasmic male sterility (male infertility, due to an interaction between mtDNA and nucleus). This is the only known case in metazoans.

Cellular Heterogeneity in the Level of mtDNA Heteroplasmy in Mouse Embryonic Stem Cells

http://www.sciencedirect.com/science/article/pii/S2211124715011730


Jitesh Neupane, Sabitri Ghimire, Mado Vandewoestyne, Yuechao Lu, Jan Gerris, Rudy Van Coster, Tom Deroo, Dieter Deforce, Stijn Vansteelandt, Petra De Sutter, Björn Heindryckx

Recent work has shown that non-pathological mtDNA variants (haplotypes) can show preferential expansion, in vivo. This is contrary to the common belief that nonpathological mutations exhibit neutral genetic drift. The authors of this study sought to study this phenomenon at the single-cell level using Mouse Embryonic Stem Cells (ESCs).

The authors established sets of cell lines, with differing proportions of two mtDNA haplotypes (NZB and BALB). The parental mice were themselves heteroplasmic in these two mtDNA haplotypes. By successive passage of the cells, the authors measure the ratio of the two haplotypes (heteroplasmy) with time. They find that, regardless of the initial ratio, the NZB haplotype tends to dominate over BALB with time (~12% over 30 passages), in this system. Furthermore, upon differentiation, cells tended to become more heterogeneous in heteroplasmy, and tended to shift back in heteroplasmy towards BALB (~8% reduction).

The results are significant, as they show that apparently neutral haplotypes have some kind of selective pressure. These dynamics are not necessarily straightforward, and seem to have some dependence on the system under study.

Friday, 23 October 2015

Direct evidence of mitochondrial G-quadruplex DNA by using fluorescent anti-cancer agents

http://nar.oxfordjournals.org/content/early/2015/10/19/nar.gkv1061.full

Wei-Chun Huang, Ting-Yuan Tseng, Ying-Ting Chen, Cheng-Chung Chang, Zi-Fu Wang, Chiung-Lin Wang, Tsu-Ning Hsu, Pei-Tzu Li, Chin-Tin Chen, Jing-Jer Lin, Pei-Jen Lou and Ta-Chau Chang

When DNA has a high content of guanine (one of the bases of DNA), under certain conditions, it can form a more exotic structure than the well-known Watson-Crick base pairing, known as a G-quadruplex. This is where four guanine bases bond to form a square-planar structure. These planes can stack on top of each other, to form the G-quadruplex. These structures can form in vivo, and are thought to have a connection to telomeres.

In this paper, the authors explore the existence of G4-quadruplexes in mtDNA. They do this by using fluorescent compounds which are able to both bind to a G4-quadruplex, and also localise in mitochondria (rather than the cell nucleus). One such agent is called BMVC-12C-P. What is curious about this particular agent is that it is able to halt the proliferation of cells in a cancer-specific manner. The agent accumulates strongly in the mitochondria of HeLa cancer cells, whereas it mainly localises in the lysosome of MRC-5 normal fibroblasts. The anti-cancer effect of this agent is robust across 3 cancer cell lines, and 3 normal cell lines, that were tested. Tumour proliferation was also shown to be slowed in mice injected with cancer cells, and treated with BMVC-12C-P.

After 72 hours of treatment, the authors find that the expression of ND3 and COX1 transcripts were severely reduced. Thus, the authors suggest that the mechanism of cytotoxicity of this agent is to prevent mtDNA transcription of these core ETC components, by targeting G4-quadruplexes in mtDNA. As well as being an interesting agent in its own right, this study provides further evidence for mtDNA being a target to alter cell proliferation.





Thursday, 15 October 2015

New compounds to directly modulate mitochondrial ROS

Selective superoxide generation within mitochondria by the targeted redox cycler MitoParaquat
Ellen L. Robb, Justyna M. Gawel, Dunja Aksentijević, Helena M. Cochemé,Tessa S. Stewart, Maria M. Shchepinova, He Qiang, Tracy A. Prime, Thomas P. Bright, Andrew M. James, Michael J. Shattock, Hans M. Senn, Richard C. Hartley, Michael P. Murphy

A mitochondria-targeted derivative of ascorbate: MitoC
Peter G. Finichiu, David S. Larsen, Cameron Evans, Lesley Larsen, Thomas P. Bright, Ellen L. Robb, Jan Trnka, Tracy A. Prime, Andrew M. James, Robin A.J. Smith, Michael P. Murphy

When mitochondria malfunction, the components of the electron transport chain may leak electrons and generate reactive oxygen species (ROS). The role of ROS in physiological and pathophysiological settings is subtle, as low levels are thought to be important in cell signalling whereas high levels may cause damage to a variety of biomolecules. In order to test the causal link between ROS and pathology, it is important to be able to directly modulate their levels and test their outcome.

In the above two papers, the Murphy group fuse a particular cation (triphenylphosphonium lipophilic cation, TPP), to two agents (paraquat and ascorbate, which are oxidizing and reducing agents repectively) allowing their localisation to the mitochondrial matrix. The resulting compounds are named MitoPQ and MitoC respectively. Once in the matrix, MitoPQ is able to generate ROS, whereas MitoC is able to mop ROS up. Importantly, this occurs at the site of ROS generation (the mitochondrial matrix). Many known agents can only modulate ROS in the cytosol, so these compounds provide more direct control over mitochondrial ROS. Furthermore, due to their direct localisation, lower concentrations of the compounds are required relative to their non-mitochondrial counterparts, to achieve the same effect.

Thursday, 8 October 2015

Consequences of zygote injection and germline transfer of mutant human mitochondrial DNA in mice

http://www.pnas.org/content/early/2015/09/30/1506129112
 
Hong Yu, Rajeshwari D. Koilkonda, Tsung-Han Chou, Vittorio Porciatt, Arpit Mehta, Ian D. Hentall, Vince A. Chiodo, Sanford L. Boye, William W. Hauswirth, Alfred S. Lewin and John Guy

In trying to understand mutations of mitochondrial DNA, biologists tend to use cells from either: 1) biopsies directly from patients; 2) early cell culture (where a biopsy from a patient has been purified in some way, then grown in the lab for a small number of generations); or 3) immortal cell lines (these are often cancer cells, which have been manipulated to contain the mtDNA mutation of interest).

Whilst all of these model system have their pros and cons (e.g. cell purity vs similarity to a natural environment), what has been lacking in this field is the ability to study human mitochondrial mutations in an animal model. This has the advantage of being able to introduce further genetic/drug perturbations to a living biological system, in the background of a mtDNA mutation. Whilst introducing nuclear mutations into mice is commonplace, it has never been attempted for mitochondrial genomes, which are held in multiple copy number.

In this study, the authors use an adeno-associated virus, which usually targets the nucleus, and add a particular protein (MT-COX8) which causes the virus to localise to mitochondria. The virus then delivers mutated human mtDNA to a mitochondrion. By exposing a mouse zygote to the virus, the authors were able to generate a mouse with a mutation in complex I, associated with LHON. The inserted viral mtDNA existed separately from the endogenous mtDNA, and was able to replicate and be transferred between generations after cross-breeding with wild-type animals. 

In humans, LHON is typically associated with retinal degeneration. The mutated mtDNA was able to express the mutant form of complex I in the mice, and cause a visual deficiency. Using mice which showed a visual defect, the authors used ocular injection with a virus containing wild-type mtDNA, and show that this was partially able to restore the visual defect, 1 month after treatment. 



Thursday, 24 September 2015

PKA Phosphorylates the ATPase Inhibitory Factor 1 and Inactivates Its Capacity to Bind and Inhibit the Mitochondrial H+-ATP Synthase

http://www.sciencedirect.com/science/article/pii/S2211124715009493

Javier García-Bermúdez, María Sánchez-Aragó, Beatriz Soldevilla, Araceli del Arco, Cristina Nuevo-Tapioles, José M. Cuezva

ATP synthase is the motor of the cell, generating most cellular ATP under normal conditions (watch a video of this here). The protein ATPase Inhibitory Factor 1 (IF1) is known to inhibit both hydrolysis and synthesis of ATP by ATP synthase, by blocking its rotation. This study investigates the mechanism of this protein's action, as well as its physiological and pathophysiological role.

Mechanistically, Protein Kinase A phosphorylates IF1 (p-IF1), which inhibits its ability to interact with ATP synthase, and so is expected to allow OXPHOS to occur. As a consequence, the authors find that dephosphorylated IF1 (dp-IF1) causes inhibition of oxidative phosphorylation and increased glycolytic flux.

Studies in yeast have shown that different energy pathways are activated, depending on the stage of the cell cycle. G1 is believed to be OXPHOS dependent, whereas G2/M is largely independent of oxygen consumption and relies on aerobic glycolysis. Consistent with this picture, the authors show that cells arrested in G1 phase had mostly p-IF1 and high levels of OXPHOS, whereas cells that were arrested in G2/M had dp-IF1 and low OXPHOS levels.

The authors also found hypoxia to be able to induce dephosphorylation of IF1, and thus inhibition of ATP synthase.  Indeed, a number of carcinomas investigated by the authors have an abundance of dp-IF1.

In terms of its physiological significance, the authors investigated the phosphorylation status of IF1 in mouse heart, in vivo. Fascinatingly, ~50% of IF1 is found in its phosphorylated state. Administration of drugs which induce an adrenaline response, causes a sharp increase in p-IF1 and OXPHOS activity. This suggests that the protein has a physiological role of fine-tuning mitochondrial output, in response to variable energy demands.


----------------
Thoughts:
It is known that the maintenance of mitochondrial membrane potential (ΔΨ) is vital for cell viability, as mitochondria perform a plethora of functions besides energy production, which are ΔΨ dependent. If cells actively inhibit their ATP synthase during hypoxia (and so can't hydrolyse ATP and pump protons), and are unable to pump protons due to a lack of oxygen, how are the cells maintaining ΔΨ? 

Friday, 4 September 2015

Dissecting tumor metabolic heterogeneity: Telomerase and large cell size metabolically define a sub-population of stem-like, mitochondrial-rich, cancer cells

http://www.ncbi.nlm.nih.gov/pubmed/26323205

Rebecca Lamb, Bela Ozsvari, Gloria Bonuccelli, Duncan L. Smith, Richard G. Pestell, Ubaldo E. Martinez-Outschoorn, Robert B. Clarke, Federica Sotgia
and Michael P. Lisanti

Telomeres are regions of non-coding DNA, which protectively cap the ends of chromosomes. After successive rounds of replication, telomeres shorten because DNA polymerase does not duplicate DNA all the way to the end of a chromosome, and induces senescence after 50-70 divisions. Telomerase (hTERT) is an enzyme which lengthens nucleotides, the overexpression of which is sufficient to immortalize a cell.

Here, the authors fluorescently tag the promoter of hTERT with GFP, to select cancer cells with high telomerase transcriptional activity, and purify so-called cancer stem-like cells. The authors, studying breast cancer cells, found that cells in the top 5% of hTERT-expressing cells (GFP-high) formed ~2.5 times more mammospheres than the bottom 5% (GFP-low). GFP-high cells also showed a 1.7-fold increase in the median MitoTracker fluorescence, indicating a strongly increased mitochondrial content in these cells.

The authors also sorted their cells by size, taking the top ~15% as 'large' and the rest as 'small'. They found that larger cells possessed a ~2.7-fold increase in hTERT activity, and 1.6-fold increase in mitochondrial mass.

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Thoughts:

Is the correlation between cell size and mitochondrial content surprising? Do ordinary cells possess a larger mitochondrial content, because they have a larger cytoplasmic volume and therefore greater energy demand? The finding that large cells have greater hTERT activity is, I think, surprising on its own terms because DNA content is independent of cell size. But disambiguating variation of mitochondrial content with cell volume, from cancer stemness is an interesting statistical question I think.

Wednesday, 26 August 2015

Mitochondrial reticulum for cellular energy distribution in muscle

 http://www.nature.com/nature/journal/v523/n7562/full/nature14614.html

Brian Glancy, Lisa M. Hartnell, Daniela Malide, Zu-Xi Yu, Christian A. Combs, Patricia S. Connelly, Sriram Subramaniam, and Robert S. Balaban


Cells need energy, especially muscle cells. Mitochondria generate part of this energy and to be able to do this they need to be supplied with various resources. Muscle cells can be quite big, so these resources (that enter the cell at its periphery) need to diffuse through the cell towards the mitochondria, which might take a long time. Is there a better, more efficient way of producing energy in large muscle cells?

In this paper they show that the mitochondrial network provides a conductive pathway for energy distribution.

Mitochondria use their Electron Transport Chain protein complexes to pump protons across their membrane, which creates an electrochemical gradient in which energy is stored. Their ATP synthase then uses this stored energy to make ATP. If many mitochondria are connected in the cell (i.e. if they all have an electrically continuous inner membrane) then a mitochondrion at one end of the cell can use the potential energy created by a mitochondrion at the other end of the cell, to generate ATP. The conduction of electric potential along the mitochondria can be faster than all kinds of resources needing to diffuse through the cell. This idea was first proposed by a Russian scientist Владимир Скулачёв (Vladimir Skulachev).

Here they show that the proteins involved in generating the electrochemical gradient are mainly found at the cell periphery (where the resources enter the cell), while proteins involved in using this energy to create ATP are found in the cell's interior. They also show that the mitochondria are indeed electrically connected to each other. The mitochondria in muscle cells are organized in a way that facilitates energy conduction.

The question remains whether this mitochondrial conductivity plays a role in all cells, or only in cells that are very energy demanding. Skin cells for example, hardly seem to need a fast conducting mitochondrial network. Nevertheless, mitochondrial fusion and network forming is seen in a variety of cells, so the fusion of mitochondria probably has other uses as well.




Tuesday, 25 August 2015

Cross-strand binding of TFAM to a single mtDNA molecule forms the mitochondrial nucleoid

http://www.pnas.org/content/early/2015/08/20/1512131112.short?rss=1

Christian Kuka, Karen M. Davies, Christian A. Wurm, Henrik Spåhr, Nina A. Bonekamp, Inge Kühl, Friederike Joos, Paola Loguercio Polosa, Chan Bae Park, Viktor Posse, Maria Falkenberg, Stefan Jakobs, Werner Kühlbrandt and Nils-Göran Larsson

Mitochondrial DNA is found to exist in protein-DNA complexes called nucleoids.  The number of mtDNA molecules per nucleoid is an important quantity to know, as it has consequences for how mtDNA is distributed amongst successive generations. The compactness of mtDNA also determines its ability to be transcribed and replicated, so the way it is packaged is also important to understand.

In their first experiment, the authors use electron microscopy in vitro, to observe how mtDNA is compacted, with increasing concentrations of the molecule TFAM (the only protein known to package mtDNA). They find that upon binding to mtDNA, TFAM causes the DNA to bend by 180°. At intermediate concentrations 1 TFAM/30 bp, dense protein-DNA spots were dispersed amongst regions of naked DNA (perhaps being a concentration appropriate for translation or replication of mtDNA). At concentrations of 1 TFAM/6 bp, mtDNA was completely compacted, and a further increase in TFAM concentration had no further effect. This may be the density of TFAM required for storage of mtDNA.

They then continued their analysis in vivo, by studying TFAM-overexpressing mouse embryonic fibroblasts (OE MEFS), which had ~2.5-fold higher mtDNA copy number. Nucleoids can cluster in cells, and confocal microscopy cannot always resolve individual nucleoids. The number of nucleoids detected in wild-type cells using superresolution STED microscopy / confocal was 1.36+/-0.76. By counting nucleoids using STED microscopy, and mtDNA copy number with rt-qPCR, they found that wild-type cells had ~1.1 mtDNA molecules / nucleoid and OE MEFS had ~1.5 mtDNA molecules / nucleoid. Thus, overexpressing TFAM has only minor changes in the mean amount of mtDNA per nucleoid. Instead, the number of nucleoids was observed to increase, relative to wild-type cells.  

Friday, 21 August 2015

Mitotic redistribution of the mitochondrial network by Miro and Cenp-F

http://www.ncbi.nlm.nih.gov/pubmed/26259702

Kanfer G, Courthéoux T, Peterka M, Meier S, Soste M, Melnik A, Reis K, Aspenström P, Peter M, Picotti P, Kornmann B


If a cell divides, how do its mitochondria get segregated into the two daughter cells?  In general, mitochondria often move along microtubules with the help of molecular motors. Specialized adaptors on the mitochondrial outer membrane  recruit these motors, one of them being the GTPase Miro. But how exactly the segregation of mitochondria during mitosis is coordinated, is not well understood.

In this paper, they identify centromeric protein F (Cenp-F) which interacts with Miro. Cenp-F is a large protein that binds to the microtubules. It was found to be strongly recruited to mitochondria at the end of mitosis.  During S/G2, a fraction of Cenp-F is found on mitochondria, located mainly at the mitochondrial tips projecting away from the cell centre. The mitochondrial Cenp-F puncta that were visible in the S/G2 phase were all colocalized with microtubules.

They further find that Cenp-F directly interacts with the GTPase domains of both Miro1 and Miro2, leading to its recruitment to mitochondria. In wildtype cells, during cytokinesis mitochondria were parallel and extended away from the division plane, whereas in cells without Miro (or Cenp-F) the mitochondria were all clustered together around the nucleus.
 
The conclusion was that Cenp-F, recruiting by Miro, connects mitochondria to the tips of growing microtubules. The mitochondria then track the tips of the microtubules. Mitochondria were also seen to influence local microtubule dynamics, it can be that dragging forces caused by the attached mitochondria play a role in this.

Maternal transmission, sex ratio distortion, and mitochondria

http://www.pnas.org/content/112/33/10162.full

Steve J. Perlman, Christina N. Hodson, Phineas T. Hamilton, George P. Opit, Brent E. Gowen

Most (but not all) multicellular organisms have uniparental inheritance of mitochondrial DNA, which is thought to prevent invasion by a more competitive lineage, and maintain compatibility between mitochondrial and nuclear genomes. Mitochondrial DNA is also subject to evolutionary pressures, and in this review the authors discuss potential (deleterious) side-effects of uniparental inheritance. 

An immediate consequence of uniparental inheritance is that one sex is an evolutionary dead-end. Thus, any selective pressure on mtDNA is principally exerted on the transmitting sex (females), and so deleterious mutations for the non-transmitting (males) sex can accumulate. This explains why male infertility is often attributed to mutations in mtDNA. A study by Innocenti et al. [1], established fly lines with variation in their mtDNA. A large fitness variation was observed, but only in males; this caused significant differential expression across the nucleus of male flies. 

The authors suggest three possible consequences of maternal inheritance of mtDNA:
  1. MtDNA mutations which are detrimental to males may fixate, if they do not affect female fitness
  2. MtDNA mutations which cause the frequency of females to increase, may fixate
  3. Nuclear symbionts carried on the nuclear female chromosome which fixate, will also cause their associated mtDNA haplotype to fixate


[1] Innocenti P, Morrow EH, Dowling DK (2011) Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution. Science 332(6031):845848.



Wednesday, 12 August 2015

An Essential Role of the Mitochondrial Electron Transport Chain in Cell Proliferation Is to Enable Aspartate Synthesis

http://www.sciencedirect.com/science/article/pii/S0092867415008533

Kıvanç Birsoy, Tim Wang, Walter W. Chen, Elizaveta Freinkman, Monther Abu-Remaileh, David M. Sabatini

When mitochondrial respiration is inhibited, it is observed that a cell's ability to proliferate is diminished. It is also known that cells with inhibited oxidative phosphorylation (OXPHOS) are still able to proliferate, if cultured in high concentrations of pyruvate (a metabolite which is the by-product of glycolysis, and feeds the tricarboxylic acid cycle). In this study, the authors screen a library of ~3,000 metabolic enzymes, treated with a low dose of complex I inhibitor phenformin, whose loss causes a severe anti-proliferative phenotype. This would reveal genes which are required in an adaptive response to mild OXPHOS inhibition.

The best scoring gene in their screen was GOT1, a component of the malate-aspartate shuttle, which transfers substrates for OXPHOS into the mitochondrial matrix. They find that GOT1-null cells are hypersensitive to phenformin, causing their proliferation to halt, at doses where wild-type cells do not.

Under normal conditions, GOT1 shuttles the amino acid aspartate, into the mitochondrial matrix. They find that, upon inhibition of complex I, GOT1 reverses its flux and exports aspartate. Aspartate is an amino acid, required for the synthesis of proteins, purines and pyramidines. Normally, it is generated in the mitochondrial matrix; the authors propose that during ETC inhibition, a drop in NAD+/NADH ratio causes aspartate synthesis to shut down, using normal pathways. Thus GOT1 reverses its flux, to become a source of this amino acid.

It is also known that supplementation of pyruvate can overcome the inhibitory effects of several ETC inhibitors. By culturing GOT1-null cells with/without pyruvate, the authors show that there is no benefit to supplementing cells with pyruvate under ETC inhibition, if cells lack GOT1. Thus a key mechanism of pyruvate supplementation is GOT1-catalyzed aspartate synthesis. Interestingly, these conclusions appear to hold in cybrid cell lines harbouring mtDNA mutations (homoplasmic mutations in CYTB and tRNA lysine were tested). When these cells overexpress an aspartate transporter SLC1A3, and cultured in high aspartate medium, their proliferation rate recovers to similar levels as wild-type cells.