Friday, 5 December 2014

Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer

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Wednesday, 3 December 2014

Explicit Tracking of Uncertainty Increases the Power of Quantitative Rule-of-Thumb Reasoning in Cell Biology

Biological quantities often come with substantial associated uncertainty, either because experimental measurements have errors, or biological systems are naturally variable (or both). This uncertainty sometimes makes it hard to fully interpret rough calculations in biology, because uncertainties in quantities can combine in non-obvious ways. This (awesome :-) ) paper introduces an approach and web tool designed to perform calculations while explicitly tracking uncertainty, so that a calculation doesn't result in a single number but rather a descriptive interpretable distribution. The web tool is linked to the BioNumbers database of experimental measurements in biology, facilitating quick and easy "back-of-the-envelope" calculations in biology.

As a mitochondrial example, here's a toy calculation of the number of protons in a mitochondrion. BioNumber #100438 gives us a guess at the volume of a mitochondrion; BioNumber #105939 tells us the internal pH (each quantity has an uncertainty). We can use the two values to estimate the number of protons in a mitochondrion:^%28-%24105939%29*6e23*%24100438*1e-15&v=105939%3Alogn%2C7.98%2C0.07%3B100438%3Alogn%2C0.5%2C0.25&x=off&n=m&h=fd&a=rad

Tuesday, 25 November 2014

Aging: A mitochondrial DNA perspective, critical analysis and an update

Inna N Shokolenko, Glenn L Wilson, and Mikhail F Alexeyev
This review discusses the recent criticisms of the mainstream view that a vicious cycle of ROS-induced mtDNA damage induces further ROS production and mtDNA damage. For instance, the authors cite evidence that chronic exposure of cells to rotenone (a complex I inhibitor and ROS generator) and hydrogen peroxide causes no significant increase in mtDNA mutation. Indeed, the superoxide radical inhibits the enzyme aconitase, suppressing the Krebs cycle and reducing the supply of NADH and FADH2, which reduces the electron flow through the ETC. Thus there may exist a negative feedback loop for ROS production in oxidative phosphorylation. The authors suggest that ROS may in fact contribute to adaptive signalling to mitigate the effects of ageing. For instance, naked mole-rats live almost 8 times longer than mice, and yet have a much higher oxidative burden, especially in their mtDNA.

Thursday, 20 November 2014

Ischaemic accumulation of succinate controls reperfusion injury through mitochondrial ROS

Edward T. Chouchani, Victoria R. Pell, Edoardo Gaude et al.

The authors investigate the mechanism of ischaemia-reperfusion (IR), which occurs when the blood supply to a tissue is disrupted and then restored, such as during a heart attack or stroke. It is already well-established that tissue damage occurs once blood supply is restored, as this causes the electron transport chain to run in reverse: using ATP to pump protons into the mitochondrial matrix, generating reactive oxygen species (ROS) and inducing cell death. This study shows that accumulation of succinate is a universal feature of ischaemia, due to complex II reversal at low oxygen concentration. After reperfusion, the large amount of succinate drives conventional electron transport in complex III and IV, whilst driving complex I to run in reverse, to generate ROS. The authors show that inhibition of complex II ameliorates reperfusion injury. This cardiprotection is lost again when dimethyl succinate is added back, indicating that succinate elimination is the key protective feature of complex II inhibition.

Wednesday, 12 November 2014

Compartmentalization of the protein repair machinery in photosynthetic membranes

Sujith Puthiyaveetil, Onie Tsabari, Troy Lowry, Steven Lenhery, Robert R. Lewis, Ziv Reich and Helmut Kirchoff

Photosynthesis relies on the functioning of the PSII complex, which is embedded in the thylakoid membranes of plant chloroplasts. This complex is large and composed of multiple subunits, of which the D1 subunit bears most of the brunt of the damage from photosynthesis. The complex undergoes a repair cycle which reduces the amount of protein synthesis required by only replacing the D1 subunit through a series of reactions designed to remove and degrade the damaged D1 subunit without destroying the entire complex, before synthesising a new D1 subunit. This repair process occurs in the stroma lamellae (which connect the stacked grana), however PSII is concentrated in the stacked grana. PSII phosphorylation triggers its disassembly before it is transported through the grana margin to the stroma lamellae for D1 replacement. The repair cycle is involved and must happen rapidly - the entire PSII complement of a plant can be turned over in just 1 hour. This requires an efficient process with minimal back-reactions.

The authors investigated the organisation of the PSII repair system through fractionation of thylakoid membranes and electron microscopy (EM) investigation of stacked grana. High-light (HL) treatment, which causes increased damage to PSII, led to growth in grana margins at the expense of grana core and stroma lamellae. By quantifying levels of key proteins involved in PSII repair in the grana core, margins and stroma lamellae, the authors deduced that localising different components in different areas allows the PSII repair system to improve its throughput by minimising back-reactions. In addition, localisation of proteolytic steps also reduces the amount of unnecessary protein degradation, by ensuring that access to proteasomes is restricted.

The authors identify discovering factors that govern the localisation of enzymes to the appropriate compartment as an important future step.

Tuesday, 11 November 2014

Transcription could be the key to the selection advantage of mitochondrial deletion mutants in aging

Axel Kowald and Thomas B. L. Kirkwood

In this paper they discuss a mechanism that could be responsible for the observed "clonal expansion" of mtDNA mutations. Clonal expansion means that in individual cells, the mitochondrial population is often taken over by a single type of mutant (as opposed to many different mutants). There have been various suggestions as to how clonal expansion occurs but none of these suggestions can account for all the experimental observations. For example, the hypothesis that clonal expansion of a single mutant happens merely by chance (random drift) can explain clonal expansion in long lived, but not short lived species.

In this paper, they propose a new mechanism of clonal expansion. The idea they propose is that normally, mtDNA replication rate decreases if concentrations of some of its products are high (a negative feedback loop). Mutants that miss that part of the genome that encodes for proteins involved in this feedback loop will not be able to suppress mtDNA replication rate through this feedback mechanism. These deletion mutations therefore have a replicative advantage over wild-type mitochondria.

By studying the position in the genome of mtDNA deletions that were observed to be clonally amplified, they found that most deletions overlap a subunit of complex I of the respiratory chain. This means that it could be that this subunit is involved in the negative feedback loop, and missing this subunit gives a replicative advantage that allows for clonal expansion.

They then provide an ODE model describing the dynamics of wildtype and mutant mtDNA as well as ATP concentration. In their model they assume that mutants have a 50% higher replication rate because they lack the negative feedback loop.  Because of this, the mutant population increases exponentially until the cell collapses (collapse is defined by a certain drop in ATP concentration and each extra mutant present lowers the ATP concentration by some amount).  Their model predicts that, if one starts with 1000 wildtype mtDNAs and 1 mutant mtDNA, at the moment of collapse the number of mutants is 9-fold higher than the number of wildtypes. This is in agreement with experimental results.

They continue to make a stochastic version of their ODE model, which can predict clonal expansion of a single type of mutant (rather than accumulated of various mutants) in both long- and short-lived species.

Thursday, 6 November 2014

A Mitochondrial ATP Synthase Subunit Interacts with TOR Signaling to Modulate Protein Homeostasis and Lifespan in Drosophila

Xiaoping Sun, Charles T Wheeler, Jason Yolitz, Mara Laslo, Thomas Alberico, Yaning Sun, Qisheng Song, Sige Zou

The authors studied a Drosophila model in which ATP synthase d (ATPsyn-d) was knocked down after reaching adulthood using a drug-inducible gene switch system (simply knocking down ATPsyn-d led to lethality before pupation). ATPsyn-d knockdown after reaching adulthood increased lifespan in female but not male Drosophila with no alteration to food intake, however overexpression did not have any effect. The lifespan extension was diet-dependent, and enhanced lifespan in high protein, low sugar diets but decreased them when the proportions were reversed.

ATPsyn-d knockdown paradoxically led to increased ATP levels through a decrease in UCP expression, but only on a protein-rich diet. It also caused significant transcriptional changes, including proteins involved in a range of protective, proteostatic and energy-generating roles.

The authors also explored the effects of ATPsyn-d knockdown on TOR and MAPK pathways, and found that overexpression of the TOR signalling suppressor Tsc2 cancelled out the longevity-promoting effects of ATPsyn-d knockdown. Feeding with rapamycin had a similar but less pronounced effect, reducing the lifespan extension due to ATPsyn-d knockdown. This is attributed to overlapping pathways of lifespan extension between ATPsyn-d and rapamycin, which are likely to include TOR signalling.

Finally, a decrease in protein polyubiquitination and polyubiquitinated protein aggregates was observed. These are biomarkers for proteostasis, leading the authors to conclude that the lifespan extension due to ATPsyn-d knockdown is at least partially accomplished through improved proteostasis. The authors suggest that ATPsyn-d and other mitochondrial proteins regulate TOR signalling, and that perhaps the beneficial effects exist in high protein, low carbohydrate diets because there TOR levels are high, whereas in low protein, high carbohydrate diets TOR levels are low so there is nothing to knock down.

Wednesday, 5 November 2014

Kinetic evidence against partitioning of the ubiquinone pool and the catalytic relevance of respiratory-chain supercomplexes

James N. Blaza, Riccardo Serreli, Andrew J. Y. Jones, Khairunnisa Mohammed, and Judy Hirst

The electron transport chain (ETC) consists of protein complexes, which pump protons across a membrane to store electrochemical potential energy. This potential energy is then converted by another element of the ETC into an energy currency: ATP. Recent studies have shown that the complexes of the electron transport chain exist in supercomplexes, where multimers of the ETC components combine, which is thought to increase their efficiency. 

The authors present evidence disputing the importance of these supercomplexes (but not their existence). Ubiquinone (Q) is a protein which ferries electrons through the lipid membrane of the ETC, and exists in a pool between the leaflets of the membrane. It has been proposed that the Q pool is partitioned such that supercomplexes have a separate pool to the TCA-cycle. However, the authors show that altering the levels of substrate for the ETC and TCA causes global changes in the Q pool, which is evidence against partitioning.

Supercomplexes are also widely cited to exist because of the observation that flux through the ETC is almost entirely controlled by both complex I and III of the ETC, suggesting they exist in a complex together. The authors here, however, question this finding because these studies rely on a particular inhibitor, rotenone, to inhibit complex I. Upon replication of previously published protocols, the authors find flux control coefficients of >100%, which is impossible. Using alternative inhibitors, the authors measured more modest control coefficients, which the authors interpret as evidence against the catalytic importance of supercomplexes.

Tuesday, 4 November 2014

Feedback regulation via AMPK and HIF-1 mediates ROS-dependent longevity in Caenorhabditis elegans

There's a wealth of stuff in this paper and it's all pretty cool. The idea is to examine the finding that inhibiting mitochondrial respiration extends lifespan. These guys pick apart a feedback mechanism involving HIF-1 and AMPK that responds to, and balances, ROS levels. They find that HIF-1 and AMPK cross-repress and regulate ROS levels in different directions, potentially allowing for fine control over ROS levels. The feedback system is coupled to free iron homeostasis (free iron can lead to the production of ROS) and intriguingly seems to modulate resistance to bacterial pathogens (suggesting that mitochondrial ROS lowers rates of infection).

(By the way, they're using ROS probes DCF-DA and Amplex Red -- not cpYFP, which we have issues with)

Monday, 3 November 2014

A Mitofusin-2 – dependent inactivating cleavage of Opa1 links changes in mitochondria cristae and ER contacts in the postprandial liver

Aditi Sood,Danny Vijey Jeyaraju, Julien Prudent, Alexandre Caron, Philippe Lemieux, Heidi May McBride, Mathieu Laplante, Katalin Tóth, and Luca Pellegrini; PNAS

In this paper, they study the liver of two groups of mice: 1) the first group was killed 2 hours after feeding 2) the second group was killed 5h after feeding. Nutrient levels become limited in the 5h group, they then studied the shape of cristae and the amount of ER-mitochondria contact in the 5h group as compared to the 2h group.

Changes in cristae structure

The number of cristae per mitochondrion had decreased in liver cells with limited nutrients. The average length per cristae remained the same.


Changes in mitochondria-ER contact
About 1 in 4 mitochondria in both groups was in contact with the ER, but in the nutrient limiting group the mitochondrial surface area in contact with the ER had increased. The ER thus wrapped more extensively around mitochondria when nutrients were limited.

OPA1 cleavage observed which is MFN2 dependent

They then continue to investigate what caused the cristae remodelling.
Total OPA1 expression levels were the same in both groups, but two new forms of OPA1 were identified in nutrient-limiting conditions. These two forms were the result of OPA-1 cleavage by an unknown cysteine protease.The sites of cleavage were named C1 and C2. Cleavage at either C1 or C2 is likely to inactive the dynamin-like activity of OPA1, but does not interfere with mitochondrial dynamics. Mfn2 was required for the observed OPA1 cleavage, further suggesting a link between changes in cristae shape and changes in mitochondria-ER contact (because MFN2 is involved in mitochondria-ER tethering).


 Mitochondria adapt to changes in nutrient availability by remodelling their cristae and changing the amount of mitochondria-ER contact. The cristae remodelling is mediated through MFN2-dependent OPA1 cleavage by a cysteine protease. The study suggests that cristae remodelling and changes in mitochondria-ER contact are coupled during nutrient depletion.

Thursday, 30 October 2014

Making Proteins in the Powerhouse

B Martin Hällberg and Nils-Göran Larsson; Cell Metabolism (5 August 2014)

This review discusses the elements of mitochondrial transcription and translation, and the pathogenic effects of defects.

Mitochondrial DNA contains essential subunits of proteins involved in the oxidative phosphorylation system, as well as the tRNA and rRNA required for translation of proteins inside the mitochondrion. Although the vast majority of mitochondrial proteins are imported, failure to correctly translate the proteins encoded by mtDNA can lead to defects in oxidative phosphorylation, which can lead to significant negative consequences for the organism. Such a failure can occur either through mutation of a gene encoding a protein, or through damage to tRNA or rRNA impairing the mitochondrial translation system as a whole. The authors give the example of two mutations in the 12S rRNA gene of mitochondria which can lead to deafness, as well as referencing a subset of mtDNA mutations found in aging which can impair mitochondrial translation.

mtDNA transcription by mitochondrial RNA polymerase (POLRMT) leads to the creation of two long transcripts, one from each strand. These are punctuated by tRNA which are then cleaved at their 5' and 3' ends to release the mRNA strands held between them. It is currently unclear how mRNAs which are not between two tRNAs are released and processed. Early transcript processing is believed to take place alongside transcription in mitochondrial RNA granules, which may be followed by a second round of processing outside of these granules. Mitochondria possess a specific polyA polymerase (mtPAP) which performs polyadenylation of mitochondrial mRNA; without this polyadenylation mitochondrial mRNA stability is impaired and translation decreases.

Mammalian tRNAs are inherently less stable than other types of tRNA due to structural differences. The authors state that this makes them more susceptible to processing and modification defects, and that over 100 mutations in mitochondrial tRNAs have been observed to be pathogenic. The aminoacyltransferases responsible for charging mitochondrial tRNAs are all encoded in the nucleus.

Mitochondrial ribosome biogenesis requires the co-ordination of both nuclear and mitochondrial processes; 12S and 16S mitochondrial rRNA must be assembled with ribosomal proteins imported from outside of the mitochondrion. Translating mitoribosomes have been reported to be tethered to the inner mitochondrial membrane. The authors also discuss post-transcriptional modifications of 12S and 16S mitochondrial rRNA and the biogenesis of the mitoribosomal subunits.

The mammalian mitoribosome has a mass ratio of RNA to protein of 1:2, whereas bacterial and eukaryotic cytosolic ribosomes have a ratio of 2:1. The authors suggest that this reflects the loss of rRNA components since absorption of the proteobacterium that formed primitive mitochondria, and the replacement of these components with nuclearly encoded proteins.

The authors discuss the fact that at least one tRNA gene is always lost in all pathogenic single large deletion mutations of human mtDNA and that these mutations always lead to heteroplasmy and a require a heteroplasmy of >60% to impair translation. Heteroplasmic tRNA point mutations are also stated to be common causes of mitochondrial disease. Nuclear mutations affecting genes controlling mitochondrial translation also have a wide variety of potential pathological effects.

Finally, the authors discuss the fact the surprising complexity of the mitochondrial translation given its limited remit, and the number of nuclear-encoded genes that must be coordinated with mitochondrial translation in order to permit correct function. They emphasise the importance of studying mitochondrial translation in order to understand both mitochondrial disease and aging.

Wednesday, 29 October 2014

Myo19 Ensures Symmetric Partitioning of Mitochondria and Coupling of Mitochondrial Segregation to Cell Division

Jennifer L. Rohn, Jigna V. Patel, Beate Neumann, Jutta Bulkescher, Nunu Mchedlishvili, Rachel C. McMullan, Omar A. Quintero, Jan Ellenberg, Buzz Baum

At cell divison mitochondria are segregated between the halves of the cell that will form the daughter cells. In order to ensure both offspring are viable they must both be provided with a sufficient complement of functioning mitochondria. The authors use a small interfering RNA (siRNA) library to target genes known to be associated with cell division errors. The resulting phenotypes were analysed by visual inspection of videos compiled from automated microscopy images to determine which of the candidate genes led to a cell division defect.

In addition to identifying a number of already-known genes, the authors identified the myosin protein Myo19 as being crucial for cell division. Myo19 was determined to be targeted to mitochondria, where it is associated with the outer membrane through a 150 amino acid domain known as MyMOMA (Myo19-specific mitochondria outer membrane association).

Inhibiting mitochondrial fission led to a failure of cell division, which the authors hypothesise may be caused by the division ring being obstructed by an excessively fused mitochondrial network. Treatment with siRNA inhibiton of mitofusin-2 (Mfn2) rescued the Myo19 depletion phentype, lending support to this idea.

Finally, and most remarkably, Myo19 inhibition led to highly asymmetric organisation of mitochondria in anaphase. This demonstrates a role for Myo19 in the correct partitioning of mitochondria at cell division; without it mitochondria are not recruited correctly to the poles of the cell and can sometimes obstruct the division ring, causing cell division to fail. Given that mitochondria are known to move along microtubules the authors suggest that Myo19 acts as a tether, regulating their poleward movement along microtubules during segregation.

Tuesday, 28 October 2014

Rapid rates of newly synthesized mitochondrial protein degradation are significantly affected by the generation of mitochondrial free radicals

A. Basoah, P. M. Matthews, K. J. Morten; FEBS Letters (November 2005)

Proteins are vulnerable to oxidation by reactive oxygen species (ROS), and mitochondrial proteins are especially at risk due to their proximity to ROS production. Nuclear proteins localised to mitochondria are at additional risk due to their partially unfolded state immediately after translocation.

Once proteins have been damaged, they are targeted for degradation by the cell's degradation machinery, however severe ROS damage can lead to proteins becoming harder to degrade. These undegraded proteins can then form protein aggregates which can prove toxic to the cell. Alternatively, if the protein degradation machinery is successful in destroying the damaged protein, this can lead to proteins being removed before they can be fully assembled. This can cause a deficiency of the damaged protein if it happens repeatedly.

The authors study a C2C12 myoblast cell culture and investigate the effects of ROS production on newly synthesised mitochondrial protein turnover. Cells were treated with menadione, which increased ROS production and led to an increase in protein degradation rate, which was observed using labelled methionine. Menadione levels were kept low so as not to affect cell viability (high doses have been shown to trigger cell death), but led to elevated ROS levels.

The changes in protein degradation were not uniform, and some proteins even showed decreased degradation rates. Confusingly, two different subunits of ATP synthase showed opposite effects, with one degradation rate increasing while the other decreased. The experimental timescale was not long enough to determine if these changes in degradation rates led to changes in steady-state abundance of the proteins concerned.

Mitochondrial ROS in cancer: initiators, amplifiers or an Achilles’ heel?

Mitochondrial ROS in cancer: initiators, amplifiers or an Achilles’ heel?

Reactive oxygen species (ROS) are typically generated by the leak of electrons from the electron transport chain (ETC) in mitochondria: the powerhouse of the cell. The function of ROS in both normal and pathological circumstances is subtle, as highlighted by this review. ROS are thought to damage mitochondrial DNA, which may result in the ETC becoming more leaky, to generate more ROS. ROS can switch on a variety of pro-survival signals such as HIF, MAPK-ERK and AMPK in cancer, as well as causing nuclear DNA-damage to increase the chances of oncogenic mutations. However, through controversial mechanisms, ROS can also act as death inducers in cancer, perhaps by spurring on apoptotic signalling. The authors argue that ROS are in fact the initiators, amplifiers and the Achilles' heel of cancer.

Monday, 27 October 2014

Enhancing nucleotide metabolism protects against mitochondrial dysfunction and neurodegeneration in a PINK1 model of Parkinson's disease

Loss of the mitochondrially-localised kinase PINK1 can cause early-onset Parkinson's disease, and a possible cause of this is through mitochondrial dysfunction following mutation of the Pink1 gene. The authors used a combination of transcriptional and metabolic profiling to discover that Pink1 mutant Drosophila have changes in nucleotide metabolism, in addition to the upregulation of the mitochondrial unfolded protein response which has been observed previously.

Following loss of pink1 a number of metabolic pathways were significantly upregulated, including glycine and serine metabolism, as well as nucleotide salvage, purine biosynthesis, and folate metabolism. The authors interpret this as a metabolic stress response induced by the cell to compensate for mitochondrial impairment due to loss of pink1.

The increase in folate metabolism was due to an upregulation of the kinase dNK, which was found to be the rate-limiting enzyme in the nucleotide salvage pathway. Pink1 mutants have upregulated dNK expression, which is shown to lead to organellar biogenesis. The authors find that inducing overexpression of dNK rescues mitochondrial dysfunction in pink1 mutant flies through enhancement of the nucleotide salvage pathway, and that dietary supplementation with deoxynucleosides also improved the suppression of mitochondrial dysfunction.

Thursday, 23 October 2014

Endogenous Drp1 Mediates Mitochondrial Autophagy and Protects the Heart Against Energy Stress

In this paper they investigate the role of Drp1 in mediating mitochondrial autophagy and stress resistance in cardiomyocytes.

Cells with down-regulated Drp1 show increases in the amount of cleaved caspase 3 (which activates the caspase and this can result in apoptosis) suggesting that Drp1 plays a role in protection against apoptosis. Also, autophagic flux was reduced upon Drp1 downregulation. Results suggest that Drp1 is required to stimulate mitochondrial degradation through autophagy.

There were significantly more mitochondria in cells with Drp1 downregulation, suggesting that the reduction in autophagy leads to an accumulation of mitochondria. Expression of PGC-1a (which causes mitochondrial biogenesis) was the same as in control cells. ATP production was lower in Drp1 downregulated cells, membrane potential was lower and mPTP opening was likely to be accelerated (increased mPTP opening could have been the reason why apoptosis was seen more). Maximum respiratory rate was lower, but the amount of proton leak was not significantly different.

Genetics of the Pig Tapeworm in Madagascar Reveal a History of Human Dispersal and Colonization

The pig tapeworm Taenia solium can cause the tropical disease cysticercosis. Humans are the only definitive hosts of the worm and pigs are the principal intermediate hosts.

The tapeworm can be divided into two mtDNA lineages, Asian and Afro-American, with disjunct geographical distributions. Recently it was found that both lineages exist in Madagascar. The first humans settled in Madagascar about 2000 years ago. Linguistic and archeological evidence suggests that people on Madagascar have ancestry from Island South-east Asia and East Africa. Recently, by studying mtDNA, a genetic contribution from India has been suggested.
By studying the genetics of the tapeworm insights for the distributional history of hosts and parasites can be gained.

In this paper, they collected larvae from pigs across five provinces on Madagascar. Their results indicate the importance of Indian influence on the diversity of people and culture in Madagascar, and that the tapeworms were introduced in Madagascar (within the past hundreds of years) multiple times with people and swines from East Africa. They also find evidence for hybridization between tapeworms with different genotypes.

Wednesday, 22 October 2014

Tumor suppressor p53 cooperates with SIRT6 to regulate gluconeogenesis by promoting FoxO1 nuclear exclusion

Tumor suppressor p53 cooperates with SIRT6 to regulate gluconeogenesis by promoting FoxO1 nuclear exclusion

p53 is a commonly mutated transcription factor in cancer, and is one of the most studied tumour suppressors. Here, the authors elucidate the interaction of p53 with the metabolism, specifically gluconeogenesis: the process by which glucose is built from non-carbohydrate amino acids, which could conceivably be essential for tumour growth. The authors show that p53 directly activates SIRT6, which induced translocation of FOXO1 to the cytoplasm, which activates the enzymes PCK1 and G6PC, which encode the rate-limiting enzymes for gluconeogenesis.

Tug-of-war between driver and passenger mutations in cancer and other adaptive processes

Tug-of-war between driver and passenger mutations in cancer and other adaptive processes

The authors generate a model of tumour growth by defining a fitness function, which depends on the number of driver and passenger mutations which have accumulated. The birth rate of cells is set by the fitness, and the total death rate saturates with the number of cells in the population. In the rare event that a driver mutation is generated, the population size increases rapidly. The population then decays due to the accumulation of passenger mutations which are assumed to reduce the fitness by a constant amount, per mutation. The resultant dynamics is a sawtooth, due to a tug-of-war between drivers and passengers. Their model predicts a critical population size, above which tumour growth is exponential, and below results in extinction. 

Monday, 20 October 2014

Hexokinase II integrates energy metabolism and cellular protection: Akting on mitochondria and TORCing to autophagy

Hexokinase II integrates energy metabolism and cellular protection: Akting on mitochondria and TORCing to autophagy

This review discusses the role of hexokinase II (HKII), a protein which is commonly misregulated in cancer. Hexokinases phosphorylate glucose, which is the first rate-limiting step of glycolysis. Glucose-6-phosphate then inhibits the action of hexokinases to form a feedback mechanism. Furthermore, HKII takes a central role in pro-survival signals, through its inhibition of apoptosis and enhancement of mitophagy. Thus, HKII can be viewed as a molecule which bridges the metabolism and cell survival.

Friday, 17 October 2014

Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis

Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis

Primary tumours spread to other parts of the body by shedding cells into the blood stream, which can seed tumours elsewhere. This process is thought to be mediated by single cells, but the authors here show that cancer cells are also found to exist in clusters when extracted from the blood, but at a very low abundance. The authors identify the factor plakoglobin which is necessary for cluster formation. Knockdown of this factor had little effect on primary tumour size, but had a striking 80% reduction in metastatic node formation in mice. This indicates that these clusters have a stronger contribution to metastases formation, than just by their abundance.

We can only speculate as to the mechanism by which these clusters gain their super-linear metastatic potential. Perhaps cooperation through sharing of a common resource makes them energetically more competent?

Thursday, 16 October 2014

The distribution of mitochondria and endoplasmic reticulum in relation with secretory sites in chromaffin cells

In this paper they investigate I) the distribution of mitochondria and the ER in chromaffin cells, and ii) how this distribution plays a role in exocytosis.

Exocytosis occurs in response to elevations of cytoplasmic calcium levels and requires energy. Mitochondria-ER interactions are important in shaping cellular calcium signals and therefore the distribution of these two organelles in the cell may well influence exocytotic events.

Mitochondria in chromaffin cells exist in two main populations, one of higher density in the cortical region and another one in the perinuclear region. Mitochondria were noticably smaller in size in the cortical region. The two populations showed different mobilities, mitochondria in the perinuclear area were faster and moved through F-actin and microtubular structures.

Distribution of the ER is more uniform (though the density increases gradually from the cortical zone to regions close to the nucleus) and ER elements were also smaller in cortical regions.

They find that the cortical populations of mitochondria and ER themselves consists of two subpopulations, one close to exocytotic sites and one further away. The local cortical subpopulations could be directly involved in the regulation of calcium signals and ATP supply in the immediate vicinity of exocytotic sites.

Wednesday, 15 October 2014

OPA1‐dependent cristae modulation is essential for cellular adaptation to metabolic demand

OPA1 mediates fusion of the inner mitochondrial membrane and is also involved in cristae remodelling. Maintenance of the cristae structure requires oligomerization of OPA1 because disruption of OPA1 oligomers is necessary for cristae opening and cytochrome c release.

In this paper, they observe that OPA1 dynamically regulates cristae shape and that OPA1 is required for resistance against starvation-induced cell death, and that these processes are independent of mitochondrial fusion (a mutant of OPA1 that does oligomerize but has no fusion activity is still able to maintain cristae structure).

They also show that some group of mitochondrial solute carriers (SLC25A) interacts with OPA1. These SLC25A transporters can sense changes in energy substrate availability. So if there are changes in energy substrate levels, SLC25A transporters respond to this and in turn interact with OPA1 which modulates cristae structure (which regulates assembly of ATP synthases) to respond to the change in energy substrate availability. All of this is independent of OPA1's role in fusion.

Why are most organelle genomes transmitted maternally?

Mitochondrial DNA (mtDNA) is maternally inherited which means it does not undergo sexual recombination. But recombination is thought to be required to prevent an accumulation of mutations (a process known as Muller's ratchet, summarized below in red). Why do mitochondria survive then? How did maternal inheritance evolve?

Paternal leakage occurs
There is increasingly more evidence that occasionally sexual recombination does occur (known as paternal leakage) and this may slow down Muller's ratchet (this is only speculated). There is, however, a selection pressure towards the evolution of uniparental transmission.

Hypotheses for uniparental inheritance
Several theoretical models for the occurrence of uniparental organelle inheritance exist, including the following:
  1. Avoiding competition between organelles and avoiding negative interaction between organelle genomes and/or other organelle genomes and the nuclear genome.
  2. The genetic bottleneck makes it possible to get rid of mutations because genetic drift to homoplasmy can occur. Paternal leakage interferes with this process.
  3. Many genes from endosymbionts have been transferred to the nuclear genome of the host cell and a lot of gene products are then re-imported into the endosymbiont. This means tight co-evolution and co-adaptation between endosymbiont and host cell is required. Mathematical models have shown that co-adaptation is enhanced by uniparental inheritance and could thus be the driving force of uniparental inheritance.

However, there are arguments against all of these hypotheses. For example, they fail to explain why , if uniparental transmission occurs, it is almost always maternal (uniparental paternal inheritance is very rare) and why killing of the paternal cytoplasm occurs (which can be costly).

In this paper, a unifying model for organelle inheritance is proposed.
They argue that uniparental inheritance evolved to avoid the spread of faster replicating organelle genomes that are incompatible with the host nucleus. This uniparental inheritance, however, is unstable (because of Muller's ratchet) and this drives a relaxation of strict maternal inheritance by paternal leakage or biparental transmission. Paternal leakage is then again susceptible to the evolution of fast replicating genomes incompatible with the host nucleus, so paternal leakage is lost again. Then it is restored again (because of Muller's ratchet), then lost again etc... They thus claim that uniparental inheritance is an unstable state. The maternal predominance is due to more mutations in the paternal cytotypes.

They then discuss some evidence for their theory.

Muller's ratchet
In asexual reproduction, genomes are inherited as indivisible blocks. If mutations occur, they will be carried over to the next generation. They will keep on accumulating and eventually the population will go extinct. In sexual reproduction, this is prevented because recombination occurs. Recombination allows for the possibility to generate genomes with fewer mutations from genomes that are highly mutated, by putting together mutation free portions of the parental chromosomes.
Note → Having a small genome reduces the probability of mutations to accumulate and therefore the effect of Muller's ratchet can be very small when genomes are small.

Activation of mitochondrial protease OMA1 by Bax and Bak promotes cytochrome c release during apoptosis

When cytochrome c is released from the intermembrane space of mitochondria into the cytoplasm, caspases in the cytoplasm become activated and they initiate apoptosis. Besides cytochrome c, other proteins that normally reside in the intermembrane space are also released into the cytoplasm, one of them is Smac which inhibits inhibitors of apoptosis. Controlling the permeability of the outer membrane of mitochondria is therefore crucial to the survival of the cell. Which event trigger the permeability to increase so that apoptosis follows?

This paper finds that first, Bax and Bak are recruited to the surface of mitochondria. This then activates OMA1, an m-AAA inner membrane protease  that is responsible for cleavage of the long isoforms of OPA1. OPA1 can shape cristae, so when it is cleaved the cristae will remodel and this is presumably what makes it possible for cytochrome c to be released.

To summarize:

  1. Bax/Bak oligomerize on the mitochondrial surface 
  2. This oligomerization somehow changes the inner membrane structure and   activates OMA1, an inner membrane m-AAA protease.  
  3. OMA1 cleaves L-OPA1 
  4. A change in the ratio of long to short isoforms of OPA1 influences cristae structure, so the cristae start remodelling
  5. cytochrome c is released

Tuesday, 14 October 2014

Mitochondrial dynamics and inheritance during cell division, development and disease

This is a nice review on mitochondrial dynamics during cell division, development and disease. A few highlights are mentioned here.

In cells lacking Drp1, mitochondria exist in elongated networks but they are still segregated to daughter cells (but less uniformly), probably because the machinery involved in cytokinesis is strong enough to cleave the mitochondria.

Mitochondria can be non-selectively removed as part of an autophagy response, but mitophagy can be selective too. Mitochondria that are experimentally depolarized attract autophagy machinery and undergo mitophagy.

The mtDNA bottleneck that occurs during oogenesis is discussed as well. A second mtDNA bottleneck occurs during early embryogenesis (there is no mtDNA replication in this stage which reduces mtDNA copy number).

A discussion about the depletion of parental mtDNA is also given, reasons for uniparental inheritance of mtDNA remain unclear..

Mitochondrial Fission Factor Drp1 Maintains Oocyte Quality via Dynamic Rearrangement of Multiple Organelles

Drp1 was knocked out in a transgenic line of female mice which were actively growing oocytes, to examine the effects mitochondrial dynamics on the development and aging of oocytes.

Effects on oocyte formation and growth
The Drp1 KO female mice produced less pups per mating (only 0.63 compared to the 6.7 pups per mating of control mice) despite normal vaginal plug formation. Few or no oocytes could be recovered from the KO mice, they therefore do not ovulate normally Follicle growth was low in KO ovaries and granulosa proliferation was blocked. Defects accumulated with age.

Effects on mitochondrial and ER morphology
Not surprisingly, Drp1 KO in oocytes lead to elongated and aggregated mitochondria. mtDNA nucleoids were clustered.  Most of the ER clustered around mitochondrial clusters. In control mice around 80% of the mitochondria were in contact with the ER, but in KO mice mitochondria tended to cluster with various other membranous structures (e.g. small vesicles). Peroxisomes and secretory vesicles were deformed.

Effects on energetics
There was no difference in membrane potential measured in mitochondria from control and KO oocytes and ATP content was not significantly affected.

Effects on calcium response
There were less calcium oscillations recorded in KO oocytes. The frequency of the oscillations was similar but the amplitude was reduced in KO mice.

Other observations
Oocytes contain a structure called the germinal vesicle, which is a nuclear structure and it is enlarged during oocyte maturation. The germinal vesicle breaks down before polar body formation. In normal mice, mitochondria move from the germinal vesicle to the cytoplasm during breakdown but this does not happen in KO mice. Mitochondrial movement is restricted in KO oocytes and the breakdown of the germinal vesicle is defective.   

OPA1‐dependent cristae modulation is essential for cellular adaptation to metabolic demand

OPA1‐dependent cristae modulation is essential for cellular adaptation to metabolic demand

It is well-established that cristae, the organized invaginations of the mitochondrial inner membrane, remodel themselves upon induction of cell death. In this study, the authors also show that substantial remodelling occurs in response to altered energetic conditions of the cell. These changes are mediated by the protein OPA-1, which is also associated with fusion of the mitochondrial network, but independent of the activity described here. The authors propose that OPA-1 can sense the presence of fuel substrates, which oligomerizes during cell starvation and tightens the cristae. These ultrastructural changes are associated with increased ATP-synthase assembly, and increased efficiency/capacity of energy production.

Monday, 6 October 2014

PGC-1α mediates mitochondrial biogenesis and oxidative phosphorylation in cancer cells to promote metastasis

PGC-1α mediates mitochondrial biogenesis and oxidative phosphorylation in cancer cells to promote metastasis

The canonical explanation for how tumour cells derive their energy is mainly through glycolysis, an anaerobic pathway. However, the work in this paper shows that circulating cancer cells (CCCs) in breast cancer favour mitochondrial oxidative phosphorylation, which can generate more energy and is aerobic. Moreover, the authors find that the protein PGC-1α, which modulates mitochondrial biogenesis, heavily influences CCCs invasiveness and ability to form distant metastases.

Thursday, 25 September 2014

Thermal adaptation and clinal mitochondrial DNA variation of European anchovy

It seems that anchovies broadly possess one of two mtDNA types, and which type a fish possesses is related to the latitudes at which it lives. This paper shows that ocean temperature is the strongest of the investigated possible determinants of anchovy mtDNA haplotype. The authors discuss the specific molecular effects of the differences between haplotypes, including some residue changes in Complex III. They speculate on the OXPHOS implications of these changes, but don't consider proton leak, which I think may be affected by the residue changes (they're on the side of the complex, though I can't see immediately if these sites are where the complex contacts the membrane). Generally -- a fun example of possible environment adaptation in mtDNA haplotypes.

Global Genetic Determinants of Mitochondrial DNA Copy Number

These guys screen yeast for nuclear genes whose deletions lead to a disappearance of mtDNA. Lots of the hits are mitochondrial proteins (54.9%), including a really big set involved in the mitochondrial ribosome. Other hits include a dozen genes involved in nucleic acid metabolism, ATP(4, 5, 14) and GRX (involved in Fe-S cluster formation) and a couple of dozen of miscellaneous functionality. Interesting to speculate on the mechanisms leading to mtDNA loss -- autophagy due to mitochondrial dysfunction, or some more direct mechanism? If the autophagy link is the case, and mitochondrial dysfunction is recognised through membrane potential, then the ATP genes are interesting, as the mitochondrion can presumably (?) maintain its membrane potential without Complex V. Perhaps there's a role for ROS signalling marking a dysfunctional mitochondrion here? If the absence of Complex V means the other complexes end up pumping protons against a higher and higher gradient, churning out more ROS as they do so?

Ten Simple Rules for Better Figures

Ten Simple Rules for Better Figures

Top tips for making figures.

Wednesday, 24 September 2014

Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming

Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming

Mitochondria contain their own genetic material: mtDNA. Each mitochondrion may contain several copies of their mtDNA, and the cell will generally contain many mitochondria. A mutation in an mtDNA can sometimes proliferate, resulting in an inhomogeneous population of wild-type and mutant mtDNA molecules. This is called heteroplasmy. The authors find that, for a particular mutation considered, changing the balance of wild-type to mutant mtDNAs, abrupt changes in the expression profile of the nuclear genome occurs, drawing an analogy with phase transitions. 

Monday, 15 September 2014

Tumour-derived PTH-related protein triggers adipose tissue browning and cancer cachexia

Tumour-derived PTH-related protein triggers adipose tissue browning and cancer cachexia

Cachexia is a condition often observed in cancer patients, associated with muscle wasting, frailty and weight loss. Although cachetic patients often ingest less food, they are also in a state of negative energy balance which cannot be corrected with nutritional supplementation. This has been linked to greater thermogenesis in brown fat tissue. The authors use a Lewis lung carcinoma murine model to identify a key secreted factor PTHrP which mediates muscle wasting in fat tissue.

Thursday, 4 September 2014

High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection

High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection

The authors generated a model to track mitochondrial heteroplasmy in cells. They simulated mtDNA, which randomly accumulated mutations at each generation, according to a Poisson process. At cell division, each mtDNA molecule was randomly chosen and replicated, so that the total copy number of mtDNAs doubled from 5 to 10. The mtDNA molecules were then randomly, but equally, split between the two daughter cells. Following successive generations of this process, the authors found consistently that a macroscopic fraction of cells in the model would contain a homoplasmic mutation. This model argues against the idea that selection is required for homoplasmy to occur, which is sometimes thought to be the case in particular forms of cancer.

Monday, 1 September 2014

Tumorigenicity of hypoxic respiring cancer cells revealed by a hypoxia–cell cycle dual reporter

Tumorigenicity of hypoxic respiring cancer cells revealed by a hypoxia–cell cycle dual reporter

The Warburg effect is the observation that, during tumorigenesis, there exists a metabolic shift from oxidative phosphorylation to glycolysis. In this report, the authors highlight the metabolic heterogeneity of cancer, by developing a dual reporter of HIF (hypoxia-inducible factor) and cell division. They find, in HEK 293T cells, that there exists a sub-population of non-HIF and non-cycling cells. These cells overexpressed certain mitochondrial genes and had an increased oxygen consumption, suggesting they respire aerobically. Despite this, they were found to be unexpectedly tumorigenic, relative to their glycolytic counterparts.

Thursday, 28 August 2014

Amino Acid Starvation Has Opposite Effects on Mitochondrial and Cytosolic Protein Synthesis

Link: Amino Acid Starvation Has Opposite Effects on Mitochondrial and Cytosolic Protein Synthesis (PLoS One)

Proteins form a substantial component of cellular mass, and their synthesis from amino acids is a one of the cell's principal energy expenditures. Amino acids have a second purpose, however - they can be catabolised and used as a a metabolite in the cell's mitochondria. Conversely, they can also be synthesised (at a significant expense of ATP) from precursor molecules, also derived partly from mitochondrial pathways. This puts the mitochondria at an important control point in protein and energy homeostasis, especially in conditions of amino acid scarcity.

In this paper, researchers from the MRC Mitochondrial Biology unit and the NIMR investigated the response of human cells to conditions of amino acid scarcity. They find that when amino acids are scarce, mitochondrial respiration and membrane potential increases, as does mitochondrial protein synthesis, but with no concomitant mitochondrial biogenesis. Cytosolic protein synthesis is downregulated, and cell cycle arrest was observed after 30 hours of amino acid starvation, 24 hours after the increase in mitochondrial protein synthesis.

Paradoxically, components of amino acid catabolic pathways were observed to be upregulated, with a decrease in amino acid anabolism, as measured by increased expression of glycine catabolism proteins and downregulation of asparagine synthetase. The authors suggest that the downregulation of cytosolic proteins is mediated by TORC1 and serves to reduce cell proliferation during amino acid scarcity, rather than as a way of reducing energy consumption. It is also suggested that this evidence shows that mitochondrial components can be replaced, rather than having to synthesise new mitochondria constantly.

Additionally, the findings in this paper indicate the citrate synthase may not be as reliable a measure of mitochondrial mass as previously thought, and that TFAM levels may not always correlate strictly with mtDNA copy number.

Tuesday, 26 August 2014

Oncogene ablation-resistant pancreatic cancer cells depend on mitochondrial function

Oncogene ablation-resistant pancreatic cancer cells depend on mitochondrial function

KRAS is an an oncogene which is found to be upregulated in many cancers. In pancreatic ductile carcinoma, KRAS mutations are known to be a driver mutation in tumorigenesis. The authors use an inducible mouse model of mutated KRAS, where the mutation is a loss of function. They show that, after KRAS ablation, a small set of surviving cancer cells persist. These are metabolically different to prototypical cancer cells, as they are addicted to OXPHOS whereas tumour cells tend to be addicted to glycolysis. The authors hypothesize that the mitochondrial hyperpolarization of these cells causes them to have a higher threshold for activating the mitochondrial permeability transition pore, which induces cell death. They find that inhibiting OXPHOS can eliminate the survivor cells.

Thursday, 21 August 2014

mTORC1 Controls Mitochondrial Activity and Biogenesis through 4E-BP-Dependent Translational Regulation (Cell Metabolism)

Paper link: mTORC1 Controls Mitochondrial Activity and Biogenesis through 4E-BP-Dependent Translational Regulation (Cell Metabolism)

Mammalian target of rapamycin (mTOR) is a protein responsible for integrating cellular signals related to energy generation and consumption - in essence it is integral to balancing the cellular energy budget. It forms two complexes, known as mTORC1 and mTORC2, and the authors find that mTORC1 stimulates both mitochondrial biogenesis and activity by phosphorylation of 4E-BP proteins. These function by binding to mRNAs and bringing them to ribosomes, and are essential for the translation of most proteins.

The authors find that when mTOR is inhibited the expression of a subset of mitochondrial proteins is repressed and the level of mitochondrial respiration decreases, lowering the cellular ATP concentration. Reduced levels of Raptor (a protein necessary for mTORC1 formation) led to decreased mitochondrial activity and copy number, whereas a reduction in Rictor (which is necessary for mTORC2) did not have these effects, and led to an increase in cellular ATP turnover, indicating that mTORC1 exerts most of the control on mitochondrial biogenesis.

This indicates that mTORC1 plays an important role in regulating nuclear-encoded mitochondrial protein synthesis to allow mitochondrial activity to match the energy demands of the cell.

Wednesday, 20 August 2014

Predicting selective drug targets in cancer through metabolic networks

Predicting selective drug targets in cancer through metabolic networks

The authors generated a general metabolic model of cancer, by looking for metabolic genes which are highly expressed across many cancer cell lines. Using a Model Building Algorithm from a previous publication, they created a minimal set of reactions which are needed to activate these highly expressed genes. From this, they investigated the effects of in silico knockdown for each gene, on the viability of the network relative to a model of healthy cells. They found significant agreement with shRNA gene silencing data in the literature. They also explored synthetic lethality, by comparing the synergistic effect of knocking down pairs of genes relative to knockdown of each individually. They identified important metabolic pathways for anticancer activity, as well as potential genetic targets for drug therapy.

Tuesday, 19 August 2014

Oxidative stress-mediated activation of extracellular signal-regulated kinase contributes to mild cognitive impairment-related mitochondrial dysfunction

They find that mitochondria of people with Mild Cognitive Impairment (MCI) (which is what you experience before Alzeimer's disease kicks in) have more MFN2. The expression levels of MFN2 are 1.8 fold higher than in control cells, meaning that the mitochondria of patients with MCI are more elongated.

There were decreased activities of complex I, III and IV in MCI cells, and ATP levels were lower in MCI cells. No difference in mitochondrial mass was observed.

Intensity of TMRM was decreased in MCI cells.

Deletion of the Mitochondrial Chaperone TRAP-1 Uncovers Global Reprogramming of Metabolic Networks.

Deletion of the Mitochondrial Chaperone TRAP-1 Uncovers Global Reprogramming of Metabolic Networks.

Chaperones are protein complexes which are used in the transport & folding of other cellular proteins. The authors found that deletion of the mitochondrial chaperone TRAP-1 led to a viable mouse model with reduced signs of ageing and age-associated pathologies such as obesity, dysplasia and tumour formation.

On a cellular level, TRAP-1 knockout reduced mitochondrial respiration, possibly by affecting complex II formation, leading to an upregulation in glyolytic activity. Somewhat paradoxically, the oxidative phosphorylation transcriptome was significantly upregulated, with a larger increase in complexes III and IV transcripts. Hsp90 (a similar chaperone) was upregulated and transported to the mitochondria in what may be a compensatory response.

Cell cultures showed reduced proliferation consistent with cell-cycle arrest, and showed a small but significant increase in ROS production.

The authors suggest that TRAP-1 knockout impairs successful folding of the SDHB subunit of complex II, which is partially rescued by dramatically upregulating all elements of oxidative phosphorylation and partially compensated for by reduced glycolysis.

It is unclear whether the cell's ability to generate energy from its mitochondria is impaired, or if the cell simply has to create more oxphos complexes to do so, however a small increase in ROS is observed, which may have a protective effect via mitohormesis and thus play a role in protecting the mice from age-associated pathologies.

Dynamics of nucleoid structure regulated by mitochondrial fission contributes to cristae reformation and release of cytochrome c

 In this paper they suggest that fission is needed to distribute mtDNA through the mitochondrial network, because if Drp1 is knocked out (and the mitochondria start to fuse) the nucleoids cluster together and large areas in the mitochondrial networks do not contain any mtDNA. This clustering starts 96 hours after Drp1 knockout (and later also 24 hours after Drp1 knockdown) and the total mtDNA content remains constant which means it really appears as though nucleoids diffuse through the mitochondrial network towards each other. If Drp1 is re-expressed, the effect is undone and the nucleoids distribute themselves again.

Knocking down Mff (mitochondrial fission factor), a protein that is also involved in mitochondrial fission, also causes clustering of nucleoids (nucleoid enlarging actually, that is what they really see). No enlarging is seen when OPA1 or MFN1,2 are knocked down and also not if both OPA1 and Drp1 are knocked down. Overexpression of MFN1 does lead to enlarged nucleoids.

When the enlarged nucleoids were observed at with higher resolution, it was clear that they consisted of several nucleoids clustered together.

They also observe that fission events tend to occur in the vicinity of nucleoids, this happened in 70% of the fission events seen (the number of which is 'several'). They then suggest that the distribution of Drp1 and Mff is responsible for nucleoid distribution.

Friday, 15 August 2014

Cyclin-dependent kinases regulate lysosomal degradation of hypoxia-inducible factor 1α to promote cell-cycle progression

Cyclin-dependent kinases regulate lysosomal degradation of hypoxia-inducible factor 1α to promote cell-cycle progression

HIF-1α is known to be important for adaptations to hypoxia, which is of interest for solid tumours which often have hypoxic regions due to their poorly formed vasculature. In addition, HIF-1α is a negative regulator of DNA replication but somehow some cells are able to replicate under hypoxic conditions. Here, the authors report that HIF-1α levels are coupled to the cell cycle through lysosomal degradation of HIF-1α. Blocking lysosomal degradation of HIF-1α through manipulation of Cdk proteins led to cell-cycle arrest in cancer cells.

The regulation of mitochondrial DNA copy number in glioblastoma cells

The regulation of mitochondrial DNA copy number in glioblastoma cells

Tumour cells and stem cells share some common traits, they are both proliferative and also appear to be more glycolytic than normal cells. In this paper, Dickinson et al. elucidate the role of mtDNA copy number in glioblastoma cells, by comparison with human neuronal stem cells. They found that depletion of mtDNA in glioblastoma enhanced their differentiation, and prolonged depletion reduced their proliferation. They observed that depleted glioblastoma cells recovered their mtDNA copy number as part of tumorigenesis, supporting the idea of a mtDNA set point.

Thursday, 12 June 2014

Mitochondrial genomes: anything goes

Mitochondrial genomes: anything goes

This is a really nice review of the crazy diversity in physical and genetic structure of mitochondrial genomes throughout eukaryotes. Because, in the early days, research focussed on animals, it was a while before this diversity became apparent. For example, it was thought that all mtDNA molecules were circular, and mapped circularly; there's now evidence for mtDNAs that map circularly but consist of many linearly concatenated sections, and mtDNAs that map linearly, and even some with multiple "chromosomes".

There's great diversity in mtDNA length and gene content, and not an obvious correlation between the two. Plasmodium parasites have mtDNA about 6 kbp long; rice's is 490 kbp (plant mtDNA in general is a bit crazy). Individual mitochondrial genes are often highly noncontiguous, broken up into many pieces that are jumbled and may lie on either strand of the mtDNA. Some interesting hypotheses are raised as to the reasons for this diversity, including horizontal transfer of mitochondrial genes, the special case of parasitism, and "competence" of plant mtDNA whereby genetic information from chloroplasts, nuclear, viral, and as-yet-unknown sources has been assimilated. Well worth a read!

mtDNA Segregation in Heteroplasmic Tissues Is Common In Vivo and Modulated by Haplotype Differences and Developmental Stage

mtDNA Segregation in Heteroplasmic Tissues Is Common In Vivo and Modulated by Haplotype Differences and Developmental Stage

Different mtDNA haplotypes can coexist inside the same cell, as a result of mutation, or as a consequence of recently-proposed medical therapies. Several studies have shown that haplotypes involving harmful mutations experience segregation -- they are outcompeted in cells over time, perhaps due to mitochondrial quality control. But little evidence exists exploring segregation between two natural and functional haplotypes, except in one model case. In medical applications, such a mixture of natural, functional haplotypes may be expected to arise, as cells will contain haplotype pairs sampled from a diverse population.

This research constructed new model mice, with their cells containing (a) mtDNA from mice captured from wild populations in Europe paired with (b) mtDNA from lab mice. This wild mtDNA was sequenced, and four different samples were chosen (a1), (a2), (a3), (a4), so that the genetic differences in the pairs (a1)-(b) ... (a4)-(b) represented the expected differences in samples from a human population. Measurements of the proportion of (a) in many different cell types was measured, and new mathematical modelling and statistics were used to powerfully compare results from across many different mice.

Segregation, surprisingly, was very common, across a wide range of tissues, including post-mitotic tissues like heart and muscle, of particular relevance for mitochondrial disease. It was often observed that (a) came to dominate over (b) (though sometimes (b) won), and the rms speed at which this domination occurred was proportional to the genetic distance between (a) and (b). Furthermore, new dynamic regimes of segregation were found, including a constant rate of proliferation of one haplotype over another, a constant proliferation during early development then stabilisation, and a constant proliferation during much of life then stabilisation in old age.

Thursday, 22 May 2014

The Intrinsic Apoptosis Pathway Mediates the Pro-Longevity Response to Mitochondrial ROS in C. elegans

The Intrinsic Apoptosis Pathway Mediates the Pro-Longevity Response to Mitochondrial ROS in C. elegans

The oxidative theory of aging suggests that mitochondrial reactive oxygen species (mtROS) are generated by defective mitochondria. mtROS in turn can damage mitochondrial DNA (mtDNA), which causes more mtROS to be generated in a vicious cycle, compromising the bioenergetic capabilities of the affected tissue. This theory is attractive, as we do indeed observe an increase in mtROS in human aged tissues.

However two organisms, namely the nematode (C. elegans) and yeast (S. cerevisiae), force us to consider a more subtle picture. We observe mtROS signalling can in fact increase chronological lifespan in these organisms. The authors found that exposing C. elegans to low levels of the superoxide generator paraquat, generates a long-lived phenotype. They observed no difference in the pattern of cell death (apoptosis) during the development of the worms, however the activation of the biomolecular machinery of apoptosis was necessary to mediate the pro-survival signal. This suggests a novel role of the intrinsic apoptosis pathway in aging.

Friday, 2 May 2014

Hepatitis C Virus Triggers Mitochondrial Fission and Attenuates Apoptosis to Promote Viral Persistence

Hepatitis C Virus Triggers Mitochondrial Fission and Attenuates Apoptosis to Promote Viral Persistence

Mitophagy is a mitochondrial-recycling process, where defective mitochondria are targeted for removal and their components broken down for subsequent use by the cell. In this study, the authors show that HCV promotes fission of the mitochondrial network, followed by increased mitophagy, mediated by a protein called parkin. This in turn attenuates HCV-induced apoptosis, or cell death. They find that HCV induces Drp1 phosphorylation, which activates fission, and silencing Drp1 prevented HCV-induced fission and an increase in apoptotic signalling. This study demonstrates how a virus may take control of the bioenergetic infrastructure of a cell, to encourage its own persistence.

Tuesday, 29 April 2014

The physiological role of mitochondrial calcium revealed by mice lacking the mitochondrial calcium uniporter

In this paper, mice lacking the calcium uniporter are investigated to see what consequences this has on mitochondrial calcium uptake, bioenergetics and cell death.

Mice lacking the calcium uniporter could not take up calcium rapidly. The basal mitochondrial matrix calcium concentration (from skeletal muscle cells) was reduced by 75% compared to that of wild type cells. Despite this, the uniporter-lacking cells showed no change in basal oxygen consumption and also the maximal maximal oxidative capacity was the same in wilde-type and uniporter-lacking mice.

Because of the lower calcium levels in uniporter-lacking mice, phosphorylation levels of the pyruvate dehydrogenase were increased which reduces its activity. This difference in phosphorylation levels was only seen in starved conditions, but dissapeared once the mice were fed. Because there were hardly any defects in basal metabolism of uniporter-lacking cells, the in vivo effects of altering matrix calcium may be most important under certain stress conditions.

When mice were placed on a treadmill, the uniporter-lacking mice were less able to exercise than the control group.

The mitochondrial permeability transition pore (PTP) opens if extramitochondrial calcium concentrations rise above a certain value. This behaviour was not seen in cells lacking the uniporter.

Effects on apoptosis
Cells were exposed to agents that induce cell death (such as tunicamycin,   doxorubicin and  thapsigargin). There was no change in the kinetics or magnitude of cell death in MEFs with or without the uniporter. Levels of cytosolic calcium and the release of cytochrome c were also the same in control and uniporter-lacking cells during cell death.

Thursday, 24 April 2014

calorie restriction changes mitochondrial ultrastructure

CR (Calorie restriction) leads to a longer life span, less cancer and fewer mitochondrial diseases. What is the effect of CR on mitochondria?

In this study they show that CR induced
  • increases in mitochondrial mass
  • increases in mitochondrial size
  • increases in the number of mitochondria per cell
  • increases in the number of cristae per mitochondrion
  • increases in the mean cristae length
  • increases in mitochondrial biogenesis.

They found that CR caused slight decreases in levels of Drp1 and Fis1. They measured only total levels of Drp1, not its phosphorylation levels. They did not find significant changes in the levels of the fusion proteins OPA1, MFN1 and MFN2.

Inverse hormesis of cancer growth mediated by narrow ranges of tumor-directed antibodies

Inverse hormesis of cancer growth mediated by narrow ranges of tumor-directed antibodies

Low levels of antibodies inside of a tumour can in fact stimulate tumour growth, by causing inflammation. This switches on pathways such as NF-κB and STAT3. However, it has long been thought that the immune system, if properly engaged, could be used to eliminate cancer cells. Here, the authors show that antibodies targeting Neu5Gc (which accumulates in human tumours) have a dose-dependent affect on tumour mass. In particular, low levels promote tumour growth, but over a surprisingly narrow dose range, the antibody suddenly begins to inhibit tumour growth.

Leaky mitochondria make you lose weight - Mitochondrial uncoupling as a treatment for obesity

In the 1930s, DNP (2,4-dinitrophenol) was introduced as a drug to treat obesity. What does DNP do? It causes mitochondrial uncoupling, i.e. it increases proton leak and as a result energy production becomes less efficient. Patients treated with DNP therefore 'waste' more energy and metabolic rate increases. An increase in energy output, while keeping the energy intake constant, means that people will start losing weight.

How does DNP work exactly? DNP is a lipid-soluble weak acid. It can pick up protons which it then carries to the other side of the membrane.  It then drops the proton, crosses the membrane again, picks up another proton, etc..

Patients treated with DNP reported feelings of warmth and increased sweating. Doses of 5 mg/kg were tolerated well and there was no increase in heart rate. Patients receiving daily  doses of 3-5 mg/kg experienced a 40% increase in metabolic rate that was maintained for at least 10 weeks. After those 10 weeks, a mean weight loss of 7.8 kg was observed. There was no need for additional dieting.

The increase in metabolic rate was clearly dependent on increase in DNP dose with an average increase of 11% for each dosage increment of 0.1g of DNP.

Because of this success, the drug became popular and it was used more and more. By 1934, about 100,000 people had been treated with the drug. However, the drug was used by inexperienced physicians who had no access to metabolic rate measurements to determine optimal doses. This lead to several people being `literally cooked to death' and the drug was taken off the market (there are reports, however, that the drug is still prescribed by US clinics)

The changing colour of fat

The changing colour of fat

It appears that fat cells come in three distinct forms: white fat cells, which specifically store energy in the form of lipids; brown fat cells, found around the head and neck which burn energy to release heat; and beige fat cells which are an immature form of brown fat cells, existing in white fat tissue. 

None of these cells are inherently "good" or "bad" under normal conditions; however, during obesity, white cells expand and proliferate at a rate faster than the development of vasculature causing a hypoxic environment. HIF-1α, a factor associated with cancer, is recruited to the tissue causing excess production of connective tissue (fibrosis). These fat cells also attract immune cells, become inflamed, develop metabolic disease and insulin resistance, which can result in diabetes.

Caenorhabditis elegans pathways that surveil and defend mitochondria

Caenorhabditis eleganspathways that surveil and defend mitochondria

Iron is a valuable resource inside the cell. The mitochondrial electron transport chain is rich in haem and iron sulphur proteins, making it an attractive target upon bacterial infection. The authors show that disruption of mitochondrial function, through drugs such as antimycin or interference RNAs (RNAis), induces xenobiotic-detoxification, mitochondrial repair and pathogen response pathways in C. Elegans. They performed an RNAi screen to identify 45 RNAis that are involved in such pathways.

Tuesday, 4 March 2014

Mitochondria from anoxia-tolerant animals reveal common strategies to survive without oxygen

Mitochondria from anoxia-tolerant animals reveal common strategies to survive without oxygen

Anoxia is the complete absence of oxygen, and various animal species have evolved to tolerate these environments for prolonged periods. The mechanisms allowing this adaptation may allow us to better understand how to combat the effects of reperfusion in cardiac tissue after myocardial infarction. The authors use examples, such as the painted turtle and the common frog, to demonstrate how adaptations to the mitochondria are important in avoiding the onset of cell death during anoxia. The overarching theme is that mitochondria must avoid the collapse of their membrane potential: failing this causes cytosolic calcium to be driven into the mitochondria during reperfusion, which leads to apoptotic signalling and cell death.

Some mechanisms which have been studied include: downregulation of respiratory chain activity; blocking of F1F0-ATPase; tighter membranes to avoid proton leak; blocking of mitochondrial calcium channels; reversal of F1F0-ATPase to maintain membrane potential; and increased ROS-scavenging enzymes. A final noteworthy example is the anoxic turtle brain, where it has been observed that the mitochondrial permeability transition pore can be transiently opened to release calcium from the mitochondria. This protective measure is not associated with mitochondrial swelling, nor release of apoptotic factors.