Mitochondrial DNA

Mitochondria contain their own DNA that is distinct from the DNA found in the nucleus. There are just 37 genes found on mitochondrial DNA (mtDNA) though more than e20,000 genes are located on chromosomes in the nucleus.

 

MtDNA was discovered in the 1960s. Margit Nass and Sylvan Nass saw threads with an electron microscope that were sensitive to DNAses, enzymes that break down DNA. Around the same time, Gottfried Schatz, Ellen Haslbrunner and Hans Tuppy found the biochemical signature of DNA in a pure mitochondrial fraction from yeast.

 

In humans, mitochondrial DNA is a circular molecule, in contrast to nuclear DNA which is linear. There are two strands of DNA entwined in each circle, an inner light chain and an outer heavy chain. Most of the genes are on the outer strand. Human mtDNA is very small – it contains just 16,569 base pairs!

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MtDNA comes in many different shapes and sizes between different species – a lot of evolution has gone on since the first event that fused a mitochondrion and a cell. It can be circular, linear or even in several pieces. Some species have very large amounts of mtDNA but this often contains lots of non-coding regions i.e. regions that don’t make a protein the organism can use.

 

Despite having 37 genes, only 13 proteins are encoded by mtDNA – all these proteins are involved in oxidative phosphorylation. There are also 22 genes that make tRNAs and 2 genes that make rRNAs that are needed for protein translation. There is also a small stretch of DNA that doesn’t code for any protein. This is involved in regulation of mtDNA replication and contains the start site for replication and for transcription.

All 13 proteins encoded by mtDNA are involved in oxidative phosphorylation.

• Seven genes in mtDNA encode subunits of Complex I – ND1, ND2, ND3, ND4, ND4L, ND5 and ND6.

• Complex II is entirely encoded by genes in the nucleus.

• One subunit of Complex III is encoded by mtDNA, the cytochrome b subunit.

• Three subunits of Complex IV are encoded in mtDNA – the COXI, COXII and COXIII subunits.

• There are two mtDNA genes encoding Complex V, ATPase6 and ATPase8.

The rest of the proteins required for oxidative phosphorylation and other mitochondrial functions are encoded by genes in the nucleus.

 

It is now thought that mtDNA doesn’t just float around the mitochondrion but is arranged in structures called nucleoids. There may be 3-7 repeats of mtDNA circles in each nucleoid held together by the protein TFAM which is also needed for mtDNA transcription. Proteins involved in mtDNA replication are often found in these structures too e.g. the mtDNA polymerase POLG, the DNA binding protein mtSSB and a helicase called Twinkle! There is likely to be more than one nucleoid in each mitochondrion as each single mitochondrion can have 10-100 mtDNA molecules!

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Amazingly mitochondrial DNA can only be inherited from your mother, unlike nuclear DNA which comes from both parents. Any paternal mtDNA found in the sperm is destroyed or lost after fertilization. This means that any mitochondrial diseases carried in the father’s mtDNA cannot be passed onto their offspring!

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Euromit 2014

20140623-195508.jpg Euromit is a big international meeting on mitochondrial pathology and was recently held in Tampere, Finland. There were more than 700 participants, tons of interesting talks and almost 500 poster presentations.

I learned some cool things at Euromit:

  • The most common deletion in mtDNA is here:

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  • Whole exome sequencing (WES) is emerging as a first line diagnostic tool
  • Mitochondria are social organelles – they interact and ‘talk’ with lysosomes, peroxisomes and the endoplasmic reticulum
  • Twinkle, the mitochondrial helicase that unwinds mitochondrial DNA during replication, is an important mitochondrial disease gene. However mutations in the same gene can cause different phenotypes – from the relatively mild progressive external ophthalmoplegia to a severe mitochondrial DNA depletion syndrome with liver and central nervous system disease and early death
  • Several children have already been born by prenatal genetic diagnosis, a technique which tests mitochondria in new embryos for mutation load before they are implanted in a woman’s womb
  • There is an unmet medical need for treatments for rare mitochondrial diseases

Tampere was also a great city to visit. There’s the Tammerkoski rapids, the Finlayson complex of museums and cafés and two beautiful lakes. The Finnish food is great: you have to try reindeer!
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Euromit 2014 was a great conference – well organised with a fantastic scientific (and social!) program. The next Euromit will be in Cologne in 2017. Can’t wait!

Other Functions of Mitochondria

Mitochondria have many other functions besides making ATP to fuel all our cells.

  1. Complex II while shuttling electrons as part of the respiratory chain also converts acetyl Co A, an intermediate between glucose and ATP, to NADH which is later converted to electrons by complex I. The pyruvate dehydrogenase complex and Krebs cycle are also found within mitochondria – in the matrix. These pathways are also involved in energy production by providing substrates for oxidative phosphorylation.

    Krebs Cycle

    Krebs Cycle

  2. Fats are another source of energy (ATP) used by cells when there is a shortage of glucose. A different pathway breaks down fat molecules but this also happens in the mitochondria. To get ATP from fats the broken down molecules (NADH and FADH2) are then metabolized in the oxidative phosphorylation system as before.
  3. Mitochondria are also responsible for haem biosynthesis by inserting iron into haemoglobin and other proteins. This process starts in the cytosol but is completed in the mitochondrion.
  4. DHODH (dihydroorotate dehydrogenase) is an essential enzyme in uridine synthesis (uridine is one of the bases in RNA). DHODH is found only in mitochondria but no one knows why!
  5. Mitochondria maintain a constant membrane potential – a difference in electric charge across the inner mitochondrial membrane due to keeping positively and negatively charged ions separate. This potential is then used to power oxidative phosphorylation and other cellular processes. Uncouplers that dissipate the membrane potential can be lethal, for example FCCCP (carbonyl cyanide-p-trifluoromethoxyphenylhydrazone) and dinitrophenol.
  6. Iron sulfur clusters are a part of many proteins such as the Rieske subunit of complex III, aconitase in the TCA cycle and DNA synthesis and repair proteins. They consist of two, three or four iron centres linked by sulfide bonds. These Fe-S proteins are synthesized in mitochondria – the amino acid cysteine is a source of sulfur and is combined with iron on scaffold proteins. Iron can be toxic so it is kept separate from the rest of the cell contents.

    Some iron sulphur clusters

    Some iron sulphur clusters

  7. Apoptosis is the controlled breakdown of cells that are sick or damaged. Cytochrome c is a normal part of complex IV in the oxidative phosphorylation system but is released from this enzyme complex when apoptosis is initiated. Cytochrome c then activates pathways that cause the whole cell to go into apoptosis.
  8. Mitochondria also generate a lot of reactive oxygen species (ROS). This happens when electrons get free from the oxidative phosphorylation system and oxidise molecules like water forming hydrogen peroxide or oxygen forming superoxide radicals (a radical is an atom with an extra electron i.e. it has a negative charge). ROS get a lot of bad press for their role in cancer and ageing as they damage DNA and proteins in tissues and lead to worn out immune cells. However ROS are also involved in signalling in the cell and communicate important messages to other cells. Activated platelets at the site of a wound release ROS to attract more platelets to aid in blood clotting.
  9. One of the more important alternative functions of mitochondria is the handling of calcium. Mitochondria can store large amounts of calcium ions. This makes them good ‘buffers’ for cleaning up extra calcium in the cytosol. Calcium also has a role in signalling between the mitochondrion and the endoplasmic reticulum.
  10. In brown adipocytes (a rare type of fat cell mainly found in babies and hibernating animals) mitochondria’s main role is to produce heat in a process called shivering thermogenesis. These specialized mitochondria use the same oxidative phosphorylation process as to make energy except instead of forming ATP at complex V the power generated by the proton gradient is lost. This power is converted into heat. When millions of mitochondria are able to do this it warms a cold body.

Mitochondria are multi-functional organelles that cannot be underestimated!

Oxidative Phosphorylation

Oxidative phosphorylation is the most important function of mitochondria! It is the conversion of glucose, the main ingredient of all our food, into an energy source that we can use. It involves the oxidation of products from the breakdown of glucose into ATP (adenosine triphosphate). ATP is our principal energy source – its structure contains strong chemical bonds that release energy when broken down. In fact for each molecule of glucose mitochondria can generate 36 molecules of ATP!

 

The oxidative phosphorylation system is made up of five main components – these are called complexes and are named by consecutive Roman numerals.

 

Complex I is a large protein complex made up of 45 subunits. It is an L shaped molecule – think of one arm stuck in the mitochondrial membrane and the other arm jutting out into the matrix.

Its function is to oxidise NADH (nicotinamide adenine dinucleotide) which is an energy rich compound that donates electrons easily. These electrons are picked up by a cofactor – coenzyme Q – and the energy from the reaction is used to move four protons (H+ ions, the opposite of negatively charged electrons) across the mitochondrial membrane. Eventually a proton gradient is formed (with more protons and therefore more positive charge outside the matrix in the space between both mitochondrial membranes (the intermembrane space)) which is then used to create ATP at complex V.

Though other proteins also contribute to the proton gradient, complex I provides a massive 40% of the proton force required to generate usable energy in the form of ATP.

Patients with a complex I deficiency often have a severe disease and die early for example, infants with Leigh disease have severe lactic acidosis and other symptoms and often die in childhood.

 

Complex II, also called succinate dehydrogenase (SDH), is a small protein complex – it consists of just four subunits imaginatively called SDHA, SDHB, SDHC and SDHD. It converts succinate to fumarate and, like complex I, reduces coenzyme Q. It moves electrons along the respiratory chain but doesn’t produce enough energy to transport protons across the membrane.

Complex II

Complex II

Surprisingly complex II has a dual function – it is also part of the TCA cycle which requires the fumarate that is produced by complex II. The TCA cycle produces energy rich compounds such as NADH which are then used in oxidative phosphorylation.

 

There are 11 subunits in Complex III. It also moves four protons across the membrane but it is not as efficient as complex I so contributes less to the proton gradient overall. A small protein with an iron atom at its centre, cytochrome c, travels through the complex taking electrons from one spot and depositing them elsewhere. The energy from these reactions is used for proton pumping. This special sequence of oxidation and reduction is called the Q cycle because coenzyme Q is also involved.

Complex III

Complex III

 

Complex IV is an important enzyme. It consists of 13 protein subunits and has two iron-containing and two copper-containing clusters. As electrons are transferred through the complex, another four protons are pumped into the intermembrane space. Eventually electrons are passed to the oxygen molecule that is trapped in between a copper and iron atom. The oxygen is reduced to water and excreted as an end product of oxidative phosphorylation.

Complex IV

Complex IV

Diseases where complex IV is reduced can also be quite severe. In fact, cyanide which is an inhibitor of complex IV can cause death within seconds if it is inhaled. A fatal dose can be as low as 75 mg for an adult!

 

Complex V has two proton domains, one of which is embedded in the mitochondrial membrane. The other domain protrudes into the matrix and rotates to produce ATP. It’s like a basketball spinning on your finger.

Complex V

Complex V

All the protons in the intermembrane space flow through the complex and cause it to whirl. As it does so, ADP (adenine diphosphate) and Pi (inorganic phosphate) are brought close together and join to form ATP, a high energy compound that is much more stable than ADP and Pi individually.

Complex V is the world’s tiniest motor! Its rotor spins 10,000 times per minute. It produces 3 ATP molecules with every revolution.an you imagine all the many complex Vs in all our many cells all making ATP? That is a lot of energy!

 

To finish, here’s a handy video of oxidative phosphorylation!

 

Evolution of Mitochondria

The evolution of mitochondria is a really interesting field however there is still so much we don’t know. Some say mitochondria originated as much as 2 billion years ago! However the oldest record of a eukaryotic fossil, that is a cell that had a nucleus, is from 1.45 billion years ago. It can be assumed that mitochondria are approximately as old as the eukaryotic state.

There are two theories as to the origin of mitochondria in eukaryotes and at the moment the field of evolutionary biology is split. The first and more traditional opinion is that a nucleus-bearing eukaryotic cell engulfed an alpha-proteobacterium containing mitochondria actively via phagocytosis, a process of eating objects or other cells in the surrounding environment. The other view suggests that a host cell acquired mitochondria before they became eukaryotic i.e. before a nucleus developed. This theory comes from the fact that the original mitochondrion was able to live with or without oxygen whereas now mitochondria function in the presence of oxygen.

The evolution of mitochondria is special as it is believed that it happened only once ever! This is suggested because the genes still encoded by mitochondrial DNA are conserved or retained across all eukaryotes with mitochondria.

There’s still so much we don’t know about how the first mitochondria came to exist inside a cell.
• What kind of species did they come from?
• What kind of cell was it that received the new mitochondrion?
• When exactly did this happen? How many billions of years ago?
• What was the advantage to the cell of having a mitochondrion in it? Just energy? Or also as a sink to detoxify excess oxygen?
• What was the advantage to the mitochondrion to being in a cell? Protection?
• How did so many mitochondrial genes get into the nucleus?
But the question that I most want the answer to is: what really came first – the nucleus or the mitochondrion??!

About Mitochondria

History of Mitochondria

Mitochondria were discovered in the 1840’s when improved microscopy made it possible to visualise these tiny structures within cells. At this time they were called bioblasts. They were not called mitochondria until 1894 and it was not until the 1940’s that they became associated with their main function – energy production.

 

By the way, mitochondria is the plural of mitochondrion.

 

Structure of Mitochondria

Mitochondria are typically oval, 1-2 um long and 0.5-1 um wide, like tiny tiny grains of rice.

 

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But they are always moving, always changing shape – they are capable of fusing and splitting apart, changing their size, form and location rapidly –more like long worms wandering around the cell, especially in the area around the nucleus.

 

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Unbelievably, there can be hundreds or thousands of mitochondria in a single cell at any one time for example a busy liver cell can have one or two thousand mitochondria which is about a quarter of the volume of the cell!

 

Mitochondria have a double membrane – the outer membrane is relatively flat but the inner membrane curls and folds in and out on itself forming loops called cristae – this increases the surface area and allows for more enzymes and channels to be attached to this membrane. The very inside of the mitochondrion is called the matrix. Both membranes are made up of fats and some proteins.

 

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There are some pores and ion channels through the membranes, some of which have gates and regulate what kind of molecules come through. In fact there are more than 1000 proteins working inside mitochondria!

 

Function of Mitochondria

Mitochondria are predominantly involved in metabolism and energy production. They are called the batteries or powerhouses of our cells because they make most of the energy (ATP) needed for our cells and our bodies to function. We wouldn’t exist if we didn’t have mitochondria!

 

ATP is adenosine triphosphate – its structure has chemical bond connections in it that are full of energy. When this molecule is broken down, the energy is released and this fuel can be used to power our muscles and our brains and our hearts.

 

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Mitochondria have other roles too. Mitochondria store calcium ions in the cell until they are needed to stimulate the cell to release neurotransmitters or hormones. They have enzymes involved in pyrimidine synthesis that are necessary to make new DNA and RNA and they also make the haem molecule needed for haemoglobin to carry iron in the blood. Some tissues have specialised roles – liver mitochondria remove toxic ammonia via the urea cycle.

 

About

Science is exciting! It’s fascinating! There are so many challenges, so many unknowns, so much left for us to discover, to find out for ourselves, to marvel at. It is truly amazing!

I think of the way the world is so varied, the way space is so vast, the way every single person is so incredible and engaging in their own way, the way mitochondria are responsible not only for fulfilling our energy requirements, regulating our calcium levels and synthesising iron carrying proteins but also have roles in ageing and neurodegenerative diseases and can you imagine they came from a little bacteria that fused with a human cell somewhere way back along the lines of evolution. They truly are the reason we are even alive!

And the brain – how can a little pathway of neurons, just long cells really, lead to all the complex emotions and thoughts and strategies that happen in our minds on a daily basis? The sheer intricacy of raw emotion we are capable of feeling and being overcome by, be it sadness, love, anxiety or lust, all comes from a few stringy neuronal cells and a mushy ball of soft tissue called the brain, truly astounding! It is actually mind-blowing.

Then there are all the other animals, plants, fish and creatures that inhabit this world along with us. Imagine that in seahorses it is the father that becomes pregnant? Imagine the HIV virus can take their DNA and make our cells copy it for them? What if there really is more than just our world out there – more life, more planets, more stars and more galaxies? – it truly is astonishing to think of it!

I love science but science is…hard. I guess what I’ve been writing about is what makes science so difficult – it is so immense! But honestly I can’t understand why scientific journals have to be written in such difficult language. Would it be too much to ask they say “we found this and we’re really excited, you should be too!” rather than the dull “here are some results, they may be important but we need more studies”… Ah, boring…

This blog will look mainly at mitochondria and all the ways they are amazing in a way that is easy to understand! Be excited!

(In case you were wondering I am currently a first year PhD student working on mitochondrial translation)