Hydrogenosome organelles found in deep sea organisms

[Moontanman]

A group of metazoans known as Loricifera contain at least three species that live their entire lives without oxygen. They depend on mitochondria like organelles called Hydrogenosomes. These organelles allow the organism to produce energy in the absence of oxygen, they live in anoxic sediments.  Not considered uniquely evolved from a new organism but actually degenerate mitochondria. . 

 

 

Spinoloricus cinziae was found in 2014. 

Quote

Spinoloricus cinziae is an animal species described in 2014 in the phylum Loricifera.[1]

It was the first described animal species that does not require oxygen at any point during its life.[2][3][4] The species, along with two other newly discovered species, Rugiloricus nov. sp. and Pliciloricus nov. sp. (all of order Nanaloricida), were found in the sediment of the anoxic L'Atalante basin of the Mediterranean Sea.[3][4]

Electron microscope images[4] show that the species' cellular innards appear to be adapted for a zero-oxygen life. Their mitochondria appear to act as hydrogenosomes, organelles which provide energy in some anaerobic single-celled creatures.[5]

At adulthood, this species is characterized by a mouth cone with eight oral ridges, a neck with eight single trichosclereids alternating with seven double trichoscalids, as well as lorical plates with spikes located at the corners.[1] More than 30 species in this group have been described.[1]

 

Edited April 28 by Moontanman

[swansont]

Link to the news?

[Moontanman]

8 minutes ago, swansont said:

Link to the news?

Shit, I deleted the point before I posted. 

Edited April 28 by Moontanman

[exchemist]

20 minutes ago, Moontanman said:

A group of metazoans known as Loricifera contain at least three species that live their entire lives without oxygen. They depend on mitochondria like organelles called Hydrogenosomes. These organelles allow the organism to produce energy in the absence of oxygen. 

 

 

Spinoloricus cinziae

 

From what I have just quickly read, these seem to have independently evolved, from mitochondria, several times in different species. So an example of convergent evolution, enabling their possessors to adapt to anoxic environments. 
 

What remains unclear to me is what the energy source is for their respiration. The flow charts I have seen seem to show pyruvate as the input, presumably from glycolysis. So that suggests glycolysis as usual, followed by some alternative to the Krebs cycle that does not require oxygen.
 

Maybe someone can explain how this works. They don’t seem to be sulphate-reducing or anything like that.

[TheVat]

44 minutes ago, exchemist said:

From what I have just quickly read, these seem to have independently evolved, from mitochondria, several times in different species. So an example of convergent evolution, enabling their possessors to adapt to anoxic environments. 
 

What remains unclear to me is what the energy source is for their respiration. The flow charts I have seen seem to show pyruvate as the input, presumably from glycolysis. So that suggests glycolysis as usual, followed by some alternative to the Krebs cycle that does not require oxygen.
 

Maybe someone can explain how this works. They don’t seem to be sulphate-reducing or anything like that.

Substrate-level phosphorylation?  Quicker and less efficient than oxidative phosphorylation.  A fermentation process, like in yeast and some bacteria.  

Oh, and erythrocytes, which have no mito.

[exchemist]

3 hours ago, TheVat said:

Substrate-level phosphorylation?  Quicker and less efficient than oxidative phosphorylation.  A fermentation process, like in yeast and some bacteria.  

Oh, and erythrocytes, which have no mito.

Yes I suppose that must be it. I was thinking of anaerobic bacteria that use alternative chemistry as fuel, like sulphate reducing or iron reducing bacteria.  

[Moontanman]

4 hours ago, exchemist said:

From what I have just quickly read, these seem to have independently evolved, from mitochondria, several times in different species. So an example of convergent evolution, enabling their possessors to adapt to anoxic environments. 
 

What remains unclear to me is what the energy source is for their respiration. The flow charts I have seen seem to show pyruvate as the input, presumably from glycolysis. So that suggests glycolysis as usual, followed by some alternative to the Krebs cycle that does not require oxygen.
 

Maybe someone can explain how this works. They don’t seem to be sulphate-reducing or anything like that.

I was wondering the same thing, when I first heard of this I thought they were metabolizing hydrogen but it clearly states that molecular hydrogen is produced not used.  

[CharonY]

A few things from above, the Krebs cycle does not provide energy, one of its functions is to generate reducing equivalents. Likewise, the cycle also does not consume or require oxygen. In aerobic organism oxygen is used as terminal electron acceptor. By coupling this redox reaction to an electron transport chain, proton pumps are are used to create a proton gradient, and that is ultimately used to generate energy (via an ATP synthetase).

Anaerobic bacteria use alternative electron acceptors, to do pretty much the same. As others have noted, this is not what is happening here. While glycolysis can happen and generate energy, the interesting bit about hydrogenosomes is another process, which is highlighted in the posted figure. ATP is generated via a multi-step process, which looks like a reversal of acetate activation (which then would go into TCA), but requires ferredoxin shuttle at which H2 is formed.

 

 

[exchemist]

7 hours ago, CharonY said:

A few things from above, the Krebs cycle does not provide energy, one of its functions is to generate reducing equivalents. Likewise, the cycle also does not consume or require oxygen. In aerobic organism oxygen is used as terminal electron acceptor. By coupling this redox reaction to an electron transport chain, proton pumps are are used to create a proton gradient, and that is ultimately used to generate energy (via an ATP synthetase).

Anaerobic bacteria use alternative electron acceptors, to do pretty much the same. As others have noted, this is not what is happening here. While glycolysis can happen and generate energy, the interesting bit about hydrogenosomes is another process, which is highlighted in the posted figure. ATP is generated via a multi-step process, which looks like a reversal of acetate activation (which then would go into TCA), but requires ferredoxin shuttle at which H2 is formed.

 

 

OK, so what is the overall reaction then? My primitive understanding of convention respiration is it essentially reverses photosynthesis, i.e. CO2 + H2O <-> (CH2O)n + O2, in which (CH2O)n is a generic carbohydrate.  This process seems to evolve both H2 and CO2. I suppose one could have (CH2O) + H2O -> 2H2 + CO2. Is that what happens? I wonder what ΔG is for a process like that. Suppose the entropy term at least will be favourable, since 3 small gas molecules are produced. 

[Moontanman]

What is the significance of the H2? Is it fuel, waste, or something else? 

[exchemist]

5 minutes ago, Moontanman said:

What is the significance of the H2? Is it fuel, waste, or something else? 

As I understand it, waste. The overall process has to release energy to make ATP from ADP, as it is ATP that is the principal energy molecule driving biochemical processes. I believe I read once that the gas in farts contains a lot of hydrogen, presumably from anaerobic metabolism by gut microbes. A schoolmate once collected some over water in the bath and claimed he set light to it. Whether it gave the characteristic “squeaky pop” of hydrogen was not clear however.

[Moontanman]

17 minutes ago, exchemist said:

As I understand it, waste. The overall process has to release energy to make ATP from ADP, as it is ATP that is the principal energy molecule driving biochemical processes. I believe I read once that the gas in farts contains a lot of hydrogen, presumably from anaerobic metabolism by gut microbes. A schoolmate once collected some over water in the bath and claimed he set light to it. Whether it gave the characteristic “squeaky pop” of hydrogen was not clear however.

Interesting, I honestly thought hydrogen in the form of protons was the energy of the cell, I seem to be lost in the bushes on this. I know there are bacteria that produce free hydrogen as part of their metabolism and bacteria that use free hydrogen as an energy source and give off methane as waste and of course there are bacteria that consume methane... brings back memories of why I was so obsessed with biochemistry in high school. I love the complexity and order of chemistry. 

[sethoflagos]

44 minutes ago, Moontanman said:

Interesting, I honestly thought hydrogen in the form of protons was the energy of the cell, I seem to be lost in the bushes on this. I know there are bacteria that produce free hydrogen as part of their metabolism and bacteria that use free hydrogen as an energy source and give off methane as waste and of course there are bacteria that consume methane... brings back memories of why I was so obsessed with biochemistry in high school. I love the complexity and order of chemistry. 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2907586/ states that 'possibly endosymbiotic' rod-like methanogenic prokaryotes were seen in close proximity to the hydrogenosomes during scanning electron microscopy. If so then perhaps the circle is closed at least in part by the reasonably exothermic (and biological carbon fixing) of CO₂ reduction by H₂.

[CharonY]

5 hours ago, exchemist said:

OK, so what is the overall reaction then? My primitive understanding of convention respiration is it essentially reverses photosynthesis, i.e. CO2 + H2O <-> (CH2O)n + O2, in which (CH2O)n is a generic carbohydrate.  This process seems to evolve both H2 and CO2. I suppose one could have (CH2O) + H2O -> 2H2 + CO2. Is that what happens? I wonder what ΔG is for a process like that. Suppose the entropy term at least will be favourable, since 3 small gas molecules are produced. 

Not quite. The net reaction of photosynthesis are two separate reactions which are not really mechanistically coupled. Specifically, it initiates an electron transfer chain (functionally similar to respiration) in order to pump protons which then chemoosmotically generate ATP. Water functions as electron donor during the water splitting event. I do think that the chemical notation masks a little bit the underlying biology, especially as carbon fixation in some bacteria happens without light,  but that is neither here nor there). I probably should add that glycolysis happens in the cytosol, and the pyruvate is then delivered to hydrogenosomes.

The reaction in hydrogenosomes is simpler and ATP formation is by substrate level phosphorylation, as mentioned before. Hydrogen is basically formed to re-oxidize ferredoxin, which is needed for the decarboxylation reaction from pyruvate to acetyl-CoA.

Not entirely sure if I get it right but it should be something like: Pyruvate + 2 [H+] + Ferredoxin(ox) -> Acetate + H2 + Ferredoxin(red) + CO2

 

2 hours ago, Moontanman said:

Interesting, I honestly thought hydrogen in the form of protons was the energy of the cell, I seem to be lost in the bushes on this. I know there are bacteria that produce free hydrogen as part of their metabolism and bacteria that use free hydrogen as an energy source and give off methane as waste and of course there are bacteria that consume methane... brings back memories of why I was so obsessed with biochemistry in high school. I love the complexity and order of chemistry. 

One way to think about this is that respiration (aerobic or anaerobic) is basically using a redox potential to energy generation, rather thinking that a particular compound being fuel or waste. Basically, if you have  a nice electron donor and acceptor pair that generate a nice potential, you can use that potential by using to drive an electron transport chain, that also pumps protons out of the cell to generate a proton gradient that is then used to generate ATP.  This means that depending on which pair the cell uses, the same compound can be used as donor or acceptor.

Hydrogen is used by many bacteria as electron donor but is also released often in fermentation processes (or the reaction above) to essentially balance the redox budget of the cell (and as you can imagine, released hydrogen can be used by other bacteria, creating interesting cycles within bacterial communities).

 

[Moontanman]

12 minutes ago, CharonY said:

Not quite. The net reaction of photosynthesis are two separate reactions which are not really mechanistically coupled. Specifically, it initiates an electron transfer chain (functionally similar to respiration) in order to pump protons which then chemoosmotically generate ATP. Water functions as electron donor during the water splitting event. I do think that the chemical notation masks a little bit the underlying biology, especially as carbon fixation in some bacteria happens without light,  but that is neither here nor there). I probably should add that glycolysis happens in the cytosol, and the pyruvate is then delivered to hydrogenosomes.

The reaction in hydrogenosomes is simpler and ATP formation is by substrate level phosphorylation, as mentioned before. Hydrogen is basically formed to re-oxidize ferredoxin, which is needed for the decarboxylation reaction from pyruvate to acetyl-CoA.

Not entirely sure if I get it right but it should be something like: Pyruvate + 2 [H+] + Ferredoxin(ox) -> Acetate + H2 + Ferredoxin(red) + CO2

 

One way to think about this is that respiration (aerobic or anaerobic) is basically using a redox potential to energy generation, rather thinking that a particular compound being fuel or waste. Basically, if you have  a nice electron donor and acceptor pair that generate a nice potential, you can use that potential by using to drive an electron transport chain, that also pumps protons out of the cell to generate a proton gradient that is then used to generate ATP.  This means that depending on which pair the cell uses, the same compound can be used as donor or acceptor.

Hydrogen is used by many bacteria as electron donor but is also released often in fermentation processes (or the reaction above) to essentially balance the redox budget of the cell (and as you can imagine, released hydrogen can be used by other bacteria, creating interesting cycles within bacterial communities).

 

I remember reading a book by Isaac Asimov where he described a planet where hydrogen was the breathing gas instead of oxygen, more recently Sara Seager has suggested that hycean worlds might support life. The bio chemistry of a metazoan that breathes hydrogen would be very interesting.  

[CharonY]

Just now, Moontanman said:

I remember reading a book by Isaac Asimov where he described a planet where hydrogen was the breathing gas instead of oxygen, more recently Sara Seager has suggested that hycean worlds might support life. The bio chemistry of a metazoan that breathes hydrogen would be very interesting.  

That would be very difficult. Oxygen is used as terminal electron acceptor as it is positioned favourably in terms of reduction potential and can couple with a wide range of donors. Conversely, hydrogen is pretty much on the other end, making it a good donor, but an extremely poor acceptor.

 

[Moontanman]

1 minute ago, CharonY said:

That would be very difficult. Oxygen is used as terminal electron acceptor as it is positioned favourably in terms of reduction potential and can couple with a wide range of donors. Conversely, hydrogen is pretty much on the other end, making it a good donor, but an extremely poor acceptor.

 

Asimov detailed it out but that was 50+ years ago so I don't remember the exact details but I do remember his talking about that very thing. He coined it as a saturation unsaturation cycle involving fats replacing proteins. He also stated that a lung full of high pressure hydrogen, I assume he was thinking this planet would have a deep atmosphere, would contain many orders of magnitude more hydrogen than a lung full of our air would oxygen but  don't remember the details beyond that. I wish I still had that book, I've tried to find it but it's one of his more obscure titles.  

[CharonY]

29 minutes ago, Moontanman said:

Asimov detailed it out but that was 50+ years ago so I don't remember the exact details but I do remember his talking about that very thing. He coined it as a saturation unsaturation cycle involving fats replacing proteins. He also stated that a lung full of high pressure hydrogen, I assume he was thinking this planet would have a deep atmosphere, would contain many orders of magnitude more hydrogen than a lung full of our air would oxygen but  don't remember the details beyond that. I wish I still had that book, I've tried to find it but it's one of his more obscure titles.  

I am not a chemist, so I have no idea if and how that would affect thermodynamics. It would be interesting to see when he proposed that- the idea that cells might be using chemiosmotic gradients was only proposed in the 60s or so. And it took a while longer until folks realized what bag of tricks bacteria had in that regard.

[exchemist]

1 hour ago, CharonY said:

Not quite. The net reaction of photosynthesis are two separate reactions which are not really mechanistically coupled. Specifically, it initiates an electron transfer chain (functionally similar to respiration) in order to pump protons which then chemoosmotically generate ATP. Water functions as electron donor during the water splitting event. I do think that the chemical notation masks a little bit the underlying biology, especially as carbon fixation in some bacteria happens without light,  but that is neither here nor there). I probably should add that glycolysis happens in the cytosol, and the pyruvate is then delivered to hydrogenosomes.

The reaction in hydrogenosomes is simpler and ATP formation is by substrate level phosphorylation, as mentioned before. Hydrogen is basically formed to re-oxidize ferredoxin, which is needed for the decarboxylation reaction from pyruvate to acetyl-CoA.

Not entirely sure if I get it right but it should be something like: Pyruvate + 2 [H+] + Ferredoxin(ox) -> Acetate + H2 + Ferredoxin(red) + CO2

 

One way to think about this is that respiration (aerobic or anaerobic) is basically using a redox potential to energy generation, rather thinking that a particular compound being fuel or waste. Basically, if you have  a nice electron donor and acceptor pair that generate a nice potential, you can use that potential by using to drive an electron transport chain, that also pumps protons out of the cell to generate a proton gradient that is then used to generate ATP.  This means that depending on which pair the cell uses, the same compound can be used as donor or acceptor.

Hydrogen is used by many bacteria as electron donor but is also released often in fermentation processes (or the reaction above) to essentially balance the redox budget of the cell (and as you can imagine, released hydrogen can be used by other bacteria, creating interesting cycles within bacterial communities).

 

OK I just about follow this, but the overall stoichiometry and thermodynamics won't be affected by the mechanism, even if various separate processes and intermediates are involved. If the starting material is carbohydrate and the waste products are hydrogen and CO2, there has to be a notional reaction scheme that accounts stoichiometrically for the relation between reactants and eventual products. That's the bit I want to understand. 

[Moontanman]

Just now, CharonY said:

I am not a chemist, so I have no idea if and how that would affect thermodynamics. It would be interesting to see when he proposed that- the idea that cells might be using chemiosmotic gradients was only proposed in the 60s or so. And it took a while longer until folks realized what bag of tricks bacteria had in that regard.

Asimov was a professor of biochemistry he has some intriguing ideas around possible alien biochemistries, he inspired me to want to be a biochemist until life had other plans, lol

[CharonY]

8 minutes ago, exchemist said:

OK I just about follow this, but the overall stoichiometry and thermodynamics won't be affected by the mechanism, even if various separate processes and intermediates are involved. If the starting material is carbohydrate and the waste products are hydrogen and CO2, there has to be a notional reaction scheme that accounts stoichiometrically for the relation between reactants and eventual products. That's the bit I want to understand. 

I get that- but being a biologist rather than chemist I understand things better if I view it from a mechanistic perspective. It just helps to explain functions better and avoids confusion for reactions that might chemically look similar, but functionally are very different (as in this case). 

 

11 minutes ago, Moontanman said:

Asimov was a professor of biochemistry he has some intriguing ideas around possible alien biochemistries, he inspired me to want to be a biochemist until life had other plans, lol

Yes, I know. His research output was low which got him in trouble regarding his teaching position. But his books were so popular, that it hardly mattered. What I meant is that in his most active years, substrate-level phosphorylation was still the basic assumption. So would be curious how much was out in lit, when he wrote the story. 

[Moontanman]

1 hour ago, CharonY said:

 

Yes, I know. His research output was low which got him in trouble regarding his teaching position. But his books were so popular, that it hardly mattered. What I meant is that in his most active years, substrate-level phosphorylation was still the basic assumption. So would be curious how much was out in lit, when he wrote the story. 

The book was one of his non fiction titles so it wasn't a story, at the time I wasn't aware of his fiction work. In fact I a pretty sure it was the first of his books I ever picked up.

I remember little from it other than it intrigued me big time. It inspired me to write a report in HS about a biochemistry based in HF as a solvent and the ecology it might support. 

Edited April 29 by Moontanman

[CharonY]

57 minutes ago, Moontanman said:

The book was one of his non fiction titles so it wasn't a story, at the time I wasn't aware of his fiction work. In fact I a pretty sure it was the first of his books I ever picked up.

Oh I see. Chances are that this around the time we started to have hypotheses how respiration actually works. Could be fun to see how folks imagined things to work and compare to what we know now.