Saturday, February 21, 2015

Random musings on carbon monoxide

There are occasional days at work when I get a lunch break. Sometimes it is long enough to get home and back, often it’s not. Given an hour of free time in the basement, what might you do?

Well, usually I go and have a look whether Nick Lane's group has any new publications up. Pondering the origins of life is a great relief from the problem solving with limited information that makes up clinical work.

In recent months I’ve usually had three browser windows open to try and get an accurate understanding of what he and his coworkers are specifically saying.

As a preamble to discussing those methanogens and acetogens which do not use cytochromes I would just like to lay it on with a trowel that these strict anaerobic organisms are not “living fossils” or in anyway primitive. They appear to be using a method of carbon fixation which is developed from that of the first prebiotic synthesis. That does not make them simple. If this is the first technique for carbon fixation it has been developing for well over 3 billion years. It’s still used nowadays because it works.

So lets go to Figure 1 sections a and b of An Origin-of-Life Reactor to Simulate Alkaline Hydrothermal Vents to have a look at the energetics of fixing organic carbon:

















This shows that hydrogen is unable to reduce CO2 to formaldehyde at pH 7. However, if you introduce a pH difference across a thin FeS barrier, it appears to be possible to put an electron or two on to FeS clusters which can then drive the reaction. At the risk of spoiling the paper, it works. Yield is low, but it's there.

Of much greater interest (to me anyway) is the ability to reduce CO2 to CO. I've added these potentials to Nick Lane's diagram like this:



















There is a lower barrier to be overcome and, given the suggested pH gradient, greater likelihood of the reaction proceeding. I think the group are interested in formate and formaldehyde because they have the potential to do many things other than generate acetate/methane plus the reactions from there onwards are exergonic.

I'm more interested in CO formation because the carbon monoxide dehydrogenase (CODH) enzyme appears to be core to carbon fixation and is conserved between archaea and eubacteria, certainly in the methanogens and acetogens which lack cytochromes and are strictly anaerobic in their metabolism. So too is acetyl CoA synthase, which is directly linked to CODH. This suggests that this enzyme complex, or the abiotic reaction is preserves, is very ancient. We need to look at Early bioenergetic evolution, Fig 2 section b for a suggestion of how prebiotic acetate synthesis might have occurred. This is the top section:























If we work down from the CO2 at the top of the dashed line rectangle we can see that CO2 is being reduced by electrons from a very low potential FeS cluster (just where it says +2[H]), generated as in my modification of the blue bar chart above, using the pH gradient across a thin FeS barrier. The FeS cluster on the right is the actual catalytic cluster and the green sphere is a Ni atom crucial to its function.

The CO diffuses to a second FeS catalytic cluster which is doped with two more Ni atoms, shown as two green spheres. This reaction does not need a low potential FeS group, so I'm not sure why the black/yellow cluster is shown to the left of the "Ni" in the diagram, excepting that modern ACS does have an FeS cluster covalently attached to the FeNiS catalytic cluster. Doesn't make the diagram particularly easy to interpret. Anyhow, the CO binds to one of the two Ni atoms and waits for a methyl donor.

The methyl source is on the far left of the diagram, shown as CH3-X. This has to be of abiotic origin in an origin-of-life scenario and the simplest is undoubtedly CH3-SH. This methyl group attaches to the CO on the Ni atom and we then have CH3-CO- attached to the catalytic site. Thiolysis using a source of sulphydryl (shown as HS-R in the diagram, below the CH3CO-Ni, still within the dotted rectangle) generates a thioester of acetate, shown (outside the rectangle) as CH3CO-SR.

We've already speculated the availability of CH3-SH in vent fluids to supply methyl groups, so we could simply replace HS-R with HS-CH3 i.e. CH3-SH can provide both the methyl group and the sulphydryl group for the above reactions. The only step requiring any energy input is the initial reduction of CO2 to CO using a low potential FeS cluster.

So when you supply CO and CH3-SH to a slurry of FeS and NiS you get CH3CO-S-CH3 of abiotic origin. This was done back in 1997 by Huber and Wächtershäuser. The trick of reducing CO2 to CO is the hard knot to pick and which needs FeS and a proton gradient, not available in the slurry.

The thioester can hydrolyse to heat and acetate but more interestingly it carries enough energy to form a phosphate derivative which retains slightly more available energy than ATP.

After translating this in to a system which has developed genes and proteins, we still the have remnants visible.

Let's now look at the lower section of Figure 2 section b. The complex series of reactions down the left is how modern acetogens generate their methyl donor source, down the right is the system from methanogens. These are both replacing the speculated abiotic CH3-SH. These pathways are not particularly relevant to any origin of life speculation but clearly are interesting in their own right as they also support CO2 reduction by H2. There are some interesting speculations as to why tungsten or molybdenum are required cofactors... Today it's still the central rectangle we are interested in:

























This is the modern version of what we have been looking at previously, with the two Ni doped FeS clusters on the right hand side. The reduction of CO2 to CO is no longer accomplished using a proton gradient, in fact these archea and eubacteria use a sodium gradient rather than a proton gradient. Instead, a low potential ferrodoxin protein with two FeS clusters is generated in the cytoplasm using electron bifurcation from molecular hydrogen (not shown, discussed here, that's the third window in my browser!). The systems used differ between methanogens and acetogens but the core energy currency for both is still reduced ferredoxin. This ferredoxin looks, to me, like a fossil of the FeS on a proton gradient which provided reducing power in the initial scenario.

The transport of CO to the second FeSNi cluster is down a molecular tunnel in the modern enzyme but the binding to a Ni atom at the end of that tunnel persists. Source of the methyl group is quite different between archaea (methanogens) and eubacteria (acetogens). This differing arrangement suggests development after the divergence of the two lineages.

The use of CH3-SH to form a thioester has been replaced by the use of coenzyme A, giving us the familiar acetyl-CoA (shown as CH3CO-SCoA) below the rectangular box. This can be used for substrate level phosphorylation of ADP to ATP or can be used as a source of cell carbon for metabolism. There is a lot of interest along these lines in this paper: The stepwise evolution of early life driven by energy conservation.

There are some interesting ideas which stem from this believable scenario.

Substrate level phosphorylation is clearly very ancient. There are suggestions from the speculated origins of ATP synthase that ATP usage may have been common before this enzyme complex was developed.

The possibility of generating an ATP-like moiety was present when all that was available was a proton gradient derived reduced FeS cluster and some CH3-SH.

Carbon fixation does not appear, initially, to have involved proton translocation, though the gradient was essential.

Carbon monoxide is utterly intrinsic to the formation of life. Strange, that.

Peter

6 comments:

Stan (Heretic) said...

Hi Peter,
Is the presence of carbon monoxide CO of biological origin, in the early Earth atmosphere, plausible? - Would you estimate it to be a major or minor component? That brings another question: are there higher evolved lifeforms at present (or the last 1/2 billion years), that are capable of tolerating atmospheric CO?
Regards,
Stan

Peter said...

Yep, there was CO in the pre biotic atmosphere and there are groups of thinkers who consider this may have been the core prebiotic reaction. There are methanogens (not sure about acetogens) which are core to CO degradation/homeostasis today.

My leaning towards CO2 comes from the massive bulk supply which was present in the early earth atmosphere. But whether CO was the spark which ignited metabolism which then produced conditions where CO2 reduction could be facilitated is interesting. There is nothing to suggest that CO2 reduction is anything but ancient and core to both archeal and eubacterial protometabolism. On the CO as origins idea, life could have originated anywhere with FeSNi minerals but only became confined to vents because they provide the environment for CO2 reduction. And a form of containment. I don't think any of the CO metabolising archea lack CO dehydrogenase, i.e. none have abandoned the fall back source of CO even if they are happy to metabolise it. Haven't checked this for certain but I think that's the case.

Peter

Stan (Heretic) said...

I was coming to those thoughts from a different angle.

Chemical potential gradient across a membrane or oceanic vents gradient, as the engine for life and driving evolution, is one possibility.

Another possibility is photo-synthesis. It does not have to be restricted only to breaking water into oxygen and hydrogen, it could also drive CO2-->CO + O, and it can also drive hydrocarbon and organic acids photo-dehydrogenation - which would directly plug into methanogenic life forms.

BTW, a digression, did you read that "Chernobyl" study paper suggesting that melanin was used by early funghi and molds, as photo-synthetic catalyst, using gamma and other ionizing radiation instead of visible light?

I was looking through some papers recently (my engineering research project), where the most promising photo-catalyst (for visible light) compounds that were investigated were iron and nickel-organic. Even metalic nickel seems to work.

http://www.ncbi.nlm.nih.gov/pubmed/24004329

There are more papers but I can't find the refs at the moment.

I was looking, as an engineering project, at various ways of producing hydrogen. Initially I thought of using water but realized that a much more promising route is dehydrogenation of hydrocarbons and fats because it avoids problems with catalysts destruction due to oxygen reactivity.
Regards,
Stan

Peter said...

Stan, I've been meaning to blog on the Chernobyl slime moulds since I read the press release and picked up a paper (or two?). A few years ago now, isn't it?

I picked up the redox potentials for this current post from the table here in Wiki:

http://en.wikipedia.org/wiki/Photoelectrochemical_reduction_of_CO2

I'm guessing you've read much further than this, for me I stopped when it gave me the info I needed.

If CO production was photo driven it must have been completely replaced by reduced ferredoxin as the source of electrons for CO generation well before the separation of archaea from eubacteria because nothing seems to remain of its existence in the metabolism of either the methanogens or acetogens in the post. Getting a high energy molecule like CO from photosynthesis does not seem like something a LUCA would lightly (accidental pun) abandon completely... I agree that non oxygenic photosynthesis using low energy photons is common, I can't see how it is primal.

Not sure what it was that had me currently thinking about Chernobyl and gamma ray "photosynthesis" unless it was the recent talk about aliens living on electricity etc. It's a very neat finding though!

Hope you are well, life here in the UK is good and looking to get better. All the best

Peter

Team Kruse said...

Peter I really hope you stay on this path........because our ideas are on a collision course. CO is a quantum gas that modern day free divers use in hypoxic environments. Your gut microbiota also makes 8-12 L of H2 a day when i is healthy and CO is in the gut without any O2.

Stan (Heretic) said...

Thanks, I am doing OK. Its nice that the UK has finally recovered after all those cutbacks (or may be because of them?), but watch those big Russian bombers ...

I find the idea of using external electricity to directly dislodge electrons in cellular processes fascinating, because it ties with some weird observations and even weirder speculations.

It ties also with my pet theory that postulates that cellular membranes, (in some instances) may create a 2-D Bose-Einstein condensate of proton-electron pairs across the membranes, allowing a leverage of a 200mV potential by a very large factors!

(From one heresy straight into another)

It then leads not only to natural gamma radiation usage by some fungi, but also perhaps to some biologically assisted nuclear reactions? 8-:)

The reports and research on that is very incoherent and not very credible but it does exist. Did you look into it?

Best regards,
Stan (Heretic)