Enzymes from nine organisms combined to create new pathway to use CO2 | Hacker News Reader

Enzymes from nine organisms combined to create new pathway to use CO2

arstechnica.com

178 pointsjseliger76 comments

This was first brought to my attention through an article at Popular Mechanics [1]. Comparing the differences between the writing and focus of the two articles leads to interesting idiosyncracies. Ars Technica seems to emphasize the challenge of combining these enzymes to produce a new cycle. It's not technical, but it does allude to some techniques.

Pop Mech emphasizes how much more carbon gets taken out of the air, compared to photosnythesis. An indication of their attention to scientific content comes from their description of the methodology:

> To oversimplify matters, they mixed together all their enzymes with some chemical fuel and calculated how much CO2 was being pulled out of the air.

I actually didn't realize these were talking about the same paper until I noticed that I had opened up the same link to the original paper twice.

[1]:http://www.popularmechanics.com/science/energy/a23938/fix-ca...

I'm always really impressed with the depth that Ars Technica goes into, considering that it's a pretty mainstream (well, sorta) site.

> The other thing is that the entire pathway can now be put inside cells, either normal bacteria like E. coli or the synthetic cells with a minimal genome that researchers are working on. If that's the case, then the need to supply all the chemical co-factors should go away, since the cells should be producing them anyway. More importantly, if the cell is made to depend on this pathway as its only source of carbon, evolution would have the chance to optimize it even further.

Immediate thought: What happens when that bioengineered E. coli or whatever, which you're hoping evolution will make work even more efficiently, leaves your carbon-sequestering vats and starts reproducing in the wild? Eventually you reach a point where we're getting record low CO2 levels. Hello, new Ice Age.

(I am sure there are many reasons this would not happen but it certainly makes for a nice bullshit explanation if I wanted to write a story set in a far-future ice planet.)

> bioengineered E. coli or whatever, which you're hoping evolution will make work even more efficiently, leaves your carbon-sequestering vats and starts reproducing in the wild? Eventually you reach a point where we're getting record low CO2 levels.

Normally, if you want to create something like this, it's an auxotroph. So it shouldn't survive outside of the carbon-sequestering vat.

Or it's all on a plasmid, so once it's out of the vat plasmid won't be maintained.

Or these will be created in "Synells" [0] that can't really replicate.

Though that's a really interesting thought. If we find a technology to do anything about CO2 levels, it seems plausible that we're going to accidentally go too far in the other direction.

[0] http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem...

I know it sounds far-fetched, but if someone develops a technology that can rapidly grow a wood-like material out of atmospheric carbon in such a way that entire buildings can be grown in single digit years, we could start seeing countries fighting over who is using too much CO2 and consuming too little

I've been meaning to try and do an estimate related to this. Just how much CO2 could be pulled out of the air by _extensive_ farming of fast growing trees. We could find ways to use as much of the wood as possible (construction materials, etc.), and just sink the remaining wood in cold water where the carbon would stay locked away for 100+ years.

Nvmind, ran the numbers... this plan sucks.

Then again, if my numbers are right, if humankind dedicated <1% of land used worldwide for food to growing trees and locking away the cellulose, we would cancel out worldwide CO2 emissions. Since most of that land is used as pasture, there is more than enough play to keep the world fed, and I could see up to 10% being tasked to this purpose , which seems doable in an emergency.

Have you accounted for moving the trees from where they grow to where they can be used? (E.g., milling, planing, curing.) That will take energy that likely offsets some of the benefits.

Likewise, moving the lumber or finished goods to consumers will also require some energy that might offset the carbon removed.

I'm confused...the numbers sucked for extensive farming in order to cut CO2, but only 1% of arable land would cancel CO2? What am I missing?

I initially thought it didn't look good when looking at the amount absorbed yearly per tree, but then was surprised by some estimates on how many trees you can fit per unit area. A more accurate estimate needs to be done though, different numbers I found put the final range at about an order of magnitude.

Also, most farming and stable forests are mostly carbon neutral. This would require continual seeding, harvesting and sequestration of the cellulose. Maybe it will be a good thing though that cellulose+lignins are so hard to breakdown.

Still plenty of room at sea. Is there a fast growing mangrove?

Future environmentalists:

We need to drill in the ocean in order to flare more CO2 into the atmosphere or sea levels will drop to catastrophic levels!

Not exactly what you're asking for, but intriguing nonetheless:

http://inhabitat.com/phillip-ross-molds-fast-growing-fungi-i...

Normaly - nuclear plants are safe.

But on humans, they aint. Humans & Technology- not even once.

Not gonna happen. Releasing these "into the wild" is like releasing glow in the dark rabbits that only eat arugula. They'll die before they make it out of the drain, let alone before they make it to any natural microbial ecosystem where they were be viciously torn apart by organisms finely tuned to that environment.

They only need to survive long enough to swap genes with existing bacteria.

https://en.wikipedia.org/wiki/Horizontal_gene_transfer

Two reasons it won't end the world.

1. This is in vitro work, and even there it is only 5x as efficient. In vivo I'd expect that rate to go down.

2. Metabolism is expensive. This is probably not a very fit pathway. It takes a lot of energy to produce the proteins and ATP necessary to power this cycle and it's product isn't more ATP. It would incur a substantial fitness cost and in the wild it would likely get out grown by wild bacteria that favor Glucose producing photosynthesis.

Not that a new ice age couldn't happen, but carbon fixation is already at a evolutionary local maximum among the six different wild versions, so I don't see why a 7th would be any different.

Then we chop down all the trees and burn them!

Indeed. One way or another, I think recent years have established that "not enough CO2 in the atmosphere" is a pretty easy problem to solve.

It depends.

One of the things that makes Earth special is the formation of carbonate rocks by life taking CO2 out of the atmosphere and falling to the bottom of the oceans; these rocks are then subducted by tectonics and the CO2 spewed out by volcanoes.

As the Earth's core cools, volcanism will diminish, and so the recycling of CO2.

But perhaps Nuclear fusion can fix everything... However I am not a geologist.

Party like it's 1999.

Free Corvettes for everyone :-)

Infinite apple juice!

>(I am sure there are many reasons this would not happen but it certainly makes for a nice bullshit explanation if I wanted to write a story set in a far-future ice planet.)

You are a bit too late to the party:

http://www.imdb.com/title/tt1706620/

Assuming they managed to make some kind of bug that was viable outside of the lab, we genetically engineer a spider to eat the fly. Obviously, this kind of thing has the potential to get out of hand as the technology improves and becomes more accessible. Maybe this is the Great Filter, or maybe the filter is not having a full enough understanding of things to solve problems before it inevitably becomes garage-level science.

I had same thought except with an all trees will suffocate plot twist. The ice age angle is interesting.

We will just burn more and more ...

Important point from paper abstract:

>The pathway is up to five times more efficient than the in vivo rates of the most common natural carbon fixation pathway.

Pretty awesome depending on how tight that "up to" bound is. As an aside, this sort of thing is why I don't worry too much about climate change - once the incentives become real I'm very confident in societies ability to invent solutions. Maybe, say, a star-trek-tier global weather control system :) The primary risk with that attitude would be if our best solutions are local in nature - this would likely result in impoverished countries and cities suffering the major brunt of climate change.

> The primary risk with that attitude would be if our best solutions are local in nature

If the major ocean-based cycles are disrupted because of salinity change / warming / acidification, then it's not going to matter where the damage was done.

People can already plant trees but don't. I don't worry about methods so much as humanity fucking itself over out of apathy.

I'm a little surprised there aren't programs to plant trees in unused midwest prairie land. Once established, trees seem to do well there.

Growing up on the High Plains I only knew trees as carefully maintained decoration and windbreaks that gale force winds, disease, lightning, hail and drought would make short work of without constant care. I remember my first trip to New York State where I was wondering about some trees blocking a view of an on ramp and why someone planted them there. Then it occurred to me. Nobody planted them. These were trees in the wild!

I grew up in Kansas. There were plenty of trees in the towns, that were planted by the settlers. I didn't see any effort whatsoever at maintaining them. There were trees in our yard, and our house bordered a greenbelt of trees. They grew just fine without assistance.

In the high plains, sure. Those areas are natural grasslands; they were grasslands before European settlers arrived and started clear-cutting forests to make room for farmland. However, east of the high plains, before the Mississippi, I'd think there'd be at least some room for new trees.

A hurricane unleashes more power than humanity is currently harnessing. I doubt we figure out how to do anything that only works locally.

Yeah, I wonder when will we have a hurricane sized wind generator (with a huge set of batteries or other storage facility)

Not just that you can't predict where the hurricanes will go, you can't really have a pop-up generator to extract power from a hurricane can you.

It is a bit extracting power from lightning strikes, it isn't going to be a good return on investment.

But hurricanes are big and affect a large area (you might be thinking of Tornadoes)

Not easy, but maybe doable

The time lag for noticing change and being able to respond may preclude the possibility of meaningful compensation

I'd like to think that as we become a more globalized society, it would be in our best interests to keep every region protected from CO2 proliferation—the 'rising tides lift all ships' philosophy.

"Rising CO2 lifts all thermometers"?

I'd stick with the tides and ships as this is one of those rare times where the common metaphor could be both literal and ironic.

Take a moment to appreciate the scale of this accomplishment. In four billion years of evolution, life has only managed to evolve six known pathways that start with carbon dioxide and build more complex molecules. In just a few years, a bunch of grad students in Zurich added a seventh.

Well done and kudos to all those involved!

Maybe this one did evolve, but others displaced it for reasons we don't know yet.

I sure hope that's what happened. I'm somehow emotionally attached to all the life forms plodding along using only those rotten old pathways, I don't know if I took kindly to lab life taking over.

But remember, that's evolution

It's like a very old system that has been patched and repatched over and over and never refactored.

10 steps that kinda works works.

Efficiencies only play a part when one resource is really limited, and even then there might be other ways of making up for it

Well no, it try's to refactor its self, randomly deleting genes, until it deletes one which can be loved without, removing some vestigial pathway or organ.

Yeah, that happens. But also this https://en.wikipedia.org/wiki/Noncoding_DNA

As cool as this is, the "20x improved efficiency" is not what that paper says it seems:

> Over the course of the optimisation, CO2 fixation efficiency in the CETCH cycle improved by almost a factor of 20 until version 5.4 (Fig. 2).

> This is comparable to the few reported attempts to measure the CBB cycle in cell extracts (1 to 3 nmol min−1 mg−1 CBB cycle protein,

So what it actually says is: They improved CETCHs efficiency by 20x during the development, but it is not 20x more efficient than plants, but rather comparable (although it seems hard to measure what plant efficiency is)

I really find the notion of designing the metabolic steps this way interesting. Converting CO2 to mallic acid, converting sugars to oil, what ever. At some point there is an organic chemistry "programming" language where you specify at a high level what you have for input and what you want for output and your biometabolic compiler spits out a bunch of RNA modules for you to link together in your holding organism to operate.

That would be an interesting compiler project.

Looking at their diagram, there appear to be multiple injections of hydrogen peroxide, but no products of hydrogen peroxide.

Maybe it just requires a finite amount to get the reaction started, or there's some subtle reaction going on that's not in the diagram.

Or they decided a trickle of conventionally produced H2O2 was an acceptable price to keep the reaction going.

Wonder what I'm missing.

Oxygen is being consumed by oxidases, producing hydrogen peroxide, and the peroxide is being turned to water and oxygen by a different enzyme. So this could be run with oxygen instead.

It looks like injected H2O2 gets recycled in the kat-mco and kat-pco reactions.

I've always maintained that the solution to carbon capture and sequestration would be biological in nature. This is great news indeed.

Man produces CO2.

Global warming.

Man produces CO2-eating organism.

Global cooling.

Snowball Earth? [1]

Wasn't there a campy French-Korean movie about this with Captain America in it? [2]

[1] https://en.wikipedia.org/wiki/Snowball_Earth

[2] https://en.wikipedia.org/wiki/Snowpiercer

Let's just hope the solution to the Fermi Paradox isn't similarly biological in nature.

Maybe CRISPR-style stuff is the Great Filter as we go and suck all the CO2 out of the ecosystem accidentally.

We know a lot of ways to replenish CO2, and if that's not enough, our two nearest neighboring planets are swimming in it. Maybe the others weren't so lucky!

Freeman Dyson would probably be pleased by this work.

No. It doesn't make sense to put this into E coli. In order to convert CO2 into usable carbon (usually, sugars), you need energy. And where is E coli going to get this energy? Breaking down sugars and burning them to create CO2?

And where is E coli going to get this energy?

From the sun? That's where plants and cyanobacteria get it.

How is E coli mysterioulsy going to convert solar energy into biochemical energy? I know how plants and cyanobacteria do it; they have photosystem.

Either by a symbiotic relationship with cyanobacteria or by transferring the genes from cyanobacteria. I mean, we're already talking about combining nine organisms into one, why stop there?

That's semireasonable: you can give e coli glucose made by a cyano (using human glucose transporter). But you're still making glucose and then burning it... Why use a middle man? Why not just transform the cyanobacteria with this system to begin with?

The energy in the system seems to be coming from ATP which is used to move energy around in both animals and plants, so it could presumably be wired to photosynthesis (which I assume is what the researchers had in mind — take the process plants use to store energy by converting water + C02 into sugar and replace it with something more efficient). And that's the limit of my high school organic chemistry.

And e coli can be modified to do photosynthesis too.

Not really. They put bacteriorhodopsin in e coli, but that's hardly photosynthetic.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892948/

> No. It doesn't make sense to put this into E coli.

So pick a strain of cyanobacteria or algae instead.

Based on the details in the arstechnica writeup, it sounds like the wetlab work was all done with cell-free systems?

what would be cool is if this could be combined with an ethanol production system. So fermentation bacteria produce ethanol, their CO2 biproduct goes straight to these enzymes, and if somehow their waste product could feed the ethanol. So you could in theory have a "sunlight in, ethanol out" plant that is almost completely neutral.

Ethanol isn't great, since combustion engines' efficiency sucks, but it would bridge a gap to reduce carbon while we still rely on combustion engines. Or the ethanol could be used in "cogeneration" facilities that use the waste heat and produce electricity to get very high utilization of energy.

This is extremely elegant work, no question. But there's a catch. The cycle requires a reducing agent (NADPH) and energy (ATP). So one would need to add components to get those from light or whatever.

Sounds like this could be a way to terraform Venus if the bacteria can float.

Floating is the easy part. The hard part would be surviving the 400C and acid rain on Venus

(Though you might get it floating to a higher altitude and lower temperature, maybe that's what you're suggesting)

If it works in vitro, why do we need it to work in vivo?

So that your system is self-replenishing. Just add some simple chemicals from time to time and monitor temperature and you no longer need to synthesize more enzymes by yourself.

Is planting a tree that difficult?

Not that difficult, but it doesn't accomplish the same thing.

First, have you noticed how long it takes for a tree to grow to a size where it's "working" at near capacity?

Second, the new pathway seems to sport higher efficiency at converting energy + CO2 into useable carbon.

Third, trees don't produce really useful carbon compounds. It takes a lot of energy to break wood down.

Fourth, the carbon in a tree is only sequestered so long as the tree is standing or its wood is processed into something durable. A tree that falls down and rots releases its carbon back into the atmosphere.

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