
Enzymes from nine organisms combined to create new pathway to use CO2 - jseliger
http://arstechnica.com/science/2016/11/enzymes-from-nine-organisms-combined-to-create-new-pathway-to-use-co2/
======
mixedmath
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...](http://www.popularmechanics.com/science/energy/a23938/fix-carbon-
dioxide-useful-products/)

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

------
egypturnash
> 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.)

~~~
sndean
> 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...](http://www.nature.com/nchem/journal/vaop/ncurrent/full/nchem.2644.html)

~~~
soreal
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

~~~
craigyk
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.

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

~~~
craigyk
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.

~~~
filoeleven
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?

~~~
craigyk
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.

------
highd
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.

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

~~~
WalterBright
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.

~~~
Procrastes
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!

~~~
WalterBright
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.

------
smaili
_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!

~~~
cronjobber
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.

~~~
raverbashing
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

~~~
AlphaSite
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.

~~~
raverbashing
Yeah, that happens. But also this
[https://en.wikipedia.org/wiki/Noncoding_DNA](https://en.wikipedia.org/wiki/Noncoding_DNA)

------
timbuchwaldt
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)

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ChuckMcM
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.

~~~
kctess5
That would be an interesting compiler project.

------
mchannon
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.

~~~
wbl
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.

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

~~~
ceejayoz
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.

~~~
mcbits
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!

------
dnautics
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?

~~~
chongli
_And where is E coli going to get this energy?_

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

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

~~~
chongli
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?

~~~
dnautics
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?

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100ideas
Based on the details in the arstechnica writeup, it sounds like the wetlab
work was all done with cell-free systems?

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digler999
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.

------
mirimir
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.

------
mikeytown2
Sounds like this could be a way to terraform Venus if the bacteria can float.

~~~
raverbashing
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)

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

~~~
yetihehe
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.

------
known
Is planting a tree that difficult?

~~~
Elrac
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.

