Mauve 👁💜 @mauve@mastodon.mauve.moe

hope everyone in new york is having a very communist morning today

Rubisco is (arguably) the most abundant protein on Earth. (LPP surely comes close, right?) It’s an enzyme that fixes CO₂ into sugars during photosynthesis.

Unfortunately, as most people learn in school, Rubisco is inefficient. Sometimes it confuses O₂ for CO₂ and wastes energy. Plants make up for this in raw concentration; up to half the soluble protein in a leaf is Rubisco.

People have been trying to engineer better Rubiscos for many decades, but it's not easy because the proteins are big, do not fold easily (they need chaperone proteins to help out), are made from 16 subunits in land plants.

But there's a new paper in Nature Plants that looks really interesting. The TL;DR is that a group in Australia figured out how to express plant Rubiscos (and all SEVEN of their folding chaperones) using a set of 3 plasmids inside of E. coli cells. This enabled them to do "directed evolution" of Rubisco in bacterial cells, and quickly find Rubisco mutants that have higher enzymatic efficiency or that fold better.

In addition to the 3 plasmids, the researchers also coaxed E. coli to make ribulose-1,5-biphosphate, or RuBP, which is the 5-carbon sugar that Rubisco smashes into carbon dioxide to make molecules of 3-PGA for central metabolism.

Now, the clever bit is that you RANDOMLY MUTATE the three plasmids encoding the Rubisco to make millions of variants. Then, you transform those mutated plasmids into E. coli. If the E. coli do NOT make a functional Rubisco, RuBP levels build up and kill the cell; the molecule becomes toxic. But if the E. coli DO make a functional Rubisco, then they keep the RuBP levels in check and live just fine.

Using this "screening assay," the researchers found 46 fast-growing colonies of E. coli. Two of those colonies encoded really useful mutations. One mutation (M116L) makes Rubisco about 25–40% faster. The other (A242V) makes it fold and assemble much more efficiently.

They put this mutation into a "hybrid Arabidopsis–tobacco Rubisco," put that into tobacco plants, and measured growth. The plants with M116L grew 75% faster than wildtype.

No guarantees this will scale to more useful crops, like wheat and corn and soybeans etc. But it seems like a nice in vitro assay for faster prototyping!

This is one of the most underrated papers from the last few months.

TL;DR: MIT scientists engineered bacteria that can be seen from hundreds of feet away, using drones or satellites, with hyperspectral cameras.

Here is how they did it.

> First, they filtered through a database of ~20,000 small molecules that organisms, across all kingdoms of life, naturally make. They calculated the electron density for each molecule to predict how each one would absorb light (both visible and infrared). In other words: if you shine white light on the molecule, they predicted the wavelengths that will be absorbed, and how strongly.

> These molecules were filtered down to those with really unique light absorption spectrums. The scientists also used computational methods to figure out how many enzymes a bacterium would need to make each molecule (fewer enzymes is better, because it's easier to engineer). The two best options were biliverdin IXα and bacteriochlorophyll a. Both of these molecules have ring structures that strongly interact with near-infrared light.

> Third, they made a hyperspectral detection algorithm. The algorithm separates the molecular signals from background "noise" in hyperspectral images. Each pixel was treated as a mix of background spectra plus, if present, the reporter molecule's fingerprint, which appears as missing light at certain wavelengths. By clustering pixels to define backgrounds and then solving for how much reporter signal best explained each pixel, they could figure out where engineered bacteria were located.

> Next, they put it all together. They engineered microbes to sense explosives and then biosynthesize biliverdin IXα in response; a living biosensor. They buried these microbes near explosives and then flew a drone overhead to see if they could spot them. (This was done with the military, iirc.)

> They used the drone to take a picture of one acre of space, covering ~4000 square meters. They were able to figure out where the bacteria were buried with a limit of detection of less than 4 million colony-forming units per squared centimeter.

This paper is more practical than it may seem, too, because hyperspectral cameras are already mounted on some satellites. And it is entirely feasible to see the locations of bacteria not only via drones, but also using satellites orbiting the Earth at much further distances (provided we can optimize these sensors even more.)

In short, these hyperspectral reporters are a long-range way to do environmental biosensing. You could, in principle, engineer bacteria to detect pathogens in soil, explosives in a warzone, or even bioleaks and then emit these hyperspectral reporters. We could use existing satellites, or launch new satellites, to monitor them from afar.

Thanks for reading.