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Apr/13

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Crowd-funding Avatar?

So there is a new project making great strides on crowd-funding platform Kickstarter: Glowing Plants: Natural Lighting with no Electricity. The aim is to produce a genetically-modified houseplant which emits light – a pretty exciting concept.

For me it brings back fond memories of 2010, when I was part of the University of Cambridge team competing in a genetic engineering competition called iGEM. We focused on bioluminescence and over a summer made bacteria which could glow.

Yours truly (right) lit by our bioluminescent bacteria. Disclaimer: they didn't seem nearly this bright.

It wasn’t revolutionary – the sequences of DNA we used had been described in the scientific literature – but we packaged them in “BioBricks” so that other iGEM teams could assemble them with their own parts to make something new. For example, last year the University of Peking used our constructs to allow bacteria in different flasks to communicate.

One of the applications we described for bioluminescence, and our original inspiration for the project, was the idea of glowing plants. Time constraints meant that we had to limit ourselves to bacteria, which take hours and not months to grow. But nobody can deny that the idea of walking down a path lit by glowing trees is pretty enticing. We took many photographs of our bacteria, but the image that attracted most attention was a 3D mockup depicting how a city lit by bioluminescence might look.

Glowing trees mockup, as featured in New Scientist and on BBC News

Now these ideas have served as the inspiration for this Kickstarter project, headed by Omri Amirav-Drory and Antony Evans. The response has been very impressive. In just three days, it has exceeded its initial $65,000 goal. So is this the model for scientific funding in future?

Not quite, I think. What has dissapointed me has been the lack of discussion as to what the team actually plan to do with the funds raised, and whether the science stacks up. To be fair to the team, they are perfectly happy to discuss it, and they have shared their DNA designs using their Genome Compiler software (the project serves in part as a case-study for it).

But most of those who have donated have done so without seeing these, or without even asking for second opinions. So here is some more information, and some personal thoughts, about the science behind this project.


What do they plan to synthesise?

The genes will come from a bacterium which lives in symbiosis with the bobtail squid

Any discussion of bioluminescence inevitably involves fireflies, probably because they are the sexiest of the bioluminescent menagerie. The firefly luciferase enzyme is indeed used in laboratories to emit light for measurement. The problem for applications like this is that we do not yet understand how fireflies make the fuel, called luciferin, that powers the luciferase. This means any plant would have to fed this very expensive luciferin, and simply wouldn’t be viable.

There are a number of other “luciferases” in nature, each with their own “luciferin”, but it is important to realise that these are for the most part entirely independent evolutions with different chemical structures. They are not cross-compatible.

This project plans to use the luxCDABEG operon from Vibrio fischeri to emit light.

V. fischeri is a bacterium which lives in symbiosis with squid. It lives in a specialised part of the squid’s body called the ‘light organ’ and emits light to camouflage them from predators. This operon of genes encodes both proteins which emit light, the luciferase, but also those involved in producing the luciferin fuel from basic building blocks.

I would absolutely agree that currently this is the best (and probably only) way to make an autonomously bioluminescent plant.


Is this new?

As the team acknowledge, the first plant was engineered for bioluminescence in 1986 – when tobacco was made to express firefly luciferase, prompting this iconic picture. However, as discussed above, this plant had to be fed luciferin to allow it to glow. A self-sufficient luminescent plant is a very different beast.

However, self-sufficient glowing plants have been made before, though to my knowledge only once. This paper from 2010 describes the creation of a tobacco plant expressing the luxCDABE operon from V. fischeri.

There were some hurdles before this achievement. One of the complications of synthetic biology is the differences between bacteria and plants. LuxCDABEG is an ‘operon’ meaning that it is a set of six (alphabetised) genes, which are read off the genome in one go. But plants, like ourselves, don’t have operons. They process each gene as a separate transcript. This would mean a lot of re-engineering to split the operon into six.

Except for one thing, plants contain chloroplasts for photosynthesis. Chloroplasts are the descendants of bacteria that entered a symbiosis with plants long, long ago. They retain the ability to read DNA in operons, and so the authors of this paper exploited that by inserting the operon into the chloroplast genome.

They write that

their glow was clearly seen after about 5–10 min of eye adjustment to darkness.

This sounds perhaps a little dimmer than our bacteria, but a similar order of magnitude. (Unfortunately the darkest room we had access to was a walk-in fridge, so we shivered excitedly as we saw our first glowing bacteria).

Brightness levels are very difficult to communicate. Photographs don't work because you can make anything look bright by increasing exposure time. The best description I can give of our light levels was that a flask of bacteria allowed enough light to read (after adapation), but only just.

All this means that the organisers shouldn’t really claim this will be ‘the world’s first glowing plant’.

However it is likely to be the first glowing plant that you can get your hands on, and that is clearly important. If the public do get their first glowing plants from Kickstarter, it will really prove the democratising effect of this approach to funding.


What is different?

The Kickstarter project plans to replicate the results obtained in tobacco, this time in the small weed Arabidopsis thaliana. This is a sensible choice of plant because it is easy to genetically manipulate, but it is difficult to say whether we can expect more or less brightness. They plan to increase the brightness by ordering DNA with a composition more similar to chloroplast DNA than bacterial DNA (a process called codon optimisation).

This technique can sometimes radically increase expression levels. In this case, because chloroplasts are bacteria, their DNA composition (‘codon usage’) is actually similar to that of V. fischeri. This makes me doubt there will be a major effect, but the only way to know is to try.

They also hope to try a number of promoters to activate the operon in order to find one which maxmises expression.

They have a number of other hypothetical designs in Genome Compiler, including one which would switch the light on only in the dark, and one which would give the plant the smell of fresh rain. One of their designs is an approach I am particularly interested in: it inserts the operon into the plant’s nuclear genome instead of the chloroplast’s. This would require re-engineering the operon to insert ribosomal skipping sequences between the genes of the operon so that the plant can understand that it is six genes and not one long gene. I have no evidence at all that it would work better, and there are arguments it could be worse because there are many chloroplasts per cell, but I think it could have promise.


How do we get brighter light?

My prediction is that this project will ship plants which have a dimly visible luminescence in a pitch-black room. That will be an exciting prospect in itself for me. With the current trajectory of the Kickstarter, the organisers may have funds left over to improve the product. The first ‘stretch-goal’ they have announced is to create a glowing rose. Cool, and good for publicity, but I think what we’ll really want is a brighter plant, of any type.

This is going to involve a better understanding of what the limiting factor for bioluminescence is. Our bacterial bubble lamp made it pretty clear that in a bacterial culture, this was oxygen levels. We put a fish-tank bubbler into the culture, which added oxygen to vastly increase the brightness levels.


In a plant the limiting factor could be the amount of a particular enzyme, or the amount of oxygen, or the amount of long-chain aldehydes needed as a basic fuel, or some other factor. Hopefully if the researchers find out what it is, they may be able to do something to widen this bottleneck and increase light output.


All in all it’s an exciting project and I wish its organisers every success. I hope they find time to fill in their wiki with some more details of the science they plan to do so that the people of Kickstarter know where their money is going.

And I hope that the people of Kickstarter start to ask for some of these details before they fork over their money. That could make for pretty effective science funding platform.

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32 comments

  • Omri · April 29, 2013 at 4:52 am

    Great writeup! I’m Omri (one of this project founders with Antony and Kyle). I’m happy you are asking this questions – both me and Kyle came from academia – both published peer reviewed papers (you can see mine here: http://www.ncbi.nlm.nih.gov/pubmed/?term=drory+o ) and we know the power of peer review in improving and backing experimental results.

    It’s funny moving from academia to this kind of project – where no matter how deep you try to explain what you are doing people will miss quote you and have only partial understanding of what you do.

    This is why we want to make it an open process – post our designs in Genome Compiler, have an open lab notes online, video experiments etc.

    We hope you could join us – this is a community project – and the first one to be so public.

    Best,

    Omri

  • Jammer · April 29, 2013 at 7:24 am

    Great write up of this project. By far the most exciting aspect of the project is the funding method. It is a potentially revolutionary way to get biotech to the people. As you discuss above, the use of luciferase is not a particularly novel idea. But then the vast majority of the public are unaware of this. I do have one question that you didn’t discuss. Who owns the IP on the luciferase gene? And would they not take some issue with these guys making money using the gene?

  • Admin comment by Splasho · April 29, 2013 at 8:25 am

    There is actually a patent application for this method of producing a bioluminescent plant, from the author of the study cited – http://www.google.com/patents/US20100192262

    I don’t know my patent law well enough to know what that means. I don’t think it ought to be patentable because I think the concept of putting the lux operon in plants to make them glow is pretty obvious (we were discussing it in 2010 before this patent was applied for).

  • Jammer · April 29, 2013 at 9:38 am

    Patent law also confuses me. Do you think they can get around this patent by “giving” the plants away as “gifts” for the kickstarter donations to the project?

  • Admin comment by Splasho · April 29, 2013 at 9:47 am

    I would be surprised, but I am not a lawyer.

  • Guillermito · May 3, 2013 at 9:19 pm

    Finally a good analysis of this Kickstarter by someone familiar with the science. Thank you. I reach the same conclusions as you do : they may get some Arabidopsis with low luminescence, which is still cool. People expecting light bulbs plants will be disappointed. Maybe I’m a bit more pessimistic than you, because I’m also concerned by the legal implications. There is a layer of good science here, covered by heavy layers of bullshit / marketing / hidden difficulties and realities.

    Here is the core of the comment I left on their blog, sorry for the copy-paste. I guess a bit of skepticism is always healthy in science :) :

    “One problem you may have overlooked : the methods you are going to use to transform Arabidopsis genome (or chloroplasts if you follow the 2010 paper you cite – because transforming the nuclear genome may not work at all) are all patented by private companies, such as the use of good old Agrobacterium tumefaciens, biolistics, selection markers, use of promoters, etc. So you cannot really release an Open Source work which contains a patented method at its core. A solution is to use open technologies (Agrobacterium alternatives) developed by Cambia in Australia. In fact, I remember now that the whole “plant transformed with luciferase / luciferine” concept was patented several times.

    Also, I don’t think the USDA and FDA will let you freely distribute transgenic seeds by mail, without a long risk assessment study in field trials before. Even for Arabidopsis.

    And comparing potential bioluminescent plants to light bulbs is a flagrant exaggeration, bordering on bullsh*t. In the best of case, getting something close to what already exists in nature (believe me, I’ve seen them all with my own eyes and grew most of them : glow worms, E.Coli with pLux, V. fisheri, dinoflagellates, mushrooms…) what you will get will look like a swarm of fireflies. Still useful for highways for example, especially if you have millions of them.

    I didn’t check your plasmid constructs yet, but I do hope you used a promoter only active at night, such as the ones used in starch degradation. No need to waste all this ATP for nothing during the day. Also, no need to produce light everywhere : concentrate it on one tissue only, or an external layer of cells to avoid re-absorption of photons. Epidermial layer would be nice, but they don’t have chloroplasts. Tinkering with promoters for a good spatio-temporal expression will take a lot of time if you want to make things the right way.

    Anyway. I’m jealous because you’re doing my old secret project I’ve thought about for many years. I planned to do it the pirate way, without telling anybody and without respecting any law, I’m kind of used to that. You take the safe legal route, but you will have problems. Many problems. Scientific and legal. The former can be solved with time and effort. Not the latter.

    I think you may get some bioluminescence on your Arabidopsis on your first shot if you are lucky, but it will be very, very, very low. People are expecting Avatar stuff : they will be disappointed. Don’t even get me started on your rose project. That’s more like a pure marketing trick. You should let the scientist on your team speak and be honest about a timeline and the real goals.

    Anyway, good luck.

    Guillermito, plant molecular biologist from outer space.
    http://www.guillermito2.net

  • Glowing plant gets funds green light | The Yann Ketchanga site · May 7, 2013 at 3:11 pm

    [...] Sanderson, a member of that Cambridge team, has blogged about the new [...]

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  • Angela · May 7, 2013 at 11:54 pm

    About patenting, if the application was done in the States, they won’t be able to sell the product in this country, however if there is not a European patent, they could sell the product in the EU too. However, I think that they would not be succesful, in case they wish to apply for a EU patent or a British patente, as the novelty’s invention is not real (already shown in the States).

    Thanks for the awesome article!

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  • Vitaly Citovsky · May 10, 2013 at 6:44 pm

    good summary of the idea and its pros and cons. i am still unconvinced as the authors suggest biolistic nuclear transformation, which has to include individual codon-optimized genes, will result in silencing of some of them (thus, they will need to transform also silencing suppressors), and likely require redirection of nuclear encoded proteins into chloroplasts (this is where the substrate is made best). so, whereas the project might ultimately succeed, its (currently available) description is too naive… (also there is the matter of IP and that BioGlow company which is already working on commercial glowing transplastomics; please note that i have NO financial, scientific, or any other connection to BioGlow)

  • How many bioluminescent plants does it need to screw in one light bulb? - wiechers.ws · May 10, 2013 at 9:31 pm

    [...] actually plan to do with the funds raised, and whether the science stacks up.” He also has a very nice blog post that explores things further, but I thought I’d chip in with some numbers, not because I [...]

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  • Synthetic biology: plant newsWeeding the Gems · May 20, 2013 at 8:47 am

    [...] Finally (and it’s not really news), just for geeky kicks take a look at this Kickstarter synbio project for glowing plants. They’ve already reached their initial goal, but you can still support the project to the ‘stretch’ goal to get your very own glowing Arabidopsis thaliana, or other less exciting goodies. There’s a very informative write-up about the project and science on Kickstarter on a blog called Splasho. [...]

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    [...] Sanderson, a member of that Cambridge team, has blogged about the new [...]

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