Carbon carbon everywhere...

A while ago I wrote about the Great Oxidation Event, the point way back in the history of the earth where a lot of little blobby organisms suddenly discovered the trick of using sunlight as energy, and in the process producing a reaction that liberated oxygen (photosynthesis). This (as I discussed in the previous post) had a major impact on all the rest of the life on earth, but it also rather majorly effected the photosynthesising organisms themselves, not so much because of the increase in oxygen, but because of the semi-simultaneous decrease in carbon dioxide.

When photosynthetic organisms first developed, there was a lot more carbon dioxide in the environment for them to use (with the world so new and all...) and therefore they weren't particularly bothered about getting hold of it. However when the carbon dioxide levels dropped (along with a potential rise in temperature) they were suddenly in very real danger of suffocating. These were marine organisms, and there just isn't that much carbon dioxide in seawater. There's plenty of carbon floating around, certainly, but it's all in bicarbonate form (HCO3- rather than CO2) and Rubisco, the main enzyme involved in photosynthesis, doesn't know how to use bicarbonate, it relies exclusively on carbon dioxide.

Our lecturer called it the 'Ancient Mariner paradox'; the ocean is full of carbon, but the photosynthesis machinery just couldn't use it:

"Water, water, everywhere,

And all the boards did shrink;

Water, water, everywhere,

Nor any drop to drink."

This left the little suffocating blobs with three options. They could stay remain tiny (as the picoplankton did) to minimise diffusion differences and therefore still survive dispite the low carbon dioxide levels. Or they could try to change the way Rubisco worked, but Rubisco has a rather compromised active site as it is, having to both distinguish between carbon dioxide and oxygen and trying to keep carbon dioxide processing levels high. Rubisco is often criticised as being an 'inefficient' enzyme, and compared to other enzymes it is, but with carbon dioxide levels at the level they are in the sea it's only ever working at half of its maximum speed. Carbon dioxide is the clear limiting factor.

So instead, these photosynthetic organisms started to develop ways to get carbon dioxide into the cell and concentrating it around the Rubisco. The main factor in this was the enzyme carbonic anhydrase, which converts bicarbonates back into carbon. However doing that inside the cell just leads to the carbon dioxide diffusing right back out again and therefore today almost all photosynthetic bacteria (and chloroplasts inside plants) contain a special internal compartment, a protein coat surrounding the Rubisco, and all the carefully hoarded carbon dioxide:

Figure above shows TEM of bacteria with carboxysomes pointed out by arrows. The scale bar on the bottom right is 100nm

Photosynthesising bacteria (apart from the picoplankton) contain a compartment called a carboxysome, which consists of a protein coat which contains carbonic anhydrase enzyme and Rubisco, allowing carbon dioxide to be produced right where it's most needed. The addition of a number of bicarbonate transporters on the outside of the cell allows bicarbonate to be brought into the cell, and the whole assembly is known as a Carbon Concentrating Mechanism, or CCM.

When these photosynthesising proto-bacteria were then picked up by free-moving proto-algae to become chloroplasts, they kept their CCMs. The CCM of eukaryotic chloroplasts is called a pyraniod, and can be seen in the picture below (from Dartmouth College) as the dark black blob in the upper left hand corner. The white things that it's surrounded by are starch grains. The big fuzzy blob below it is the cell nucleus, and the little grey membrane-filled circles are the mitochondria. The long black threads are either thylakoid membranes (inside the chloroplast) or endoplasmic reticulum:

The first algae would have been marine as well, and would have needed the CCMs in their chloroplasts in order to produce energy. Sea water tends to be alkaline, which means that the biocarbonate: carbon dioxide ration is insanely large. Gasses don't diffuse very well in water either, carbon dioxide takes about about 10 000 times longer to get anywhere in liquid compared to air.

In fact the best thing to do to get as much free carbon dioxide as possible is to leave the water altogether, and head out onto the land. But that is different story.

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Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, & Yeates TO (2008). Atomic-level models of the bacterial carboxysome shell. Science (New York, N.Y.), 319 (5866), 1083-6 PMID: 18292340

Metabolomics

'Omics' words tend to get a large amount of bad press in biology. Starting fairly sensibly with genomics, the group expanded to include such things as proteomics, metabolomics, transcriptomics and then when a bit crazy, with seemingly every branch of biology (and possibly even a couple of physicists) wanting to find an 'omics' to work on. The 'Tree of Life' blog even started giving out awards to some of the more hilarious ones.

Omics words are like the cool silent kids in black leather jackets with a hint of drug-taking about them. One of them is fine, a couple of them can be fun but if you get too many it just starts getting messy and looks a bit gratuitous. And eventually people realise there's nothing particularly amazing about them and they become Public Enemy Number One. Which is a pity as many of them are actually quite sensible and can be very useful.

As far as I've been lead to believe 'ome' means 'complete set of '. The genome is the set of all the genes in a cell, proteome the set of all proteins, transcriptome the set of all mRNA transcripts made from the DNA and the metabolome is the set of all metabolic reactions taking place in the cell. 'Omics' is the study of 'omes'.

On the face of it, metabolomics looks to be a mindnumbingly insane task. To study and document every metabolic reaction happening in a cell, to create a model of it, and then use that model to predict how levels of substances change in response to changing conditions seems almost impossible. Just to give some idea of the task, here's a quick diagram of a couple of metabolic pathways involving manipulation of carbon chains:

Diagram taken from the SYSFYS project carried out by the University of Helinski Computer Department. This picture is one of two reasons I am currently studying biochemistry.

Each little dot on the diagram above represents a metabolite, and that diagram doesn't include enzymes, or the things that affect enzymes, or any method of regulation. It doesn't include quantitative analysis of the flux through every pathway, and how different concentrations of metabolites or regulators affect that flux. All of that information is tied up in metabolomics.

One of the first things that's noticeable about that diagram (other than that it looks like the London Tube Map as designed by Tim Burton) is that all the branches appear to be interconnected, everything is joined together. They become a lot more interconnected when you start considering regulation of each step, as many of the metabolic enzymes are regulated by similar compounds (ATP, for example). And what that means is that a change in the levels of one metabolite can have an unprecedented effect on the levels of another. More importantly, anything that accidentally gets missed out of the diagram could cause the model to work incorrectly. To put it in (slightly) more mathematical terms: there are a lot of parameters floating around.

How do you even start studying something like that?

Analysis can be split into two broad categories, open and closed. Open analysis involves taking a sample, and looking for metabolites. It's primarily used to find novel entities, and is rather open ended, in that you start without much of an idea of what you're going to find. 'Looking for metabolites' is done by pretty much any method used to detect proteins; mostly NMR spectroscopy, Liquid and gas chromatography, various Mass Specs and chromatography methods which would take up a whole blog post on their own (which I can write, if anyone's interested, it will be good revision).

Closed analysis focuses on a specific molecule (or molecules) and tries to find out as much as possible about them; what they interact with, what interaction rates are, how it's reactions are controlled, etc. This can be a lot more sensitive than open analysis, and you start with a clear idea of what you're searching for. Apparently it's better for producing papers as well.

By looking for different proteins, and then examining them in detail, a picture can be gradually built up of the metabolic pathways and their interactions. While I'm sure this has many uses in humans (for medical purposes) one of the applications I've been most exposed to is (surprise, surprise) in bacteria, where an understanding of existing metabolic pathways can be used to enhance synthetic ones. By playing around with the enzymes and fluxes of pathways involved in (say) a certain antibiotic precursor, you can encourage bacteria to be far more productive in antibiotic synthesis.

Like all things, metabolomics is at it's best when combined with other methods to give a fuller picture. The information gained from both metabolomics and transcriptomics was used in the reference below to find a key transcriptional compound, Stearyl-CoA desaturase, involved in fatty liver production. Fatty liver is formed from lipid accumulation in the liver, caused by orotic acid supplementation in rats, and excessive drinking in humans. The metabolic diagram below shows the effects of the orotic acid addition (green denotes an increase in a substance, and red a decrease) which for anyone who is not instantly able to pick out glycerol substrates (like me) simply shows just how much work is involved in metabolomics, and how complicated it can get.Despite my fascination with metabolomics and the pretty diagrams they produce, I don't think it's an area I would really go into. Nevertheless it's produced some very fascinating results, with some very worthwhile applications for many different scientific disciplines.

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Griffin, J. (2004). An integrated reverse functional genomic and metabolic approach to understanding orotic acid-induced fatty liver Physiological Genomics, 17 (2), 140-149 DOI: 10.1152/physiolgenomics.00158.2003

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Multicellular bacteria

Part of my NatSci course at the moment involves group supervisions, which are made up of around ten people; a mix of students and faculty (all from the Biochemistry department). About halfway through last term we had a supervision about nuclei, and one of the supervisors raised the question, "Is it possible to be multicellular without a nucleus?" (by nucleus he meant chromosomes wrapped up in a membrane, rather than the bacterial arrangement of coiled up DNA loosly attached to the outer cell membrane). His opinion, and the overall consensus that the group seemed to come too, was no, they didn't. I managed to get a few words in about bacterial hunting packs, and sporulation and things, but they weren't really convincing enough. Also I am still just a little Lab-Ratting undergrad obsessed with bacteria, the group knows this and the general opinion seems to be that I see bacteria everywhere now. Even in multicellular form :p

Which was why I was very glad to come across a paper last week that reviewed in great detail a bacteria that is multicellular beyond all reasonable doubt. They do exist, and I feel very rightous about the whole thing, even if I'm not quite brave enough to bring it back up in supervisions.

First, a brief step back to consider just what makes something multicellular. After all, just having lots of cells in close proximity is not enough, otherwise a large colony of Staph aureus, or bits of swept up dried insect would count as multicellular. True multicellularity requires the following:

• Cell-cell adhesion: the cells must be stuck together in a fairly permanent manner
• Intercellular communication: the cells must be able to signal to each other
• Cell differentiation: probably the more important point, the cells must be doing different jobs, and must depend on the surrounding cells to survive.

Can bacteria do all that? Not very many of them can, true, or there would be large multicellular bacterial 'animals' roaming the plains. But there are a number of photosynthetic bacteria are able to form truly multicellular structures, albeit rather small ones:

Those long chains are technically all one organism, a photosynthesising cyanobacteria. The outer cell wall surrounds the whole organism in one continual envelope, and fulfills the first requirement for multicellularity. The arrows point towards larger cells which fulfill the third, these cells are different from the ones surrounding them, they have differentiated to form specialised cells whose only job is to uptake nitrogen and 'fix' it into a usable form.

The reason they've done this is simple, the enzyme required to fix nitrogen (i.e turn it from a useless inorganic form into a usable organic form) does not work in the presence of oxygen, which unfortunately is needed for respiration. That's why most animals and plants can't fix nitrogen and instead rely on food sources, or surrounding soil bacteria. Bacteria respond to this problem either by becoming totally anaerobic (not using any oxygen at all), or differentiating.

(There is a third strategy, which is to become a nitrogen fixing bacteria by night, and an aerobically respiring bacteria by day, but this requires huge amounts of energy as it means that the cell has to do a complete enzyme turnover every twelve hours)

The differentiated cell is called a heterocyst. It has a thicker cell wall to stop oxygen diffusing into the cell, and all cellular processes that might produce oxygen have been removed. Once the cell has turned into a heterocyst it cannot change back again, and is completely dependant on the cells surrounding it for the products of respiration (which it cannot carry out by itself) likewise, the surrounding cells are dependant on the heterocyst for the provision of nitrogen.

In order for the bacteria to survive, both cells are therefore vital. Furthermore the patterning of these cells are vital, having three heterocysts in a row would mean the one in the middle would be deprived of energy and could die. Each heterocyst must be surrounded by normal respiring cells, and they must also be at regular intervals, to provide nitrogen for all the cells in the organism.

This is where the cell signalling comes in. Heterocysts are created when the cells are being starved for nitrogen. Low levels of nitrogen lead to the activation of a protein called NctA, which activates another protein called hetR. These two proteins both lead to more production of each other in a positive feedback loop, until the levels of both are high enough to turn on the genes that will turn the cell into a heterocyst. It also turns on two other important genes; PatA and PatS.

PatS suppresses heterocyst formation, and this diffuses out into the surrounding cells, preventing them from differentiating. The function of PatA is a little uncertain, but it is thought to stop PatS from having an effect in the heterocyst cell itself. This means that the heterocyst will be surrounded by non-differentiated cells, which can supply it with all the energy it needs, and is shown schematically below:

As well as heterocysts, individual cells can also differentiate into other structures, such as spore like cells, which in times of nutritional stress will break up and lie dormant, turning back into fully functioning cells (and replicating to produce a fully functioning organism) when conditions improve. Several cyanobacteria can also form little lines of very small cells, called hormogonia, which have a variety of interesting functions. They show gliding motility (using either pili or slime) and can produce internal gas vesicles, which makes them bob up to the surface in water. Hormogonia are also the first infection units in symbiosis. When a cyanobacteria wants to form a symbiotic relationship with (say) a plant, it sends out these little hormogonia cells to invade the plant. Like the spore-cells, these can then turn back into normal, undifferentiated cells.

I do think it's a pity that there isn't a course here purely for studying bacteria. On the other hand, it's probably better for me as a scientist to have a slightly greater range of knowledge beyond all things prokaryotic. Especially for the upcoming exams!

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Flores, E., & Herrero, A. (2009). Compartmentalized function through cell differentiation in filamentous cyanobacteria Nature Reviews Microbiology, 8 (1), 39-50 DOI: 10.1038/nrmicro2242

Pictures of my microbes

I'm usually very reluctant to put my own work on this blog, as none of it has yet been published. Depite the CC logo at the bottom of the page I'm still very much aware that anything you put on the internet can potentially be taken away and used for nefarious purposes, without acknowledgement. Also I really don't want to 'out' any of my research.

But this is so amazing I had to share it. It's from the control of a failed experiment anyway, so shouldn't be giving too much away. It's taken with a light microscope, and shows a species of Streptomyces bacteria (complete with contamination):

I feel very proud of that picture, and not only because it took ages fiddling around with a microscope and two broken slides (don't ask!) to produce. The big blob in the middle is the Streptomyces, but it's not one Streptomyces bacteria it's a whole network of integrated hyphae; long branching filamentous cells. This can be seen particularly well in the largest blob in the middle, which has a filamentous 'tail' like structure coming out of it, these are the mycelium branching out and breaking away. Some of them will branch off completely as single cells, and differentiate to form spores.

If you look up at the top right hand corner of the picture, you can just about make out some little dark dots. These are E. coli! My sample is clearly contaminated, those little dots were actually wriggling around under the microscope which made it look slightly freaky. Although the contrast in the picture doesn't show it, the little wriggling E. coli are pretty much everywhere, surrounding the larger Streptomyces structures.

My PI was shaking her head and going "Oh dear, it's all contaminated" but I was just staring into the microscope, fascinated at the amazing world presented inside it. It was like that bit in 'The Borrowers' when The Boy peeks under the floorboards and sees a world full of little people, a whole universe of life which he never knew existed. I went a bit mad taking pictures:

The picture above is a closeup of the hyphae, at a higher magnification. You can make out individual threads, which are formed by long thin cells growing forward in a line. This picture shows the meeting point of three different Streptomyces colonies and an area which is miraculously free from contamination.

In a way, I think I preferred seeing the contamination, despite the fact that I now have to grow the things all over again. It was a reminder that the bacterial world isn't just a collection of similar shaped blobs floating around together. Seeing this little snapshot of the Streptomyces in their huge hyphae fortresses surrounded by little scurrying E. coli reminded me that the bacterial world is as diverse in size and shape as the animal one, just on a far smaller scale. In fact, biochemically, it's more diverse than the animal world and just as dangerous.

Anyway, now I have to stop gushing and go do some actual work :)

Bacteria in Cancer Research

One of the most important things a researcher has to do is justify their existence; explain why they should continue to be paid for the work they're doing. When working with bacteria finding a reason isn't too difficult (although getting it accepted can be another matter). Most researchers can draft something up about medical superbugs, or industrial chemical production and then get back to ferreting out just how these amazing organisms function, in their little cellular world.

However sometimes research can be justified with more than just a passing nod to the realms of General Usefulness. Ananda Chakrabarty, possibly best known for patenting a bacteria capable of metabolising oil, and therefore eating up oil spills has been producing papers for about ten years concerning bacterial chemicals that have the potential to induce apoptosis (cell death). Most interestingly, they seem to bind preferentially to certain cells, in particular cancerous cells.

Azurin was first discovered as the toxin that attacks cellular macrophages. It's produced by the bacteria Pseudomonas aeruginosa the 8821M strain of which was found to produce a high concentration of Azurin. When applied to both normal and cancerous cells (taken from a breast cell carcinoma) the Azurin preferentially entered the cancerous cells, as shown below:



The picture on the right shows the carcinoma cells while normal epithelial cells are on the left. Cells are stained blue, which Azurin is stained green. Both cells are shown twenty four hours after the Azurin treatment. The cancerous cells have taken up the Azurin and are starting to be degraded by it.

The exact mechanism for Azurin-mediated cell death is not yet fully certain, but it does interact with p53, a cell cycle control protein which can lead to cell death in normal cells if overactivated. The graph below shows cytoxicity (cell killing) levels in cells containing p53 (B) and cells that did not (C):


In both cases the wild type Azurin (in contrast to the mutated Azurin, which is non-functional) leads to some cytoxicity, but when p53 is present the effects are far greater, suggesting a role for the p53 protein, which is usually upregulated in cancer cells.

Further research managed to isolate the active component of Azurin; the section of the protein that was actually binding to p53 and causing the cancer cells to die. By simply chopping bits off the protein and seeing which parts were essential for it's activity, they managed to isolate a region between amino acids 50-77 and subsequently called it p21 (p usually stands for 'protein' in these circumstances, because bacteriologists are not always very imaginative about names). p21 is currently undergoing stage I clinical trials for cancer treatment; first stage of testing in human subjects.

Azurin isn't just useful as a potential cancer treatment however, it also has several other potentially quite amazing properties. Azurin is able to bind to the surface protein MSP1 of the malarial parasite Plasmodium falciparum and significantly reduces parasitemia (the number of parasites found in the blood). Azurin also forms an attachment with CD4 receptors of HIV, the sites of attachment of the T4 cells, and leads to suppressed HIV-1 growth at early stages in the infection.

All of this is very exciting, as it shows that despite the drop-off in antibiotic discovery, molecules produced by bacteria still have plenty of applications that are waiting to be discovered. As to why the bacteria might have evolved to kill cancer cells and malarial parasites as yet there's no idea! Probably the best explanation at the moment is that like antibiotics they were originally intended for something completely different, yet they have properties which allow them to be more useful too us than they can ever have imagined.

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Yamada, T. (2002). Bacterial redox protein azurin, tumor suppressor protein p53, and regression of cancer Proceedings of the National Academy of Sciences, 99 (22), 14098-14103 DOI: 10.1073/pnas.222539699

Punj V, Bhattacharyya S, Saint-Dic D, Vasu C, Cunningham EA, Graves J, Yamada T, Constantinou AI, Christov K, White B, Li G, Majumdar D, Chakrabarty AM, & Das Gupta TK (2004). Bacterial cupredoxin azurin as an inducer of apoptosis and regression in human breast cancer. Oncogene, 23 (13), 2367-78 PMID: 14981543

Chaudhari A, Fialho AM, Ratner D, Gupta P, Hong CS, Kahali S, Yamada T, Haldar K, Murphy S, Cho W, Chauhan VS, Das Gupta TK, & Chakrabarty AM (2006). Azurin, Plasmodium falciparum malaria and HIV/AIDS: inhibition of parasitic and viral growth by Azurin. Cell cycle (Georgetown, Tex.), 5 (15), 1642-8 PMID: 16861897

MolBio Pick of the Week!: Tumour cell ecosystems, electrical crayfish and fluorescing corals

This week, I'm hosting the MolBio Pick Of the Week, usually hosted on the MolBio Research Highlights Blog. The picks of the week are taken from researchblogging.org, which contains a number of great science blog posts from all areas, however this post only chooses topics aggregated under 'biology'

1) Tumour cells are cells in the body that have escaped the control system of the surrounded cells and are therefore about to diversify and mutate to a far greater extent than the cells surrounding them. Iayork at Mystery Rays From Outer Space discusses the ecosystem within tumours that is created by this lack of control:

"A tumor, by the time we can detect it, is a collection of many cells, at least billions of them, and those cells are not all the same... Even cells that are unambiguously cancerous are very different within a tumor."

The appreciation of different cell types within a tumour creates new considerations for treatment. Rather than targeting the 'average' cell within a tumour, treatments can be geared towards the most dangerous cells, the ones most likely to lead to metastasis or spreading of the tumour.

2) Different animals use different systems to detect their surroundings. Recent research by Patullo and Macmillan into explores the idea that Crayfish use electrical signals to interact with their environment, making them one of the smallest fish to use electrical impulses as signals. So far, research has shown that Crayfish can respond to biologically relevant electrical signals (such as those produced by tadpoles, which they prey on) although as yet there is no neuronal data to support this. Marmorkrebs blog discusses this in detail.

3) Coral reefs are some of the largest and most beautiful symbiotic structures on earth. Lucas Brouwers explains that even those corals without much colour can still look beautiful: by producing fluorescence:

"When some of these corals are exposed to light of the right wavelength, they return the favor by fluorescing with amazing colours. The diversity of colours displayed by these fluorescent corals is remarkable, ranging from azure blue to a deep crimson red."

A recent study by Field and Matz looked at the evolution of these different fluorescent proteins, and created some amazing phylogenic trees drawn with fluorescing bacteria on Petri dishes.

That's it from me this week!

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Some of the articles discussed in this week's selected posts:

Patullo, B., & Macmillan, D. (2010). Making sense of electrical sense in crayfish Journal of Experimental Biology, 213 (4), 651-657 DOI: 10.1242/jeb.039073

Park SY, Gönen M, Kim HJ, Michor F, & Polyak K (2010). Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. The Journal of clinical investigation, 120 (2), 636-44 PMID: 20101094

Field, S., & Matz, M. (2009). Retracing Evolution of Red Fluorescence in GFP-Like Proteins from Faviina Corals Molecular Biology and Evolution, 27 (2), 225-233 DOI: 10.1093/molbev/msp230

Dancing through life

I'm heading off for a weekend away as soon as my other half wakes up, so no time for a proper paper analysis today, just a quick video of some algae dancing:



The organisms shown above are microalgae called Volvox carteri. The large circle is a surrounding membrane which holds within it normal volvox cells (the little white spots) and larger germ line cells (the large white spots) which later hatch to form new Volvox. The reason the three cells above look like they're dancing is because they move by beating little hair like structures called cilia all in time, causing them to move or spin. The three algae shown above have manage to get their cilia moving together at the membrane surface, and are momentarily stuck together because of it.

Here's another video of them dancing on a surface:



Move videos, along with some of a swimming Chlamydomonas, can be found at the Goldstein Labs Youtube channel.

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Drescher K, Leptos KC, Tuval I, Ishikawa T, Pedley TJ, & Goldstein RE (2009). Dancing volvox: hydrodynamic bound states of swimming algae. Physical review letters, 102 (16) PMID: 19518757

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Chameleon plants!

This is a picture of a small cyanobacteria under red light:

And this is a picture of exactly the same organism under blue-green light:

Some cyanobacteria (both freshwater, marine and soil varieties) have the ability to change their colour depending out external conditions. The reason they do this is because they photosynthesise and therefore require light for energy. The light is harvested by the bacteria using special protein complexes called phycobilisomes which contain (among other things) two proteins capable of absorbing energy from light: Phycocyanin (PC) and Phycoerythrin (PE).

These two proteins both absorb light at different wavelengths, and the light wavelengths that they don't absorb get reflected away from the bacteria and (if you're standing by) into your eyes where after complex eye/brain interactions, you perceive them as colour. This is why plants look green, because chlorophyll in the leaves absorbs all the red and blue light. The two light absorbing complexes in the phycobilisome both absorb at different wavelengths as shown in the absorbence spectrum below:
The colour bar below shows what wavelengths of light are being absorbed by the PE and the PC. PE absorbs green light and therefore looks red, while PC absorbs red light and therefore looks green.

One of the main systems involved in controlling this colour change is called the Rca system (stands for Regulator of Complementary Chromatic Adaptation). This consists of three main proteins, imaginatively called RcaE, RcaF and RcaC (other letters were found but have either not been properly characterised, or turned out to be less important). Unsurprisingly, given that this is a bacterial system, it's mostly a modified two-component response. RcaF is the sensor, with a chromophore binding domain that holds a light-sensor, and a terminal kinase domain that passes the signal on the the receivers.

RcaF and C are both response regulators, although it's proposed that RcaF is an intermediate responder, which passes the message on to RcaC. RcaC contains a DNA binding domain, which allows it to activate the genes required to turn on genes for PC production (absorbing red light and turning the cells green). As usual with two-component systems, the signal is passed on by phosphorylation.

Under green light everything gets dephosphorylated and the PC production is turned off. This dephosphorylation causes RcaC to bind to the promoter for the genes that produce PE (absorbing green light and turning the cells red). Green light also activates another system called the Cgi system (which stands for Control of Green light Induction). This turns on PE production, although it hasn't been properly characterised as yet, so the actual biochemical mechanism for this is unknown.

What the paper doesn't say, and what I really want to know, is whether anyone's tried to make tartan patterned bacterial populations with this...

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Kehoe, D., & Gutu, A. (2006). RESPONDING TO COLOR: The Regulation of Complementary Chromatic Adaptation Annual Review of Plant Biology, 57 (1), 127-150 DOI: 10.1146/annurev.arplant.57.032905.105215

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