Carboxysomes are small compartments inside photosynthetic bacteria where the machinery for capturing carbon dioxide is concentrated. You can see carboxysomes and their characteristic virus-like shape when you look at slices of these bacteria under an electron microscope:
Until recently, no one had looked at carboxysomes under the microscope in cells that were still alive. My labmates Dave and Bruno developed a way to label carboxysomes with fluorescent proteins and track them under a microscope as the cells grow, and their amazing paper in Science details some of the fascinating systems they discovered about how carboxysomes are controlled.
They noticed something very interesting right away: the carboxysomes in live cells are all lined up, evenly spaced, down the central axis of the rod-shaped bacteria. They hypothesized that there must be something holding the carboxysomes in place, preventing them from diffusing through the cytoplasm. All bacteria have a "skeleton," a mesh of proteins that maintains their shape, helps them divide, and can hold chromosomes and other cellular parts in place. When they deleted one of these mesh proteins out of the genome of the photosynthetic bacteria they saw that the cells would become rounder, not able to hold their shape as well, and that the carboxysomes weren't evenly spaced any more (figure B). When they knocked out a different skeleton-associated protein, parA, they saw that it seemed to exert special control over the carboxysomes. Deleting this gene allowed the cells to stay rod-shaped, but the carboxysomes weren't lined up anymore (figure C).
In the mutants without parA and no even carboxysome spacing, sometimes when a cell divided, one of its daughter cells wouldn't get any carboxysomes. Without the machinery to capture carbon dioxide, the cell grew much slower until it was able to get enough protein together to make a new carboxysome. In the video below you can see this happening. The red arrow points to a cell that gets no carboxysomes after division, and the white arrow points at its sister cell that got them all. The empty cell doesn't divide again until it forms carboxysomes (the green dots), while the cell that got the carboxysomes has already divided by that time. This shows why the cell would invest so much energy holding the carboxysomes in place; without even spacing a certain number of cells wouldn't be able to grow at the optimal speed, decreasing the fitness of the whole population.
When they fluorescently tagged parA in wild type cells, they saw something amazing: this "skeleton" protein isn't just a static structure that the carboxysomes cling too, but an oscillating wave, ping-ponging back and forth down the length of the bacteria. As the wave moves through the cell parA makes sure that the carboxysomes are evenly spaced along the whole axis. In other species of bacteria, this skeleton wave can control the even spacing of genetic material along the length of the cell or keeps proteins associated with the tips of rod-shaped bacteria where they belong. You can see the wave traveling through the cell in the second video, where the carboxysomes are labeled in red and the wave protein in green.
With a deeper understanding of the cell biology of the carboxysomes and how they are controlled in the cell, as well as the genetic tools that Bruno and Dave developed for putting the fluorescent proteins into the photosynthetic bacteria, synthetic biologists in our lab and others will be better poised to engineer the carboxysomes for any number of synthetic purposes, to design novel bacterial micro-factories.
The fight over genetically modified foods, whether they're safe, healthy, good for the environment, or just plain "unnatural," has been going on for a long time now. Most people in the scientific community agree that genetic modification in general is a good thing, able to create crops that need less water, less fertilizer, less pesticide, or that contain extra vitamins and nutrients that are otherwise difficult to come by in certain parts of the world. Many would also argue that fighting against such life-saving, often environmentally sustainable modifications is a sign of an ignorant anti-science backwardness. Two recent articles in The Guardian and The Economist show that the issues surrounding the acceptance of genetically modified food technologies are a lot more complicated than a simple rational/irrational or scientific/ignorant divide.
In The Guardian article, plant scientist Eoin Lettice points out that most of the genetically modified (GM) plants brought to market today primarily benefit giant multinational corporations rather than the consumer. Tomatoes designed to last longer during long-distance shipment end up tasteless and mealy, and the most common genetically modified foods are designed to be resistant to the weed killer that Monsanto produces, the chemicals in which may actually contribute to health problems (although the numbers in the one study are worst than shaky and a lot more work needs to be done). Moreover, Monsanto and other GM producing corporations aggressively patent their products, holding back research in plant science by not allowing university researchers to use naturally occurring plant gene regulatory sequences that they have patented, and forcing small farmers around the world out of business. Government delays in approving the use of GM products cause a lot of problems for these corporations, and it is in their best interest to make their products seem natural and good and their opponents seem crazy and stupid. Lettice puts it well when he writes:
Perhaps I'm being presumptuous, but I can't imagine many Irish or European consumers lying awake at night worrying about lost revenues for [the German chemical company] BASF. What Irish consumers are interested in, however, are real and tangible benefits from their foods.
For the most part, real and tangible benefits from current GM technology are not going to be felt by well-fed consumers in Europe and the U.S., but already GM technology has made an impact on the yields and quality of food produced by farmers in developing countries around the world. According to The Economist, 90% of the farmers currently benefiting from GM technology live in poor countries, where soil quality and access to water and fertilizer can make it difficult to grow at the high yields needed to feed the community. The spread of the technology has also made an impact on how companies like Monsanto think:
Attitudes are also changing at Western agribusinesses, some of which used to dismiss poor farmers as mere "seed pirates". As developing countries develop GM crops of their own, these firms are now pursuing public-private partnerships or joint ventures with local firms and otherwise softening their stance. Monsanto, a hard-nosed pioneer of transgenic crops, is donating its drought-resistant technology to a coalition called Water Efficient Maize for Africa, for example.
As plant engineering technology develops further, these issues will only become more important, and scientists around the world need to consider how their work and their support can go to real people, not just corporations.
Animal cells are made up of many smaller membrane-bound compartments called organelles that perform highly specialized functions necessary for life. Incredibly, several of these organelles have been shown to be evolutionarily related to free-living bacteria, captured and incorporated inside a larger cell billions of years ago in a complex mutually beneficial relationship, known as endosymbiosis (a partnership between two species where one of the species is inside the other). The mitochondria that power our cells, generating energy by breaking down sugars are in fact relatives of regular old bacteria, even having retained some bacterial genes that they replicate on their own. In some (very very rare) cases, the bacteria-ness of your own mitochondria can actually be bad for you, activating an aggressive immune response after a serious trauma releases the contents of lots of mitochondria into the bloodstream!
Bacteria themselves are much smaller and much simpler cells, performing many of the same cellular functions without the spatial organization of organelles, all the cell's enzymes and genetic material are instead floating freely in the cell. Some types of bacteria, however, do have compartments that have specialized functions, separating certain enzymatic activities from the rest of the cytoplasm. These compartments are surrounded by a protein shell, not a membrane, so they aren't technically organelles, but they're still pretty amazing.
Many species of photosynthetic bacteria (the precursor to the chloroplast organelle that makes plants photosynthetic) have protein-bound compartments that separate the carbon dioxide capturing machinery from the rest of the cell, called carboxysomes. The enzyme that captures the carbon dioxide and turns its carbon atoms into chemical forms that the cell can use is called RuBisCO and it kind of sucks. Every carbon atom in a photosynthetic cell comes from this enzyme's function, but the reaction happens much much slower than most enzymatic reactions and if there's too much oxygen around it doesn't happen at all. In the carboxysome, RuBisCO is so tightly packed that oxygen can barely fit through the cracks, and the high concentration of the enzyme can help to overcome some of the inefficiency of the reaction. The carboxysome protein shell is made up of interconnecting proteins shaped like hexagons and pentagons that link together to form a complex polygon, kind of like a soccer ball.
This soccer-ball protein geometry is also used by some species of viruses to form a protective shell. Some carboxysomes have a geometry that is more complex than the standard icosahedral viral capsid, indicating that carboxysomes may have not actually originated from the same common ancestor as the virus, but that their similarity is the result of convergent evolution. However, the question of whether carboxysomes are the result of endosymbiosis between bacteria and viruses that have evolved over billions of years is still open. This matryoshka doll concept of evolution and cellular substructure, with animal cells housing bacteria housing viruses is wonderful and fascinating, pointing to a rich diversity of interspecies cooperation in nature.
There's still a lot that we don't know about carboxysomes, and there's a lot of active research going on in my lab about how carboxysomes are formed and controlled inside of photosynthetic cells, with the goal of being able to engineer special protein substructures inside any bacterial cell. Stay tuned for more on that shortly!
We designed a metabolic circuit in bacteria that produces hydrogen (a potentially useful fuel) from natural precursors in the cell. The proteins in our synthetic pathway work to make hydrogen by transferring high-energy electrons from pyruvate, a common metabolite, to protons that are freely floating in the watery cytoplasm. The electrons transfer between the proteins through quantum-mechanical tunneling, which makes hydrogenases and other electron transferring proteins some of the craziest enzymes ever.
This tunneling happens so fast once two electron carrying proteins (of which there are many different types in the cell) hit each other, that it's difficult to make sure that all of the electrons from the original metabolite are getting to hydrogen. While sometimes the analogy between synthetic biology and electronics can be a bit tricky, in this case we really have to "insulate" the "wires" that are transferring electrons by preventing them from connecting to other "wires" and "shorting" the "circuit" (sorry to go overboard with the quotation marks but you get the idea). We tested a bunch of different biological methods to insulate the pathway, and all of them made small but significant improvements in the amount of hydrogen that we could produce. These methods can be used not only to optimize the amounts of hydrogen that we can make biologically, but can be applied to many other synthetic biology circuits that use electron transfer to get things done.
My labmates and I love Lady Gaga. Like, love love love. Enough to make a parody fan video of Bad Romance. It is my pleasure to present to you "Lab Romance", a production of Hydrocalypse Industries. Enjoy!
Some of the responses to my post about synthetically expanding the genetic code have highlighted some of the weaknesses in my argument about the safety of using a different genetic code. Namely, that "life finds a way", that we can't really ever know for sure what will happen when we release a synthetic organism in the wild, or how natural selection will act on them. The science fiction scenarios where engineered organisms escape, break out of the designed restrictions on their growth and take over in new and terrifying ways are compelling, frightening, and instructive for thinking about biosafety and synthetic biology, but it is also important to be, dare I say, realistic.
Muldoon: What about the lysine contingency? We could put that into effect!
Dr. Ellie Sattler: What's that?
John Hammond: It is absolutely out of the question.
Ray Arnold: The lysine contingency - it's intended to prevent the spread of the animals is case they ever got off the island. Dr. Wu inserted a gene that makes a single faulty enzyme in protein metabolism. The animals can't manufacture the amino acid lysine. Unless they're continually supplied with lysine by us, they'll slip into a coma and die.
Dr. Ellie Sattler: How could we cut off the lysine?
Ray Arnold: No real trick to it. Just stop running the program, leaving them unattended.
I argued that organisms engineered with alternate genetic codes, who need an external source of unnatural amino acids in order to survive, would not be able to survive in the wild where these unnatural amino acids do not exist, just like the "lysine contingency" in Jurassic Park. Of course, humans can't make their own lysine either, requiring it in our diet in order to survive (this is why it is an essential amino acid), and thank goodness lysine is everywhere in the environment, in the proteins of the plants and animals that we eat. In the case of unnatural amino acids it is possible to design chemicals that don't exist in nature, and molecules that cannot be made enzymatically. While it may be possible that in many many millions of years a biological pathway could evolve to create such an unnatural amino acid, it is vastly more likely that the escaped synthetic bacteria will have died first, its atoms scavenged by other micro-organisms that can't even read its DNA. Moreover, the mutations introduced are small, incremental changes to protein structures that better allow us to understand how proteins work rather than give the cells any vastly new behavior. In many respects, the products of synthetic biology are almost identical to natural cells. We shouldn't bush off concerns over safety with eye-rolling, but we also shouldn't let unrealistic fear take over either. What do you think?
Almost every living thing shares an identical genetic code, with three nucleic acids in an RNA sequence coding for a single amino acid in the translated protein sequence. While there are 64 three-letter RNA sequences, there are only 20 amino acids and degeneracy in the code allows some amino acids to be coded by multiple codons. Chemists and synthetic biologists in the past few years have been working to expand this genetic code, with unnatural nucleotides that can be incorporated into DNA and RNA sequences and unnatural amino acids that can expand the chemical functionality of proteins. These amino acids can add chemical groups that are not usually present in proteins to create new biochemical reactions, or to create more stable bonds inside the protein for enzymes that are more resistant to harsh environments. Because each three-letter RNA codon already is matched to a specific amino acid, it's very difficult to incorporate these unnatural amino acids into proteins of live cells. Some researchers have mutated one of the "stop" tRNAs in E. coli (there are three codons that tell the ribosome to stop, each corresponding to a different tRNA molecule that will terminate the amino acid chain) so that instead of stopping translation it inserts the unnatural amino acid instead. A cell with each of the "real" stop signals in the genome mutated to one of the other two stop codons would be a perfect "chassis" for using one of these unnatural amino acids.
But what if instead of mutating individual tRNAs, you could make a whole parallel genetic code in a living cell? An awesome paper in this week's Nature makes progress towards this goal, by using directed evolution to design a ribosome that reads four letter codons instead of the normal three. With a four letter code, you could potentially program 256 different amino acids, to create altered proteins or entirely different biological polymers. For a lot more detail on how the researchers went about "reprogramming the code of life" check out the webcast of a presentation by the senior author, Jason Chin.
Expanding the genetic code to include unnatural biological building blocks is an interesting problem for synthetic biology. Most synthetic biologists aim to recombine natural systems in unnatural ways, making new connections between existing or slightly modified proteins to create a new function. Using different chemical building blocks has the potential to create totally new chemistries with fascinating implications for how we understand and use living systems. An editorial in the most recent issue of New Scientist addresses some of the typical concerns that arise with any new synthetic biology technology:
This is a fundamental advance that could lead to new drugs, materials and energy sources. But tampering with life's operating system will inevitably raise safety concerns - and it's true that we have no way of predicting the fallout of this work. Synthetic biologists need to confront openly and honestly public fears that they are "playing God". If such deeply felt concerns go unanswered, the huge potential of this breakthrough could come to naught.
Designing unnatural amino acids can seem, well, unnatural, but most research in synthetic biology is primarily about better understanding how natural living things work. Moreover, realistically, we can't change all that much without wrecking proteins and killing the cell. It is very hard to predict how a protein will fold from just looking at the protein sequence (with today's computer technology it's impossible for more than a handful of amino acids), and when you throw in unnatural amino acids with different chemistry it gets even harder. Unnatural amino acids may become gradually incorporated into research of how proteins fold and how they function chemically.
In many ways, the use of unnatural nucleotides and amino acids in laboratory strains of bacteria has the potential to actually create safer synthetic systems. Unnatural amino acids have to be chemically synthesized and supplied to the cell in the growth medium, thus preventing the cells from being able to grow in the wild if they were to escape. More importantly, wild-type cells would be unable to "read" the synthetic genes in a cell with an expanded genetic code, so any gene transfer between engineered cells and natural cells would make protein "gibberish" (most random protein sequences don't actually fold in the cell, and thus would not lead to any new function). Instead of simply relying on the hand wave-y argument of "lab strains are already probably unfit for survival in the wild", these sorts of "failsafe" systems may soon be feasible to ensure environmental health and safety for all new biological designs.
The future potential of synthetic biology is usually discussed in terms of applications in fields like medicine, food science, and the environment. Genetically engineered life forms are being designed to make medicines cheaply, to target tumor cells, to make more nutritious food, or to make agricultural plants that are easier to grow with less of an environmental impact, to clean up pollution or produce sustainable biofuels. What if synthetic biology systems were instead designed for use in culture or entertainment?
David Benqué, a student in the Design Interactions program at the Royal College of Art in London, explores using hypothetical genetically engineered plants to create an acoustic sound garden. Bugs engineered to chew specially designed nuts in rhythm, whistling termites, lilly pad speakers, and popping seed pods populate this imaginary garden.
This Acoustic Botany is fascinating in terms of synthetic biology, rethinking and expanding the potential scope of genetic design, as well as having implications for how we think about natural ecologies of sound. As Nick writes over at Noise For Airports:
Primarily, this seems like a very interesting way to create an opposing form of acoustic ecology. Most work in acoustic ecology is about reducing human sonic influence in nature, and protecting "natural" soundscapes. Genetic engineering (or at least the implausibly specific and sonic version Benqué describes) offers another way to get into nature's sounds and alter the soundscape.
Synthetic biology aims to replace a great deal of chemical manufacturing, medical technologies, and fuel production. Although it's unlikely that synthetic biology will replace many entertainment technologies, it's interesting to think about how synthetic biology may alter the way we interact with and enjoy our environment. It's fun to design new living systems, maybe it will be fun to use them too.
Notes, thoughts, and news on synthetic biology by 
Until recently, no one had looked at carboxysomes under the microscope in cells that were still alive. My labmates Dave and Bruno developed a way to label carboxysomes with fluorescent proteins and track them under a microscope as the cells grow, and their amazing paper in Science details some of the fascinating systems they discovered about how carboxysomes are controlled. 
They noticed something very interesting right away: the carboxysomes in live cells are all lined up, evenly spaced, down the central axis of the rod-shaped bacteria. They hypothesized that there must be something holding the carboxysomes in place, preventing them from diffusing through the cytoplasm. All bacteria have a "skeleton," a mesh of proteins that maintains their shape, helps them divide, and can hold chromosomes and other cellular parts in place. When they deleted one of these mesh proteins out of the genome of the photosynthetic bacteria they saw that the cells would become rounder, not able to hold their shape as well, and that the carboxysomes weren't evenly spaced any more (figure B). When they knocked out a different skeleton-associated protein, parA, they saw that it seemed to exert special control over the carboxysomes. Deleting this gene allowed the cells to stay rod-shaped, but the carboxysomes weren't lined up anymore (figure C).
