Thursday, December 20, 2018

We’ve added letters to the genetic code – and the results are amazing


This is amazing.  Turns out that the system of life is both simple and crude as one would expect from a proof of concept but is wide open to refinement and optimization.  This is the real future of biology.

Again it is early days and progress will be slow but the foundation is even now tightening up.

This also tells us that my open conjecture in terms of alien lifeforms been engineered to task is not unreasonable at all.  Agricultural man was designed close to the planets own life ways but still a robust jump.  Yet the Alien Greys are so clearly designed for space itself and could have trouble competing on Earth.  We ourselves mostly lack the robustness we would actually need..

We’ve added letters to the genetic code – and the results are amazing

5 December 2018

The first life forms with a six-letter genetic code are already pumping out drugs and other materials that nature has never seen before
By James Mitchell Crow

MAKING a living thing is no mean feat, what with the billions of components that need putting together. Nature manages it with one molecule: deoxyribonucleic acid, better known as DNA. It is the instruction manual for building everything from songbirds to scorpions, seahorses to schoolchildren. Yet Steven Benner is unimpressed. “When you look at DNA, what you see is imperfection,” he says.

He has a point. It may be a guide to making wondrous things, but DNA uses an alphabet of only four letters. What if we could sprinkle in a few extra ones? Do that, and the variety of materials that living cells could manufacture goes through the roof. We might even use that power to meet some of our most pressing needs, not least for new medicines.

Benner and a few others have been chasing the dream of expanding the genetic alphabet for decades. Finally, one of them has succeeded in creating a life form that is not only founded on entirely novel genetic letters, but is also capable of using the instructions to assemble materials that incorporate wholly unnatural building blocks. This is life, but written with a whole new alphabet.

The DNA double helix is a molecular icon. Its twin strands of genetic code, curled like a spiral staircase, has an elegance befitting the recipe of life. The sturdy rails of the staircase are made of the sugar deoxyribose and phosphate molecules. The steps are collections of atoms called bases. There are four types of base in DNA, each with slight chemical differences: adenine, thymine, cytosine and guanine, also known as A, T, C and G. These are the letters of the genetic code.

Things get interesting when sections of the DNA strands unpeel, copies are made, and these are sent to the cell’s manufacturing centre, the ribosome. Here the sequence of letters is read, and used to determine the order in which molecules called amino acids are stitched together. Strings of amino acids then coil and fold into proteins, the biomaterials that make up everything from fingernails to the immune system. This system has driven evolution across the epochs.

“When you look at DNA, what you see is imperfection. We thought we could do better”

Nevertheless, the molecule at its heart doesn’t impress Benner, who established the Foundation for Applied Molecular Evolution, a research outfit in Florida. It isn’t just DNA’s tiny alphabet he finds underwhelming. Take the forces holding the double helix together. These are nothing but hydrogen bonds, a much weaker type of bond than the covalent sort that typically holds molecules together. “It is surprising you would entrust your genetic inheritance to hydrogen bonding,” he says. “DNA looks like such a hopeless design, we thought we could do better: better binding, more letters.”

This was no overnight job. To work properly and be passed down the generations, new bases need to form an exclusive pair and be accepted by the biological machinery that copies DNA. In the natural stuff, patterns of hydrogen bonding ensure that C pairs with G, and A with T – no exceptions. The fidelity of the copying process relies on this. Any extra pair of letters must be equally faithful.

Decades ago, biochemists sketched out novel pairs of bases with similar structures to the existing ones, but that would be joined using different patterns of hydrogen bonding. In the late 1980s, Benner set out to make and test each of these hypothetical pairs. But he found that their atoms tended to scramble around, leading to mispairings.

Floyd Romesberg entered the field around the same time. From the start, his team avoided hydrogen bonding altogether, trying to develop base pairs that stuck together because of their mutual dislike of water. It wasn’t exactly a shortcut. “We spent 15 years,” says Romesberg, who is based at the Scripps Research Institute in California. But after screening thousands of candidates, they found a pair that worked. Another researcher, Ichio Hirao, then at the RIKEN research institute near Tokyo, also made some impressive unnatural bases that worked according to the same principles.

Benner, meanwhile, stuck with his beefed-up hydrogen bonding patterns and found ways to overcome the atomic scrambling. By 2004, he had shown that what he calls his “funny bases” could be incorporated into strands of natural DNA without the whole helix falling apart – and how useful the result could be.

A Californian company called Chiron used Benner’s bases to develop a test that measures the number of viruses in blood. It was handy for detecting when someone’s HIV medicine was failing, among other things. The test involves a DNA strip with two sections, one matching the genes of the virus and one including Benner’s funny bases. The first section binds to virus DNA, and the second acts as a handle researchers could use to fish it out. They just exposed the blood sample to a complimentary sequence of bases – nothing else would stick to the unique bases.

Getting unnatural DNA to work in living cells and be passed on when they replicate was another matter. True, it isn’t difficult to introduce it into a bacterium such as E. coli. Bacteria routinely pass loops of DNA called plasmids to each other, and Romesberg mimicked that trick to smuggle in his six-letter code. But unless they were supplied with spare copies of the extra letters, the bacteria would have no materials with which to make copies of the unnatural DNA.

“It was the first self-replicating life form with a six-letter genetic alphabet”

Romesberg realised that some algae happen to possess a protein channel that sucks up his unnatural bases. Engineering the E. coli so that they also had these channels meant he could spike their food with his bases, whereupon they would automatically take them up and incorporate them into their DNA. By 2014, he had created the first living, replicating organism with a six-letter genetic alphabet.
“Romesberg’s work is fantastic,” says Benner, who has a $5-million programme aiming to introduce his own bases into cells. One headache is that Romesberg’s version, triphosphates, are expensive. Benner is trying a different solution, giving the cells a cheap precursor they can metabolise into the bases. The other problem, back then, was that no researcher had got their unnatural bases doing anything interesting.

The potential, however, was huge. After all, a living cell is a chemical factory. Fed by DNA instructions, it makes proteins with an efficiency and precision human chemists can only marvel at. “Biology can do things no man-made chemistry or technology can do,” says Michael Jewett, co-director of the Center for Synthetic Biology at Northwestern University in Illinois. We already harness life’s synthetic prowess. Re-engineered yeast and bacterial cells pump out insulin for people with diabetes at a rate chemists could never match. But DNA, with its limited alphabet, can only instruct the cell to build with a small selection of bricks.

When chemists look at the mere 20 amino acids nature uses to make proteins, they see 20 shades of beige. These molecules are all composed of carbon and hydrogen atoms with the odd oxygen, nitrogen and sulphur. The rich chemistry across the periodic table is untapped.

helical art
DNA’s double helical structure has become iconic, inspiring art and sculpture
Still, it isn’t difficult to spice things up, adding exotic elements to create unnatural amino acids. For instance, metal-binding amino acids could cling to iron, making them electrically conducting or magnetic. “If you can build little handles into whatever protein you make, that gives you molecule-by-molecule precision. You could think about making better displays, better sensors, better energy-harvesting devices,” says Timothy Lu, a synthetic biologist at Massachusetts Institute of Technology.
There are ambitious, long-term things we could do with those building blocks (see “Jellyfish pseudo-creatures”). But there are two, more immediate, obvious applications, says Jewett.

The first is catalysis. There is a near endless list of products we need to make using chemical reactions, from pigments to fuels. Catalysts turn many reactions from sluggish non-starters to nippy procedures, but finding the right ones is no picnic. We already get genetically engineered bacteria to churn out lots of proteins, then screen them in the hunt for promising new catalysts. But with extra amino acids the potential soars.

Protein rugby tackle

The second is medicines. Traditionally, drugs are made from small molecules. Proteins are larger structures that take out their biological target in a rugby tackle compared with a small molecule’s tap on the wrist. “Proteins are remarkable drugs, but incredibly limited in terms of the properties they have, which is set by the amino acids they are built from,” says Romesberg. Semi-synthetic super proteins could incorporate components that recognise and dismantle their medical target. Equally, they could be engineered to help the protein fight off the immune system, which breaks down many drugs within a few hours, meaning you need multiple doses.

For any of this to become reality, you need a way to tweak the recipe for life so it asks cells to build with unnatural bricks. Which brick to pick is defined by groups of three bases called codons. The four letters of the natural code can be arranged into codons in 64 ways, each of which fits with specific versions of molecules called transfer RNA (tRNA). These shunting engines pick up amino acids and slot them into place (see “Diagram”).

Exotic alphabet
A basic way of monkeying with this set-up emerged in the 1990s. We knew that several different codons instruct the ribosome to add a particular amino acid. For instance, the codons AGC and AGT both code for the amino acid serine. There are also several sequences that translate as “stop”, telling the ribosome to cease adding amino acids. Peter Schultz at Scripps set his sights on one of these stop codons. He developed a way of attaching an unnatural amino acid to the tRNA corresponding to the so-called amber stop codon. With that, he succeeded in doing something no one else had done: getting a bacterium to produce proteins with an unnatural amino acid in the spot he wanted.

Borrowing the stop codon was a feat that should have snagged Schultz a Nobel prize, says Romesberg. Even so, Schultz couldn’t prevent the codon from continuing to act as a stop instruction, he just competed with that role. That meant that sometimes, instead of incorporating a new amino acid, ribosomes would just stop building, yielding a useless stump of a protein.

In 2013, Farren Isaacs at Yale University and George Church at Harvard University overcame that problem. They redesigned the entire genetic code of E. coli, replacing the amber stop codon with an alternative in any DNA sequences they didn’t want to affect. This approach stopped the stumpy protein problem and was a huge enabler for researchers like Jewett. Soon, he and his team had managed to incorporate 40 identical amino acids into a protein. “That’s a pretty big step forward,” says Jewett.

It may even be possible to install several different amino acids using the same sort of approach. Church has published a design for an organism with seven freed up codons.

“Exotic building blocks could make proteins magnetic or conduct electricity”

Romesberg’s work with unnatural bases could push things much further. “We thought, instead of trying to steal or trick nature into giving you an extra codon, let’s just give nature a whole bunch of new codons,” he says. He was in an excellent position to do that. Having increased the genetic code from four to six letters, there were now 216 possible codons.

In late 2017, Romesberg put the first two of those new codons to use. He created a six-letter E. coli that used them to incorporate unnatural amino acids into a protein at the positions he desired. At that stage, the modified protein didn’t do anything special beyond fluoresce. But the glow proved the technology works. “We are continuing to modify the cells, to simultaneously incorporate three or four different unnatural amino acids into a protein at once – things nobody has been able to do before,” says Romesberg. He has also started a company called Synthorx, which is using his technology to make protein therapeutics.

By creating new letters of genetic code in the lab, Romesberg has stripped DNA of a little of its mystique. “One of the things we have shown is there is nothing magic about DNA,” he says. But in another way, his efforts make it seem more enigmatic. Why and how did life pick the four genetic letters it did? Synthetic biology has plenty to say about the future of life, but that is one question it can’t answer.

Jellyfish pseudo-creatures

In the sparkling, turquoise waters around the Great Barrier Reef, a jellyfish-like creature pulses hypnotically, pushing gently against the tide. Suddenly, as if an internal switch has been flicked, the languid creature jolts into life. Thousands of identical partners materialise out of the blue and together they swarm into the distance.

At the University of the Sunshine Coast in Australia, Nina Pollak is engineering synthetic creatures that look like juvenile jellyfish. She has developed designer cells based on heart cells that will be attached to a flower-shaped scaffold. As the cells beat, the petals contract, pushing the pseudo-creature along. The point of these things, which are still at the development stage, is to seek and destroy environmental toxins, such as a pesticide that has been washed into the ocean. The cells contain a strip of genetic code that tells them how to produce a biosensor that detects the toxin and an enzyme that destroys it.

Synthetic organisms have been suggested as useful agents in plenty of other environmental remediation jobs, such as reversing desertification.

Now researchers are developing synthetic amino acids and additional artificial DNA letters that are needed to tell cells how to assemble them into novel proteins (see main story). That would come in handy here. In Pollak’s case, plucking a known enzyme off the shelf should work. But adding synthetic amino acids should be even better, she says. “The enzyme could definitely be enhanced to make it work faster, more efficiently.” In principle, the unnatural DNA makes the organism more containable too. Fail to supply it with those artificial bases, which it can’t make itself, and it can no longer function.

No comments: