Researchers at The Scripps Research Institute (TSRI) claim to have created the first stable semisynthetic organism with extra bases added to its genetic code. The single-celled organism is also able to continually replicate the synthetic base pair as it divides, which could mean that future synthetic organisms may be able to carry extra genetic information in their DNA sequences indefinitely.
The cells of all organisms contain genetic information in their DNA as a two-base-pair sequence made up of four molecules – A, T, C, G (Adenine, Cytosine, Thymine, and Guanine). Each of these is known as a nucleotide (consisting of a a nitrogenous base, a phosphate molecule, and a sugar molecule) and are specifically and exclusively paired, so that only A is coupled to T and C is coupled with G. These nucleotides are connected in a chain by the covalent (electron-coupled) bonds between the sugar of one nucleotide and the phosphate of the next, which creates an alternating sugar-phosphate "backbone."
The team from TSRI have added two synthetic bases that they call "X" and "Y" into the genetic code of a E.coli carrier organism – a single-cell bacteria – and then chemically tweaked it to live, replicate, and survive with the extra DNA molecules intact.
The paper is available via PNAS:
Yorke Zhang, et al.,A semisynthetic organism engineered for the stable expansion of the genetic alphabet (DOI: 10.1073/pnas.1616443114)
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New Natural Selection: How Scientists Are Altering DNA to Genetically Engineer New Forms of Life
Before human beings wrote books or did math or composed music, we made leather. There is evidence hunter-gatherers were wearing clothes crafted from animal skins hundreds of thousands of years ago, while in 2010 archaeologists digging in Armenia found what they believed to be the world's oldest leather shoe, dating back to 3,500 B.C. (It was about a women's size 7.) For a species sadly bereft of protective fur, being able to turn the skin of cows or sheep or pigs into clothing with the help of curing and tanning would have been a lifesaving advance, just like other vital discoveries Homo sapiens made over the course of history: the development of grain crops like wheat, the domestication of food animals like chickens, even the all-important art of fermentation. In each case, human beings took something raw from the natural world—a plant, an animal, a microbe—and with the ingenuity that has enabled us to dominate this planet, turned it into a product.
[...] Modern Meadow's microbes can produce collagen much faster than it would take to raise a cow or sheep from birth, and the company can work with brands to design entirely new materials from the cell level up. "It's biology meets engineering," says Andras Forgacs, the co-founder and CEO of Modern Meadow. "We diverge from what nature does, and we can design it and engineer it to be anything we want."\
That is the promise of synthetic biology, a technology that is poised to change how we feed ourselves, clothe ourselves, fuel ourselves—and possibly even change our very selves. While scientists have for decades been able to practice basic genetic engineering—knocking out a gene or moving one between species—and more recently have learned to rapidly read and sequence genes, now researchers can edit genomes and even write entirely original DNA. That gives scientists incredible control over the fundamental code that drives all life on Earth, from the most basic bacterium to, well, us. "Genetic engineering was like replacing a red light bulb with a green light bulb," says James Collins, a biological engineer at the Massachusetts Institute of Technology and one of synthetic biology's early pioneers. "Synthetic biology is introducing novel circuitry that can control how the bulbs turn off and on."
The article discusses a number of topics, including microbe-grown collagen for leather, Genome Project-write, synthetic cells, a company using yeast to make perfumes and other products, and the falling (but still high) cost of DNA synthesis.
Related: Project to Synthesise Genes Mooted
Scientists Engineer First Semisynthetic Organism With Three-base-pair DNA
Scientists Create Independent Synthetic Cell With Smallest Known Genome
In 2014, scientists engineered Escherichia coli to incorporate new bases they called 'X' and 'Y' in addition to adenine-thymine (A-T) and guanine-cytosine (G-C). Now it has been demonstrated that these synthetic base pairs can be transcribed into RNA and used to produce a protein containing "unnatural" amino acids.
The addition of the new bases could increase the amount of amino acids from 20 to a possible total of 172.
A semi-synthetic organism that stores and retrieves increased genetic information (DOI: 10.1038/nature24659) (DX)
Since at least the last common ancestor of all life on Earth, genetic information has been stored in a four-letter alphabet that is propagated and retrieved by the formation of two base pairs. The central goal of synthetic biology is to create new life forms and functions, and the most general route to this goal is the creation of semi-synthetic organisms whose DNA harbours two additional letters that form a third, unnatural base pair. Previous efforts to generate such semi-synthetic organisms culminated in the creation of a strain of Escherichia coli that, by virtue of a nucleoside triphosphate transporter from Phaeodactylum tricornutum, imports the requisite unnatural triphosphates from its medium and then uses them to replicate a plasmid containing the unnatural base pair dNaM–dTPT3. Although the semi-synthetic organism stores increased information when compared to natural organisms, retrieval of the information requires in vivo transcription of the unnatural base pair into mRNA and tRNA, aminoacylation of the tRNA with a non-canonical amino acid, and efficient participation of the unnatural base pair in decoding at the ribosome. Here we report the in vivo transcription of DNA containing dNaM and dTPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and their efficient decoding at the ribosome to direct the site-specific incorporation of natural or non-canonical amino acids into superfolder green fluorescent protein. The results demonstrate that interactions other than hydrogen bonding can contribute to every step of information storage and retrieval. The resulting semi-synthetic organism both encodes and retrieves increased information and should serve as a platform for the creation of new life forms and functions.
Previously: Scientists Engineer First Semisynthetic Organism With Three-base-pair DNA
Related: How Scientists Are Altering DNA to Genetically Engineer New Forms of Life
NASA-Funded Research Creates DNA-like Molecule to Aid Search for Alien Life
In a research breakthrough funded by NASA, scientists have synthesized a molecular system that, like DNA, can store and transmit information. This unprecedented feat suggests there could be an alternative to DNA-based life, as we know it on Earth – a genetic system for life that may be possible on other worlds.
This new molecular system, which is not a new life form, suggests scientists looking for life beyond Earth may need to rethink what they are looking for. The research appears in Thursday's edition of Science Magazine.
[...] The synthetic DNA includes the four nucleotides present in Earth life – adenine, cytosine, guanine, and thymine – but also four others that mimic the structures of the informational ingredients in regular DNA. The result is a double-helix structure that can store and transfer information.
[Steven] Benner's team, which collaborated with laboratories at the University of Texas in Austin, Indiana University Medical School in Indianapolis, and DNA Software in Ann Arbor, Michigan, dubbed their creation "hachimoji" DNA (from the Japanese "hachi," meaning "eight," and "moji," meaning "letter"). Hachimoji DNA meets all the structural requirements that allow our DNA to store, transmit and evolve information in living systems.
Also at NYT, Discover Magazine, and ScienceAlert.
Hachimoji DNA and RNA: A genetic system with eight building blocks (DOI: 10.1126/science.aat0971) (DX)
Related: Scientists Add Letters X and Y to DNA Alphabet
Scientists Engineer First Semisynthetic Organism With Three-base-pair DNA
How Scientists Are Altering DNA to Genetically Engineer New Forms of Life
Synthetic X and Y Bases Direct the Production of a Protein With "Unnatural" Amino Acids
(Score: 4, Insightful) by ikanreed on Thursday January 26 2017, @02:57PM
Are there RNA molecules that match up to these nucleotides? If not, it's just random chemical garbage injected into DNA, right?
If the polymererase hits an X or a Y during transcription, what happens?
(Score: 1, Funny) by Anonymous Coward on Thursday January 26 2017, @03:52PM
lp0 on fire?
(Score: 0) by Anonymous Coward on Thursday January 26 2017, @04:12PM
If the polymererase hits an X or a Y during transcription, what happens?
One would expect that it would be flagged as DNA damage and "repaired" (not sure if procaryotes have repair pathways for this, but in eucaryotes they are present).
(Score: 0) by Anonymous Coward on Thursday January 26 2017, @10:30PM
If you RTFA, you'll see that the claim to fame isn't that they got the new bases into DNA, that's been done before, it's that they've rejiggered the needed protein machinery to make the bases persist over generations. It doesn't do anything but take up space, yet, but this is the first step.
(Score: 1, Interesting) by Anonymous Coward on Thursday January 26 2017, @03:22PM
...and just suppose that this thing threatens to escape the containment of the laboratory. [wikipedia.org]
What then? Hmmm? [wordpress.com]
-- OriginalOwner_ [soylentnews.org]
(Score: 1) by YeaWhatevs on Thursday January 26 2017, @03:54PM
The plot line from Evolution becomes a reality.
(Score: 2) by ikanreed on Thursday January 26 2017, @04:00PM
Then... it'll probably not be able to compete against unmodified bacteria and go extinct rapidly?
I mean, that's the general case for GMOs across the board. They tend to suck at the whole "Survive and reproduce" thing without human intervention. Because most of the human-created modifications make them more useful to humans, not better adapted to their environments.
(Score: 0) by Anonymous Coward on Thursday January 26 2017, @04:45PM
Yes, but evolution is not something easily turned off. If an organism has poor hand dealt to it by its human creator, mutations will give it opportunity to adapt better, starting from next generation in the wild.
(Score: 2) by ikanreed on Thursday January 26 2017, @04:58PM
Yes, but, again, the bacteria all over the fucking place have a few billion years on them for this "adapting to the environment" thing.
(Score: 3, Insightful) by sjames on Thursday January 26 2017, @06:09PM
That hasn't worked out very well for starlink corn, Scotts bentgras, or roundup ready canola.
A more interesting uise for synthetic base pairs would be creating organisms that cannot synthesize a critical base pair that also isn't found in nature. That way it would depend on a specialized growth medium.
(Score: 0) by Anonymous Coward on Monday January 30 2017, @05:58AM
> That hasn't worked out very well for starlink corn, Scotts bentgras, or roundup ready canola.
Uh...but their dna is found all over in fields with other strains near where they've been grown?
> A more interesting uise for synthetic base pairs would be creating organisms that cannot synthesize a critical base pair that also isn't found in nature. That way it would depend on a specialized growth medium.
100% best idea in this post. Patent the idea and release it as free.
(Score: 2) by HiThere on Thursday January 26 2017, @08:08PM
Where's it going to find the X and Y nucleic acids in the non-lab environment? If you need them to build your genetic code, you need them to grow.
That said, to answer an earlier question, (in at least one reported organism of this variety) the ribosomes have been modified to respond to additional RNA signals to attach the additional amino acids to build proteins when codons containing X or Y are encountered. Last I heard only a couple of proteins were encoded that way, but that was nearly a year ago.
Think of this as a security measure. The stuff can only grow in an environment containing X and Y, and it's been modified to depend on their presence in order to grow. (Again, that's based on a different story. I think that one was from Craig Ventener's lab rather than Scripps. But it was also based on E. Coli.)
Javascript is what you use to allow unknown third parties to run software you have no idea about on your computer.
(Score: 0) by Anonymous Coward on Thursday January 26 2017, @06:53PM
Call the United Galactic Sanitation department..
(Score: 2) by edIII on Thursday January 26 2017, @08:21PM
Wow. I wonder how many people around here are old enough to remember that :)
They don't make ship's navigators like that anymore.....
Technically, lunchtime is at any moment. It's just a wave function.
(Score: 0) by Anonymous Coward on Thursday January 26 2017, @08:44PM
arrgh. wrong story..
(Score: 0) by Anonymous Coward on Thursday January 26 2017, @11:25PM
This is an interesting story, but my mind interpreted the headline initially as, "Scientists Engineer First Semisynthetic Orgasm With Three-base-pair DNA." Which would be quite a different story, I believe. And I'd volunteer for any field trials of that one.
(Score: 0) by Anonymous Coward on Friday January 27 2017, @08:29AM
All your base-pair belong to us!