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Reprogrammed Bacterium Speaks New Language of Life
wabrandsma writes "New Scientist reports that 'A bacterium has had its genome recoded so that the standard language of life no longer applies. Instead, one of its words has been freed up to impart a different meaning, allowing the addition of genetic elements that don't exist in nature. ... The four letters of the genetic code are usually read by a cell's protein-production machinery, the ribosome, in sets of three letters called codons. Each codon "word" provides instructions about which amino acid to add next to a growing peptide chain. Although there are 64 ways of combining four letters, only 61 codons are used to encode the 20 amino acids found in nature. ... The three combinations left over, UAG, UAA and UGA, act like a full stop or period – telling the ribosome to terminate the process at that point. ... A team of synthetic biologists led by Farren Isaacs at Yale University have now fundamentally rewritten these rules (abstract). They took Escherichia coli cells and replaced all of their UAG stop codons with UAAs. They also deleted the instructions for making the release factor that usually binds to UAG, rendering UAG meaningless. Next they set about assigning UAG a new meaning, by designing molecules called tRNAs and accompanying enzymes that would attach an unnatural amino acid – fed to the cell – whenever they spotted this codon."
Or did they mean 3 letters of four symbols?
4*4*4 = 64.
But that's not what the article said. Bad article.
I should use this sig to advertise my book ISBN-13 : 978-1501515132.
64 ways of combining four letters taken 3 at a time to form a codon.
If you reply, do so only to what I explicitly wrote. If I didn't write it, don't assume or infer it.
I see you didn't even make it through the summary. Good form.
I would approve of requiring labeling on food if it was produced by one of these.
Note that the only examples of words had 3 letters.
4^3 = 64
So what they meant to say was that there are only 64 ways of combining four letters in 3 letter words.
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Sheesz people, we've been rprogramming trna to use nonnatural amino acides for over 10 years now! Theres even a few companies st up that do just that. The principle of trna modification is old, just their method is new
If an experiment works, something has gone wrong.
If you had an infinitely long one of these, it would be kind of like a Turing machine.
If you had one three billion long you could have Turing himself.
Does this mean geneticists just figured out how to overclock cells?
No. Just added custom instruction set.
But you didn't. If you read what it said you would have:
26x26x26x26 = 456,976
Assuming you have 26 letters in your alphabet. Irish has less, German has more.
It's the genetic equivalent of adding the Euro sign into your system fonts.
That's actually a remarkably accurate analogy, if you add the Euro sign at ascii position 0x09 (aka ^I, aka HT) and modify your software (e.g. C compiler) to treat tabs as a normal character instead of whitespace.
Codons are sets of three letters. Every creature has its own unique codon table - every three letters (GATC) make up one codon, so there are 64 possibilities. But the fun thing is that many codons actually code for the same amino acid, but take different times to complete the process. Either because some molecular rotation is taking place or just because it's a time delay to allow folding to complete elsewhere. Then sometimes the sequence is used in reverse order (creating a back-to-front version of whatever is made) and sometimes even the sequence of letters is read with an offset of one or two letters, so essentially one group of letters can code for six different chains of amino acids.
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Well, if you only had one of them, you would only have a very tiny bit of Turing himself.
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Some years ago, when Venter's synthetic genome bacteria was created, I came up with a plan to do this on a more extensive scale.
(1) Sequence the genome of a bacterium, and edit the genome (on computer) to use no codons ending in 'T" or "A". (The redundancy of the genetic code allows this.)
(2) Also edit genome so that it has tRNA for the codons ending T or A which entirely change their meanings (but still using the standard amino acids.) (Transfer RNA - tRNA - are the mechanism by which the codon code is decyphered to amino acids.)
(3) Synthesize the edited genome, and replace the genome of a living bacterium with it. Breed for a few generations, to check that all is well, and to eliminate any of the old tRNA.
(4) Edit the genome to use entirely the new codons. Also edit replacement tRNA for the remaining codons, ending G or C.
(5) Replace the genome of one of our modified bacteria with this one.
Result: a bacterium which has an entirely rewritten genetic code, and is incapable of reading the old code.
However, I don't think I was the first to think this all up. In any case, Science didn't accept my letter proposing it.
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Sorry, I made the mistake of reading what it said, not what it meant.
That's ok, you'll just evolve to do better next time.
Bad article: most of the aspects discussed were first done ~10 years ago by Peter Schultz: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299037/
Codons are sets of three letters. Every creature has its own unique codon table - every three letters (GATC) make up one codon, so there are 64 possibilities.
Almost. Every species has its own take on tRNA codong, but there is a lot of similarity up to the Kingdom level
But the fun thing is that many codons actually code for the same amino acid, but take different times to complete the process. Either because some molecular rotation is taking place or just because it's a time delay to allow folding to complete elsewhere. Then sometimes the sequence is used in reverse order (creating a back-to-front version of whatever is made) and sometimes even the sequence of letters is read with an offset of one or two letters, so essentially one group of letters can code for six different chains of amino acids.
Uh, no...not molecular rotation or time delay....this is actually more of a planned overlap. Pretty neat how nature planned this one. And as for mRNA being converted to a protein using tRNA (tranlation), it is strict one-way encoding (5' to 3' IIRC). dsDNA (but not ssDNA) (transscription) may be read in either direction, but mRNA not so (is is very much like ssDNA)
Well, if you only had one of them, you would only have a very tiny bit of Turing himself.
Well, his mommy had only that much at one point. Fortunately, it was capable of self replication :P
But there aren't 26 letters in the DNA alphabet. There are 4.
4 letters (base pairs), "sets of 3 letters called codons". "Although there are 64 ways of combining 4 letters ...", in that context, is clear and correct.
Well, if you only had one of them, you would only have a very tiny bit of Turing himself.
It's f-ing TURING dude!
Code includes a "do - until" replication loop.
"If you had one three billion long you could have Turing himself."
Not as interesting. We already know that Turing halts.
In 1954.
"If you had one three billion long you could have Turing himself."
Not as interesting. We already know that Turing halts.
In 1954.
That wasn't a error halt. Turing code correctly detected hostile external attacks and shut itself down to avoid further damage.
Plus - this would be TURING 2.0 !
But the summary didn't say DNA alphabet, I thought we were reading the summary completely literally without taking into account any context.
All life *is* the result of run-amuck assemblers.
.6 micro meters cubed. Or 6x10^-19 m3. In optimal conditions its replicated every 20mins. Lets say 30mins. So 48 replication cycles per day. After one day of uninhibited replication we now have about 168ml of ecoli. After 2 days we have about 47 cubic kilometers. After 3 days its 1.3x10^25 m3, compare to the volume of earth of just 6x10^20 m3. The same effects that prevent ecoli from unrestricted replication, apply to anything else that can replicate.
Consider that the grey goo hypothesis requires that the assemblers need to break the laws of thermodynamics and requires advanced alchemy to work as advertised.
Ecoli has a volume of about
The grey goo disaster happened 3 billion years ago. Earth as we know it is the result.
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