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GM Organism Produces New Amino Acid
blamanj writes "Scientists led by Scripps Research Institute chemistry professor Dr. Peter Schultz have engineered a version of the E. coli bacteria that can produce an amino acid not found in nature. Story at the Environment News Service and Science Daily."
So now we can... em.. er.. Anyone? Development's great, but as far as I can see new Amino Acids would have no purpose whatsoever :?
puts ("Python r0cks\n");
A bacteria with a new amino acid is like a...'mule with a spinning wheel - no one knows where [we do now ;] he got it, and danged if he knows what to do with it!'
Sure I'm paranoid, but am I paranoid enough?
This is interesting and certainly Scientific Progress, but not revolutionary by any means. While quite rare, there are still 5 or 6 cases already known of organisms that use abnormal amino acids. This may lead to some answers to current questions a decade or two down the line, and there's even the off chance that it could mean something really revolutionary, but for now it's no more and no less than interesting.
How do we know that this amino acid is not produced in nature? Last time I checked we had not catalogued every living creature on earth let alone analyzed all of the chemicals that each of them produce.
From the article:
"This allows you to have a totally autonomous organism that you can 'race'in one pot by evolving the new bacterium alongside its ancestors with 20 amino acids," says Christopher Anderson, a researcher at Scripps and another author of the paper. By racing the organisms -- exposing both to selective pressures at the same time and watching their development -- the researchers hope to see if the organism with the expanded genetic code has an evolutionary advantage over natural organisms.
Geez, is this where the reality tv show "Survivor" is going? "Don't miss the new SURVIVOR 6: YOUR COLON where natural and unnatural E. Coli bacteria compete for control of your ASS!" We already knew it's a shitty show, but it CAN get worse.
Other useless thoughts...
"It's a bona fide unnatural organism now."
--Wasn't this a bad guy's line from a SciFi Channel original movie?
"Our unnatural organism will always live in the lab. We have no intention of putting it out in the wild or in commercial products where it could 'get out.'"
-- Oh yeah, it wasn't the bad buy that said these things, it was the unwitting scientist-stooge of the bad guy.
"We are now focusing on more 'useful' unnatural amino acids such as ketone- and PEG-containing amino acids," Anderson says. PEG stands for polyethylene glycol, a polymer that can be connected to proteins used in medicines to enhance their therapeutic value. "I don't think it is at all unrealistic to imagine that in the not-too-distant future there will be a transgenic goat that can biosynthesize a PEG amino acid and incorporate it into therapeutic proteins secreted into the animal's milk," Anderson says.
--Isn't polyethylene glycol otherwise known as antifreeze? Imagine ice cream that melts in the freezer -- YUM!! Now THAT'S REALLY USEFUL.
I guess that's all for now.
Too
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Slashdot..
Brain... function
decreasing.
Cerebral cortex failure imminent.
What Would Satan Do?
Did they use Ninnle Linux to run the analysis on this? Ninnle's capable of it, don't you know?
The majority of the nonstandard amino acids present in protein come about by post-translational modification; they start off as a standard amino acid and either are modified by another protein or are simply unstable in their environment as a standard amino acid. Oxidation of cysteines to cysteine sulfenic (-inic, or -onic) acids is one example, phosphorylation of tyrosines is another. Selenomethionine and selenocysteine are sometimes examples of this as well (enzymatic replacement of the sulfur with selenium), although in some special cases are coded in the DNA as specifically being selenomethionine and selenocysteine as opposed to methionine and cysteine. What the group at Scripps did was engineer E. coli to change how it recognizes a codon or a set of codons, presumably ones that E. coli rarely uses (can't find the original article, damnit!) and incorporate a new amino acid, p-aminophenylalanine in place of whatever normal E. coli put in a polypeptide before when it hit that codon. This is cool because previous efforts used modified growth media to "trick" the bugs into putting something similar in a protein in place of a standard amino acid whereas here the bugs are using 21 (23 if you're being tight with your definitions and including selenocysteine and selenomethionine) amino acids. The goal of the study is to try and look at why we've ~all got 20 (22) amino acids and not some other number. I wish them luck on that one, but at least they've got a start on the tools necessary to figure that out.
The first 20 are hard enough to learn. I never learned them, but my biochem roommate did and if he had told me the structure of valine one more time I was going to kill him.
What's the use of it? Well, imagine getting a whole new shape of Lego piece to design around.
There's two more surprises in this pipeline that will be coming out of shultz group. this is the tip of the ice berg.
...) and thus can be given in lower doses and less frequently. Currently Most plausible protein therapeautics are not effective for exactly these reasons: they get digested two quickly or would have to be delivered in toxic doses. With the extremley large amino acid substitution set available, it would be theoretically possible to redesign drugs in a computer much faster than pathogenic organisms could evolve machinery to destroy each new variation.
First lets explain what shultz achieved that was new. with 4 bases there are 4^3 = 64 possible 3 base-codons. Think of these as the word (or byte) size used in computer that uses base-4 rather than base 2 logic. (so this is equivalent to a 6 bit byte). continuing this analogy, like the ascii character set, these bytes code for the 'amino acid' cheracter set.
However, these are non-uniquely mapped to 20 amino acids (plus an end-of-line character) by the ribosome. In keeping with the ascii analogy, more than one bit pattern is interpreted as the same letter. In principle one could have as many as 63 different amino acids represented in this coding scheme but in practice there are only 20.
Because nature designed ribosomes and tRNAs so long ago you just cant fiddle with this machinery very easily and expect any orgnaism to be viable. (sort of like messing with the lowest level of the bios). To fiddle with it successfully you would have to fiddle with many poorly understood parts simultaneously.
The above statement is almost true. There are a few organims that happen not to use one or two of the 64 codons. these codons are called amber and ochre in the literature. In such an organism these codons are "undefined" and not used anywhere in the DNA of the organism. (oversimplification warning).
If one edits the organism's DNA to add these codons into a gene, and also simultenouesly supplies the organism with the ability to translate these codons to a new amino acid, then you can get the organism to build proteins using 21 amino acids one of which is defined by you. By "simultenouesly supplies the organism with the ability to translate these codons" I mean specifically supplying the organism with the specially modified tRNA which has on one end the signal to recognize the new codon, and on the other end is a gripper that holds the synthetic amino acid.
This has been done many times previously. However in all these cases the magic tRNA is chemically synthesized and then 'fed' to the organism. Shultz's work here is to get the organism to do the synthesis of this amber recognizing tRNA and the new amino.
Shultz's group has something even more revolutionary in the pipeline. They are working on adding two more bases to the 4 base set of DNA.
this gives 6^3 = 216 codons. of which only 64 are currently spoken for with natural tRNAs. For practical purposes this is an unlimited number of novel amino acids that could be incorporated into a protein.
Actually If I remeber correctly they have already created a working 6 base DNA, as well as created tRNAs that a ribosome can use to generate proteins. So now 'all' they have to do (I guess) is incorporate the tRNA and non-natural amino acids synthesis into the bug itself. in the mean time they can of course do this synthetically and 'feed' the tRNAs to the bugs.
This is pretty damn exciting stuff. there are an amazing number of possible uses. I'll name two
first, protein's built from unusual amino acids will escape many cellular mechanisms for degrading or cutting up proteins. Medicines built out of these proteins will thus be able to last longer in the host (human or bacteria or
A second application is there is no limit to the chemical functionality that could be placed on the bussiness ends of these amino acids. This would probably be a bad idea for use as therapeuatics, but would be a great way to make chemically active self-assembling nano materials. We let e coli built rigid protein scaffolds in any shape we want and then use this tehcnology to put reactive chemicals at precise locations on the scaffold. You can think of this like designer molecular sized cresent wrenches that can be shaped and chemically coded to grip only certain other shapes. the old lock and key analogy.
It is a modest exaggeration to imagine not just molecular sized transistors, but entire self-assembling mulit-molecular sized circuits and logic gates. That's a ways off. Before we get there there will be other sorts of molecular sized self-assembled doodads from molecular machines to chemical processing systems to optical coatings to information storage.
Some drink at the fountain of knowledge. Others just gargle.
I'm amazed that nobody has make a Jurrassic Park snide remark regarding the researchers making the bacteria unable to produce the amino acid leucine.
The work talked about is an accomplishment, but I think that one very important point has been neglected. Yes, DNA codes for 20 amino acids, but post-translational modifications, such as phosphorylation, increases that number by a bit (sorry, don't know the exact number), so there are more than 20 functional chemical groups found on proteins in nature. Another thing to keep in mind is that there are a couple less common residues beyond the normal 20. The fungus trichoderma viride produces a peptide called alamethicin which is filthy with (alpha)-aminoisobutyric acid (probably misspelled, but abbreviated Aib). The peptide gramicidin is loaded with amino acids that have the opposite structural handedness of normal amino acids.
Essentially, this bacterium can be added to a minimal media (salts and a basic carbon source) and it's able to do the rest.
We crippled the organism's ability to biosynthesize leucine [one of the 20 essential amino acids] to avoid any risk that the organism could propagate outside a controlled lab setting ...
So which is it? Minimal media or media supplemented with leucine? If those are the *safeguards*, then that's pretty weak. Surviving on minimal media means that only a carbon source (abundant) and salts (abundant) are necessary for growth/reproduction. If the bug is a leucine auxotroph then it's not much better, as there is plenty of leucine around "in the wild" to supplement the deficiency.