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Home https://server7.kproxy.com/servlet/redirect.srv/sruj/smyrwpoii/p2/ Science https://server7.kproxy.com/servlet/redirect.srv/sruj/smyrwpoii/p2/ Scientists are creating their own E. coli genome, compressing their genetic code

Scientists are creating their own E. coli genome, compressing their genetic code



  Like all other E. coli but different
enlarge / Like all other E. coli, but different.

Genetic code is the basis of all life, allowing information on DNA that will be translated into proteins that perform most of the cellular functions. And yet it's … kind of mess. Life usually uses about 20 amino acid sets, and the genetic code has 64 possible combinations. This incompatibility means that redundancy is raging, and many species have evolved in different ways that would otherwise be a universal genetic code

So is the code itself important, is it something of a historical event recorded in the distant evolutionary past of events? The answer to this question has not been chosen so far, as single codes appear in hundreds of thousands of sites, even in the genes of the simplest organisms. However, as our ability to increase DNA is increased, it has been possible to synthesize the entire genome from scratch by allowing for wholesale reproduction of the genetic code.

Now scientists declare that they have repeated the bacterial genome E. coli to get rid of some genetic code release. The resulting bacteria grow slightly slower than the normal strain, but otherwise it is difficult to distinguish them from non-synthetic peers.

Codes and redundancy

The genetic code is set out in three DNA base sets. Each of the three positions may have any of the four bases, that is, there are 4 x 4 x 4 possible combinations, or 64. Conversely, there are only 20 amino acids, and at least one of the remaining codons must be used to tell the cell to stop translating the code. This does not match 43 codes that are not necessary. Cells use those additional codes as redundancy; instead of one-stop code, most genomes use three. Eighteen of the 20 amino acids are encoded in a set of more than three bases; two have six possible codes.

Is this dismissal helpful? The answer is sometimes. For example, many DNA sequences are doubled, encoding both protein and regulatory information that controls gene activity or allows specific RNA structures to be formed. Over-flexibility makes one sequence easier to achieve two goals. Release can also allow the regulation of gene activity, as some codes are more efficiently translated into proteins than others. These factors suggest that the release of the genetic code may have been necessary for the body.

However, the test is whether it is a little nightmare. Even the most compact genomes have hundreds of genes ( E. coli strains from 4,000 to 5,500), and each single code can occur several times each. Editing each one is possible, but it would take a long time.

So scientists simply recorded things on a computer. Focusing on one of the amino acids with many unnecessary codes, they compressed the sequences so that more than 1

8,000 individual two-code usage was replaced by unnecessary choice. Designed with a synthetic genome, it was only divided into pieces that can be ordered from a DNA synthesizer

It's easier than it seems, according to one of the researchers (and a regular Ars reader) Wolfgang Schmied. "With a project where you ask questions about the rules of the genetic code, you have to commit at some point to ordering the genome of the synthetic DNA," he said, a rather large financial commitment rather than a simple push of a button. “But press […]

Some assembly is needed

Unfortunately, there is a big gap between the DNA synthesis device and the multi-base long genome. The group had to carry out the entire collection process by sliding the small pieces into a large segment in one cell and then bringing it to another cell with a large segment of overlap. "Personally, my biggest surprise was indeed how well the collection process was going," Schmied said. "The success rate at each stage was very high, which means we were able to do most of the work with standard bench methods."

During the process, there were several sites where the synthetic genome ended up with problems – at least one case, two genes coincided. However, scientists have been able to improve their version to find out the problems they have identified. The final genome also had some bugs that occurred during the collection process, but none of them changed the three key codes that were given.

After all, it worked. Instead of using 61 of the 64 potential amino acid codes, the new organism, called Syn61, is only used for 59. The researchers could then delete the genes that normally allow E. coli to use directed codes. Usually these genes are necessary; Syn61, they can be deleted without problem. This does not mean that the Syn61 strain is good; it has grown slower than regular peers. However, this is probably the result of all the cases described above, where DNA sequences have performed more than one function. It may be that over time the strain may develop to normal growth rate

In addition to answering questions about basic biology, the Syn61 strain may ultimately be useful. There are many more amino acids than 20 people and many of them have interesting chemical properties. However, in order to use them, we need backup genetic codes that can be directed to artificial amino acids – precisely what this new job has given.

Nature 2019. DOI: 10.1038 / s41586-019- 1192-5 (About DOI)


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