28 March 2014

How to get live artificial yeast


Kirill Stasevich, Compulenta

To understand the structure of something, we first take it apart, analyze the "insides", and then try to assemble something similar from what is there. If the created works in the same way as the original, it means that we did well and understood everything correctly.

We have long learned to disassemble the genomes of a wide variety of organisms, both bacteria and eukaryotes, both unicellular and multicellular, for "spare parts". Moreover, we are able to correct other people's genomes so that they continue to work, but in a slightly different way, taking into account our corrections. The most common example is the introduction of a new gene (say, a fluorescent protein gene) into a bacterium or eukaryotic cell: the cell does not die at all, but begins to glow.

However, such modifications still preserve, so to speak, the natural basis – the gene is embedded in the natural chromosome of a bacterial or eukaryotic cell. It is clear that sooner or later researchers would want to create the entire chromosome from scratch, making not just an artificial copy, but a copy "corrected and supplemented". This is exactly what a large group of scientists led by Jef Boeke from Johns Hopkins University and New York University (both USA) managed to do: in the journal Science, they describe a seriously edited chromosome they created for a yeast cell (Annaluru et al., Total Synthesis of a Functional Designer Eukaryotic Chromosome).

Edited yeast chromosome; colored "pins" and white diamonds mark the places of dot editing,
the areas cut from the chromosome are highlighted in yellow. (Illustration by Lucy Reading-Ikkanda.)

The yeast Saccharomyces cerevisiae has sixteen chromosomes; the researchers chose the third one for their experiment. Of the 317,000 nucleotides, 50,000 were edited. At the same time, of course, they were changed, cut out and inserted not in an arbitrary order: manipulations were performed when it could greatly improve the technological assembly of the chromosome; first of all, "jumping" genes associated with mobile elements were cut out, but completely new sequences were introduced so that later with their help it was possible to purposefully remove some kind of gene.

That is, additional possibilities were laid in this hybrid chromosome for subsequent revisions.

This, of course, is not the first time that scientists have created an artificial genome: in 2010, Craig Venter and his institute did a similar job. Mr. Venter is a well–known figure in the world of genomic research and synthetic biology, and the experiments of 2010, when he and his colleagues managed to recreate the complete genome of the bacterium Mycoplasma mycoides, only strengthened his reputation. However, although the mycoplasma genome is at least three times larger than the third chromosome of yeast, the researchers did not make any significant edits to it at that time. As for yeast, then, as already mentioned, almost every sixth nucleotide has been edited.

A synthetic chromosome was introduced into yeast and the viability of the resulting strain was checked. The environmental conditions for the cells varied in 19 different ways, but SynIII, as the new strain was called, was no different from its natural counterpart: both grew and multiplied equally in a variety of conditions, whether it was altered acidity of the medium, DNA-damaging stress, etc.

Moreover, SynIII was able to push for sexual reproduction by cutting out a gene that prevents this type of reproduction.

Such a "chromosome constructor" is not just art for art's sake, scientists expect to learn with its help some fundamental facts about the structure of the genome. The DNA of living organisms contains many genes, but which of them are necessary to a greater or lesser extent, without which it is impossible to live, what hierarchy exists between them, how they interact with each other, etc. – all this we have yet to find out. And this can be done just with the help of these artificial chromosomes, which allow you to insert and delete genes at the request of the researcher.

Moreover, yeast and I have 6,000 genes in common, so this may help to learn something about our own molecular genetic cuisine. And, of course, we should not forget about the purely practical benefits: by experimenting with synthetic chromosomes, we can create an organism with the desired properties, which, say, will produce some kind of biofuel with terrible force.

Prepared based on the materials of the Langon Medical Center at New York University:
Scientists Synthesize First Functional “Designer” Chromosome in Yeast.

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