A path towards artificially produced life – From designer bacteria to designer humans?

Meanwhile, everyone is talking about the genetic scissors “CRISPR”: The news at the end of November 2018 that the Chinese researcher He Jiankui had genetically modified two embryos to protect them from HIV and then implanted those into a woman’s uterus who subsequently gave birth to genetically modified twins (“CRISPR babies”) shocked the world far beyond the research community. It was the first gene technological intervention within the human germ line. But anotherfear as well as awe-inspiring biological field has long since established itself: the creation of artificial life. Or in concrete terms: the synthesis of artificial genetic sequences for the purpose of research into biological phenomena or the production of new bio-molecules. Like CRISPR, this field also has enormous potential to unlock remaining secrets of life and thus potentially open up entirely new technological horizons, as well as raising a multitude of disturbing questions – scientific and technological as well as philosophical and ethical ones.

When the controversial genetic engineering pioneer Craig Venter announced nine years ago that he had created a complete organism exclusively with artificial genetic material for the first time, the media response was still rather contained. In May 2010, Venter’s team succeeded in building an artificial genome in the laboratory and implanting it into a cell of the bacterium Mycoplasma capricolum that had previously been freed from its natural DNA. It was a milestone in modern genetic engineering that was immediately associated with the great human dream of creating artificial life. “Life from scratch” has since been the goal of the geneticists. Less than four years later, US-American researchers led by biologist Jef Boeke did not attract much more public attention after they had rebuilt a complete yeast chromosome in the test tube with some artificial modifications. Yeast is a so-called eukaryotes, i.e. a living organism with a cell nucleus (bacteria do not yet have their own cell nucleus, which is why they are called “prokaryotes”). Their genome is much more complex and, above all, much more extensive than that of bacteria and viruses in Venter’s studies. In the meantime, Boeke’s teamhas already produced six artificial chromosomes and are about to reproduce the entire set of 16 yeast chromosomes.

The method behind Venter’s and Boeke’s work of creating new artificial life is in principlequite simple: From a database of many millions of genes, the genetic engineers simulate the properties of a very large number of possible gene combinations that have not yet been realized in nature. Genome sets with certain desired properties are then identified, chemically synthesized and produced with the help of machines before being introduced into the nucleus of the target organism, which has been freed from its original genome. The chemical synthesis corresponds to the assembly of Lego pieces: The calculated sequence is simply assembled from the four nucleic bases adenine (A), cytosine (C), guanine (G) and thymine (T). Designed on the computer and brought to life by machines in the laboratory – this is how the creation of the new creatures can be summarized. Genetic engineers also speak of “DNA printing”. The cell provided with the artificial DNA then produces copies of that DNA just like natural cells do.

At this point it should be noted that this method does not produce entirelyartificial cells (Venter’s assertions at the time were somewhat misleading in this respect). Although the artificially produced DNA sequence contains the information for all protein syntheses within a living being, these are always carried out in the context of the surrounding cell and the culture medium in which it is located. Without the cell, DNA would be nothing more than a collection of carbonaceous material, just like software is just a string of lines of code that needs to be implemented on a piece of hardware in order tounlock the power of a computer. After his success, Venter therefore spoke of a new “digital era” in biology, in which DNA can be programmed as the “software of life” targeting the creation of microorganisms on demand. These microorganisms could then produce precisely desired amino acid sequences, i.e. proteins, which, for example, enables the production of new drugs that are yet very difficult and expensive to produce. It is not that unusual for microorganisms to produce drugstoday, as e.g. genetically modified bacteria produce the hormone insulin, which diabetics use to regulate their blood sugar level.

But the ambition of genetic engineers already goes much further: they want to learn nothing less than to use the programming language of life to produce better genomes than nature has done. In principle, any form of biological data can be coded by rewriting the DNA. This could enable completely new organisms with very real benefits: The genetic engineers are hoping for above mentioned applications in medicine (new drugs), but also in energy production (e.g. electricity-producing bacteria), food production and agriculture.

A next milestone in artificial DNA synthesis has now been reached: Scientists led by Jason Chin from Cambridge University in England have succeeded in equipping Escherichia coli bacteria, i.e. coli bacteria as they occur in our intestines (and the same bacteria used by biochemists for insulin production), with a completely synthetic genome (J. W. Chin, Total synthesis of Escherichia coli with a recoded genome, Nature, Volume 569, p. 514-518 (15 May 2019)). It is the largest artificial genome ever inserted into a bacterium and contains four times as many DNA building blocks as Venter’s bacteria. The really extraordinary thing about this new work, however, is that the new organism gets by with less genetic information than natural organisms. Genetic engineers speak of a “recoding” of the genome. Natural cells use 64 different triple combinations of the four nucleus bases A, C, G and T (there exist 64 – four to the three – triple combinations from these four bases) to encode the 20 amino acidsoccurring in living beings that make up all the proteins produced by natural organisms (the so called “canonical amino acids). In other words, a triple combination of the four nucleic bases (a so-called “codon”) stands for one amino acid each. Remarkably, all living beings use the same genetic code: Each amino acid is always represented by the same codon. With 64 possible triple combinations for 20 amino acids (plus a stop codon), this “hereditary code of nature” is highly redundant: many amino acids are represented by several different codons. In a way, nature thus offers itself a great luxury (the reason is that errors in the coding during cell division, so-called mutations, are in many cases less pronounced or critical for the organism). In theory, life could manage with a codon for exactly one amino acid. All other redundant respective codons could be replaced by that one codon. The researchers around Chin have now modified the synthetic genome of the new artificial bacterium in such a way that it produces all the necessary amino acids with only 61 codons. This leaves space in the genome for the coding of three additionalamino acids that natural cells are unable to produce. Such artificial amino acids could be used to produce proteins that have completely new properties, such as those that can be used as drugs or by the chemical industry.

However, the new artificial creature has yet another very special characteristics. Because it has its own code for protein synthesis, it can only decipher its own genome. This in turn means that it cannot interact with other (natural) organisms. It cannot read their genetic code and vice versa. In particular, the artificial bacterium cannot be infected by viruses. If a virus enters the cell and tries to take over the genetic machinery of the cell to produce more viruses, it would get stuck in the process of DNA decoding, so to speak. It could not lead the cell to produce viral proteins and thus replicate itself –which is exactly what happens during a viral infection. If human DNA could be re-encoded in this way, the corresponding cells would be resistant to HIV, hepatitis, influenza or any other form of virus. Such cells would be the ultimate basis for stem cell therapy. Jef Boeke thus recently said: “The ultra-safe human cells could do for stem cell treatments — regenerative medicine — what pasteurization did for milk”.

The researchers around Chin used the CRISPR methodology to produce the latest artificial genome(which Venter did not have available to himself nine years ago). With it they gradually introduced the new, artificial genome into a normal E. colicell until the natural code was completely replaced and no longer contained a piece of natural DNA but only those that were modelled after the natural code. The synthetic genome furthermore differed from the original one in 18’214 positions (for comparison: Venter’s artificial organism from 2010 contained only 25 modifications).

How will the field of synthetic biology develop further? Jef Boeke’s team has been working for some time on a complete replica of the entire set of yeast chromosomes. This consists of a total of 12 million base pairs. Will it one day be possible to artificially reproduce the entire human genome, and this if necessary with corresponding modifications? It is clear that enormous ethical questions arise here. But technologically this is hardly foreseeable any time soon. The human genome is many times more complex than that of a bacterium or yeast: instead of four or twelve million, 3.3 billion base pairs would have to be reconstructed and inserted. For now this significantly exceeds the capabilities of current genetic engineering tools.

But we should not be too complacent in that respect. In technological terms, the leap from zero to one million is often much greater than the leap from one million to several billions and more. And indeed, biologists are already talking about the “Human Genome Project-write”. Once completed, this would give them access to the blueprint for all life andthus the ability to cure diseases and repair ecosystems, or even, as some geneticists say, “to preserve humanity in an environmentally friendly way”. We could even give the artificial human genome the ability to produce amino acids that our body cannot produce itself. This could e.g. prevent malnutrition. More generally, we could get our body to produce itself most of the substances it needs for its own metabolismas well as fighting off diseases(except for the energy that due to fundamental principles in physics – second law of thermodynamics – has to come from outside). In any case, the result would be a new, better human being.