In 2002, the journal Science announced to the world the synthesis of a virus in a test tube. That is, a working genome had been created from inert chemical compounds. “It caused a sensational stir,” says project coordinator Eckard Wimmer of Stony Brook University in New York. In the blink of an eye, science had gone from reading genes to writing them . ” They called us irresponsible for synthesizing the polio virus , but also for divulging how we had done it,” recalls the scientist.
Despite the criticism, the advance gave rise to a new branch of research: that which considers biological systems as machines , to recreate, replace, eliminate and use each of their parts at will. We are talking about synthetic biology.
Famous for his ambition to be the first to sequence the human genome, it took biologist and entrepreneur John Craig Venter just a year to follow in Wimmer’s footsteps. At the end of 2003 he announced the synthesis of the genome of a somewhat more complex virus. It was a bacteriophage, a viral agent that only infects bacteria. Since that date, the research Institute that bears his name has patented techniques and discoveries with one obsessive and single objective: to discover the minimum amount of DNA capable of sustaining a living organism.
“Life evolved through random changes,” Venter explains in his recent book Life at the Speed of Light . “Our goal is to discover which are the basic modules, those responsible for chromosomal replication or cell division. Once these parameters have been established, we will be able to manipulate the parts so that the cell can carry out the functions that interest us ”.
It is not a new approach. For centuries, humans select and use microorganisms at their convenience. Yeasts, for example, ferment beer and bread ; the fungus Penicillium chrysogenum produces penicillin; and without lactic acid bacteria, wine would be something else. However, Venter believes that designing microbes with synthetic DNA will mark a paradigm shift. It is easy to say, but very difficult to achieve.
Mycoplasma genitalium , the smallest known bacterium, has 525 genes. To define the minimum viable genome, the research team at the J. Craig Venter Institute (JCVI) began working with this species, whose genome had been sequenced in 1995. “About a hundred genes of M. genitalium are not essential, because we disable them and the cell is still alive ”, explains Venter. “However, we don’t know which ones we can do without at the same time .”
Solving these mysteries could take too many years, precious time that Venter did not want to waste. With the support of a team that includes the best molecular biologists in the world, our man then decided to ignore the genomes he had worked with and play God . In other words, synthesize from scratch, piece by piece, a functional molecule.
To put their idea into practice, JCVI scientists previously developed new methods. In 2007, they successfully performed the first transplant of genetic material in history. Broadly speaking, they removed the DNA of a bacterium and implanted it inside the empty cell belonging to another species. The degenetized organism began to behave as if it were the donor.
Six months later, JCVI molecular biologist Daniel Gibson’s team assembled their first artificial genome. Nothing new, if we take into account that Venter himself had created a virus five years earlier. However, now the challenge was to adapt the techniques already developed to a larger DNA: that of the bacterium Mycoplasma genitalium . Applying engineering principles, the scientists divided the DNA of this microorganism into 101 fragments to work with more manageable sequences. As Gibson explains, “the problem was that DNA synthesis tends to degenerate. The larger the sequence, the greater the probability of errors. So we had to develop methods that would allow us to put the pieces together little by little ”.
It took Gibson and his team less than two years to achieve their goals. After manufacturing a genome from scratch in the laboratory and transplanting it into an empty cell, they announced in the journal Science the creation of “the first living being whose progenitor is a computer”, in the words of Craig Venter. The new species was called Mycoplasma mycoides JCVI-syn1.0.
Did the JCVI experts create artificial life? Many believe not. “The importance of these results has been exaggerated,” says David Baltimore, a biologist at the California Institute of Technology, in the US ” It is a question of scale rather than a pure scientific advance. They have not created life: they have imitated it ”.
Venter does not object. “Indeed, creating life implies that the genome models the cell where it is found, not taking over an existing one, as if a hermit crab took possession of an empty shell,” he explains. And he adds: “Our work does not pretend to recreate the genesis. In fact, we could not do it without living beings that have evolved over 3.5 billion years. ” To generate the synthetic cell, Gibson worked with two different species. First, he synthesized a genome based on that of the bacterium Mycoplasma mycoides , larger than that of M. genitalium , but also with a greater capacity to multiply. Then he transplanted that molecule into an empty cell, belonging to the Mycoplasma capricolum species.
“We define the result as a synthetic cell” says the researcher. “But in reality – he continues – the only artificial thing is its DNA: the cytoplasm is still that of M. capricolum . Of course, as the new bacterium replicates and forms a colony, its descendants do not harbor information about the original species , but about the genome that we have implanted in it ”.
Last April, another bioengineering experiment returned to the front pages of newspapers: the creation of a synthetic chromosome in a being more complex than the viruses or bacteria hitherto featured in this news. It was Saccharomyces cerevisiae , better known as beer yeast, whose DNA is encapsulated within a nucleus.
The team led by Jef Boeke, from NYU Langone Medical Center in New York, developed a synthetic and functional version of chromosome number 3 – S. cerevisiae has sixteen – thanks to a cut-and-paste technique similar to that developed by Gibson. ” The real milestone is that it is integrated into a living organism ,” explains Boeke. “Cells that carry this chromosome are perfectly normal, but they can do different things than their natural counterparts.” Over seven years, scientists made more than 50,000 modifications to the yeast genetic base, removing repeats and other sequences with no apparent function. “One wrong change and the cell dies. Our intervention shows that the synthetic chromosome is very resistant ”, says the expert.
What are these Frankensteins of the microbial world for? Two examples: the biotechnology company Amyris already works with yeasts that generate artemisinin, the main ingredient in malaria treatment; while DuPont has succeeded in creating a bacterium that produces superior quality polyester. At the JCVI they are investigating another couple of applications: the synthesis of vaccines and hydrocarbons.
Craig Venter spends a large part of his budget traveling the planet. He wants to collect as many microorganisms as possible , sequence their genome and find out what they are capable of doing with it. A decade ago he sailed with members of his team for two years and discovered more species than anyone in history, especially microalgae.
“They are the perfect candidates to give rise to an artificial organism”, explains the North American entrepreneur. “They consume energy from the sun, they don’t need food. In addition, they synthesize hydrocarbons to store energy ”. People have tried to make fuels from algae for a long time, but the costs are too high. Since 2009, JCVI has been working with ExxonMobil to correct a problem that, the oil company itself has admitted, may have another 25 years of investigations left.
Although Venter announced a year ago that the dream of creating completely artificial DNA, without copying that of any species, was just around the corner, the task seems Herculean. Incredibly simple if we consider its functions, the genetic code is based on four chemical compounds: adenine (A), cytosine (C), thymine (T) and guanine (G). Once attached to a sugar backbone, these nitrogenous bases form the DNA double helix. Each set of three letters – called a codon – encodes one of the twenty essential amino acids , the raw material of all proteins. Well, this universal code, unchanged since the dawn of terrestrial life, has gained two letters.
In early 2014, scientists at the Scripps Research Institute in California, led by Floyd Romesberg, announced the happy result of more than fifteen years of research: a living cell whose DNA has two extra bases. In the pages of Nature , Romesberg explained that his objective is to encode in these new units information that allows the synthesis of non-essential amino acids. “With more letters we can invent words,” he says. We are no longer talking about improving what exists, as Venter proposes, but about producing something different from everything that has existed.
In anticipation of criticism, the enriched cells incorporate a control mechanism that prevents survival outside the laboratory. According to Boeke, his yeasts would also be unable to do so, but, if we talk about bacteria or algae synthesized in the JCVI, the situation is not so clear. “By treating the genome as an alphabet, we can write anything in the non-coding areas of DNA. In the first synthetic cell, we put the 46 names of all those who contributed to this advance and some quotes from famous people ”, Venter explains.
Critics claim that such security marks will disappear after successive cell divisions. Furthermore, they would not prevent laboratory microbes from surviving in the wild. There are still many doubts and obstacles to resolve.
