Synthetic bacteria: famous scientists on the achievement of the Venter Institute
Life in the era of synthetic life
Anton Chugunov, "Biomolecule"
It does not often happen that a scientific discovery, even published on the pages of the most prestigious scientific publication, instantly flew around the whole world, even on the pages of tabloid newspapers. However, at the end of May 2010, the mass media around the world were stirred by a revolutionary scientific achievement – scientists have created an artificial form of life! With a special appetite, newspapers littered the biography of the "godfather" of the project – an ambitious molecular geneticist and organizer of science, adventurer, avid surfer and racing driver, Vietnam War veteran, founder of a private company that shared the laurels of the "pioneer" of the human genome, charismatic businessman and rich man, founder of the scientific institute named after himself (J. Craig Venter Institute, JCVI) – J. Craig Venter.
Craig Venter at the helm of his yacht "Enchanter II", which, although not as big and expensive as Roman Abramovich's ship, was used for much more interesting purposes than a voyage to the World Cup in South Africa. A few years ago, Venter circumnavigated the world on this yacht, during which he "fished out" the genetic information of thousands of previously unknown viruses and bacteria from the waters of five oceans (Williamson S.J. et al., PLoS One; 2008). Such genetic sequences obtained from natural systems have come to be called the metagenome.
Venter also wrote a paperback book of the type "my way of life". Why aren't he, but Ksyusha and Paris, the stars of the screens?
Photo: Wombatunderground1 @ Flickr.
JCVI assembled, modified and implanted a synthesized "from scratch" genome into a bacterial "shell", resulting in a "working" microorganism Mycoplasma mycoides (Gibson D.G. et al., Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science, published online May 20, 2010).
Bacteria with a chemically synthesized genome multiply rapidly and outwardly practically do not differ from the "wild" Mycoplasma mycoides bacteria.
Colonies of bacteria with a synthetic genome (above) are colored blue because their genome contains the lacZ gene encoding the enzyme beta-galactosidase. In the nutrient medium there is a substance X-gal, which is converted by this enzyme into a blue dye (5.5’-dibromo-4.4’-dichloro-indigo). The "wild" bacteria M. mycoides (below) do not have this gene, so their colonies remain white.
Drawings from an article in Science.
Nature magazine also responded to this major event by collecting and publishing the opinions of eight well-known scientists in the field of synthetic biology (and not only), ranging from skeptical to inspired: Life after the synthetic cell. Nature 465 (2010), 422-424. We provide a translation of this column.
Strength and weakness
Mark Bedau, Professor of Philosophy and Humanities, Reed College, Oregon (USA)
Craig Venter's "synthetic cell" (Gibson D.G. et al., Science 2010) is a common bacterium with an artificially created genome. And since the genome makes up no more than 1% of the dry mass of the cell, only a small part of it can be called synthetic. However, the genome is a special component that carries all the hereditary information and "controls" all the processes taking place in the cell.
The ability to create artificial genomes is undoubtedly a huge step forward compared to the long–familiar engineering of individual genes. The artificial genome synthesized at the Venter Institute actually repeats the genome of an existing microorganism, with the exception of a small number of places where the synthesis occurred with an error, and specially added "watermarks" (in particular, the email addresses of some of the authors of the work). No technological limitations prevent us from moving on: any part of this genome can be modified in a way pleasing to researchers. Compared to the "today" obtained in JCVI, the "tomorrow" synthetic cell will really be a new form of life that the Earth has not yet seen.
However, the most important thing here is something other than just biotechnological (and in particular genetic engineering) innovations: I will list only four of the most obvious scientific and social consequences of these achievements.
Cheaper, please
George Church, Geneticist, Harvard Medical School (USA)
It is wonderful that we live in an era of fantastic achievements, similar to the work of the Venter Institute. But can we, without lying, say that JCVI really created artificial life? Hardly. The semi-synthetic mycobacterium does not differ at all from its "wild" counterparts in most parameters. Copying an ancient text is not the same as understanding what it says. The DNA built into the cell and working is far from new, although earlier it was, of course, not about whole genomes, but about individual genes. It is much more difficult to understand the structure of the whole machine as a whole – the apparatus that executes the "instructions" recorded in the genome. Biochemists, geneticists and structural biologists still have many years (if not centuries) to study all this.
Synthetic life is able to tell us something new about "ordinary" life. The "dissection" of genomes can show what we have missed in terms of speed, efficiency and sustainability. According to these parameters, fast and stable Escherichia coli is the industry standard compared to slower and whimsical mycoplasma. However, advances in the field of genomic DNA synthesis in the future allow dreams to come true, possible only with operations on whole genomes – for example, the creation of cells resistant to all kinds of viruses, enzymes or chemicals. From these positions, the new achievement of Venter's team – 1.08 million pairs of nucleotides (against the 0.58 that they had before) – is a significant leap forward.
Now that the creation of new forms of life with potentially dangerous properties is becoming a reality, it is necessary to pay special attention to the procedures of regulation and control that protect nature and society from the mistakes of researchers or acts of biological terrorism. These should be realistic laboratory ecosystems for monitoring the development and behavior of new life forms, their sustainability, the ability to integrate into existing ecological networks and exchange genetic information "at will".
What is really needed now is the ability to design and test millions of genetic combinations using protein and RNA biosensors that register the features of metabolism and intercellular signaling of new microorganisms. In addition to the technologies that were shown at the Venter Institute (but, of course, many times cheaper), this will allow researchers to develop a new approach to obtaining new dosage forms, biotechnological fuels, stereospecific chemicals and bio (nano)materials.
And finally,
"Bottom up" would be more honest
Steen Rasmussen, Professor of Physics, University of Southern Denmark
Creating a synthetic genome and putting it inside a cell is the most important milestone on the way to understanding the mysteries of life. However, genetic engineering according to the uncompromising "top-down" principle, which is adhered to by Venter's associates, does not quite correspond to my understanding of the "synthetic cell".
Both opposing camps of synthetic biologists – adherents of the "top–down" and "bottom-up" approaches - are trying to penetrate the foundations of life. Apologists of the "top-down" methodology, whose prominent representatives are Venter and his comrades, are trying to "rewrite" the genetic program and run it on the same hardware (that is, to make the modified genetic code work in the same cell). Researchers working on the "bottom-up" principle (to which I belong) strive to synthesize life – both "hardware" and "code"! – in the simplest possible form, even if the result does not exactly coincide with the generally accepted idea of the living.
Researchers who adhere to the "bottom-up" concept in synthetic biology are confident that the "assembly" of life from materials other than those used by nature, and even according to other "drawings", will teach us much more than when we simply copy familiar forms.
Until recently, our two camps practically did not intersect – mainly because of the different angle of view on the seemingly common goal, as well as because of the completely different methods used. Now, after a number of successes in both camps, the interaction appears and becomes closer: many projects already include supporters of both approaches – a great example of this is the synthetic genome.
The End of Vitalism
Arthur Kaplan, Professor of Bioethics, University of Pennsylvania (USA)
Venter and his colleagues have demonstrated that "banal" manipulations with objects of the material world can be used to create what we call Life. Their achievement undoubtedly brings to an end the debate about the nature of life, which has been going on for thousands of years. Perhaps, in terms of importance for understanding the place of man in the universe, this work is on a par with the discoveries of Galileo, Copernicus, Darwin and Einstein.
More than a hundred years ago, the French philosopher Henri Bergson postulated that life cannot be explained solely from a mechanistic standpoint. Accordingly, life cannot be created by combining synthesized molecules together. He claimed that there is an "élan vital" – a vital force that fundamentally distinguishes between living and inorganic matter. And no manipulation of inanimate matter is fundamentally incapable of creating anything to which the word "alive" applies.
This point of view, called vitalism, has been brought to our days through the centuries. Galen wrote about the "spirit of the living" in the second century; Louis Pasteur, in order to explain the existence of life in 1862, was looking for a "life-giving impulse"; biologist Hans Driesch spoke about the "life-giving force" as an unchangeable attribute of life in 1894. However, the science of the XX century – with molecular biology at the forefront – stubbornly selected arguments not in favor of vitalism, analyzing more and more new life processes to materialistic "gears". At the same time, Christianity, Islam and Judaism, as well as other religions, continued to assert that the soul is at the heart of life – at least human life.
And suddenly, all these metaphysical views are overshadowed by scientific research, which rather unceremoniously creates life from inanimate "pieces", albeit so far made according to the "patterns" of a living cell. The works of the Venter Institute seem to destroy the argument that some special immaterial force is necessary for the existence of life. In my opinion, this alone puts these achievements on the pedestal of the most significant scientific discoveries in the history of mankind.
Synthesis at the helm of innovation
Steven Benner, Foundation for Applied Molecular Evolution, Gainesville, Florida (USA)
Synthesis itself is not a scientific field. However, this is the basis of a research strategy in any field of science where technology allows you to design new objects for research. Thus, the technology of chemical synthesis for a long time allowed the theory in the field of chemistry to develop at a more intensive pace than in areas where synthesis was not available, for example, in planetary science or biology.
In biology, a turning point occurred in the 1970s, when biotechnology first introduced biological synthesis tools. At first, biologists and genetic engineers could only cut or insert individual genes, only "mixing" what was initially available. Later, in the early 1980s, synthetic biologists managed to deviate from the path laid down by nature, synthesizing genes and creating artificial genetic systems and proteins with a number of amino acids exceeding the natural twenty. [By the way, "orthogonal" ribosomes have already been obtained, capable of reading the genetic code not by triplets, but by quadruplets, using non–natural amino acids for protein synthesis – see, for example, "A four-letter Word." - A. Ch.]
However, in order to achieve more than just mixing the initial components, the synthetic approach must necessarily be "ahead of the whole planet", forcing scientists to struggle with more and more new questions. Thus, synthesis manages the course of research and determines the direction of technological innovation in a fundamentally different way than just observation and analysis.
The main thing that can be learned from the latest publication of Craig Venter's collaborators is that the synthesis and cloning of a genome with a size of 1.08 million nucleotide pairs is something more than just an "extension" of the 1984 work on the synthesis of a gene with a size of about 330 bp (Nambiar K.P. et al., Science 223, 1299-1301; 1984). An increase in the length of the synthesized DNA section by more than 3,000 times has given birth to an impressive bouquet of technologies for the synthesis, verification and manipulation of large volumes of genetic information.
The results of the JCVI researchers may even bridge the gap between chemistry and natural history. Based on the genome sequences of those mycoplasmas with which the scientists worked – M. capricolum, M. genitalium and M. mycoides – it is possible to restore the genetic code of extinct microorganisms – the ancestors of modern mycoplasmas. New technologies allow us to "revive" such organisms and study their metabolism and "habits". These data can tell a lot about the ecology of microbial communities that existed on Earth for 100 million years. years ago, and one day even planetology will benefit from cooperation with synthetic biology.
No one has canceled the natural limits yet
Martin Fussenegger, Professor of Biotechnology and Bioengineering at the Swiss Higher Technical School in Basel
JCVI researchers have an impressive track record: transplantation of entire genomes between related prokaryotic species, assembly of modified genomes from extended sections of synthetic DNA, targeted modification of chromosomes to circumvent the limitations existing in the cell. Now another bright line is added to this list: they have assembled the genome "from scratch" with high accuracy, actually "programming" an entire microorganism.
Of course, this is a technological rather than a conceptual breakthrough. Chimera organisms have long been created by crossing, and more recently by "transplanting" whole genomes into cells with a missing nucleus. Interestingly, nature in all cases seems to "resist" too much pace of genetic changes: mules, although remarkable in many qualities, are sterile, and genetic clones, like the famous transgenic sheep Dolly, inherit the biological age of the genome donor (in other words, they die quickly).
Venter's technological demonstration clearly shows how it is possible to "move from being able to read the genetic code to writing it." However, there is no guarantee that what is written will carry at least some meaning. And if it does, then everything can end like a fairy tale, drama, science fiction or a documentary thriller – to choose from.
During its existence on the planet, humanity has rarely created something fundamentally new; for the most part, it was an improvement and complication of what already existed. It's the same now: the new technology will simply increase the speed at which new organisms can be obtained.
But this speed, together with the frenzied pace of biotechnological innovations, is already causing discomfort, always, however, accompanying technological breakthroughs. And if an organism with a synthetic genome really turns out to be practically useful, it will have to get out of the "greenhouse" conditions of the laboratory and move to ecosystems more natural for living organisms (even if it is just a biotechnological vat). And in these conditions, it will already become clear whether these microorganisms will be able to provide themselves with a decent existence among their "wild" brethren.
Chimeric organisms contain synthetic, but still natural "components", which means that they are subject to an evolutionary process that has not yet been canceled (and cannot be bypassed). Whether "synthetic" organisms will encounter natural limits in the wild, such as reduced fertility and/or life time, only time can tell.
There are spare parts, but there is no manual
James Collins, Professor of Biomedical Engineering, Boston University (USA)
Relax – the hysteria in the press, inflating the achievements of Venter's colleagues to the scale of an act of divine creation, can be safely equated to "jeans". Their work, undoubtedly, significantly advances us in copying living organisms, but it cannot be called the creation of life "from scratch" in any way.
The microorganism from Venter's article is synthetic in the sense that its DNA has been synthesized, and not in the fact that a new form of life has actually been created. That is, the new genome is a copy of the DNA of an existing microorganism – with very small changes.
Researchers working in the field of synthetic biology create artificial "circuits" of proteins, genes or simply DNA fragments that should give the body new qualities. However, these "schematics" are extremely simple and consist of a maximum of a dozen genes – and this simply pales in comparison with hundreds and thousands of genes of a living cell. In fact, it is very difficult to make a normally functioning system even from just two genes – the behavior of the cell too often turns out to be simply unpredictable. Biology is fundamentally complex and confusing, and in most cases does not obey the principles of rational design.
Imagine that scientists have learned to program cells so that they grow into an artificial heart ready for transplantation (by the way, this is not such an unrealistic picture). Of course, a lucky person whose life will be saved using this organ will not be considered a form of artificial life or a synthetic organism. Venter's microorganism is in exactly the same situation – only they don't transplant his heart, but a synthetic genome.
To be honest, scientists just don't know enough to create artificial life. And although the Human Genome project gave us a list of "spare parts", in order to assemble a working cell from them, one little thing is missing – "operation and repair manuals". The situation somewhat resembles an attempt to assemble an airbus from its original parts without the help of specialists - in fact, an impossible task. Some of the synthetic biologists may suffer from megalomania, but our real goals are actually quite modest.
The origin of life is getting closer
David Deamer, Professor of Biomolecular Engineering, University of California, Santa Cruz (USA)
The achievements of scientists from JCVI are biomolecular engineering of the highest standard. However, what the authors themselves do not hide, they intentionally reproduce already existing components of life, and, for example, the cytoplasm of a "synthetic" cell, together with all its contents, is by no means synthetic. This means that the statement of the 17th–century physician William Harvey remains in force: "Omne vivum ex ovo" - "every life from an egg". However, apparently, it won't be for long.
People mastered the embedding of functional genes into bacteria in the 1970s, when they "invented" recombinant DNA. The bacterium captures the plasmid, expresses the gene and produces the required protein. The first commercial use of this phenomenon is on the account of the San Francisco biotech company Genentech, which managed to "persuade" the E. coli bacterium to produce recombinant insulin - this gave rise to a multibillion–dollar industry.
The work of Venter and his colleagues has taken this process to a new level – now it is possible to synthesize and embed a whole genome, rather than individual genes. To prove the potential of this technology, scientists from JCVI intend in the future to obtain a photosynthetic bacterium that could use light energy to split water (to produce hydrogen), similar to how yeast makes alcohol from corn raw materials. If this works out, it will be possible to free millions of hectares from inefficient and burdensome corn cultivation for arable land, and instead get hydrogen in environmentally friendly bioreactors located in the vast expanses of deserts.
Now that the possibility of synthesizing the bacterial genome is becoming commonplace, there is an opportunity to answer one of the most pressing questions of biology – how did life originate? Using the tools of synthetic biology, it will be possible to put aside proteins and DNA, concentrating on a molecule that itself can both catalyze reactions and transfer genetic information – RNA. If it is possible to design and synthesize RNA that catalyzes its own reproduction in an artificial membrane, then it will be possible to seriously talk about creating artificial life in the laboratory, which may repeat the path traversed by the first living forms on Earth about four billion years ago.
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16.06.2010