Synthetic biology

Constructing life in the laboratory?

Synthetic bio cell
Synthetic bio cell
23 JUL 2016
by

Judging from the first international meetings on this term, synthetic biology (SB) is only 20-25 years old. The brochure of the last synthetic biology congress in London (2014) opens up with a sentence stating that SB was predicted to be worth 10.8 billion dollars by 2016. Not bad, then, for a new branch of life sciences. For some, however, SB is not really a novel branch of science, but actually a new dress for bioengineering within the broader field of biotechnology. But there was something qualitatively new and very ambitious in the program of SB: to create new forms of life, alternative to the extant ones. This, mostly with the aim to tackle the energy problems of our world (new biofuels), and to produce new drugs. In fact, most of its success is due to the interest that SB induced in the pharma industry, the perspective of new drugs; but SB is under study also for the perspectives of making fine chemicals, as well as for making biofuels. Just to give an idea, Richard Kitney of the Imperial College in London introduced the notion of “from oil-based feedstock – which gives all possible products to bio-based feedstock,” looking namely at the importance of SB in plants.

The field of SB has several working directions now, and, correspondingly, is being classified into different sub-fields. For me, the fundamental difference is between the genetic engineering approach (genetic manipulation) and the kind of SB that is based on chemical synthesis or chemical procedures without interfering with the extant genomes.

The case of engineering SB

Engineering is the most popular branch of SB. As already said, this mostly involves genetic engineering, namely the manipulation of genes, and/or entire genomes. I have summarized in the notes some examples of relatively recent papers, not at all an exhaustive list, but just to give an idea of the breath of the field.

What are the operations performed by molecular biologists to carry out their genetic manipulations? I cannot give here the molecular biology details, but only the principles. To do so, look at Figure 2. This may represent the genome of an organism containing, for the sake of simplicity, only four genetic elements A, B, C and D.

In Figure 2 (a), one or more elements are eliminated, in what is generally called the “knockout procedure.” A well-known example is the work of Venter’s group with Mycoplasma genitalium, where the original 475 genes have been reduced to 380. Figure 2 (b) illustrates instead the case in which one gene is added to a pre-existing organism. The organism is now supposed to perform all his previous functions, plus the new ones due to the added E element. Figure 2 (c) illustrates the replacement of a genomic part. A good example is the work by Lee et al. (2008), who operate on the metabolic engineering for enforcing – or removing – the existing metabolic pathways toward enhanced product formation.

The extreme case of Figure 2 (c) is when the entire genome is substituted. This has been the case with the work of Venter with Micoplasma genitalium. In this case, the entire genome has been synthesized in vitro, and exchanged with the original, natural one. The modified organism was viable, which was taken by the mass media (but not only) as an indication that life was synthesized from scratch. This is, of course, not true, as we are seeing here a kind of organ transplant.

From this simple illustrations, and from the examples cited in the notes, one can understand that, from a philosophical point of view, we are dealing with a form of reductionism: bacterial life is seen as the sum of elements or circuits which can be eliminated and added as independent parts. And we are dealing with a teleology scheme, in the sense that the aim is predetermined and all operations are finalized to achieve such an aim. For the full philosophical implications, the reader is referred to the second edition of my book on The Emergence of Life (Cambridge Univ. Press, 2016).

Chemical SB

You see things as they are and you say, “Why?” But I dream things that never were, and I say, “Why not?
(George Bernard Shaw)

It is proper to say that SB has a double soul. One corresponds to the bioengineering approach outlined above, with the aim of changing the extant bacterial life to bend it to our needs. The other “soul” corresponds instead to a more philosophical, basic question: “why did nature do things in a certain way, and not in another one?”. Why 20 amino acids, and not 15, or 50? Why do nucleic acids contain ribose instead of glucose? Must mammalian hemoglobin be constituted by four chains, why not six or twelve? And: why didn’t nature make much simpler cells?

SB possesses the tools that may permit us to tackle this kind of questions: let us synthesize the alternative form, and see whether there are some reasons why nature did so and not otherwise. And you can do that without genetic manipulations-just using the classic old tools of chemistry. This kind of questioning (why this and not that?) links to the dichotomy between determinism and contingency: are the things of nature the way they are, simply because there were no other ways to make them (“absolute determinism”)? Alternatively, are they the way they are, due to contingency – something that some time ago, less properly and less fashionably, we used to call “chance”?

Take the example of the work by Albert Eschenmoser and collaborators at the Swiss Federal Institute of Technology in Zurich (ETH-Z). The question here was “why has nature chosen ribose as the sugar to associate to nucleic acids? Why not glucose, which is more stable, and more diffuse in nature?” This is a typical “why this and not that” question, and can be tackled with SB, “simply” making in the lab the synthesis of nucleic acids containing pyranose instead of ribose. The authors did so, and on the basis of their work, they arrived at some important conclusions on the possible relevance of ribose and RNA in nature.

Still in the vast camp of nucleic acid, there is the question of the four bases, A, T, G, and C. Are they the product of determinism, in the sense that the genetic code and DNA replication can only work with these particular chemical structures? Or then, again, are they the product of contingency, and DNA could have worked with different the chemical structure?

This important question has been tackled by Steve Benner and his group in 2005, who synthesized nucleic acids built up with bases different from the canonical ones. And jumping from nucleic acids to proteins, take the work of Doi et al. in Yanagawa’s group on proteins with a reduced alphabet of amino acids. They were able to make functional enzymes having 15 or even less different amino acids.

To the world of proteins belongs an even more fundamental question: why these proteins which we have now, and not others? This question has led in 2006 to the synthesis of proteins which do not exist in nature – the so-called “never born proteins” -(see details in my cited new book). And there is another important question that comes to mind, and that can be tackled with the tools of chemical SB: “why are cells, even the simplest bacterial ones, so complex, being constituted by thousands of genes?”. Isn’t possible to make by SB simplified cells constituted, for example, by a few dozens of genes?” –as they probably were at the beginning of life on Earth?

These questions, lead the way to the attempt to make cellular life in the laboratory- indeed one of the main general targets of SB. For that, the reader is again referred to more specific sources.

By way of conclusion

The notion of “new forms of life” has evoked strong reactions from the mass media, mostly because of the fear of engineered new, unknown, and potentially dangerous forms of life: bacteria, for example, that can bring about some new epidemic disease. I believe, as many professionals in the field do, that such fears are out of place; that SB will further develop giving us rich surprises; and that, at the same time, bioethical questioning must always be present in this kind of work.

About that, there is a general point. SB on bacteria must in fact be seen within a larger frame of higher organisms - think of the cloning experiments of Dolly’s memory, all the GMO problems, and stem cells, organisms hybridization…This is a new dimension in human history, an additional step in the Baconian dominion on nature: mankind, after having taken the dominion over the sky, the ocean, the ores, all lands and forests, and over all animals, is taking power over the last stronghold of nature: life itself.

There is no way to stop this, as this is part of our own evolution. The only thing we can do is to remain alert, and do community work so as to shift this evolution towards goals which enrich humanity- canceling without hesitation all those which, being founded on profit or insanity, will carry us instead towards more destruction.

References: titles of some characteristic papers in the field of bioengineering of SB (sorry that for space reason, the full references with Journal and page number could not be given).

Engineering a synthetic dual organism system for hydrogen production (Waks and Silver, 2009)
Metabolic engineering for advanced biofuels production from Escherichia coli (Atsumi and Liao, 2008) Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels (Lee et al., 2008)
Light- energy conversion in engineered microorganisms (Johnson and Schmidt- Dannert, 2008)
Towards systems metabolic engineering of microorganisms for amino acid production (Park and Lee, 2008). And some, where you see clearly the notion of circuits, e.g., Principles of cell-free genetic circuit assembly (Noireaux et al., 2003)
Engineering prokaryotic gene circuits (Michalodimitrakis and Isalan, 2009)
Reconstruction of genetic circuits (Sprinzak and Elowitz, 2005)
Toward scalable parts families for predictable design of biological circuits (Lucks et al., 2008)
Digital switching in a biosensor circuit via programmable timing of gene availability). And just a couple about pharmaceuticals, e.g. from Fussenegger’s group (Weber et al., 2009) on biotin- triggered genetic switch, which enabled dose-dependent vitamin H control in certain cell lines; Chang and Keasling (2006) on production of isoprenoid pharmaceuticals by engineered microbes; and that by G. Stephanopoulos’ group (Ajikumar et al., 2008) on terpenoid synthesis from microorganisms. There is a lot of work on yeast chromosome biology, and in this regard, one should mention that there is now an international consortium (United Kingdom, Germany, United States, and France) for the work on yeast, the so-called Saccharomyces cerevisiae 2.0 (Sc2.0) project (Dymond et al., 2011; Annaluru et al., 2014).
The Sc2.0 project aims specifically at designing synthetic chromosomes and to generate eukaryotic cells driven by these fully synthetic chromosomes.