Modifying life: advances in synthetic biology – Magazine ?

Like manipulating Lego game pieces, scientists design and assemble biological circuits that do not exist in nature. With them they seek to produce vaccines, drugs, biofuels and new materials at low cost.

A biotechnologist sits in front of his computer screen. He clicks and dozens of pages with databases on microorganisms are displayed before him. Among them he selects a bacteria. He now accesses another page full of genetic information. He is assisted by a computer program and, as if editing a text, he dedicates himself to copying and pasting groups of letters that represent DNA fragments to give shape to a novel design. These particular fragments are genetic circuits, that is, sets of genes that result in the “on” or “off” of other genes.

Like a child manipulating the pieces of a Lego-type puzzle, the scientist continues with the selection and assembly of combinations of genetic circuits that will allow him to assemble an “a la carte” microorganism, which does not exist in nature and that will be able to develop pre-programmed functions. .

Once the gene assembly is completed, the researcher uses it in the laboratory to produce the new microorganism with a specific purpose that may be to generate biofuels, detect genetic diseases or eliminate malignant tumors. With the advances in synthetic biology, this scene no longer seems like science fiction.

Goats and spiders

In 2012, researchers from Utah State University, United States, led by Randy Lewis, announced the successful completion of a daring experiment to produce authentic living chimeras: goats to which a spider gene was introduced so that they produced in their milk a essential protein to make spider web.

To produce spider webs on a massive scale, millions of these arthropods would need to be raised and “milked.” But molecular biology professor Randy Lewis decided to try a simpler route: when his goatspiders If they started lactating, I would simply collect and purify their milk to obtain the desired protein.

There could be no shortage of criticism of this and other similar experiments with transgenic animals: many accused Lewis of “playing god” or altering the natural order. The truth is that, despite its spectacular nature, the advances in genetic engineering could soon pale in comparison to the range of possibilities that synthetic biology is opening up.

Now the intention is not only to modify or reconfigure existing organisms, but to design – with the support of computer programs and the large amount of information derived from the explosive rise of genomic sciences – others with desirable characteristics, which may or may not be found. In nature.

“In this field, not only are small modifications made to the genetic information, but genetic circuits are also designed, manipulated, simulated and introduced to organisms,” point out Daniel Aguilar and Isabel Ángeles in their article “Synthetic biology: designing biological systems with genetic pieces”, published in the magazine Biotechnology in 2012.

With this approach – state the authors of the article – “different technological problems are being addressed, such as new forms of synthesis and production of biofuels, biopharmaceuticals and nanostructures.”

artificial organisms

When in 2010 the famous Californian scientist Craig Venter revealed the assembly and self-replication of a bacteria Mycoplasma mycoides —whose artificial genome was inoculated into the carcass of another bacteria devoid of its own DNA—the scientific world was shocked (see As you see? No. 140). Venter’s successful experiment showed that it was possible to design a genome by computer, manufacture it with the necessary chemical elements in the laboratory and implant it in a cell that in turn produces a new one capable of replicating itself following the “instructions” of the synthetic genome. However, by then synthetic biology had already taken other important steps.

“The challenge that Craig Venter faced was technical, but not conceptual, since he was able to build entire chromosomes for the bacteria.” Mycoplasma mycoides”Daniel Aguilar explains in an interview. According to this biotechnologist who graduated from the Biomedical Research Institute, Venter’s merit is that before that work, very long complete DNA fragments had not been produced or synthesized in the laboratory.

In 2003 Jay Keasling, from the University of California, United States, managed to introduce a genetic circuit to produce in the bacteria Escherichia coli a chemical precursor to artemisinin, a drug used against malaria. And in 2010, the American company LS9 genetically modified this same microorganism to produce alkanes and alkenes, which are the basic constituents of gasoline, diesel and jet fuel. This work demonstrated that it is feasible to transfer between organisms the ability to manufacture certain proteins and enzymes, which opens the possibility of transforming carbohydrates into low-cost fuels.

In Mexico there are also groups that have ventured into this discipline. This is the case of the Synthetic Biology and Biosystems Laboratory of the Center for Research and Advanced Studies (Cinvestav) Irapuato Unit. In this laboratory, as its owner, Agustino Martínez Antonio, explains in an interview, lines of research are followed focused on understanding how genetic circuits work and engineering those pieces.

“We want to obtain the minimum elements to make a self-replicating system; That is, a DNA molecule with the genes necessary for a protein or protein complex to form and make copies, like a robot that self-assembles, but at the molecular level.”

Dr. Martínez’s work group, which already has agreements with Mexican companies, also seeks to assemble genetic circuits that can be used to produce compounds used in the food industry such as lycopene, beta-carotene and melanin, in addition to biofuels, at a lower cost.

Another brick in the wall

Some groups within synthetic biology have put their hopes one step further: to make accessible to anyone both the “inventory” of pieces of the puzzle of life and the procedures for assembling them. The goal is that the advances of this science serve the interest of the entire society.

One of the boldest initiatives along these lines is from the Biobricks Foundation (BBF), a non-profit association founded in 2006 at the Massachusetts Institute of Technology (MIT), United States, at the initiative of biologist and computer engineer Tom Knight. Biobricks seeks to establish a common platform with technical standards for the manufacture of interchangeable synthetic biological parts, as is done when building cars or electronic circuits.

“We envision a world in which scientists and engineers work together using freely available standardized biological parts that are safe, ethical, effective and publicly accessible to provide solutions to the problems facing humanity,” says a BBF statement on its website.

Assembly protocol 10, developed by Knight and based on the use of restriction enzymes, which function as “molecular scissors” to cut DNA fragments, was the first to be used. This method allows you to build – continuing with the Lego game analogy – modules that are functional, but has certain limitations. For example, when linking two biobricks, “scar” base pairs are produced between them that are not recognized by restriction enzymes (they do not completely “fit” into the puzzle), which prevents the formation of chimeric proteins, that is, resulting from the fusion of two or more genes that originally coded for two different proteins.

For this reason, in the last decade, other more effective standards were introduced that allow overcoming the obstacles that limit the assembly of biological parts, such as Silver and Freiburg.

The first—introduced by researcher Pamela Silver, from Harvard University and also known as Biofusion—allows the length of the “scar” to be reduced from eight to only six “letters” of DNA, and with it the fusion of proteins.

The other method, developed by a group at the University of Freiburg, Germany, introduced the use of additional restriction enzymes to cut the genetic fragments. Although the size of the “scars” remains at six base pairs, they encode other proteins that are more stable.

Other DNA amplification and synthesis methods such as Gibson assembly or SLIC (Sequence and Ligation Independent Cloning) allow the assembly of multiple biological parts without the need to cut or glue segments, since they do not require restriction enzymes, according to Daniel Aguilar. Both the Gibson method—invented in 2009 by Daniel Gibson of the J. Craig Venter Institute—and the SLIC—developed in 2007 by researchers Mamie Li and Stephen Elledge—make it feasible to join many DNA fragments in a single reaction, without the need for that the parts are compatible. The latter enables a more efficient and reproducible assembly of recombinant DNA with five or even 10 fragments simultaneously, as described by its authors in an article published in the journal Nature Methods in February 2007.

“With these two techniques, you only need nucleotides (the “letters” of the genetic code, A, C, G, T) that have sequences in common with the two pieces that are going to be glued and then, through a chain reaction of the polymerase (RPC) the entire segment is amplified,” details Aguilar. PCR allows multiple copies of DNA fragments to be obtained; It was developed by the American biochemist Kary Mullis and for this he received the Nobel Prize in Chemistry in 1993.