Synthetic Biology and Genetic Engineering: No, We Aren’t Creating X-Men

November 7, 2023
Science Magazine

Will genetically modified crops turn us into X-men? What if scientists accidentally create zombies in the lab? Is the government going to zap us into clones of each other?

As biotechnology enters the public sphere, misunderstandings surrounding recent biotechnological advancements—especially those involving gene editing—have inevitably arisen.

So what exactly is synthetic biology, the field that encompasses gene editing? The dictionary definition describes “a multidisciplinary field of biotechnology that involves engineering the genetic material of organisms to have new characteristics.” But in reality, synthetic biology isn’t that different from selective breeding. Technically speaking, domesticated dogs and cats are genetically modified organisms (GMOs). Centuries of farming have optimized the genetic traits of plants we use to cook since before we used the term “DNA.” Synthetic biology is simply a faster and more controlled way of accomplishing this selection among organism traits—and it can produce a wider range of beneficial effects.

Proteins and nucleic acids, two of the most important types of biomolecules, act at the center of synthetic biology. Proteins are responsible for many functions: they connect cells into stronger tissues, act as hormonal signals and signal reception devices, regulate welcome and unwelcome microbes, and facilitate every important chemical reaction that occurs within organisms. 

As a result of these many functions, most synthetic biology research seeks to insert or modify genetic sequences to gain or modify a known protein. Given the diverse set of functions these proteins have, synthetic biology could become a pathway to solving a wide range of problems. 

So what exactly would this look like in a lab? Recombinant DNA—DNA produced by combining sequences of multiple organisms—is one of the most fundamental synthetic biology techniques. Due to its simplicity and accessibility compared to other bacteria, E. coli is commonly used as the base organism for synthetic biology and can be engineered with recombinant DNA to produce proteins that are usually produced in other organisms, including humans. 

Above: Plasmids combining the DNA sequences of multiple organisms are inserted into bacteria, making recombinant bacteria. Courtesy of the National Human Genome Research Institute

To begin the process of producing recombinant proteins using E. coli, researchers must first find and select the desired gene sequence. For example, researchers could focus on the human genome sequence that encodes insulin, a hormonal protein that signals body cells to uptake blood sugar. Next, researchers design and synthesize the genetic sequence. As a bacterium, a significant amount of E. coli’s genetic information is encoded in plasmids, or circular structures of DNA. To convert a human gene to a plasmid form, researchers can either redesign a plasmid that contains the sequence of insulin or insert the insulin gene into preexisting, cut-open plasmids. After the genes are inserted, the new plasmid is re-inserted into an organism—though this process varies between organisms. In E. coli, electricity or heat can create pores in the bacterial membrane, allowing the plasmids to enter. Lastly, by providing nutrients and other necessary chemicals for protein synthesis, the gene of interest within the plasmid can be expressed at high amounts, and the protein produced by the bacterium can be harvested for medical purposes. 

Thus, synthetic biology presents a wide range of advantages:

  • Using a simple base, such as E. coli, and a simple DNA structure, such as a plasmid, allows scientists to easily construct functional complex genomes. 
  • Inserting genes from complex organisms into simpler organisms such as E. coli lessens the chance of interfering with other biochemical processes, and environmental factors can be controlled in a lab.
  • Over time, higher-efficiency bacterial expression and reproduction methods will result in cheaper, more accessible products.
  • Recent innovation suggests that synthetic biology could play a role in developing eco-friendly materials as well as more sustainable production methods.
  • Unlike selective breeding, synthetic biology is not limited to organisms that reproduce sexually or traits that currently exist within the targeted organism.

Recombinant DNA is already an astonishing technique that can lead to impressive results: mass-producing other protein drugs, producing natural proteins (such as spider silk) for usable materials, or even causing new traits (such as fluorescence from green fluorescence protein) to arise in other organisms. However, the example of insulin production is only a small piece of the field that synthetic biology has developed into. Rather than being limited to single genes, researchers can completely rethink and reconstruct plasmids, achieving more complex methods including metabolic engineering, genetic circuits, and directed evolution. 

Metabolic Engineering

Metabolic engineering is another method within synthetic biology that utilizes recombinant DNA. Instead of being limited to the direct collection of a protein, metabolic engineering often uses the expression of enzymes or enzyme cascades, which can continuously generate protein and non-protein products from given reactants. If employed in the right organisms, this technique removes the need for researchers to intervene in the process of harvesting and using the products. 

The classic example of metabolic engineering is the Golden Rice Project, which uses enzymes to synthesize beta-carotene out of preexisting compounds and create a new genetically modified crop. A more recent example is the bioremediation—or use of organisms to process environmental pollutants—of a toxic plastic processing chemical called DEHP. Researchers constructed a plasmid containing two enzymes discovered in a strain of Gordonia bacteria, which are respectively capable of hydrolyzing DEHP into MEHP and hydrolyzing MEHP into phthalic acid, which is less harmful to the body. 

Above: Enzyme cascades required for the production of beta-carotene from GGPP in “Golden Rice” (left) and the degradation of phthalic acid esters including DEHP into phthalic acid (right). Courtesy of the Golden Rice Project and the Journal of Agricultural and Food Chemistry

Genetic Circuits

Genetic circuits are another new concept within synthetic biology. This technology has become important in environmental protection efforts as well as human health and safety protection. Genetic circuits use various combinations of genes and different inputs—like heat, light, or chemicals—to produce different outputs. 

One application for genetic circuits is biosensors, which use biomolecules to generate signals that indicate the level of a certain substance in a given environment. One study used a transcription factor—a protein that acts as an “if…then” statement for protein production—to create a biosensor for phthalic acid, a product of DEHP degradation. In the genome they constructed, researchers modified a transcription factor, allowing it to bind to phthalic acid and induce expression of green fluorescence protein. By inserting this genome into E. coli, researchers were able to then use these E. coli to accurately detect concentrations of phthalic acid in water by measuring the level of fluorescence produced by the bacterial colonies. 

Above: Transcription factor proteins that bind to phthalic acid can bind to subsequent parts of the genome and induce the expression of detectable proteins. Courtesy of ACS Synthetic Biology

Directed Evolution

Another interesting method derived from synthetic biology is directed evolution. This concept involves making a large number of small modifications to a genome and screening the results for desirable effects, thus simulating genetic diversity and natural selection. By using techniques such as recombinant DNA and metabolic engineering, desired target genes for directed evolution can be isolated for modifications, while genetic circuits can be used adjacently for efficient and effective screening. 

In fact, the long-term goal of the phthalic acid biosensor study at East China University is to employ directed evolution on the DEHP biodegradation enzyme cascade. Error-prone PCR, a type of PCR that uses a faulty polymerase, intentionally inserts a wide variety of mutations into the DEHP-degrading genome created through metabolic engineering. Then, the fluorescence biosensor for phthalic acid can easily detect the speed and capacity at which different variants of the cascade can break down DEHP. As a result, researchers can identify mutated versions of the enzyme cascade that are more effective by simply measuring fluorescence over time. 

Above: A cell that contains a plasmid for the enzyme cascade, as well as a biosensor plasmid, is able to measure the effectiveness of the DEHP degradation enzymes by increasing fluorescence as more DEHP is biodegraded. Courtesy of ACS Synthetic Biology.

Scientists are only beginning to uncover the potential of synthetic biology. Whether breaking down pollutants, increasing the nutritional value of agriculture, mass-producing important protein therapeutics, or producing biological sources of energy, possibilities seem limitless for this ever-growing field of science and engineering. 

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