11.3: Synthetic Biology

Biotech Focus

Can you synthesize an organism's entire genome?

The answer to this question is yes. In 2002, scientists in the US synthesized an "artificial" viral genome for the first time when they recreated the polio virus genome from scratch. Their work brought attention to the risk that synthetic biology could be used to develop biological weapons.The first synthetic bacterial genome was completed 6 years later with the synthesis of the Mycoplasm genitalium genome, a bacterium that causes urinary and genital tract infections in humans. In 2017, another group of scientists partially synthesized the genome of Saccharomyces cerevisiae, the yeast that is used to make bread and brew wine and beer. Today, researchers are continuing to push the limits of synthetic biology and DNA-synthesis technology in order to help understand how genomes work. Researchers

One group of researchers, called the "Genome Project-Write" (GP-Write)", is seeking to synthesize, or "write" the human genome, in addition to the genomes of other plants and animals important to agriculture and public health. However, like the work on the polio virus, ethical concerns have been raised in association with GP-Write. What is the exact purpose of artificially creating a human genome? Will the work be restricted to cell lines or be used to alter human embryos. How synthetic biology and artificial genomes will continue to develop will definitely be an area to keep an eye on.

To learn more about synthetic biology and what it can do, check out the National Institute of Health (NIH) webpage on synthetic biology.

Introduction

Synthetic biology is a field of science that combines biology and engineering to design and build new biological parts, systems, or organisms. In synthetic biology, organisms are often completely "redesigned" to give them new abilities, like produce a produce a new therapeutic compound, detect a toxin, or make enzymes that turn sugars into biofuels. Alternatively, entirely new organisms can be built from the "ground up". Synthetic biology is analogous to computer programming, but instead of writing code, scientists use DNA, RNA, and proteins to write new genetic "software" that makes "old" cells behave in "new" ways.

Synthetic biology is often confused with genetic engineering. Genetic engineering is the direct modification of an organism's DNA using biotechnology. It focuses on using genes that are already found in nature and involves the insertion of new genes into an organism's genome, or the editing of the genome by either deleting a gene or changing its sequence. Based on this, genetic engineering is part of synthetic biology. However, synthetic biology is a more advanced and design-oriented field that builds new biological parts, systems, or even organisms that may not exist in nature at all.

Learning Objectives

Synthetic biology combines the techniques of biology and engineering to create new biological systems. At the end of this page, you will be able to:

• Explain synthetic biology and its importance
• Explain BioBricks and list some of the common parts used

Synthetic Biology Applications

The applications of synthetic biology are wide and varied. Examples include building synthetic circuits in bacteria to make them behave like computers or creating entirely new synthetic genomes like the Synthetic Yeast Project. However, one of the most well-known examples of synthetic biology is the production of lab grown "meat". Since the introduction of the first cultured beef hamburger in 2013, snthetic biology is allowing researchers to rethink meat production by growing meat without animals. To do this, a sample of animal cells (e.g. cow or chicken muscle cells) is collected without harming the donor animal. The cells are placed into a bioreactor containing a nutrient-rich culture medium that mimics what they would be exposed to in the animal's body. The cells are induced to grow rapidly, differentiate into muscle and fat tissue, and then formed into something that resembles meat. Improvements in this technology have allowed for improved taste and texture, enhanced nutritional content, and cell growth using synthetic alternatives to animal serum. Today the global lab-grown meat "market" has increased, with companies like Upside Foods (USA) and GOOD Meat (Singapore) being among the first companies to sale lab-grown "chicken" to customers.

Figure \(\PageIndex{1}\): The Cultivated Hamburger. Lab-grown meat can be used to make delicious hamburgers. (First cultivated hamburger by Mosa Meat; CC BY 4.0)

Lab-grown meat is a more conventional application of synthetic biology, but there are others that may seem more in the realm of science fiction than science. Today, researchers are exploring the use of synthetic biology in order to produce self-healing materials like concrete, metal, and plastic. For this, scientists engineer microbes or biological components (like proteins or enzymes) and embed them in a material. When damage happens, these biological agents activate and “heal” the material. Engineered bacteria, like Bacillus subtilis, have been mixed into concrete to product a "bio-concrete". This bio-concrete, when cracked, allows the entrance of water and activates the bacteria to begin to produce limestone, thus sealing the crack. Synthetic biology and bio-concrete have been proposed as a way of extending the life of roads, bridges, and buildings. Similarly, scientists have embedded engineered yeast or E. coli into hydrogels and plastics, enabling them to detect stress or damage and respond by producing repair proteins that mend the material. This approach could be used to make materials more sustainable rather than disposable and could even be used on spacecraft or space stations to repair damage on their own.

BioBricks

BioBricks are standardized DNA sequences (i.e. "parts) that encode biological functions and can be easily assembled together physically to build new biological "circuits". These synthetic biological circuits can then be incorporated into living cells to construct new biological systems.

Examples of BioBrick parts include the:

1. promoter which directs gene expression
2. ribosome binding site (RBS) that helps start protein production via translation
3. gene or coding sequence
4. terminator which tells the cell when to stop translating the coding sequence

BioBrick parts are used according to a specific hierarchy (Figure \(\PageIndex{2}\)). Specifically, the BioBrick parts (e.g. promoter, RBS etc...) are combined to form a "device" - a genetic circuit to perform a defined function. A complementary set of devices can then be combined as a biological system to perform a high-level task.

Figure \(\PageIndex{2}\): Biobricks are used in synthetic biology. Each BioBrick, known as a "part", is a DNA sequence. The BioBrick parts of promoter (P), ribosome binding site (RBS), coding sequence (CDS), and terminator sequence (T) are ligated together in a plasmid to form a "device" or biological circuit. Several circuits are combined to form a "system" or biological system (BioBricks by Patricia Zuk, CC BY 4.0; modified from Abstraction Hierarchy by Shammie23, CC BY-SA 3.0)

To create a synthetic system using BioBricks, each part is cloned into a plasmid. The sequences flanking each part are specific restriction sites that allow the BioBrick parts to be digested out of their plasmid and then ligated into another plasmid in a specific order - not unlike snapping several Lego bricks together to make a bigger toy. These restriction sites are standardized across all BioBricks. The "prefix" restriction site at the start of the part's sequence is either EcoRI, NotI, or XbaI. The "suffix" restriction sites found at the end of the sequence are either SpeI, NotI, or PstI. Ultimately, when these parts are ligated to one another in their desired order, the majority of the restriction sites are eliminated to prevent the accidental removal of a key BioBrick part. However, the flanking sites at the extreme ends are still intact, allowing for the addition of more parts or the transfer of the assembled parts. To learn more about restriction sites and ligation, go to Chapter 4.1 Principles of Genetic Engineering and Chapter 4.2 Creating Recombinant DNA.

Concept in Action

BioBrick Assembly

Testing of BioBrick systems are often done using cell-free systems or a "chassis" - a host organism (like E.coli or yeast) that is used to "run" synthetic genetic circuits. A chassis in synthetic biology is not unlike the hardware of the computer that runs the newly written software. Choosing the right chassis is important in synthetic biology. This is because different chassis have different metabolisms, growth rates, and tolerances. Others are better for industrial-scale production, drug delivery, or biosensoring.

Common chassis organisms used in synthetic biology include:

• E. coli - fast-growing, well-studied, and easy to modify
• Saccharomyces cerevisiae - a eukaryotic chassis used for more complex tasks, like producing drugs of biofuels
• Cyanobacteria - used as photosynthetic chassis to produce energy
• Mammalian cells - used for advanced medical or therapeutic applications

Numerous applications of BioBricks are being proposed each and every day. One way could be in the creation of biosensors within cells capable of detecting biotoxins like heavy metals in cells (Figure \(\PageIndex{3}\)). Others include detection systems for pests in agriculture, systems for carbon capture, and the creation of chemical "factories" that would produce things like complex flavors, fragrances, and materials.

Figure \(\PageIndex{3}\): Heavy metal detection using BioBricks. BioBricks are assembled in Circuit 1 for the expression of a DNA-binding protein that act as a molecular "switch" (Switch A) for the detection of arsenic (As). A similar switch protein (Switch B) that detects mercury (Hg) is expressed using Circuit 2. These switch proteins control gene expression from Circuit 3. Switch protein A binds arsenic (A-As) which then binds to its promoter, driving expression of green fluorescent protein (GFP) from its coding sequence. Switch protein B binds mercury (B-Hg). Binding of this switch to its promoter drives expression of red fluorescent protein (RFP). (BioBrick Detection of Heavy Metals by Patricia Zuk; CC BY 4.0)

Key Concepts

Synthetic biology is a combination of biology and engineering and is used to modify or create genetic "circuits" in cells that changes the function of a cell

Some important concepts to remember are:

• synthetic biology uses engineering principles on biological systems
• synthetic biology treats DNA like software code, editing it or creating it, in order to given an organism a new function
• synthetic biology can be applied to medicine, agriculture, energy, and the environment
• one aspect of synthetic biology is the use of BioBricks
• BioBricks are standardized DNA sequences that can be linked together to form a "circuit" - a system for expression of a gene multiple circuits can be combined to create synthetic biological systems

Glossary

 

Bioengineering - the application of engineering principles to biological systems for the development of technologies and products

BioBricks - standardized DNA sequences called "parts" with defined functions that can be combined to build synthetic genes and circuits; includes parts like promoters, ribosomal binding sequences, coding sequences, and terminator sequence

Biosensor - a device that uses a biological component, like an enzyme, antibody, cell, or DNA sequence ) to detect and measure specific chemicals, substances, or conditions and convert them into a signal (like light, electricity, or color change)

Cell-free system - a synthetic environment outside living cells where biological reactions can occur using extracted cellular components like enzymes and ribosomes

Coding sequence (CDS) - the sequence of DNA that is ultimately translated into a polypeptide by ribosomes

Genetic circuit - a designed combination of genes and regulatory elements that control how a cell behaves, similar to electronic circuits

Genome - the totality of genetic information found within a cell

Promoter sequence (promoter) - a sequence of DNA where the RNA polymerase binds; determines the site of transcription initiation

Restriction enzyme - an endonuclease that cuts the DNA at a specific sequence called a restriction sequence

Restriction sequence - the sequence of DNA cut by a restriction enzyme

Restriction site - the physical location of a restriction sequence in a DNA sequence

Ribosomal Binding Site (RBS) - a short sequence found in messenger RNA (mRNA) that signals the ribosome where to start translating the mRNA into a protein

Synthetic genome - a genome that has been entirely built from synthetic DNA rather than copied from nature

Terminator sequence - a short sequence found in mRNA that signals where the ribosome stops its translation