Authors: S. V. Amitha Mithra*,1, Amolkumar U. Solanke1 and Basavaprabhu L. Patil2
1ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi
2ICAR-Indian Institute of Horticultural Research (IIHR), Bangalore
*Corresponding author: amithamithra.nrcpb@gmail.com
Synthetic Biology refers to the engineering part of biology i.e., creating complex systems based on biological concepts and inputs (individual amino acids or proteins, or cells or tissues or organs or complete organisms), which display functions that do not exist in nature. Structures of living organisms are an engineer’s delight as they can grow, self-assemble, regulate, heal and adapt themselves to change in both external and internal environments. Thus Synthetic Biology tends to engineer complete life or component life forms which eventually might have practical applications such as designing of new organs, new shapes etc., for practical applications such as bioenergetics, bio-computation, organ replacement, cancer treatment and information storage. Synthetic Biology inputs are bases, amino acids, genes, proteins, and circuits, which can self-assemble to create new biological function(s). Synthetic Biology can operate at all levels from proteins to organs.
Seeds of synthetic biology were sown when in-vitro DNA synthesis of oligonucleotide primers and probes were initiated which later extended to synthesis of complete genes and gene constructs. Stomatostatin was the first artificial gene synthesized. In 2004, a synthetic, ~32 kbp long polyketide synthase gene cluster from Escherichia coli was synthesized, assembled and its functionality was tested. This was a huge feet towards development of Synthetic Biology as till then only fragments as long as 5 Kbp (equivalent to size of a small virus genome) could be synthesized. This is a marvellous accomplishment as longer the DNA strands, more brittle they are, and their assembly is highly complicated. A real mile stone in synthetic biology was achieved in 2017 by Craig Venter’s research group which demonstrated synthesis and assembly of ~ 6 Mbp long genome of a disease causing bacterium, Mycoplasma genitalium strain JCVI-1.0. Only at this point Biotechnology could be truly described as Synthetic Biology. But still this is only DNA synthesis but not engineering of a complete living cell.
At functional level (DNA is structural while RNA, protein, metabolite and cell and its components are functional), Biotechnology has already made it possible to improve the production of enzymes or hormones or metabolites by manipulating some of the components in its metabolic network using standard molecular biology tools. Synthetic Biology is beyond such manipulations wherein new metabolites are engineered by exogenous supply of the components (such as bases, amino acids and some essential proteins) followed by self-synthesis and assembly of the components. Engineering of proteins, new circuits and organs with new functions or properties is the essence of Synthetic Biology. Some examples of advancements made in this direction are briefed below:
- Ribozyme switches marked the beginning of Synthetic Biology. They were designed with their functionality based on ligand binding and structure on RNA framework, for use as gene-regulatory systems. Such switches possess very desirable properties like target specificity, inducible regulation, better cleavage kinetics and design modularity. Their functionality has been demonstrated has been demonstrated in bacteria, yeast and mammalian systems.
- Designing new genetic circuits in bacteria and eukaryotes is the major area of Synthetic Biology that has witnessed remarkable developments. Another such major area is protein design which had provided us with a lot of insights on protein folding, stability and function.
- Partial redesigning of the T7 bacteriophage with the hypothesis that overlapping regions are non-essential is a notable example of a larger system that has been redesigned. Such experiments help in contributing to gain fundamental insights into biological processes such as gene transcription and translation, cell communication, the role and sources of biological noise and the existence of biological modules.
- A recent development in this direction has been made by Toda et al (2018). In nature, Notch receptors present on cell membranes have the ability to sense Delta proteins which are present on the surface of neighbouring cells. Notch receptors have intracellular ligand binding domains called as effectors which help in mediating gene expression and subsequently signalling. This common signalling pathway, called as Delta-Notch, has inspired Toda et al. to design a cell communication system called synNotch3. In synNotch, the natural core of the Notch protein is used while the ligand that is sensed and the effector domain that responds are customizable. Using this principle, it is possible to create multiple ligand and effector pairs resulting in modifiable cell–cell communication. Cadherin proteins mediate cell–cell adhesion, and so are essential for spatial organization of tissues. Toda et al., used synNotch sensors and genes encoding cadherin proteins tagged with fluorescent proteins and successfully demonstrated formation of shapes upon mixing of different cell types. This is a major feet towards development of shapes using developmental programs.
References:
1. Chan LY, Kosuri S, Endy D (2005) Refactoring bacteriophage T7. Mol Syst Biol 1: 0018
2. J. Craig Venter Institute. "Scientists Create First Synthetic Bacterial Genome -- Largest Chemically Defined Structure Synthesized In The Lab." ScienceDaily. ScienceDaily, 24 January 2008.
3. Kennedy AB, Vowles JV, d'Espaux L, Smolke CD (2014) Protein-responsive ribozyme switches in eukaryotic cells. Nucleic Acids Res. 42(19): 12306-12321.
4. Kodumal SJ, Patel KG, Reid R, Menzella HG, Welch M and Santi DV (2004) Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Nat. Academy Sci., USA, 101 (44): 15573-15578.
5. Serrano L (2007) Synthetic biology: promises and challenges. Mol Syst Biol. 3: 158.
6. Toda S, Blauch LR, Tang SKY, Morsut L and Lim WA (2018) Programming self-organizing multicellular structures with synthetic cell-cell signalling. Science Vol. 361, Issue 6398, pp. 156-162
About Author / Additional Info: