Bansod Akash Anand1 & A C Reddy2*
*aswinchilakala@nipgr.ac.in
1- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore
2- National Institute of Plant Genome Research, New Delhi.
Abstract:
Synthetic biology is a new interdisciplinary field of biology which is emerging as a powerful tool which will be able to design, engineer, and synthesize life forms which were never existed before. Synthetic biology firstly involves modification of existing genetic material by incorporating synthetic DNA sequences and/or removing the junk pieces in it or secondly by completely synthesizing a new genome and incorporating it in live cells. The approaches used for engineering synthetic genomes, its methodology are discussed. Furthermore, insights on recent advances, current challenges, governing authorities across nations, and future prospects of synthetic biology has been included in the current article.
Introduction
Since the dawn of human civilization, humans have a strong urge to be superior to the rest of the planet’s living things. This urge never stopped; instead, it stayed there for generations, increased enormously with evolution, and still existed in the modern era. In today’s world, most developed nations show their power and strength through the means of military and nuclear weapons they possess. The industrial revolution has made such difficult things possible. But wait, what if I tell you that a nation declares itself as a superpower as they have created real-life Superhuman, aka Superman.
What is SYNTHETIC BIOLOGY? For understanding it clearly, we will simplify the complex meaning behind it. As the name suggests, Synthetic biology simply means artificially made/engineered (synthetic) genomes (life). Basic biology says that all the 2303320living organisms existing are made up of cells controlled by the genetic material inside them. It is called nucleic acids (genetic material/ All the genes present in an organism). These nucleic acids control all the necessary and metabolic activities to carry out the cell’s life functions. In synthetic biology, these genes, genetic pathways, and genetic networks are altered or rearranged to produce the desired organism.
Now let’s discuss in detail Synthetic genome engineering (SGE), a sub-discipline of synthetic biology; this aims to (re-)design and fabrication of biological entities or components and biological systems that do not already exist on planet earth. It also combines the chemical synthesis of DNA (synthetic DNA) to manufacture cataloged DNA sequences and their assembly into whole new genomes. This creates another question regarding the existing genetic engineering technology and CRISPR technology.
How a Synthetic genome engineering (SGE) is different from Genetic engineering (Genome editing), there may be a doubt? Let’s clear it, according to the National Institute of Health (NIH), in genome editing, researchers typically use specific techniques and tools to make small but significant changes to the organism’s DNA. In contrast, synthetic genome engineering involves long stretches of DNA (genes found in other organisms or be completely novel) to be stitched together to create an artificially synthesized genome. Moreover, synthetic genome engineering facilitates us to make changes throughout the genome, which seems over the limits of genome editing. Only a small stretch of DNA is being manipulated.
There are two approaches for it as explained in Figure 2: 1) Top-down: An older model can be redesigned to make the existing model more efficient (reducing the complexity of the existing system and creating a small-sized system), and the second one is 2) Bottom-up:
A new model can be designed from scratch (individual parts are synthesized and reassembled to create a new system). For SGE, mostly, the bottom-up approach is used.
Methodology: When we look for the methodology of synthetic genome engineering, it starts with designing a prototype or blueprint of the genome we wish to engineer using platforms like J. Craig Venter, CEO of Synthetic Genomics Inc. Biostudio. This software enables us to explore four main aspects such as 1) Recoding: it is one of the simplest features which is mostly used for the purpose of recording the codons (3-digit code of amino acids which are building blocks of proteins), designing restriction sites and PCR tags. Next is 2) Modularization: which allows designing the DNA fragment sizes required for the assembly of genome, 3) Add-in: which allows us to add the desired sequences from existing organisms and 4) Simplification: which involves reducing errors and removal of unnecessary genes, sequences and making the model amenable to survival and performance. After this, a trial-and-error analysis is performed to reveal the model’s flaws, and necessary actions have been taken.
Figure 3: J. Craig Venter, CEO of Synthetic Genomics Inc.
Applications: So next thing which makes us curious is what has happened/recent advances till the date in this evolving field. One can see the achievements in the picture below: Starting from creating a simple synthetic phage genome to creating complex synthetic true yeast chromosomes, the area has flourished significantly. One of the pioneers of SGE, J. Craig Venter Institute, has excelled in their research. In 2003, they assembled bacteriophage PhiX74 genome (5386 bp long) in about two weeks and later in 2006, they created a completely synthetic genome of a minimal bacterium, Mycoplasma laboratorium.
Further, they are putting efforts to make it function in a living cell. Another jewel in the crown of synthetic biology was added in 2019 which reveals a microorganism (bacteria Escherichia coli) which has modified genome (possibly artificial) and is able to code 59 codons instead of the natural number of 64 codons to encode 20 amino acids.This paradigm shifts from “genome reading” to “genome writing” tells us about humankind’s advancements so far.
Interestingly, Dr. Jef Boeke from Johns Hopkins University leads a project called “The Sc2.0 Project” with the team of international collaborators, which is first attempt to design and synthesize a eukaryotic genome- Saccharomyces cerevisiae, i.e., our Baker’s Yeast, which aims at synthesizing the entire yeast genome, which consists of 16 chromosomes, nearly 6,000 genes and a total of 12 megabases of non-redundant of DNA. They designed the Synthetic Chromosome Recombination and Modification by LoxP-mediated Evolution (SCRaMbLE) system for gene rearrangements. They introduced more than 5,000 LoxP sites (if it is getting hard to understand, Wikipedia is there to help you) so as to introduce desired rearrangements and deletions. They have also introduced neochromosome (a completely new chromosome) having tRNA genes, ditched destabilizing transposons, which makes it stable, removed “junk sequences,” which made it leaner, and as already mentioned, introduced SCRaMbLE system, which makes it a built-in inducible diversity generator.
So far, we have talked about the applications of SGE relevant to microbes only, which needs an update and upgrade, so what do you think! Do we have something to talk about on higher organisms? Absolutely yes! Currently, we can find few published examples of synthetic plant biology, which involves the production of synthetic sensors and synthetic metabolic pathways, but the research is still in its initial stages and faces difficulties in creating plant synthetic genome like 1) scarcity of well-characterized and interchangeable parts and modules of plant genome, required for their modeling and assembly, and fine-tuning of synthetic gene networks 2) context-dependency ofbiological parts and modules which makes the synthetic process unpredictable 3) Host-compatibility issues like codon optimization, genetic instability, regulatory incompatibilities and genomic position effects after integration of synthetic devices into a plant can create major malfunction of model.
So what could be looked at as the next step to progress in plant SGE? The answer is Synthetic plastome (genome of a plastid, a type of organelle found in plants) engineering. There are certain advantages in using plastome for synthetic modification, such as the plastome’s prokaryotic nature may help in building synthetic circuits in plants. A tiny plastid genome with fewer but important components will be of great value for two reasons:
1) The regulatory network responsible for plastid functioning can be deciphered, and
2) It can be used in biotechnological research by serving as template for engineering plastomes
Challenges and Future prospects: Using SGE to create synthetic plastomes can serve as the breakthrough to open a gateway for plant genome engineering. Practically speaking, there is still the lack of availability of well-characterized genetic parts, modules, strictly controlled expression devices, and thorough knowledge of plastid gene expression. As human nature tends to see hope even in the darkest hours, so in the future, this emerging field can be seen as a threshold to alleviate the problems related with biotic and abiotic stresses and to help in increasing the production of food, secondary metabolites, and even completely synthetic life forms. Advancement in technology has paved road for development of new algorithms, various models, and precise softwares which will help in better characterization and standardization of the orthogonality of more biological parts and modules, as well as better rational designs. Encouragingly, funding agencies in different countries have started to look into plant synthetic biology projects. We also hope that advances in the field of science and technology will show us the miracles in need of an hour.
Perspective creates a different scenario and differs from person to person. One perspective says whether this technology is safe and raises concerns over bio-terrorism, the environment, and the human race. Whereas, other perspective focuses on advancement in SGE to fasten the process and creation of meaningful and useful models for the desired output. Still, wherever there are concerns over safety, there need to be governing authorities to control experiments. At the International level, several treaties contain provisions that apply to synthetic biology; these include: -The Convention on Biological Diversity (CBD),-Biological Weapons Convention, -Cartagena Protocol on Biosafety, -Nagoya–Kuala Lumpur Supplementary Protocol on Liability, and -Australia Group Guidelines.
Conclusion:
As far we have seen SGE, we can truly say … this technology not only enables us to create something new, but to understand the process of how life works, gives the promising opportunity to create crops with high yields, better resistance to pest and diseases, and better adaptability on introduction to new areas as well in case of humans it might allow us to tackle incurable genetic diseases, to know the evolutionary process and can help us to predict the mysteries of genetic material. So, in the end, we can say that this field challenges the laws of nature. Still, as someone has said, “if we eat GMOs, we may die, but if we do not eat GMOs, then we are definitely gonna die,” which might be said in the context of increasing demand and decreasing supply. So, bringing Superplants with unbelievable qualities and comic characters like Superman, Spiderman into reality is not just Stan Lee’s job anymore; it can be done by scientific researches too.
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