Synthetic biology: A dream of today is future of tomorrow
SYNTHETIC BIOLOGY also known as SynBio, is synthetic genomics or system biology. In earlier days the branches of sciences such as chemistry, biology, physics, etc, performed their work independently. Recently scientists have focused to emerge all sciences together in a multidisciplinary way for the betterment of mankind. One of the approaches to enhance the performance of scientific research is the development of a platform known as synthetic biology. To be more specific to the terminology, the field not only focuses on the synthesis of different parts of cell, which will be available in the market and ready to assemble for the synthesis of new lives in near future.
Today the genetic engineering, which is the earlier version of synthetic biology, deals with cutting, copying, and pasting of genetic material such as DNA. As time goes on, the improvement in these techniques makes scientists capable to synthesize DNA by chemical process. Synthetic biology brings important changes in the direction of genetic technology which previously was dependent on gene sequencing of short fragments; nowadays we can sequence whole genome with a short period of time (thousands of base pair per minute) with the help of next generation sequencing.
As the biology proceeds with time, the future (synthetic biology) will be similar to that of making electronic circuits by designing it on computer (dry lab work), assembling of different parts and obtain the final machine (genetically engineered micro-organisms). Similarly, with the synthetic biology, we can access thousands of genomes already sequences and present in the databases such as NCBI (http://www.ncbi.nlm.nih.gov), e.g. we can select target genes of interest in database and the selected gene is synthesized commercially (Syntehtic DNA). The synthetic DNA is assembled like the computer parts to synthesize micro-organism with novel functions not existed before.
Synthetic biology believes that all parts of life can be made synthetically, the DNA codes are referred as a software for constructing the synthetic DNA, while the cell membranes and all other components are regarded as hardware of the cell.
The DNA synthesis mechanism was discovered by Nobel laureate Gobind Khorana in 1966 by arranging four nucleotides such as adenine, guanine, cytosine and thymine (A, G, C, and T). The people started synthesizing short stretches of DNA known as oligonucleotides by chemical process. Furthermore, the world first commercial biotech industry for the synthesizing DNA started in 1976 by the name Genentech in United States. The researchers around the world started amplifying genes of their interest by synthesizing oligonucleotides also known as primers. The genes synthesis companies are growing rapidly in different parts of the world, the United States is centre of all.
Synthetic biology also praises the great effort of the bioinformatics by creating and designing different models which make the biology easy. Such as development of software for simulations of genes/genomes assembly, metabolic networks in different cells including prokaryotes and eukaryotes. There are also many other applications of bioinformatics in the field of synthetic biology is to find out different targets inside the cell which are not possible experimentally, one example for this is the identification of SNPs (short nucleotide polymorphism) and many more.
In my personnel experience, I tried to synthesize the DNA fragment of one gene having the size of 1 kb (kilo base pairs) using recombinant PCR. I designed around 20 nucleotide fragments using BIOEDIT software, and assembled it by recombinant PCR. The drawback of this method is it took much time up to one year because of having mutations in the gene. One can synthesize DNA by ordering the sequence to Biotech Company e.g. DNA 2.0 (USA) and GeneArt (Germany) and will get the gene/DNA cloned in any described vector. In simple words we can say the DNA synthesis or synthetic DNA is getting cheaper and easily accessible to any part of the world.
There are different research areas of synthetic biology:
A. Minimal genomes microbes
B. Assembling BioBricks
C. Artificial cell construction
D. Metabolic engineering
A. Constructing minimal genome microbes:
John Craig Venter (born October 14, 1946) is an American biologist and most famous for his role in being the first to sequence the human genome. His group started deleting the unnecessary genes from a bug named Mycoplasma genetalium, which has the smallest genome of 590.000 bps. He started working by knocking out genes which were not essential for the growth. They successfully identified the minimal set of genes need for survival.
The aim of constructing the minimal genome micro-organism was to use as a platform for the industrial purposes, such as engineering metabolic pathway for production of chemicals and fuels.
Recently, J. C Venter and his colleagues successfully constructed the first ever synthetic life on the earth. He replaced the whole synthetic genome of Mycoplasma genetalium in other bacteria by the method of genome transplantation discovered by his team. His work was published in science 2010.
B. Assembling BioBricks
Synthetic biologists, researchers, graduates and undergraduate students throughout the world share their ideas and experiences under the platform of iGEM (Internationally Genetically Engineered Machine Completion). The iGEM programme is run by undergraduate students. The iGEM competition facilitates by providing a library of standardized parts (called BioBrick standard biological parts) to students, and asking them to design and build genetic machines with them. Student teams can also submit their own BioBricks. To be creative one can have many ideas about making their own BioBrick libraries by collaborating with different synthetic biology laboratories throughout the world. BioBricks is the strand of DNA, which is designed to perform a unique function and can easily be assembled and compatible with another BioBricks to construct a synthetic circuit inside the cell.
The engineered circuits are then transformed into host cell for expression and production of desired metabolites.
C. Artificial cell construction:
The aim is to construct an artificial cell without the use of DNA. This idea was given by a theoretical physicist named Steen Rasmussen. The artificial cell can be synthesized from bottom up approach, where three basic requirements for life, such as energy generating system such as metabolism, information storing molecules such as DNA and membrane to hold all. One example of creating the artificial cell is Los “Alamos Bug”, which is droplet of oil, mimicking the cell membrane, and having PNA instead of DNA. PNA is peptide nucleic acid similar to DNA and is not existed in nature. PNA has the same nucleotide bases (A, T, C and G) but having peptide backbone instead of phosphodiester linkage.
D. Metabolic engineering:
Another great advantage of synthetic biology is to design microorganisms with novel properties. In nature, microorganism with desired properties is difficult to isolate and grow in laboratory conditions. The metabolic engineering helps us in designing new circuits and metabolic network inside a cell.
The desired genes from various species are synthesized and assembled in plasmid, cassettes (insertion into genome) expressed in heterologous host. A number of examples are available such as chemicals (1, 2 propane-di-ol), plastics (polyhydro-xyalkanoate), fuel (ethanol, butanol, biodiesel) are produced by engineering Escherichia coli.
E. Future perspectives:
Synthetic biology is considered to be a possible solution to the current problems of the world such as global warming, environmental security, global peace, cheaper availability of medicine and vaccines and many more. To be specific to these points one can engineer, construct microorganism according to his need. The solution of global warming, environmental security and global peace is all related to fossil fuel availability and demand. These three main factors can be solved by producing alternative biofuels using the synthetic biology approaches. Similarly, the vaccines and drugs produced by engineering microorganisms are cheaper and having low risk of contaminants to that which are produced from natural resources.
The writer is a PhD scholar at Korea Advance Institute of Science and Technology (KAIST), South Korea. He can be reached at email@example.com