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Asian Journal of Basic Science & Research
Volume 5, Issue 3, Pages 40-49, July-September 2023
ISSN: 2582-5267
40
An Overview on Synthetic Biology: its Classification, Engineering Approaches, and
Applications of Synthetic Biology
Hassaan Bin Sajid1, Areeba Afzal2, Soha Fatima3, Nimra Tabassum4, Muhammad Hamza Awan5 & Muhammad Asif Raheem6*
1-6University of Agriculture Faisalabad (UAF), Pakistan. Email: asifraheem74641@gmail.com*
DOI: http://doi.org/10.38177/AJBSR.2023.5304
Copyright: © 2023 Hassaan Bin Sajid et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Article Received: 22 May 2023 Article Accepted: 24 July 2023 Article Published: 30 July 2023
░ 1. Introduction
Synthetic biology is a collaborative field of science that concentrates on living organisms and systems, and it uses
engineering methods to develop new biological devices, systems, and parts [1]. The roots of synthetic biology can
be seen in landmark research by Francois Jacob and Jacques Monod in 1961, in their research of lac operon in E.
coli gave them to predict the presence of regulatory network that support the response of a cell to its surrounding
[2]. In mid nineteenth century, the development of a detailed new direction in chemistry, instead of studying old
molecules chemist began to synthesize them or making new molecules that did not exist before. This old and new
approaches changed chemistry, this synthetic chemistry laid down the development of synthetic biology, an
emerging field in which the goal is to develop biological systems [3].
The increase in molecular biology generated the field of synthetic biology, as computer scientists and biologists
began to combine computation and experimentation to reverse engineer cellular pathways [4]. The study on
restriction nucleases not only allowed us to make recombinant DNA molecules or to analyze single gene, but also
took us into new world of synthetic biology where new gene can be constructed and analyzed [5]. In 2010,
1.08Mbps genome of Mycoplasma mycoides designed, synthesized, and assembled starting from digitizing genome
sequence information and its transplantation into a M. capricolum (receiving cell) to create new M. mycoides cells
that are controlled by the synthetic chromosome [6].
Synthetic biology is fetching engineers and biologists together to design and construct novel biomolecular parts,
circuits, and pathways, and use these constructs to reconstruct, reanalyze and reprogram organisms [7]. Synthetic
ABST RACT
Synthetic biology is an interdisciplinary field that focuses on living organisms and systems, employing engineering techniques to create innovative
biological devices, systems, and components. It represents the convergence of old and new approaches, bridging the gap between chemistry and
biology, with synthetic chemistry laying the foundation for its emergence. At its core, synthetic biology aims to develop and engineer biological
systems by bringing together engineers and biologists to design and construct novel biomolecular parts, circuits, and pathways. These constructs are
then utilized to reconstruct, reanalyze, and reprogram organisms for various purposes. There are five primary categories within synthetic biology:
bioengineering, synthetic genome, protocell synthetic biology, unconventional molecular biology, and in silico techniques. Traditionally, four
engineering approaches have been employed in synthetic biology, including top-down, parallel, orthogonal, and bottom-up methods. These
approaches provide a systematic and rational way of reassembling and reconstructing biological components, enabling the creation of functional
biological devices, systems, and organisms with known, useful, and novel functions. Synthetic biology holds the promise of providing efficient
solutions to various significant challenges in the modern world, encompassing areas such as chemicals, pharmaceuticals, agriculture, energy, and
bioremediation. By leveraging engineering methods in the realm of biology, synthetic biology benefits from over 50 years of molecular biological
and functional genomic research, along with advanced technologies that allow for the analysis, synthesis, assembly, modification, and transfer of
genetic components into living organisms. In essence, synthetic biology offers an exciting avenue to unlock the potential of biological systems and
revolutionize multiple industries through innovative modifications and breakthrough innovations.
Keywords: Synthetic biology; Artificial life; Biological systems; Bioengineering.
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biologists divided into 2 broad classes, one uses the artificial molecules to reproduce emergent behaviors from
nature biology, with aim of creating artificial life, and the other finds exchangeable components from natural
biology to assemble into systems that function unnaturally [8]. Synthetic biology has a large scope, still in that it
tries to recreate in unnatural chemical systems the evolving characteristics of living systems, like inheritance,
genetics, and evolution [9].
Synthetic biologists search to assemble parts that are not natural to generate chemical systems that support
Darwinian theory by carrying out the assembly in a synthetic way, these scientists hope to interpret non synthetic
biology, that is natural biology [8]. Recently, an engineering team has given further. Meaning to the term. This
community searches to extract from living systems exchangeable components that can be tested, validated as
construction units, and reassembled to create devices that might or might not have counterparts in living systems
[10] Synthetic biology already has many accomplishments to its credit. The effort to generate synthetic genetic
systems has yielded diagnostic tools, such as Bayer’s branched DNA assay, which annually helps improve the care
of some 400,000 patients infected with HIV and hepatitis viruses [11].
░ 2. Classifications of Synthetic Biology
There are five categories of synthetic biology that are bioengineering, synthetic genome, protocell synthetic
biology, unconventional molecular biology, and in silico techniques [12].
(a) Bioengineering
The field of bioengineering focuses on making novel regulatory and metabolic pathways and these days drawing
the attention of many researchers and funding. When using the word bioengineering it cannot be confused with
traditional genome engineering, which involves adding a single gene into the organism. Bioengineer utilized
synthetic biology to give more detailed and substantial ideas to alter organisms and biological systems.
Bioengineering strives to achieve innovative biological systems by employing simplified and abstracted metabolic
and regulatory modules, along with standardized parts that allow for flexible combinations to develop new
pathways or organisms. This approach not only opens the door to countless novel applications but also promises
greater predictability and control compared to conventional biotechnology [12].
(b) Synthetic Genomic
The development of animals with a chemically manufactured genome is another milestone of synthetic biology that
is pointed out by synthetic genomics. The field synthetic biology contributed in the DNA synthesis technology,
which now makes it easy to make DNA molecules with thousands of base pairs at minimal cost. The aim is to
merge these molecules and transfer them in living organism cell, replacing the host genome or its metabolic
pathways for different functions [12].
(c) Protocell Synthetic Biology
The generation of synthetic cells in vitro is the protocell branch of synthetic biology. Lipid vesicles can be used to
create these cells because they have all the necessary function as a complete system. In the end, the aim is that these
synthetic cells should be alive means capacity to self-replicate, self-maintenance, and evolution. Lipid vesicles can
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carry out specific functions with cell extracts and biological macromolecules. They may perform tasks like PCR or
protein synthesis. Protocells offer versatile applications in synthetic biology, including biopolymer and medicine
production [12].
(d) Unconventional Molecular Biology
The aim of unnatural molecular biology is to create new varieties of life that are based on different type of
molecular biology, such as new types of nucleic acids and new genetic code. Novel nucleotides with distinct
properties can be synthesized by modifying specific DNA or RNA components, such as the bases or backbone
sugars. Organisms with genomes based on synthetic nucleic acids or new coding systems for synthetic amino acids
could form a new type of life. This offers potential benefits but also introduces new risks. These synthetic
organisms may lack the ability to exchange genes with natural species and could struggle to survive outside
controlled environments if they escape. However, if they adapt successfully, they might possess advantages over
natural organisms, such as resistance to predators and viruses, leading to uncontrolled proliferation [12].
(e) In Silico Technique
Different methods and synthetic biology in silico are connected to each other. The production of complex designs
like metabolic pathways, vital cellular processes, whole genome, is one of the major obstacles faced by the methods
mentioned above. That is why, synthetic biology has a strong in silico branch like system biology, that aims to
make computational models for the design of common biological components or synthetic circuits for the
stimulation of synthetic organisms [12]. Integrating the five domains of synthetic biology as a cohesive field of
study is a logical approach. Despite their distinct focuses on different aspects of life, including metabolic
regulation, essential elements, and biochemical makeup, these five strategies share a common goal: the creation of
novel living organisms. Furthermore, the diverse methodologies employed in this field stem from various
methodological approaches, contributing to the wide range of synthetic biology approaches [12].
Figure 1. Overview of Synthetic Biology [13]
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░ 3. Approaches that are Used by Synthetic Biology
Traditionally there were 4 engineering approaches that has been used by synthetic biology: top down, parallel,
orthogonal, and bottom up [13].
Synthetic biology employs unnatural chemicals to replicate emergent behaviors found in natural biology, while
also seeking to assemble interchangeable components from biological systems to create non-natural systems. This
ambitious goal compels researchers to explore new frontiers and tackle challenges beyond the scope of
conventional analysis. As a result, novel paradigms emerge, driving innovation in ways that traditional analysis
alone cannot achieve. Beyond creating playful gadgets like oscillating or creeping devices, synthetic biology has
also given rise to diagnostic instruments that significantly improve the treatment of patients with infectious diseases
[8].
(a) Top-Down Approach
Synthetic biology utilizes metabolic and genetic engineering techniques to introduce new functionalities into living
cells (Schwille, 2011). One approach involves comparing universal genes and removing non-essential ones to
create a simplified genome, aiming to reduce the complexity of existing cells. However, recent research suggests
that the tree of life, composed of eukaryotic and prokaryotic cells, may have evolved from a group of primordial
cells rather than a single cell. Consequently, the quest for the "minimum genome" akin to the Holy Grail has
become elusive, as eliminating non-essential functions can compromise an organism's fitness and result in "fragile"
genomes [13].
(b) Bottom-up Approach
This approach involves the creation of new biological systems in vitro by assembling 'non-living' biomolecular
components,[15] often with the goal of constructing an artificial cell. The three fundamental self-organizational
principles considered for this purpose are reproduction, replication, and assembly. Reproduction involves the
concept of "hardware" in cells, where a container and metabolism are combined. Replication, on the other hand,
pertains to systems duplicating perfect copies of themselves, like DNA, which is akin to "software." Assembling
occurs when vesicles or containers, such as Oparin's coacervates, formed of tiny droplets of organic molecules like
lipids or liposomes, aggregate to create membrane-like structures composed of phospholipids [13].
This area of study, including protocells and other in vitro synthetic biology initiatives, aims to produce minimal
cells, metabolic pathways, "never-born proteins," and mimic physiological functions like cell division and growth.
Although the in vitro enhancement of synthetic pathways may no longer be strictly classified as synthetic biology
research, it holds significant potential to impact other synthetic biology sectors, including metabolic engineering.
This essential research warrants proper recognition as a part of synthetic biology exploration [13].
(c) Parallel Approach
Parallel engineering, also known as bioengineering, is rooted in the fundamental genetic code, utilizing
conventional biomolecules such as nucleic acids and the 20 amino acids to construct biological systems. This
versatile field encompasses various applications in biocomputing, bioenergy, biofuels, bioremediation,
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optogenetics, and medicine. It involves standardizing DNA components, engineering switches, biosensors, genetic
circuits, logic gates, and cellular communication operators. To direct the expression of two or more genes and/or
proteins, many of these applications rely on the use of vectors or plasmids. Plasmids are small, circular,
double-stranded DNA units commonly found in prokaryotic cells, and occasionally detected in eukaryotic cells,
capable of autonomous replication independent of chromosomal DNA [13].
(d) Orthogonal Approach
Also known as perpendicular engineering or chemical synthetic biology, this approach aims to modify or expand
the genetic codes of living systems using artificial DNA bases and/or amino acids. Connected to xenobiology, this
field explores the use of "alien" or xeno molecules as genetic information carriers by creating compounds like DNA
canonical bases [13]. By altering or enlarging the genetic code, information beyond the 20 conventional amino
acids can be expressed. Researchers have successfully incorporated noncanonical moieties into DNA and proteins,
leading to advancements in creating biological systems with diverse biomolecules. Directed evolution is utilized to
produce orthogonal enzymes, enabling the incorporation of XAAs into proteins and the development of "mirror
life" systems [13].
Figure 2. Proposition of four engineering approaches encompassing all synthetic biology research [13]
░ 4. Applications of Synthetic Biology
Synthetic biology guarantees to give efficient solutions to many big problems of modern world through
modifications and innovations in chemicals, pharmaceuticals, agriculture, energy, and bioremediation [16]. By
using engineering methods to biology, synthetic biology has become the science of reassembling and
reconstructing biological components in a systematic and rational manner to create and engineer functional
biological devices, systems, and organisms with known, useful, and novel functions. Synthetic biology has ability
to use different biomolecular parts compiled over 50 years of molecular biological and functional genomic research
[17] as well as technology that has made it possible to analyze, synthesize, assemble, modify, and transfer genetic
components into living organisms [18].
(a) Biosensors
A biosensor is an engineered organism, often a bacterium, designed to detect and report specific environmental
conditions, such as the presence of heavy metals or toxins. One notable example is the Lux operon found in
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Aliivibrio fischeri, [19] which encodes for the enzyme responsible for bacterial bioluminescence. By placing this
operon downstream of a responsive promoter, the luminescence genes can be expressed in response to a particular
environmental stimulus [20]. One application of this technology involved creating a biosensor with a
bioluminescent bacterial coating on a photosensitive computer chip to detect petroleum pollutants. When the
bacteria detect the pollutants, they emit luminescent light, providing a visible indication of the presence of
contaminants. Another instance is the use of an engineered E. coli reporter strain capable of detecting TNT and its
main degradation product DNT, resulting in the production of green fluorescent protein (GFP) when these
substances are present. This mechanism allows for the detection of landmines using the bacteria as a sensing tool.
These biosensors offer promising opportunities for environmental monitoring and detection of various substances
in a reliable and cost-effective manner [21].
(b) Biological Computers
A biological computer is a product of engineered biological systems capable of performing computer-like
operations, representing a significant paradigm in synthetic biology. Scientists have successfully constructed and
analyzed various logic gates within different organisms, [22] showcasing both analog and digital computation
abilities in living cells. Through their research, they have shown that it is feasible to engineer bacteria to execute
analog and/or digital computations, opening up new possibilities for advanced biological computing [23].
(c) Cell Transformation
Cells use gene circuits, composed of interacting genes and proteins, to carry out various functions like responding
to signals and making decisions. Synthetic biologists have designed gene circuits that control gene expression at
different levels, such as transcriptional, post-transcriptional, and translational levels. With the introduction of
foreign genes and directed evolution, traditional metabolic engineering has been advanced, enabling the production
of valuable substances like the precursor of the antimalarial drug, Artemisinin, [24] in E. coli and yeast. Although
creating entire organisms from scratch is still a challenge, new DNA can be integrated into living cells to bestow
them with desired capabilities and phenotypes. Through cell transformation, biological circuits can be constructed
and manipulated to achieve specific outputs [25].
(d) Designed Proteins
Natural proteins can undergo engineering through techniques like directed evolution, leading to the creation of
novel protein structures that can match or even surpass the functionalities of existing proteins. For instance, one
group developed a helix bundle that mimicked hemoglobin's oxygen-binding properties but didn't bind carbon
monoxide [26]. Another group produced a structurally and functionally novel ATPase [27], while a different
protein structure supported various oxidoreductase activities [28]. Computational approaches are also employed to
engineer novel functionalities or protein specificity. In one study, two computational methods were utilized: a
bioinformatics and molecular modeling method to mine sequence databases, and a computational enzyme design
method to reprogram enzyme specificity. These methods resulted in designed enzymes with significantly enhanced
specificity for producing longer chain alcohols from sugar [29]. Furthermore, researchers often explore expanding
the natural set of 20 amino acids. While 61 codons have been identified, generally only 20 amino acids are coded in
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all organisms. By engineering certain codons, alternative amino acids like O-methyl tyrosine or exogenous amino
acids such as 4-fluorophenylalanine can be incorporated. These projects often rely on re-coded nonsense
suppressor tRNA-Aminoacyl tRNA synthetase pairs from other organisms, requiring substantial engineering in
most cases [30].
(e) Designed Nucleic Acids
Scientists have achieved the remarkable feat of encoding digital information onto a single strand of synthetic DNA.
Back in 2012, George M. Church successfully stored one of his books on synthetic biology using DNA, totaling 5.3
Mb of data, which was over 1000 times larger than the previous record for information stored in synthesized DNA
[31]. Another exciting project involved encoding William Shakespeare's complete sonnets in DNA. In the broader
context, several algorithms like NUPACK, ViennaRNA, Ribosome Binding Site Calculator, Cello, and
Non-Repetitive Parts Calculator [32] have been developed, enabling the design of novel genetic systems.
Furthermore, various technologies have emerged for incorporating unnatural nucleotides and amino acids into
nucleic acids and proteins, both in laboratory settings (in vitro) and within living organisms (in vivo). These
advances represent significant milestones in the field of synthetic biology [33].
Utilizing microorganisms for bioremediation to remove contaminants from water, soil, and air.
Modified rice produces beta-carotene, a substance preventing vitamin A deficiency, benefiting hundreds of
thousands of children at risk of losing their vision and dying from infectious infections.
Yeast is engineered to produce rose oil, offering a sustainable and environmentally friendly alternative to
using fresh roses for perfumery.
Some other applications are space exploration, synthetic life, drug delivery platforms, engineered bacteria,
engineered yeast, cell-based platforms, biofuels, pharmaceuticals, and biomaterials.
Figure 3. Overview of Synthetic Biology [34]
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Declarations
Source of Funding
This study did not receive any grant from funding agencies in the public or not-for-profit sectors.
Conflict of Interest
The authors declare that they have no conflict of interest.
Consent for Publication
The authors declare that they consented to the publication of this study.
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