by Catherine Jefferson, Filippa Lentzos and Claire Marris
"Synthetic biology, a field that aims to ‘make biology easier to engineer’, is routinely described as leading to an increase in the ‘dual use’ threat, i.e. the potential for the same piece of scientific research to be ‘used’ for peaceful purposes or ‘misused’ for warfare or terrorism. Fears have been expressed that the ‘de-skilling’ of biology, combined with online access to the genomic DNA sequences of pathogenic organisms and the reduction in price for DNA synthesis, will make biology increasingly accessible to people operating outside well-equipped professional research laboratories, including people with malevolent intentions. The emergence of DIY biology communities and of the student iGEM competition has come to epitomize this supposed trend towards greater ease of access and the associated potential threat from rogue actors. In this article, we identify 5 ‘myths’ that permeate discussions about synthetic biology and biosecurity, and argue that they embody misleading assumptions about both synthetic biology and bioterrorism. We demonstrate how these myths are challenged by more realistic understandings of the scientific research currently being conducted in both professional and DIY laboratories, and by an analysis of historical cases of bioterrorism. We show that the importance of tacit knowledge is commonly overlooked in the dominant narrative: the focus is on access to biological materials and digital information, rather than on human practices and institutional dimensions. As a result, public discourse on synthetic biology and biosecurity tends to portray speculative scenarios about the future as realities in the present or the near future, when this is not warranted. We suggest that these ‘myths’ play an important role in defining synthetic biology as a ‘promissory’ field of research and as an ‘emerging technology’ in need of governance."
"The method dubbed Assembly of Designed Oligonucleotides (ADO) is a powerful tool in synthetic biology to create combinatorial DNA libraries for gene, protein, metabolic, and genome engineering. In directed evolution of proteins, ADO benefits from using reduced amino acid alphabets for saturation mutagenesis and/or DNA shuffling, but all 20 canonical amino acids can be also used as building blocks. ADO is performed in a two-step reaction. The first involves a primer-free, polymerase cycling assembly or overlap extension PCR step using carefully designed overlapping oligonucleotides. The second step is a PCR amplification using the outer primers, resulting in a high-quality and bias-free double-stranded DNA library that can be assembled with other gene fragments and/or cloned into a suitable plasmid subsequently. The protocol can be performed in a few hours. In theory, neither the length of the DNA library nor the number of DNA changes has any limits. Furthermore, with the costs of synthetic DNA dropping every year, after an initial investment is made in the oligonucleotides, these can be exchanged for alternative ones with different sequences at any point in the process, fully exploiting the potential of creating highly diverse combinatorial libraries. In the example chosen here, we show the construction of a high-quality combinatorial ADO library targeting sixteen different codons simultaneously with nonredundant degenerate codons encoding various reduced alphabets of four amino acids along the heme region of the monooxygenase P450-BM3."
"Saccharomyces cerevisiae can serve as a key production platform for biofuels, nutraceuticals, industrial compounds, and therapeutic proteins. Over the recent years, synthetic biology tools and libraries have expanded in yeast to provide newfound control over regulation and synthetic circuits. This review provides an update on the status of the synthetic biology toolbox in yeast for use as a cell factory. Specifically, we discuss the impact of plasmid selection and composition, promoter, terminator, transcription factor, and aptamer selection. In doing so, we highlight documented interactions between these components, current states of development, and applications that demonstrate the utility of these parts with a particular focus on synthetic gene expression control."
"Recent advances in synthetic biology have made it possible to replicate an unnatural base pair in living cells. This study highlights the technologies developed to create a semisynthetic organism with an expanded genetic alphabet and the potential challenges of moving forward..."
by Maria-Eugenia Guazzaroni and Rafael Silva-Rocha
"The understanding of how the architecture of cis-regulatory elements at bacterial promoters determines their final output is of central interest in modern biology. In this work, we attempt to gain insight into this process by analysing complex promoter architectures in the model organism Escherichia coli. By focusing on the relationship between different TFs at the genomic scale in terms of their binding site arrangement and their effect on the target promoters, we found no strong constrain limiting the combinatorial assemble of TF pairs in E. coli. More strikingly, overlapping binding sites were found equally associated with both equivalent (both TFs have the same effect on the promoter) and opposite (one TF activates while the other repress the promoter) effects on gene expression. With this information on hand, we set an in silico approach to design overlapping sites for three global regulators (GRs) of E. coli, specifically CRP, Fis and IHF. Using random sequence assembly and an evolutionary algorithm, we were able to identify potential overlapping operators for all TF pairs. In order to validate our prediction, we constructed two lac promoter variants containing overlapping sites for CRP and IHF designed in silico. By assaying the synthetic promoters using a GFP reporter system, we demonstrated that these variants were functional and activated by CRP and IHF in vivo. Taken together, presented results add new information on the mechanisms of signal integration in bacterial promoters and provide new strategies for the engineering of synthetic regulatory circuits in bacteria."
"Karmella Haynes was among scientists and engineers to address national leaders at a recent U.S. Congressional briefing on issues raised by the emerging field of synthetic biology.
Haynes is an assistant professor in the School of Biological and Health Systems Engineering, one of Arizona State University’s Ira A. Fulton Schools of Engineering. She is among educators and researchers using synthetic biology techniques in pursuit of solutions to many of society’s major biotechnology and medical challenges.
The field combines biological sciences and engineering in designing and creating new manufactured biological systems and devices, as well as redesigning existing natural biological systems to maintain and enhance human health.
Researchers are using the capabilities of synthetic biology to probe the fundamental makeup of biological systems, enabling them to do things such as modifying and reprogramming body cells and DNA to perform medicinal functions. Such techniques are also being used in plant biology to enhance agriculture.
The rapid advance of synthetic biology has prompted discussions about how to weigh the benefits of the research against potential social and ethical implications, and concerns about safety.
Haynes and two colleagues – Steve Evans and Jay Keasling – gave presentations on those questions to staff members representing members of Congress, National Science Foundation officials, science journalists and other interested parties.
Evans is a research fellow at Dow AgroSciences, a part of the Dow Chemical Company that focuses on sustainable agriculture.
Keasling is the chief executive officer of the Joint BioEnergy Institute, assistant director at the Lawrence Berkeley National Lab and a professor of biochemical engineering at the University of California, Berkeley. He is also director of the National Science Foundation-supported Synthetic Biology Engineering Research Center (SynBERC), which helped to organize the Congressional briefing. Haynes is an affiliate researcher with SynBERC.
The speakers stressed the importance of increasing public awareness of synthetic biology as a way to foster confidence about the methods and the goals of researchers. “We want to inform more people to prevent unfounded fears that might hinder work that has great value for addressing society’s needs,” Haynes said after the briefing.
The audience was also told it will be increasingly important to have experts in the field working with the Environmental Protection Agency and the Food and Drug Administration to help keep government regulations up to date on rules related to biological research and biotechnology development. Current regulations “need to be more aligned with technology that is coming from synthetic biology,” Haynes said.
Arizona State University “was highly visible” at the briefing, she said, due particularly to talk about the Workshop on Research Agendas in the Societal Aspects of Synthetic Biology to be hosted by ASU in November.
“We hope we convinced everyone at the briefing that sustained support for biomedical engineering is in the best interests of the nation,” Haynes said."
"As in other engineering fields, progress in synthetic biology depends on the exchange of parts and designs by researchers and will be most effective if designs adhere to common standards. A group of experimental and computational researchers from many different institutions in several countries, coordinated by Herbert Sauro from the University of Washington, describes such a data standard: the Synthetic Biology Open Language (SBOL). SBOL uses standard graphical notations—for example, for promoters, 5′ untranslated regions, coding s…"
Sami Ullah Jan, Burhan Ullah, Aimal Khan, Muhammad Asif Shahzad, Zeeshan Ali Yousaf, Atif Shafiqu1and Muhammad Ali Abbas
"Genomics and its related studies boosted explorations when applied in various dimensions of biology. The most common concept employed is to mix natural abilities of various living organisms or distant biological sources in the form of genes targeted for their products. With the advent of 21st century, this field gained a pace due to the attention by various scientific communities worldwide. Though, many hurdles still exist on its way but synthetic biology has led the basis for advanced outcomes by merging the potentials of genetic engineering and electronic techniques. This piece of literature reviews the research and development of synthetic biology accomplished since past in various life sciences with emphasis on pharmaceuticals, vaccines and biofuel development. The efforts of international scientific community and international organizations are also highlighted, who developed regulations and transmitted the importance to applied level. The production of biofuel, anti-microbial drugs, vaccines or other biological components with the help of genetic engineering technology was the first generation which after integration in synthetic biology has successfully transferred to a new generation. Along with the past, this paper also forecasts the future of synthetic biology in minimizing the limitations and problems faced in biological research with the help of synthetic biology. "
"A cornerstone of synthetic biology and biological engineering is achiev- ing regulatory control of genes of interest. Typically, this is attempted by placing binding sites for classic transcription factors upstream of genes. However, gene regulation is multilayered beyond transcription factor recruitment; thus, a new study has characterized how diverse chro- matin regulators might provide a flexible and powerful way to regulate different aspects of gene expression.
Chromatin states in eukaryotic cells are modulated in various ways — including by DNA methylation, histone modifications and nucleo- some remodelling — thus providing opportunities for ‘fine-tuning’ the regulation of gene expression. An emerging approach to assess the gene regulatory effects of specific chromatin regulator proteins is ‘epi- genome editing’, in which chromatin regulators are fused to sequence- specific DNA-binding proteins to allow their recruitment to a chosen locus. Such a strategy has so far characterized only a few chromatin- modifying enzymes. So, Keung et al. took a systematic approach by generating a library of 223 yeast chromatin regulators fused to zinc- finger (ZF) DNA-binding proteins, although the system is potentially also applicable to the transcription activator-like effector (TALE) and CRISPR–Cas genome targeting systems. ..."
comment to: ORIGINAL RESEARCH PAPER Keung, A. J. et al. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158, 110–120 (2014)
by Dejana Jovicevic, Benjamin A. Blount andTom Ellis
"A team of US researchers recently reported the design, assembly and in vivo functionality of a synthetic chromosome III (SynIII) for the yeast Saccharomyces cerevisiae. The synthetic chromosome was assembled bottom-up from DNA oligomers by teams of students working over several years with researchers as the first part of an international synthetic yeast genome project. Embedded into the sequence of the synthetic chromosome are multiple design changes that include a novel in-built recombination scheme that can be induced to catalyse intra-chromosomal rearrangements in a variety of different conditions. This system, along with the other synthetic sequence changes, is intended to aid researchers develop a deeper understanding of how genomes function and find new ways to exploit yeast in future biotechnologies. The landmark of the first synthesised designer eukaryote chromosome, and the power of its massively parallel recombination system, provide new perspectives on the future of synthetic biology and genome research."
"The last 20 years of metabolic engineering has enabled bio-based production of fuels and chemicals from renewable carbon sources using cost-effective bioprocesses. Much of this work has been accomplished using engineered microorganisms that act as chemical factories. Although the time required to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead."
Hamilton Smith is scientific director of synthetic biology and bioenergy at the J. Craig Venter Institute in La Jolla, California. He shared the 1978 Nobel Prize in physiology or medicine for his discovery of an enzyme that cuts DNA, an advance vital to genetic engineering. He told Kat Austen he...