Synthetic Biology

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Project

  1. Matthew Chang: Synthetic programmable microbes for engineering applications
  2. Rong Rong Jiang: Microorganism engineering from itstranscription level
  3. Chueh Loo Poh: Project title: Development of computer-aideddesign tools for Synthetic Biology Design: A Platform Technology
  4. Hao Song: Microbial electrosynthesis in converting carbondioxide to value-added chemicals via synthetic biology strategies
  5. Sierin Lim: Engineering bacteria for metal sequestration
  6. Eileen Fong: Enhanced biological phosphorus removal process(EBPR)
  7. Zhao Xun Liang: Biosynthetic mechanism of secondarymetabolites 
  8. William Chen: Metabolic Engineering of Yeast Cells
  9. Par Nordlund and Tobias Cornvik: A high throughput protein production platform

Project title: Synthetic programmable microbes for engineering applications.
Prof Matthew Chang’s group focuses on developing synthetic microbes that show programmable behaviors for engineering applications such as infection treatment and prevention, and biochemical production. Synthetic biology aims to engineer genetically modified biological systems that perform novel functions that do not exist in nature, with reusable, standard interchangeable biological parts. The use of these standard biological parts enables the exploitation of common engineering principles such as standardization, decoupling, and abstraction for synthetic biology. With this engineering framework in place, his group aims to make the construction of novel biological systems a predictable, reliable, systematic process, and to implement engineering principles to facilitate the construction of novel biological systems. His current research projects include the development of therapeutic synthetic microbes, and auto-regulatory genetic circuits that enable efficient biochemical production.

Project title: Microorganism engineering from its transcription level
Prof. Jiang Rongrong’s group focuses on improving microorganism performance under stressful bioprocessing conditions (high temperature, organic solvents, pH, oxidative stress, and osmotolerance and etc.). Breeding industrial microorganisms with desired properties has been achieved by classical strain engineering methods in the past, such as spontaneous adaptation and mutagenesis with UV/chemical mutagens, which are simple but inherently time-consuming and labor-intensive. Metabolic engineering tools have also been employed to pursue improvement in fermentation performance of microorganisms since its advent, but it requires prior strain genetics and physiology knowledge. In recent years, transcriptional engineering has started to attract attention in strain engineering, which addresses the limitations of classical strain engineering methods. Our group is focusing on engineering transcription factor to improve stain performance under stressful conditions. We brought directed evolution technique from protein engineering to strain engineering and used it to introduce mutations to a transcription regulatory protein. Compared to classical strain engineering methods, this approach can greatly shorten the selection period from weeks/months to 3 − 5 days. We have successfully enhanced E. coli resistance under various stresses through transcriptional engeering so far, including biofuels (bioethanol, biobutanol), organic solvents (toluene, hexane, cyclohexane…), oxidative stress (H2O2, cumene hydroperoxide), low pH, acetate stress and osmotic pressure (high sugar concentration).

Project title: Development of computer-aided design tools for Synthetic Biology Design: A Platform Technology
Prof. Chueh Loo Poh’s group has been focusing on the engineering of beneficial microbes for the sensing and killing of infectious pathogens, development of biomodels and modeling techniques for optimization of synthetic genetic circuits design, characterization of Bioparts and development of information systems for Synthetic Biology. The overall aim of his synthetic biology research is to make engineering of biology more predictable and efficient. He has key expertise in synthetic biology, computational biomodeling related to genetic circuit design and engineering, and biomedical informatics, with publications in Molecular Systems Biology, IEEE Trans on Information Technology in Biomedicine, Computer Methods and Programs in Biomedicine, Molecular and Cellular Endocrinology, Biointerphases and Journal of Digital Imaging. He was invited as international judge for international synthetic biology competition (iGEM - 2011) and he has since filed 3 patents in which one of them relates to engineered microbes for infectious pathogen. He also sits in the program committee of the flagship synthetic biology conference (SB6.0) which will be held in July 2013. Recent awards include best application awarded at international synthetic biology conference SB5.0 2011. As the engineered genetic circuits become more complex, computational tools that aid the design process become essential. His group is currently developing computer-aided design tools to assist the design of genetics circuits for engineering of complex biological systems, enabling the study and optimization of the systems in silico before the actual construction. Using the tools developed, his group is working on optimizing the pathogen sensing and killing microbes which are designed to combat infectious diseases caused by pathogens.

Project title: Microbial electrosynthesis in converting carbon dioxide to value-added chemicals via synthetic biology strategies
Prof. Song Hao’s group focuses on genetic engineering of microorganisms by rational strategies taken from Synthetic Biology & Metabolic Engineering, and Systems Biology (various Omics technologies). He aims at industrial applications related with energy and environmental biotechnologies, in particular (1) Renewable bioenergy production (bioelectricity, biofuels); (2) Bioproduction of chemicals/drugs and functional foods (nutraceuticals); and (3) Petroleum and environmental microbiology and microbial consortia. His group adopted synthetic biology strategies to successfully engineer a number of microbial consortia and a variety of microorganisms to achieve high electricity energy production in microbial fuel and electrolysis cells, which have many applications in energy and environmental biotechnologies. His group has published over 40 papers in high-profile biotechnology Journals, including Nature Chemical Biology, Molecular Systems Biology, ACS Chemical Biology, etc. Currently, his group is actively working on engineering bacterial electron transfer and metabolic pathways, and its applications in redox reactions for energy and chemicals production. Specifically, (1) Engineering conductive bacterial biofilms for bio-electrochemical systems via synthetic biology, including: (i) microbial fuel cells (MFC) for wastewater treatment and bioelectricity production; (ii) microbial electrolysis cells (MEC) for hydrogen production; and (iii) microbial nanoparticles biosynthesis; and (2) Microbial electrofuels: Biological recycling of CO2 to chemicals & biofuels by microbial electrosynthesis and metabolic engineering.

Project title: Engineering bacteria for metal sequestration
The rapid advancement of nanotechnology in the past decades results in developments of individual units that can be assembled to form hyrarchical systems with varying complexity. Prof. Sierin Lim’s lab focuses on the design, engineering, and development of hybrid nano/microscale devices from biological parts by utilizing protein engineering as assembly tool towards future healthcare and sustainable earth. In a recent work, we have successfully engineered E. coli to to synthesize iron nanoparticle by increasing the metal intracellular sequestration and production of protein cage as the biological template. The protein cages are formed by self-assembly of multiple subunits forming highly uniform hollow spherical cage structures of nanometer size. Expression of both the FeoB iron transporter and ferritin under inducible promoter results in the production of approximately 10 mg of protein cage/liter of culture; loaded with up to 200 Fe/cage forming an iron core of ~8 nm. This loading can be optimized in vitro with the highest loading observed at 7000 Fe/cage. Besides serving as template, the protein cages have been shown to assist the solubilization and prevent the aggregation of the nanoparticle. Applications of these metal sequestering bacteria include environmental toxin removal and templated-synthesis of nanoparticle production.

Eileen Fong: Enhanced biological phosphorus removal process (EBPR)
Prof. Eileen Fong’s is interested in genetically engineering microbes found naturally in activated sludge, to increase their capacity for phosphate uptake. It is hoped that such genetically modified microbes will lead to higher efficiency and reduced costs of EPBR operations.

Zhao Xun Liang: Biosynthetic mechanism of secondary metabolites
Prof. Liang Zhao Xun’s lab works on polyketide-derived natural products from bacteria, fungi and plants represent a large family of secondary metabolites with unique molecular structures and potent biological activities. He is interested in several polyketide natural products that are assembled and functionalized by the so-called iterative polyketide synthases (iPKS) and the associated ancillary enzymes. His laboratory is examining the biosynthetic mechanisms of these structurally complex metabolites by expressing the enzymes in heterologous hosts, identifying the biosynthetic intermediates, and characterizing the structure and function of the enzymes. In addition to the potential of discovering novel enzymes as biocatalysts, the studies will open the door for future protein or metabolic engineering to produce structural derivatives with improved pharmacological properties.

William Chen: Metabolic engineering of yeast cells for enhanced biofuel precursor production

  • Prof. William Chen’s group aims to metabolically engineer the yeast Saccharomyces cerevisiae for enhanced biofuel precursor production. The idh1 and idh2 genes involved in citrate turnover in tricarboxylic acid cycle (TCA cycle) were disrupted to generate ∆idh1/2 mutant strain and the citrate production level was increased to 5- times higher. A heterologous ATP-citrate lyase (ACL), responsible for cleavage citrate to acetyl-CoA was overexpressed in this yeast mutant strain to generate ∆idh1/2-acl engineered strain, which served for the fatty acid biosynthesis. The final fatty acids production increased and especially, the mono-unsaturated fatty acids (C16:1 and C18:1) in engineering strain showed 92 % and 77 % higher. The comparative 2D LC-MS/MS proteomics analysis between engineered S. cerevisiae strain with enhanced biofuel precursor synthesis and wild type strain were investigated. The results revealed the metabolic pathway shift, sugar utilization shift, solvent stress response mechanism in the engineered strain. Together with GC-MS based metabolites analysis, the proteomics approaches not only provided an overview of ubiquitous cellular changes in ∆idh1/2-acl strain, but also help explore the metabolic mechanism of engineered strain, which served better for further modification of yeast cells for enhanced biofuel production.

  • Project title: Metabolic engineering of yeast cells for medium chain biofuel synthesis
    Prof. William Chen’s group aims to build a whole-cell catalyst to produce medium chain biofuels efficiently with Saccharomyces cerevisiae as producer. In preliminary research, the aldehyde with carbon chain length of nine, precursor of the target medium chain biofuel molecules, was synthesized with S. cerevisiae as producer. Preliminary results also suggested a possible unparalleled functioning in the peroxisomal membrane transporting complex. The excessive dependence of industrial development on fossil fuels has led to energy crisis which then stimulated renewable biofuel discovery. Here we present a novel approach to synthesize medium chain biofuels, alkanes and alkenes, potential substitutes for aviation fuels with unique and outstanding properties, stepping forward to exploit biotechniques of low-cost renewable transportation fuels production. LOX, HPL and AD with high specificity would be cloned in S. cerevisiae, as an enzymatic engineering approach to synthesize medium chain alkanes or alkene (carbon chain length of eight) with aldehydes (carbon chain length of nine) as the intermediate.
  • Project title: Malonate uptake and metabolism in Saccharomyces cerevisiae
    Prof. Willam Chen’s group aims to enhance malonate uptake and metabolism in Saccharomyces cerevisiae. MatB gene from the bacteria Rhizobium leguminosarium bv trifolii encodes for a malonyl-CoA synthetase which catalyzes the formation of the Malonyl-CoA directly from malonate and CoA. However, results from HPLC performed proved that Saccharomyces cerevisiae itself does not contain enough cytoplasmic malonate within them and is unable to uptake exogenously supplied malonate in the form of malonic acid. A dicarboxylic acid plasma membrane transporter with the ability to uptake exogenous malonic acid was identified from another species of yeast known as Schizosaccharomyces pombe and the gene encoding this transporter is identified as the mae1 gene. From the experiments thus far, the mae1 gene had been successfully cloned and transformed into Saccharomyces cerevisiae. The expression and functional ability of the encoded plasma membrane dicarboxylic acid transporter were also demonstrated and verified using specialized technologies such as RT-PCR, yeast immunofluorescence, HPLC and LC-MS. Subsequently, the malonyl-CoA synthetase from the matB gene would then be cloned next into the yeast. Tests will be run to verify the presence of these cloned genes and to verify their intended functions inside the cells and toxicity caused to the cells if any. Once all verification tests are done, an overall increase in the production in Malonyl-CoA by exogenously supplying malonate would be expected. Following which, an overall increased in the production of fatty acid within the cells would be expected which can then be further processed into biofuels.
  • Project Title: Genetic and protein engineering of yeast for increased fatty acid synthesis
    Prof. William’s group aims to find out the reason for the particular and extraordinary high lipid accumulation ability in oleaginous yeast strains and the essential factors involved and affected in the lipid accumulation and metabolism pathways. Time-course comparative proteomics profile using LC-MS/MS method and metabolic profile using GC/MS method were conducted. Essential proteins and metabolites were identified through comparison among high lipid content yeast strain, medium lipid content yeast strain and S. cerevisiae (low lipid content level). Utilizing the investigated important metabolites and proteins, we could increase the amount of biofuel precursors- fatty acids through metabolic engineering and genetic engineering strategies in the model yeast strain.


Par Nordlund and Tobias Cornvik: A high throughput protein production platform
Profs. Par Nordlund and Tobias Cornvik work on a high throughput protein production platform at the School of Biological Sciences at the Nanyang Technological University. The platform has to date collaborated with/served more than 45 different principal investigators at NTU, A*STAR and NUS. The platform has cloned more than 8000 different protein constructs and delivered over 1500 protein batches to the customers. The proteins have been used for a wide range of applications such as structural biology, enzymatic assays, drug development and antibody generation. The platform has an average throughput of screening 200 expression constructs/month and 50+ purifications/month, enough to serve additional projects e.g. synthetic biology and commercial entities.

Other Synthetic Biology Activities
Other efforts to grow synthetic biology at NTU include the following:
  • Winning gold and silver medals at the international Synthetic Biology competition held at MIT;
  • Developing new synthetic biology courses for undergraduate education; and Organizing the first International Symposium on Synthetic Biology in 2010 (an event widely reported in the local media).
  • Establishing strong collaboration links in synthetic biology with Imperial College London, through the NTU-Imperial College Joint PHD program started in 2009.


Other International Collaborators