RESEARCH

SYSTEMS BIOTECHNOLOGY

Biotechnology is undoubtedly recognized as 21st century-leading technology due to the potentials of producing high-profit pharmaceuticals, replacing commercial chemical products, and generating new markets with innumerable products from biodiversity. Biotechnology also meets the needs for clean technology through biodegradable products and environment-friendly bioprocess. Until now, biotechnology processes have been developed through labor- and time- intensive way. High cost and time taking development process has been unavoidable due to complexity of cellular networks, difficulties in biological experiments, and unpredictable outcomes. 

Rational reengineering of biology for the purpose of bioremediation, bioenergy or biorefinery requires deep understanding of all functional interactions of relevant components within native cell(s). The rational circuit design is becoming critical to develop bioprocesses for overproduction of bioproducts. The high throughput experimental tools conducting thousands of analyses in parallel, genome-wide experiments and rapid accumulation of biological data provide a foundation for profound understanding of biological process. Integration of multiple omics data and in silico modeling and simulation of biological networks thereby is becoming critical to design and re-engineer microorganisms for the efficient industrial production of recombinant proteins, biofuels, and a variety of bioproducts. This means biotechnology process can be developed in rational and systematic way – we referred this as ‘systems biotechnology’ - rather than traditional trial and error approach. Systems biotechnology can provide deep insight of identification of target gene or pathway for overproducing desired products and influence the speed and efficiency of process development.

Modeling and simulation of cellular process is extremely helpful to organize the available metabolic knowledge and to design the right experiments. Simulation of biological systems through metabolic modeling can provide crucial information concerning cellular behavior under interested genetic and environmental conditions, and thus lead to development of efficient biotechnology process with its predicting power. 

We are conducting integrative analysis of genomic architecture and composition, transcriptome and proteome structure/function, protein-protein and protein-DNA interactions and metabolic/regulatory networks to re-engineer industrial microorganisms. A key aspect of our approach is to use the power of systems biology to understand how complex biological processes operate. Our systems approach will reduce time and labor significantly to develop biotechnology processes for pharmaceuticals and biorefinery products such as biopolymers and key chemical products.

STRAINS OF PARTICULAR INTEREST

- Escherichia coli BL21(DE3)

Derivatives of E. coli B have been the major workhorse for production of recombinant foreign proteins and various biomaterials including biofuels in the labs and in industry. Strain REL606 has been used for experimental evolution studies, while BL21(DE3) is a favorite of molecular biologists, structural biologists, protein engineers, and production managers of the bioindustry. B strain often shows phenotypes distinct from those of K-12 - faster growth rate in minimal media, lesser production of acetate, superiority in foreign protein expression, and lesser tendency for degrading foreign proteins during purification.

We have determined genome sequences of B strains - REL606 which has been applied to long-term experimental evolution study and BL21(DE3) which has been a cell-factory for overproducing recombinant proteins, biofuels, and a variety of bioproducts on an industrial scale. Until now, the bioprocess optimization using B has been carried out in a rather trial-and-error manner. This inefficient approach has been unavoidable, because of insufficient information about the metabolism and physiology of B. Therefore, systematic understanding of cellular physiology and metabolism of the strain is essential not only to determine culture condition and, but also to design recombinant hosts.

- Pseudomonas putida S12 

Pseudomonas putida is a gram-negative gamma-proteobacterium widely distributed in soil and water environments. P. putida has a broad metabolic range and can tolerate and degrade various organic compounds. Therefore, it has been extensively used in bioremediation to remove organic pollutants from contaminated sites. This bacterium exhibits rapid growth, metabolic versatility, and inherent robustness to physicochemical stresses, making it an ideal candidate for producing biofuels, bioplastics, and other industrial products using renewable feedstocks.

P. putida S12 is exceptionally tolerant to various organic solvents and aromatic compounds that are toxic to most bacteria. It was first isolated using styrene as the sole carbon source, and it can grow on supersaturated concentrations of styrene, octanol, or heptanol as the sole carbon source. Due to its high solvent tolerance and versatile metabolism, S12 has been used in the synthesis of organic compounds such as phenol, p-hydroxystyrene, p-hydroxybenzoate, and 2,5-furandicarboxylic acid.

- Escherichia coli Nissle 1917

The nonpathogenic Escherichia coli strain Nissle 1917 (EcN) is among the most studied probiotic bacteria [1,2]. Over 100 years, EcN has been actively used as a phar-maceutical product (trade name: Mutaflor) for the treatment of intestinal disorders, such as inflammatory bowel disease, ulcerative colitis, and diarrhea [2]. EcN is a suc-cessful colonizer of the human gut, possessing strong antagonistic activity against en-tero-pathogens and immunomodulatory properties. The persistent colonization of EcN confers an advantage over Gram-positive probiotic strains, such as lactic acid bacteria, which transiently colonize the gut mucosa [1].

EcN has been genetically engineered to diagnose, prevent, and treat diseases ow-ing to its facile genetics and biosafety profile [3]. Recombinant EcN was constructed to secrete human epidermal growth factors to heal wounds in human intestinal epithelial cells [4]. It was engineered to sense and kill Pseudomonas aeruginosa in Caenorhabditis elegans and mouse infection models [5]. EcN can selectively colonize and replicate in solid tumors, and its tumor-targeting ability has been exploited to bind to cancer cells and produce cytotoxic compounds in tumor-bearing mice [6–8]. EcN was developed as a live microbial therapeutic to treat metabolic disorders, such as phenylketonuria [9] and hyperammonemia [10]. With advances in synthetic and systems biology, EcN is expected to be engineered to develop safer, cheaper, and more effective therapeutics for a wide range of diseases [3].

- Lactobacillus strains