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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

Systems Biology-Enabled Biosystems Design

C zofingiensis starch

Cryo-soft x-ray tomography shows substantial accumulation of starch (yellow) in chloroplasts of C. zofingiensis as part of research on the alga's physiological and genetic response to changes in glucose availability. This will help identify target genes for developing new engineered strains that accumulate high amounts of biofuels and bioproducts. [From Roth, M. S., et al., The Plant Cell, DOI: 10.1105/tpc.18.00742. Cryo-soft X-ray tomography capabilities supported by DOE Office of Basic Energy Sciences.]

Rationale

Multidisciplinary systems biology approaches are necessary for analyzing disparate types of genome-scale data to enable a deeper understanding of plant and microbial systems. Recent advances in the integration of computational biology with omics-enabled analytical technologies allow complex biological networks to be dynamically modeled and displayed. Genomics and systems-level predictive understanding of biological systems, pioneered by the Genomic Science program, are uncovering foundational design rules that govern system behavior to the extent that rational genome-scale redesign of organisms is becoming possible. Also referred to as "synthetic biology," this new but rapidly developing field already is providing novel tools for collaborating teams of biologists and chemical engineers to construct biological systems and organisms that address unique challenges and enhance understanding of complex biological systems.

The merging of biology, chemistry, physics, and engineering has the potential to transform fundamental and applied science by shedding light on the basic principles of biological system organization and evolution. This understanding can then be used to extend and enhance the capabilities of natural organisms to solve significant practical problems associated with the production of biofuels and related coproducts from renewable biomass. Extensive modification of existing networks or design of specific synthetic systems can both advance the understanding of biological systems and provide novel tools for interrogating basic biological function. Just as early trial and error in airplane design refined the understanding of fundamental fluid dynamics laws and enabled today's fully automated designs, iterative design cycles in biology will reveal the complex interconnections among biological laws, experimental observations of biological systems, and design of new biological behaviors.

A number of recent breakthroughs have piqued keen interest in genome engineering and biological design. New regulatory circuits can be constructed and evaluated for high-level function and control, and complete metabolic pathways can be assembled, engineered, and introduced into living cells to produce high-value compounds. Entire bacterial genomes can be replaced with modified synthetic counterparts. Orthogonal molecular processes have been developed to incorporate unnatural amino acids into proteins, conferring new functions by codon replacements through directed evolution. Novel nucleases with customizable specificity for genome engineering have been developed from bacterial transcription activator-like effectors (TALEs) and the type II clustered, regularly interspaced, short palindromic repeats (CRISPR)/Cas9 system. Substantial progress also has been made toward constructing synthetic eukaryotic chromosomes. Finally, the vast amount of comprehensive data available for genes, transcripts, proteins, and metabolites under different conditions for multiple individual organisms has dramatically advanced network analysis and computational modeling of biological systems.

Coincident with the development of these new technologies and approaches is an increased awareness of the potential security implications of intentional or unintentional misuse associated with applications enabled by advancements in genome editing, gene drives, and genome synthesis technologies. Consequently, federal agencies are supportive of taking a proactive stance in biothreat characterization through evaluation of the efficacy of biological detection and identification systems, fundamental research to inform risk mitigation of an accidental release of a biological material, and improved modeling and forecasting capabilities (see box, Secure Biosystems Design Initiative).

Secure Biosystems Design Initiative

Research activities under a new secure biosystems design initiative aim to develop genome-scale engineering tools to test fundamental principles that drive biological systems, with the specific goal of conferring enhanced stability, resilience, and controlled performance in DOE-relevant plant and microbial systems. These activities will be carried out under the Biosystems Design component of the Genomic Science program, integrating ongoing efforts in plant and microbiome science, environmental genomics, and sustainability research in mission-relevant ecosystems.

The initiative focuses on developing emerging technologies for manipulating microbial and plant platforms, while also facilitating coordination and exchange between experimental research platforms and environmental biological detection or sentinel systems. Another area of emphasis is understanding plant-microbe or microbial community interactions (including pathogenic or symbiotic relationships) well enough to create new synthetic biology and computational toolkits and design stable nanohybrid biological systems with predictable functionality.

Research topic areas cover:

  • Understanding the behavior of engineered organisms, including signaling and interactions, in different environmental conditions to devise new strategies for detecting and responding to intentional or unintentional biological escapes.
  • Developing novel biosystems design strategies to control or prevent the growth of engineered organisms outside the laboratory.
  • Advancing innovative biosystems design approaches to enhance and control the stability, resilience, and performance of engineered organisms in field conditions.
  • Engineering plants or microbes to detect or control other engineered organisms released into the environment.

Additionally, the initiative will generate large, heterogeneous datasets that integrate modern genomic and omic surveys with biochemical and biophysical measurements. This data, combined with new computational algorithms, will enable analysis and refinement of current knowledge, generating new insights and identifying biological paradigms.

Systems Biology Approaches

These advances also open new doorways to understand the foundational principles governing the systems properties of living organisms and to develop novel approaches for large-scale manipulation of functional properties that would not be possible via more traditional metabolic engineering approaches. For example, biodesign approaches applied to biomass feedstock plants could lead to new crops that express their own nitrogen-fixing enzymes without the need for bacterial symbionts or that incorporate components of the C4 and crassulacean acid metabolism (CAM) carbon fixation pathway into C3 plants. Such modifications could result in plants with significantly decreased fertilizer requirements, more efficient water utilization, and greatly improved sustainability characteristics. Understanding and improving stress tolerance in microbes is another critical issue that could benefit from biosystems design approaches. Currently, almost every fermentation process is limited by the microbe's tolerance to the final product. A novel way to overcome this problem might be the complete redesign of cell membrane composition by introducing genes to synthesize new membrane lipids. For example, the lipids making up archaeal membranes are very different from those of bacteria. Thus, moving the pathways for lipid biosynthesis from archaea to other microbes could create engineered organisms more tolerant to alcohol and thus more resilient to the stress of biofuel production. In eukaryotes, subcellular compartmentalization in organelles allows cells to contain metabolic pathways and sequester toxic compounds. Engineering cells with repurposed organelles could enable the production of high intracellular concentrations of biofuel molecules without affecting cytoplasm conditions.

Research Awards by Year

BER Program Manager for Biosystems Design

Dr. Pablo Rabinowicz
U.S. Department of Energy
Office of Biological and Environmental Research
Phone: 301-903-0379
Email: pablo.rabinowicz@science.doe.gov

Featuring

Genome Engineering for Materials Synthesis Report [06/19]


Biosystems Design to Enable Next-Generation Biofuels (Summary of Funded Projects) [12/17]


Biosystems Design Report [04/12]

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