Genomics:GTL

Technologies for Systems Biology

Technology Overview

The GTL program is founded on major advancements in genomics and emerging technologies for 21st Century biology. Biotechnology will be a major strategic factor in achieving DOE mission goals in industrial biotechnology—a critical arena of national economic competitiveness. Comprehensive suites of technologies will enable a new era in biology, building on the national investment in genomics.

The research community increasingly is recognizing the need for global analysis of myriad simultaneous cellular activities and is calling for a new research infrastructure. “Progress in microbiology always has been enabled by the technology available, a fact that is still true today. However, many researchers are stymied by lack of access to the expensive instruments that would enable them to make the greatest strides.” (Schaechter, Kolter, and Buckley 2004, p. 13; see also Aebersold and Watts 2002; Buckley 2004a; Stahl and Tiedje 2002).

Science and Technology Rationale

In the simplest interpretation, an organism’s genome contains encoded information to produce the proteins that are the cell’s workhorses. Central to the scientific and technical strategy of GTL, however, is the fact that information encoded in the genomes of microbes, plants, and the metagenomes of microbial communities goes well beyond encoding proteins. Genomes control biological structure and function at many spatial and temporal scales—molecular, machine, cellular, organism, community, and ecosystem—through an intricate set of interrelated and communicating regulatory and control processes (see figure below). Biological systems display such strong interactions that capabilities are needed to explore these systems in a comprehensive and integrated way at all levels. A comprehensive technology suite must be established to dramatically improve research performance, throughput, quality, and cost.

Examples of performance challenges include producing and characterizing complex proteins (e.g., membrane and multidomain); isolating, characterizing, and modeling large or tenuous molecular machines; measuring the full molecular profile of microbial systems; and imaging molecules as they carry out their critical functions in cells in structured communities. Examples of throughput challenges include providing insight into the functions of hundreds of thousands of unknown genes and their modifications; processing thousands of molecular machines; analyzing molecular profiles of thousands of microbial samples under different conditions; and spanning the full range of conditions and processes governing microbial-community behaviors. Quality control includes developing and implementing strict protocols and providing the most sophisticated diagnostics. High-throughput methods and resource sharing among community members will lower the unit cost for production and analyses. The GTL program supports numerous pilot studies targeting key technologies and their integration for systems biology.

The figure above depicts elements of technology and experimentation that must be spanned to build an integrated body of knowledge about behavior, from genomic interactions through ecosystem changes. Simultaneously studying multiple mission problems is powerfully synergistic because enduring biological themes are shared and general principles governing response, structure, and function apply throughout. The biology underlying the challenges of one mission will inform those of the others. Accumulating data as they are produced, the GTL Knowledgebase and the computational environment that GTL will create will act as the program's central nervous system, allowing this information to be integrated into a predictive understanding.

The Office of Science has a tradition of strategic basic research in a multidisciplinary team environment for national missions. These new suites of technologies will bring together the biological, physical, computational, and engineering sciences to create a new infrastructure for biology and the industrial biotechnology needed for the 21st Century. DOE’s technology programs can work with industry to apply such capabilities and knowledge to a new generation of processes, products, and industries.

A New Trajectory for Biology

As we have learned from the genome projects, consolidating capabilities and focusing on aggressive goals will drive dramatic improvements in performance and cost. As depicted in this image, GTL’s development of new technologies in a coordinated and integrated way will accelerate discovery and reduce the time for useful applications. With this higher level of performance, systems biology is sufficiently tractable and affordable to support the next generation of industrial biotechnology for the coming decade and beyond.

Capsule Technology Descriptions

The GTL program, working with the scientific community, analyzed a complementary set of technologies and their products, which were consolidated into suites with a common technical, intellectual, or infrastructure foundation. Two of these technology suites are focused on analysis of properties and functions of cellular components, proteins, and molecular machines.

• Production and Characterization of Proteins and Molecular Tags
• Characterization and Imaging of Molecular Machines

Two suites focused on analysis of biological-system responses and functions at the molecular, cellular, and community levels:

• Whole Proteome Analysis
• Modeling and Analysis of Cells and Communities

This technology suite discusses each set of technologies in further detail—the science that drives them, how they function, their strengths and weaknesses, and how they might be developed. Capsule descriptions follow.

Technologies for Production and Characterization of Proteins and Molecular Tags

Technologies for Protein Production and Characterization will use DNA sequence to make proteins and reagents for interrogating cell function. Specifically, a number of emerging technologies support the capability to produce all proteins encoded in any genome on demand; create molecular tags that allow each protein to be identified, located, and manipulated in living cells; and, to gain insights into function, perform biophysical and biochemical characterizations of proteins produced. Creating high-throughput in vitro and in vivo techniques will lower the cost of producing proteins to allow comprehensive analysis of all proteins within the cell as needed to understand critical features of cell function. A natural adjunct to protein production will be generation of “affinity reagents.” These small proteins or nucleic acids will permit detection and tracking of individual proteins in living systems, including complex molecular assemblages; intracellular position of all proteins and their spatial dynamics; if exported, extracellular localization and interaction with other community members; and techniques for manipulating protein activity in the environment.

Core instrumentation being explored within GTL pilot studies:

• Gene synthesis and manipulation techniques
• High-throughput microtechnologies for protein-production screening
• Robotic systems for protein and affinity-reagent production and characterization
• Computing for data capture and management, genomic comparative analyses, control of high-throughput system and robotics, and production-strategy determination

Technologies for Characterization and Imaging of Molecular Machines

A variety of instruments and methods are emerging to identify and characterize molecular assemblies and interaction networks. These include capabilities to isolate and analyze molecular machines from microbial cells; image and localize molecular machines in cells; and generate dynamic models and simulations of the structure, function, assembly, and disassembly of these complexes. To understand the makeup and function of molecular machines, scientists must identify molecular machine components, characterize their interactions, validate their occurrence, and determine their locations within the cell—ultimately analyzing the thousands of molecular machines that perform essential functions inside a cell. These analyses are a key step in determining how the network of cellular molecular processes works on a whole-systems basis by completely understanding individual molecular machines, how each machine is assembled in 3D, and how it is positioned in the cell with respect to other components of cellular architecture.

Core instrumentation being explored in GTL pilot studies:

• Robotic culturing technologies to induce target molecular machines in microbial systems and support robotic techniques for molecular complex isolation
• Culturing and pull-down experimentation coupled with mass spectrometric analyses to determine the interactome in cellular systems
• Numerous sophisticated mass-spectroscopy and other techniques specially configured to analyze samples of purified molecular machines for identification and characterization of complexes
• Various advanced microscopies for intracomplex imaging and structure determination
• Imaging techniques for intracellular and intercellular localization of molecular complexes
• Computing and information systems for modeling and simulation of molecular interactions that lead to complex structure and function

Technologies for Whole Proteome Analysis

Emerging technologies based on genomic analyses can provide insight into microbial functions by identifying (1) all proteins and other molecules that a microbe (or microbial community) creates under controlled conditions and (2) key pathways and other processes. An organism selectively produces portions of its proteome in response to specific environmental or intracellular cues. Studying its constantly changing protein expression thus leads to a better understanding of how and why an organism turns portions of its genome “on” and “off.” A suite of technologies is emerging to achieve a comprehensive understanding of biological responses to environmental cues by identifying, quantifying, and measuring changes in the global collections of proteins, RNA, metabolites, and other molecules. These molecules, including lipids, carbohydrates, and enzyme cofactors, are important in understanding biological processes mediated by proteins. Integrated diverse global data sets can be utilized to parameterize computational models to predict systems functions and responses, inferring the nature and makeup of metabolic and regulatory processes and structures.

Core instrumentation being explored in GTL pilot studies includes:

• Large farms of chemostats to prepare samples from highly monitored and controlled microbial systems under a wide variety of conditions
• Numerous specialized mass and nuclear magnetic resonance spectrometers and other instrumentation capable of analyzing the molecular makeup of ensemble samples with thousands of diverse molecular species
• High-performance computing and information capabilities for modeling and simulation experiments of living system functionalities under different scenarios to inform the design of experimental campaigns focused on systems-level goals and to infer system molecular processes from ensuing data

Technologies for Modeling and Analysis of Cellular Systems

Ultimate analytical capabilities will allow systems-level study of living cells in complex and dynamic structured communities or tissues and knowledge synthesis to then enable a predictive understanding and modeling of organism, cell, and community function critical for systems biology. Imaging methods will monitor proteins, machines, and other molecules spatially and temporally as they perform their critical functions in living systems. Organisms such as plants and microbial communities contain numerous microniches that elicit unique phenotypic and physiological responses from individual species of microbes. Determining the detailed molecular makeup of specific structures within living systems is a grand challenge for biology that must be addressed before scientists can predict the behavior of these systems and take advantage of their functional capabilities. Modeling will then describe essential features of biological interactions with the physicochemical environment and predict how they will evolve in structure and function.

Core instrumentation targeted in GTL pilot studies include:

• Highly instrumented cultivation technologies to prepare structured microbial communities to simulate natural conditions under highly controlled conditions
• Instruments integrating numerous analytical imaging techniques that can spatially and temporally determine, in a nondestructive way, the relevant molecular makeup and dynamics of plants, microbial community environments, and the microbes that comprise it
• Computing and information capabilities to model and simulate complex microbial systems, design experiments, and incorporate data

Relationships and Interdependencies of Technologies

Each technology suites is technically distinct in the nature of its instrumentation, methods, and overall goals. Depending on the application—as a general capability to serve many programs or as part of a vertically integrated set focused on a particular mission challenge—the instruments will be designed to maximize quality and throughput and reduce unit costs, to reach new levels of performance, or combinations of both. These technologies, when used together, have complementary strengths that can help provide complete systems knowledge. The figure Interrelationships Among Key Analytical Methodologies Used in Systems Biology illustrates how these core functions are complementary to each other. The key interactions shown demonstrate their interdependencies and necessary exchange of all information through the GTL Knowledgebase and the program’s communication and computing infrastructure.

Research Scenarios

As described in the Missions Overview and related appendices, each mission example has a unique endpoint and research strategy for developing the needed understanding, predictive models, and research capabilities. Table 1. Research Scenarios on Microbial Processes and Table 2. Science Roadmaps for Natural Systems present conceptual research-scenario roadmaps for six cases as illustrations related to Science Milestones and GTL Technologies. Although these systems and problems cover a breadth of biological phenomenology and system behaviors, they can be studied using the same foundational capabilities. Each GTL milestone, as denoted in the left column of Tables 1 and 2, drives the technical core.

This Webpage adapted from Genomics:GTL Roadmap, DOE/SC-0090, October 2005. See References PDF.