DOE Microbial Genome Program Evolves
Rapid DNA Sequencing Generates Abundant Data for Gene Discovery, Insights
From its beginning in 1994, the DOE Microbial Genome Program (MGP) sparked a revolution in microbiology. Since the complete genome sequence of Haemophilus influenza was published by Craig Venter’s group (then at The Institute for Genomic Research, TIGR), genome sequences of some 51 microbes have been completed and published. Sequencing of at least a dozen more is complete but not yet published, and about 140 additional microbes are in varying stages of progress. Activity in the private sector also has been intense. Sequencing technologies have progressed to the point where a high-throughput facility such as the DOE Joint Genome Institute (JGI) can draft the sequence of a 2.5-Mb microbe in a day and 65 Mb of microbial sequence (about 17 to 20 microbes of different-sized genomes) in a month.
These sequences are enabling the discovery of new genes and pathways, as well as the insight that the horizontal transfer of genetic information may have been remarkably frequent in microbial evolution. Even in the 470-gene sequence of the smallest known free-living microbe Mycoplasma genitalium, perhaps as many as 100 to 150 genes are not required for life. With many microbial genomes finished or nearly finished (and thus sufficient for gene analyses), scientists have found that about 50% of each genome characteristically comprises genes of unknown function. Microbes have been isolated (and their genomes sequenced) from many different environments characterized by extremes: low pH, temperatures above that of boiling water, pressures more than 200atmospheres, high toxic-metal concentrations, high-radiation fluxes, high salinity, and just about every other inhospitable condition imaginable. Most microbes do not cause diseases and, in fact, increasingly are thought to play important roles in maintaining the earths ecology. DOE hopes to use the unique capabilities of microbes to fulfill its missions in carbon sequestration, bioremediation, cellulose degradation, energy production, biothreat reduction, and biotechnology.
The new awards represent a departure from the past. Instead of focusing on the high-throughput production of microbial genome sequence data (a mission now given over to JGI), MGP has evolved towards sequence analyses. MGP goals include functional analyses of microbial genomes; bioinformatics tools for microbial genome analyses; studies of lateral gene transfer (LGT), including its frequency and biological constraints; novel technologies for genomic characterization; and studies of microbial consortia and communities. Of more than 70 applications to the program, 28 awards were made in 2001.
Functional Studies
- John Battista (Louisiana State University): Enhance understanding of Deinococcus radiodurans and define the novel protein family responsible for DNA damage repair; identify genes required for radiation resistance as well as those whose expression changes after exposure, and compare them with genes in other radiation-resistant bacteria.
- Ray Gesteland (University of Utah): Use computation and experimentation to understand the phenomenon of “genome recoding,” the determination of additional expressed proteins from a known gene.
- David Wilson (Cornell University): Study genes coding for plant polysaccharide-degrading enzymes in the virtually complete Thermobifida fusca genome sequence; use the sequence to study the expression regulation of genes involved in cellulose digestion.
- Derek Lovley (University of Massachusetts, Amherst): Identify genes and proteins involved in the electron transfer system matrix of the environmentally significant bacterium Geobacter sulfurreducens.
- Brian Palenik (Scripps Institute of Oceanography): Explore transport proteins and their regulation in Synechococcus WH8102; add to the knowledge of nutrient transport in anenvironmentally important photosynthesizer.
- Caroline Harwood (University of Iowa): Use new microarray technologies to determine genes expressed during carbon dioxide and nitrogen fixation by the photosynthetic bacterium Rhodopseudomonas palustris.
- Daniel Arp (Oregon State University): Describe in Nitrosomonas europaea the gene regulatory networks that respond to changes in nutrients and other conditions; infer gene function using microarrays.
- Jizhong Zhou (Oak Ridge National Laboratory) in collaboration with James Tiedje (Michigan State University, MSU), Kenneth Nealson (University of Southern California), Harwood, and Arp: Construct whole-genome microarrays for several key microbes relevant to DOEs missions to elucidate gene-expression profiles under various growth conditions and to characterize different genetic mutants.
Bioinformatics Tools
- Owen White (TIGR): Continue the Comprehensive Microbial Resource, a coherent collection of careful, consistent annotations of microbial genome data that integrates all of TIGRs microbial sequencing and bioinformatics expertise in an easy-to-use Web interface.
- Mark Borodovsky (University of Georgia): Enhance gene-finding algorithms to better detect atypical genes in microbial genomes; analyze these genes to identify those that might have been laterally transferred.
- Jeremy Edwards (University of Delaware): Develop novel computational and high-throughput experimental tools to analyze DNA-repair pathways in D. radiodurans and the influence of metabolic flux distribution on DNA repair.
- Charles Lawrence (Wadsworth Center): Develop technologies for identifying transcription regulation networks in genomes of microbes sequenced by DOE-funded projects.
- Gary Olsen (University of Illinois, UI): Use tools and concepts of molecular phylogenetics with those of molecular biology to build an integrated computational tool for constructing and editing multiple sequence alignments.
- Monica Riley (Marine Biological Laboratory): Construct a metabolic database for Shewanella oneidensis; examine proposed pathways for missing functionality, experimentally validate the pathways, and attempt to identify candidates for the missing functions.
- Larry Wackett (University of Minnesota): Extend the University of Minnesota Biocatalysis/Biodegradation Database (called UM-BDD) to incorporate data on microbial metabolism relating to metals, metalloid, and organometallics.
- Diane Makowski (Argonne National Laboratory, ANL): Identify small molecule binding sites on microbial proteins genome wide.
- George Garrity (MSU) and Bergey’s Manual editors: Use a variety of statistical analyses to view information on bacterial species so the species can be clustered functionally and evolutionarily.
- William Cannon (Pacific Northwest National Laboratory, PNNL): In association with Richard Smith, develop computatonal tools for analyzing the output from high-throughput mass spectroscopy of microbial proteins.
Horizontal Gene Transfer
- Gary Olsen with Carl Woese (both at UI): Explore LGT to estimate the frequency of recent gene transfers to diverse microbial lineages; determine traits that correlate with high acquisition rates of external genetic information; identify donor lineages of ancient gene transfers; determine any relationship between gene transfer and biologically important events.
- Karen Nelson (TIGR): Substantiate and expand recent findings from whole-genome sequencing of Thermotoga maritima and other high-temperature archaea showing extensive genomic homologies that could have arisen only by LGT; apply biochemical methods to identify common and unique regions among the genomes of some 50 high-temperature bacteria and archaea.
- Terry Marsh (MSU): Investigate genomic plasticity in Ralstonia eutropha and R. pickettii,environmental isolates important in such processes as hydrocarbon degradation and resistance to high metal concentrations.
- Howard Ochman (University of Arizona): Investigate a set of 30 conserved and universally distributed genes to assess their involvement in LGT; establish LGT’s effects on shaping bacterial genomes.
Novel Technologies
- David Schwartz (University of Wisconsin, Madison): Characterize some 12 widely diverse microbial genomes by optical mapping over a 3-year period; coordinate microbe selection with JGI.
- Jay Keasling (University of California, Berkeley, UCB): Develop chip microfabrication arrays that will enable the automated testing of a large range of culture conditions; expose difficult-to-grow organisms to different environmental conditions to discover their growth requirements; test the effects of different metabolic substances on the physiology of established cultures.
Microbial Consortia and Hard-to-Culture Species
- Jill Banfield (UCB): In association with JGI, characterize the genetics and biochemistry of a community of acid-tolerant microbes; study LGT events between community members by utilizing the BAC libraries made by Ed DeLong (Monterey Bay Aquarium Research Institute).
- Fred Brockman (PNNL): Explore microbial subgenomes from undefined microbial consortia in contaminated subsurface sediments; characterize a genomic “signature” for the microbes in highly radioactive aquifer sediments.
- Cheryl Kuske (Los Alamos National Laboratory): Further the characterization of microbial backgrounds and isolate useful genes by determining the abundant and active microbial species in soils and sediments contaminated by radionuclides and metals, flow-sorting such cells, and developing methods to simplify microbial DNAs to generate libraries for future sequencing analyses.
- David Kirchman (University of Delaware): Address a key aspect of carbon cycling in the biosphere by studying how insoluble biopolymers are broken down to enter the food chain, especially in the marine bacterium Cytophagales.
Daniel Drell, with contributions from John Houghton and Anna Palmisano, DOE
A more detailed version of this article is at (http://microbialgenomics.energy.gov/announcement/2001awards.shtml).
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v12n1-2).
