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DOE JGI Finishes 100th Microbial Genome
May 23, 2006ORLANDO, Florida - Microbes, thriving in even the world's most extreme environments, are capable of performing myriad biological functions, learned over the billions of years they have inhabited the planet. Those lessons, and how they can be captured to render clean renewable sources of energy and to repair damaged environments, are among the many secrets encoded in their DNA sequence. On May 23, at the general meeting of the American Society of Microbiology (ASM), the U.S. Department of Energy Joint Genome Institute (DOE JGI) will announce that it has finished the sequence of 100 microbial genomes and released this information for the benefit of the global research community.
ASM President Dr. Stanley Maloy, who will touch on DOE JGI's achievement in his President's Forum remarks, said that the 100 microbes represent a rich portfolio of the vast and mostly uncharacterized microbial world. "DNA sequencing has opened a particularly productive vein to mine in exploring and expanding the frontier of microbiology. Especially where, through conventional culture methods, we are unable to shed light on the metabolic profiles of these microorganisms and their environmental implications, DNA sequencing provides us a welcome set of tools."
"The power of DOE JGI sequencing microbes, and other organisms, is that it gives us the complete genomic 'parts list' of those organisms," said Dr. Raymond L. Orbach, Director of the DOE Office of Science. "With this list in hand, we can explore how microbes use these parts to build and run their key functions, many of critical importance to DOE because they can break down plant materials to produce such useful sources of energy as ethanol and hydrogen, and clean up toxic waste sites. We know that microbes can perform these and a multitude of other amazing tasks and with the proper technology we can harness these capabilities."
DOE JGI, a national user facility, has sequenced or is in the process of sequencing over 380 organisms, more than any other institution in the world. DOE JGI averages over 3.1 billion bases or letters of sequence generated per month, or roughly the equivalent of a human genome once over. As microbes range in size from typically five to tens of millions of bases, several microbes could be sequenced in one day. However, the sequencing process, in order to meet rigorous quality standards and to satisfy the demands of the scientific community, is an iterative one, requiring six- to eight-times coverage. The term "finished," associated with the 100 microbial genomes accomplished by DOE JGI, is a technical designation referring to a standard of accuracy established for the Human Genome Project of tolerating no more than one mistake in 50,000 letters of genetic code with no gaps.
The microbes sequenced by DOE JGI, both single-celled and those multi-celled organisms invisible to the naked eye, cross all main branches of the tree of life: Eubacteria, Archaea, and even the Eukaryota, which include microscopic fungi, plants, and animals.
The 100th microbial genome, a project originally proposed by Dr. Kevin Sowers of the Center of Marine Biotechnology at the University of Maryland Biotechnology Institute (UMBI), is Methanosarcina barkeri fusaro, a methane-producing organism that exploits a unique metabolic pathway to do the job. This microbe, while isolated from a freshwater mud sample, also lives in the rumen of cattle where cellulose and other polysaccharides are digested.
"We are delighted that the DOE JGI's 100th genome is a microorganism that one of our UMBI faculty members has been studying to evaluate its potential for bioremediation and as an alternative energy source," said Dr. Jennie Hunter-Cevera, UMBI President. "By sequencing this and other important organisms, DOE JGI is helping to accelerate biotechnology discovery and innovation."
Microbes are critical micromanagers in the balance of nature. DOE JGI collaborator Dr. Donald A. Bryant, Ernest C. Pollard Professor of Biotechnology and Professor of Biochemistry and Molecular Biology at Penn State University, elaborates.
"Green sulfur bacteria, Chlorobi, are extremely important players in the global cycling of carbon, sulfur, and nitrogen," said Bryant. "Thanks to DOE JGI, the availability of multiple genome sequences for the Chlorobi has turbocharged our functional genomics studies. This has allowed us to make remarkable progress in understanding sulfur and ferrous iron oxidation, carotenoid and chlorophyll biosynthesis, photosynthetic light harvesting, oxygen tolerance, and many other aspects of the physiology and metabolism of the green sulfur bacteria."
The search for microorganisms that can inform solutions to energy and environmental challenges can go to the extremes-the boiling hot pools in Yellowstone National Park, for instance-and lead to new biotechnology products.
"DOE JGI has played an invaluable and otherwise unavailable role in the development of new enzymes for industrial use," said David Mead, President & CEO, of Lucigen Corporation. "The sequence acquisition of DNA from superheated thermal aquifers and other unique sources has resulted in the discovery of a new class of thermostable DNA polymerases and unique thermostable cellulase and hemicellulase enzymes. Without the DOE JGI these valuable molecules would not have made it into the marketplace."
The list below features highlights of some of the finished 100 and references the collaborating institutions and the roles of the organisms in their environment.
Bioenergy
Acidothermus cellulolyticus ATCC 43068. Alison Berry, University of California, Davis. Isolated from acid hot spring in Yellowstone; degrades cellulose, source of high-temperature enzymes.
Clostridium thermocellum. David Wu, University of Rochester; Mike Himmel, National Renewable Energy Laboratory. Cellulose degrader.
Cytophaga hutchinsonii ATCC33406. Mark McBride, University of Wisconsin Milwaukee. Cellulose degrader.
Frankia Cc13. Louis Tisa, University of New Hampshire. Fixes nitrogen; promotes formation of woody-biomass energy source.
Pichia stipitis. Thomas W. Jeffries, University of Wisconsin, Madison, USDA, Forest Service, Forest Products Laboratory, with José M. Laplaza; Volkmar Passoth, Swedish University of Agricultural Sciences (SLU), Yong-Su Jin, MIT: Ferments xylose to ethanol; potential to oxidize products of lignin degradation and plays a role in cellulose degradation.
Saccharophagus degradans 2-40. (formerly Microbulbifer degradans) Ronald Weiner, University of Maryland. Marine microbe degrades and recycles insoluble complex polysaccharides; potential for conversion of complex biomass to energy.
Thermobifida fusca YX. David Wilson and Diana Irwin, Cornell University. Major degrader of organic materials.
Moorella thermoacetica ATCC39073. Steven Ragsdale, University of Nebraska. Fixes carbon dioxide in absence of oxygen.
Nostoc punctiforme. Jack Meeks, University of California, Davis. Fixes carbon dioxide and nitrogen; produces hydrogen; survives acidic, anaerobic, and low-temperature conditions.
Bioremediation
Burkholderia species. Jim Tiedje, Michigan State University. Outstanding degrader of polychlorinated biphenyls (PCBs).
Chromohalobacter salexigens DSM 3043 (formerly Halomonas elongate). Laszlo Csonka, Purdue University; Brad Goodner, Hiram College; Aharon Oren, The Hebrew University of Jerusalem. Extremely salt tolerant; displays metal resistance; degrades aromatic hydrocarbons and toxic organics.
Deinococcus geothermalis DSM11300. Michael Daly, Uniformed Services University of the Health Sciences, James K. Fredrickson, Pacific Northwest National Laboratory, Kira S. Makarova, National Institutes of Health. Resists radiation; can bioremediate radioactive mixed waste.
Desulfovibrio desulfuricans G20. Judy D. Wall, University of Missouri. Reduces sulfate, uranium, and toxic metals; corrodes iron piping; "sours" petroleum with hydrogen sulfide.
Geobacter metallireducens. Derek Lovley, University of Massachusetts. Important player in the carbon and nutrient cycles of aquatic sediments and in the bioremediation of organic and metal contaminants in groundwater.
Rhodobacter sphaeroides. Samuel Kaplan, University of Texas Health Sciences Center at Houston. Metabolically diverse, grows in wide variety of conditions; photosynthetic, providing fundamental insights into light-driven, renewable-energy production; can detoxify metal oxides.
Shewanella species. Jim Fredrickson, Pacific Northwest National Laboratory. Degrades metals including uranium, technetium, and chromium; important in carbon cycling in anaerobic environments.
The entire list of the DOE JGI 100 can be found at: http://genome.jgi-psf.org/microbial.
DOE JGI provides the scientific community at large with access to DNA sequencing for DOE-relevant projects based on scientific merit as judged through independent peer review. Nominations, due August 10, 2006, are currently being sought for candidate microbes, microbial consortia, for draft genomic sequencing in support of DOE's Office of Biological and Environmental Research (BER) Bioenergy Program element within its Genomics: GTL Program. Nominated candidates must be relevant to the BER mission to determine genomic sequences of microorganisms involved in energy production, particularly conversion of lignocellulosic material to ethanol, or hydrogen, or other biofuels.
The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up. DOE JGI's Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
U.S. Department of Energy Joint Genome Institute
DOE JGI, a national user facility, has sequenced or is in the process of sequencing over 380 organisms, more than any other institution in the world. DOE JGI averages over 3.1 billion bases or letters of sequence generated per month, or roughly the equivalent of a human genome once over. As microbes range in size from typically five to tens of millions of bases, several microbes could be sequenced in one day. However, the sequencing process, in order to meet rigorous quality standards and to satisfy the demands of the scientific community, is an iterative one, requiring six- to eight-times coverage. The term "finished," associated with the 100 microbial genomes accomplished by DOE JGI, is a technical designation referring to a standard of accuracy established for the Human Genome Project of tolerating no more than one mistake in 50,000 letters of genetic code with no gaps.
The microbes sequenced by DOE JGI, both single-celled and those multi-celled organisms invisible to the naked eye, cross all main branches of the tree of life: Eubacteria, Archaea, and even the Eukaryota, which include microscopic fungi, plants, and animals.
The 100th microbial genome, a project originally proposed by Dr. Kevin Sowers of the Center of Marine Biotechnology at the University of Maryland Biotechnology Institute (UMBI), is Methanosarcina barkeri fusaro, a methane-producing organism that exploits a unique metabolic pathway to do the job. This microbe, while isolated from a freshwater mud sample, also lives in the rumen of cattle where cellulose and other polysaccharides are digested.
"We are delighted that the DOE JGI's 100th genome is a microorganism that one of our UMBI faculty members has been studying to evaluate its potential for bioremediation and as an alternative energy source," said Dr. Jennie Hunter-Cevera, UMBI President. "By sequencing this and other important organisms, DOE JGI is helping to accelerate biotechnology discovery and innovation."
Microbes are critical micromanagers in the balance of nature. DOE JGI collaborator Dr. Donald A. Bryant, Ernest C. Pollard Professor of Biotechnology and Professor of Biochemistry and Molecular Biology at Penn State University, elaborates.
"Green sulfur bacteria, Chlorobi, are extremely important players in the global cycling of carbon, sulfur, and nitrogen," said Bryant. "Thanks to DOE JGI, the availability of multiple genome sequences for the Chlorobi has turbocharged our functional genomics studies. This has allowed us to make remarkable progress in understanding sulfur and ferrous iron oxidation, carotenoid and chlorophyll biosynthesis, photosynthetic light harvesting, oxygen tolerance, and many other aspects of the physiology and metabolism of the green sulfur bacteria."
The search for microorganisms that can inform solutions to energy and environmental challenges can go to the extremes-the boiling hot pools in Yellowstone National Park, for instance-and lead to new biotechnology products.
"DOE JGI has played an invaluable and otherwise unavailable role in the development of new enzymes for industrial use," said David Mead, President & CEO, of Lucigen Corporation. "The sequence acquisition of DNA from superheated thermal aquifers and other unique sources has resulted in the discovery of a new class of thermostable DNA polymerases and unique thermostable cellulase and hemicellulase enzymes. Without the DOE JGI these valuable molecules would not have made it into the marketplace."
The list below features highlights of some of the finished 100 and references the collaborating institutions and the roles of the organisms in their environment.
Bioenergy
Acidothermus cellulolyticus ATCC 43068. Alison Berry, University of California, Davis. Isolated from acid hot spring in Yellowstone; degrades cellulose, source of high-temperature enzymes.
Clostridium thermocellum. David Wu, University of Rochester; Mike Himmel, National Renewable Energy Laboratory. Cellulose degrader.
Cytophaga hutchinsonii ATCC33406. Mark McBride, University of Wisconsin Milwaukee. Cellulose degrader.
Frankia Cc13. Louis Tisa, University of New Hampshire. Fixes nitrogen; promotes formation of woody-biomass energy source.
Pichia stipitis. Thomas W. Jeffries, University of Wisconsin, Madison, USDA, Forest Service, Forest Products Laboratory, with José M. Laplaza; Volkmar Passoth, Swedish University of Agricultural Sciences (SLU), Yong-Su Jin, MIT: Ferments xylose to ethanol; potential to oxidize products of lignin degradation and plays a role in cellulose degradation.
Saccharophagus degradans 2-40. (formerly Microbulbifer degradans) Ronald Weiner, University of Maryland. Marine microbe degrades and recycles insoluble complex polysaccharides; potential for conversion of complex biomass to energy.
Thermobifida fusca YX. David Wilson and Diana Irwin, Cornell University. Major degrader of organic materials.
Moorella thermoacetica ATCC39073. Steven Ragsdale, University of Nebraska. Fixes carbon dioxide in absence of oxygen.
Nostoc punctiforme. Jack Meeks, University of California, Davis. Fixes carbon dioxide and nitrogen; produces hydrogen; survives acidic, anaerobic, and low-temperature conditions.
Bioremediation
Burkholderia species. Jim Tiedje, Michigan State University. Outstanding degrader of polychlorinated biphenyls (PCBs).
Chromohalobacter salexigens DSM 3043 (formerly Halomonas elongate). Laszlo Csonka, Purdue University; Brad Goodner, Hiram College; Aharon Oren, The Hebrew University of Jerusalem. Extremely salt tolerant; displays metal resistance; degrades aromatic hydrocarbons and toxic organics.
Deinococcus geothermalis DSM11300. Michael Daly, Uniformed Services University of the Health Sciences, James K. Fredrickson, Pacific Northwest National Laboratory, Kira S. Makarova, National Institutes of Health. Resists radiation; can bioremediate radioactive mixed waste.
Desulfovibrio desulfuricans G20. Judy D. Wall, University of Missouri. Reduces sulfate, uranium, and toxic metals; corrodes iron piping; "sours" petroleum with hydrogen sulfide.
Geobacter metallireducens. Derek Lovley, University of Massachusetts. Important player in the carbon and nutrient cycles of aquatic sediments and in the bioremediation of organic and metal contaminants in groundwater.
Rhodobacter sphaeroides. Samuel Kaplan, University of Texas Health Sciences Center at Houston. Metabolically diverse, grows in wide variety of conditions; photosynthetic, providing fundamental insights into light-driven, renewable-energy production; can detoxify metal oxides.
Shewanella species. Jim Fredrickson, Pacific Northwest National Laboratory. Degrades metals including uranium, technetium, and chromium; important in carbon cycling in anaerobic environments.
The entire list of the DOE JGI 100 can be found at: http://genome.jgi-psf.org/microbial.
DOE JGI provides the scientific community at large with access to DNA sequencing for DOE-relevant projects based on scientific merit as judged through independent peer review. Nominations, due August 10, 2006, are currently being sought for candidate microbes, microbial consortia, for draft genomic sequencing in support of DOE's Office of Biological and Environmental Research (BER) Bioenergy Program element within its Genomics: GTL Program. Nominated candidates must be relevant to the BER mission to determine genomic sequences of microorganisms involved in energy production, particularly conversion of lignocellulosic material to ethanol, or hydrogen, or other biofuels.
The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up. DOE JGI's Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
U.S. Department of Energy Joint Genome Institute
Establishing standard definitions for genome sequences
In 1996, researchers from major genome sequencing centers around the world convened on the island of Bermuda and defined a finished genome as a gapless sequence with a nucleotide error rate of one or less in 10,000 bases.
Duckweed genome sequencing has global implications
Three plant biologists at Rutgers' Waksman Institute of Microbiology are obsessed with duckweed, a tiny aquatic plant with an unassuming name. Now they have convinced the federal government to focus its attention on duckweed's tremendous potential for cleaning up pollution, combating global warming and feeding the world.
454 Life Sciences and Baylor College of Medicine complete sequencing of DNA pioneer
454 Life Sciences Corporation, in collaboration with scientists at the Human Genome Sequencing Center, Baylor College of Medicine, announced today in Houston, Texas, the completion of a project to sequence the genome of James D. Watson, Ph.D., co-discoverer of the double-helix structure of DNA.
Genome of PURAC's lactic acid-producing micro-organism completed by Greenomics™
PURAC and Greenomics™ (Plant Research International B.V.) announced the completion of the whole-genome sequencing of a production strain of PURAC that produces high amounts of lactic acid. Greenomics™ conducted the shotgun cloning and high quality sequencing of the genome up to a zero-gap situation. The closed genome is accompanied by an automated annotation and a functional classification of all the genes by bioinformatics tools. The positive results obtained so far has encouraged PURAC to continue the research in this field and to collaborate further with Greenomics™ in a comparative genomics project involving another lactic acid producing strain. The collaboration is not
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