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Unleashing the Power of Genomics: Understanding the Environment and Biological Diversity

Since The Institute for Genomic Research first decoded the complete genetic material of a free-living organism (Haemophilus influenzae) in 1995,1 we have seen an explosion in the number of completed genomes. The total completed genome count is about 150, a number that is likely to double in 2004. Next year, we will experience a greater shift in genomics, from simply obtaining the genetic code of organisms to comparing and interpreting them, eventually understanding how the four-letter (ACGT)

By | December 1, 2003

Since The Institute for Genomic Research first decoded the complete genetic material of a free-living organism (Haemophilus influenzae) in 1995,1 we have seen an explosion in the number of completed genomes. The total completed genome count is about 150, a number that is likely to double in 2004.

Next year, we will experience a greater shift in genomics, from simply obtaining the genetic code of organisms to comparing and interpreting them, eventually understanding how the four-letter (ACGT) code leads to such diversity of life.

Mathematical, computational, and strategic advances, as well as new analytical instruments, have completely revolutionized genomics; more than 1,000 sequenced genomes should be finished by the end of 2005. These same tools are now being used to characterize and understand the environment. As a result, a new discipline is emerging: "environmental genomics." Through The Institute for Biological Energy Alternatives, we are expanding the environmental applications of genomics and are already seeing exciting new vistas.

Environmental genomics traces its origins to 1996, when the sequence of Methanococcus jannaschii, an obscure and unseen organism, was completed;2 it was isolated from a deep-sea volcanic vent off the coast of Mexico. M. jannaschii is from the Archea, the third branch of life, between Bacteria and Eukaryotes, to which humans belong. Found to be an autotroph, this organism uses only inorganic constituents as its food and makes everything for its survival from those elements. It comes to life at about 60°C, with an optimum temperature for growth at about 85°C.

Some of what is captivating about this and similar organisms are their catalytic reactions for producing cellular energy. M. jannaschii uses ambient carbon dioxide (CO2) as its carbon source and hydrogen electrons as its energy source to generate cellular energy and methane, supporting the idea that biology could be harnessed to help with CO2 sequestration and clean energy production.

These photosynthetic microorganisms evolved about three billion years ago. They could capture photons from sunlight and use the energy to split water-producing oxygen and hydrogen ions. They released the oxygen into the atmosphere and used the energy from the hydrogen ions to help capture CO2. The carbon was converted into sugar as a mechanism of stored energy.

While the scientific community has long looked for biological processes to produce energy, most efforts have fallen short due to the slow intrinsic rate of the chemical reactions in microbial and plant cells. However, with new molecular biology and genomic tools to enable genome engineering, reaction rates could be theoretically changed by 10,000-fold. Such changes would make biological energy production both economically and environmentally competitive.

To do so, we need to find new proteins in the environment with desired properties, or modify existing systems. With each new genome sequenced (including the human) we discover that 40% to 60% of the genes are new to biology. With 150 genomes decoded, the fraction of new genes hasn't diminished, proving that the global gene pool is enormous. It is estimated that less than 1% of microbial species on our planet have been discovered, in large part because most cannot be grown in the laboratory.

To enhance discovery of new organisms and biochemical pathways, we are gathering organisms from various ocean depths and simultaneously sequencing their genomes using the shotgun sequence approach. Recently, we completed a test project in a portion of the North Atlantic Ocean called the Sargasso Sea, off Bermuda. We chose this water body because it's considered to have a low diversity of species due to its nutrient-poor environment.

The data are stunning: From 200 liters of sea-water we have found thousands of new species and more than one million new protein-coding genes (about 10 times the total number of genes discovered to date). The new genes include hundreds of new photoreceptors that capture energy from sunlight. If the same extent of microbial diversity exists across the oceans, it is not inconceivable that hundreds of millions of genes could be discovered. These powerful genomic tools may become the method of choice to monitor ocean environments.

J. Craig Venter is founder of the nonprofit J. Craig Venter Science Foundation Joint Technology Center, which supports research at The Institute for Genomic Research, The Center for the Advancement of Genomics, and The Institute for Biological Energy Alternatives.

References
1. R.D. Fleischmann et al., "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.," Science, 269:496-512, 1995.

2. C.J. Bult, "Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii," Science, 273:1058, 1996.

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