By Debbie Strickland

Staff Writer

With the help of a U.S. Department of Energy grant, the genome of a second methane-producing Archaea organism has been sequenced, yielding a stack of information that could be used to harness its fuel production machinery.

Waltham, Mass.-based Genome Therapeutics Corp. (GTC), in collaboration with Ohio State University, sequenced the genome of Methanobacterium thermoautotrophicum and published the research in the November issue of the Journal of Bacteriology.

M. thermoautotrophicum is an archaeon, one of a group of bacteria-like organisms that make up the third branch of life, the other two being procaryots (bacteria) and eucaryots (everything else). Discovered just 20 years ago, archaeons typically reside in such hostile environments as toxic waste dumps, extreme ocean depths, boiling temperatures and saturated salt solutions. The hardy critters have potential applications ranging from the clean-up of radionuclides to food processing.

Last year, the Institute for Genomic Research (TIGR), formerly associated with Human Genome Sciences Inc., of Rockville, Md., sequenced a similar archaeon, methane-producing Methanococcus jannaschii.

"We now have a unique opportunity for comparative genetic analysis," said Bernd Seizinger, executive vice president and chief scientific officer at GTC. "With two Arcahea bacteria, we can look for common denominators."

"A big surprise," he added, "is that the [two methane-producing] Archaea bacteria share only a relatively small number of genes. About 20 percent have homologies of more than 50 percent. They have fewer genes in common than we would have anticipated."

A total of 1,855 protein encoding genes have been identified, and approximately 44 percent have been assigned putative functions. About 27 percent of M. thermoautotrophicum's genes "are absolutely new," said Seizinger.

M. thermoautotrophicum is an anaerobic archaeon with rod-shaped cells that grows optimally at 65° Celsius. The organism produces methane through the reduction of carbon dioxide with hydrogen gas. The 1.8 million base-pair sequence was obtained by using a whole-shotgun sequencing approach. The complete circular map of the genome is available on the company's home page at

In 1994, the Department of Energy Microbial Genome Project selected a group of sequencing projects to fund via multimillion-dollar grants totaling more than $10 million. GTC was to receive $4.6 million for the M. thermoautotrophicum effort, although the company declines to disclose how much it actually received.

Due to the government funding, the M. thermoautotrophicum sequence is a part of the public domain, but GTC retains commercial rights. The company may seek a licensing or research collaboration deal with an energy company, Seizinger said.

GTC, which specializes in sequencing genes and genomes with human therapeutic applications, is not sequencing additional archaeons, although it is working under the same DOE grant program to complete the sequence of the genome of Clostridium acetobutylicum — a spore-forming, solvent-producing bacteria that belongs to a genus associated with diseases such as botulism, tetanus and gangrene. The company in September made available initial sequence data from C. acetobutylicum.

GTC's shares (NASDAQ:GENE) closed Thursday at $8.25, down $0.125. *