LONDON - The genome of the thermophilic organism, Thermoplasma acidophilum, has been sequenced, providing a new crop of genes encoding thermophilic enzymes for biotechnology exploration. Details of the genome also suggest that, contrary to theories suggested by some evolutionary biologists, the organism is not an ancestor of eukaryotic cells.
T. acidophilum used to be classified as a thermophilic mycoplasm but has now been classified as a member of the Archaea - the so-called "third domain of life," the other two being bacteria and eukaryotes. Isolated during the 1960s from self-heating coal refuse piles, T. acidophilum has no cell wall and lives at temperatures as high as 59 degrees Celsius and at pH 2.0 or even lower.
Andreas Ruepp, postdoctoral research fellow at the Max Planck Institute for Biochemistry in Martinsried, Germany, told BioWorld International: "We decided to sequence T. acidophilum partly because of the extreme environment it lives in, but mainly because its genome is not that big, and because we had already worked on visualizing many of its proteins using 3-dimensional electron microscopy."
Ruepp and his colleagues, who include Craig Volker at SmithKline Beecham Pharmaceuticals in Collegeville, Pa., report their findings in a paper in the Sept. 28, 2000, issue of Nature titled, "The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum." Using a new rapid technique they call "shotgun primer walking," they identified more than 1,500 protein-coding sequences within the organism's genome, which has 1,564,905 base pairs. Many of the genes closely resemble sequences found in another thermophilic archaeon, Sulfolobus solfataricus.
Don Cowan, reader in molecular microbiology at University College London in London, told BioWorld International, "One reason why this paper is important is because it clears up some of the speculation that T. acidophilum may be a precursor of eukaryotic cells. The results show that there is not enough eukaryote-like material in the genome for that - in fact, a lot of it looks like bacterial genetic material."
Cowan, who is the author of a News and Views article on the paper in the same issue of Nature, titled, "Use your neighbour's genes," added that one of the most interesting features of T. acidophilum is that it is one of the few organisms to exist without a cell wall. "Unfortunately, the genome does not directly tell us much about how it copes without a protective cell wall," he said.
From the point of view of the biotechnology industry, the genome provides another resource in the search for enzymes suitable for particular processes, Cowan added. "Thermophilic enzymes have attracted a lot of attention in the field of biotechnology, particularly in the biotransformations area, partly because of their thermal stability and partly because of their higher level of stability to organic solvents and denaturants than non-thermophilic enzymes."
Ruepp said one of the most interesting features of the paper is the analysis of proteins called chaperones, which help polypeptide chains fold in the correct way to form proteins, and proteases, enzymes that break down proteins. "With this information we were able to draw up a scheme of proteolysis and protein folding, and the pathways which connect them. This is the first time this has ever been done for an organism," he said.
The genome also shows that many of the genes of T. acidophilum are very similar to those of S. solfaricus. Ruepp said, "We think that the genes of organisms sharing this extreme environment are exchanging their genetic material between themselves to adapt to this specific environment. The distribution of the genes which are similar is not random - there are five "hotspots" where a lot of these proteins which are similar occur."
Cowan added that this finding strengthened scientists' view that organisms are able to readily exchange parts of their genomes. "This discovery adds to the growing perception that microorganisms are really very good at spreading their genes around. This is of considerable evolutionary significance," he said.