Thinking Small Paying Off Big In Gene Quest
By NICHOLAS WADE
Published: February 3, 1997
HILTON HEAD, S.C., Jan. 28— Working in the shadow of the vast project to decode human genes, biologists are rapidly deciphering the genetic makeup of much smaller organisms, including microbes that cause disease.
The result, these scientists say, is that the full DNA, or genomes, of many pathogens is likely to be decoded in the next several years, offering new drug and vaccine strategies.
They say their field will have an impact far sooner than will the better known $3 billion project to decipher the human genome, which began in the late 1980's and is not expected to be completed before 2000.
''It is absolutely clear that the availability of whole genomes has changed the way we are doing science,'' said Dr. E. Richard Moxon, an infectious disease specialist at Oxford University.
Aside from their medical importance, the small genomes are also of interest in two other arenas. Biologists hope that by comparing diverse genomes, they will be able to trace the tree of evolution back to the origin of life, or at least to its earliest branches. And industrial chemists are screening genomes from the poles to the deep sea in search of enzymes with special properties.
Sequencing a genome means determining the nature and order of all the chemical building blocks, each represented by a letter, of an organism's DNA. The smallest known bacterial genomes contain as few as 500,000 letters in their genetic instruction set. That is just a few pages, compared with the 3-billion-letter tome of human DNA, but it is still daunting enough that the first bacterial genome was sequenced only two years ago.
Sequencing a small genome costs $1 million to $15 million, depending on the length of the organism's DNA. Despite the costs, which are enormous by the usual standard of biological research, plans are now under way for sequencing the organisms that cause diseases like malaria, syphilis, Lyme disease, typhus, gastric ulcers and gonorrhea.
The agencies financing the work are so eager to stake out claims that the National Institutes of Health and the Wellcome Trust of London each formed plans to sequence the tuberculosis bacterium before deciding to join forces instead.
To the human eye, the printed result of a computer-generated genome sequence is a meaningless string of A's, G's, T's and C's, representing the four chemical components of the genetic code. Sequencing has long been regarded by biologists as about as thrilling as running an index fund, but the power of the computer has begun to modify that.
Computers can annotate the text of a genome, marking where its genes probably start, flagging the on and off gene switches that are found in DNA regions between the genes and marking the hidden viruses that have slipped their DNA into their host's genome. Most important, computer programs can identify the likely role of many genes by comparing their DNA sequence with the thousands of genes of known function whose sequences have now been deposited in data banks.
Genomes annotated in this way are transformed from gibberish to draft blueprints of a living organism. For scientists, the annotated genomes of pathogenic bacteria are like a decrypted top-security message about the enemy's strategy and tactics. They lay bare every inherited weapon and defense, even though much is not yet understood.
The era of small-genome sequencing began in 1995 when Haemophilus influenzae, a bacterium that causes ear and throat infections (and is no relation of the flu virus), was sequenced by a team led by Dr. J. Craig Venter, of the Institute for Genomic Research, now in Rockville, Md., and Dr. Hamilton O. Smith, of Johns Hopkins University School of Medicine in Baltimore.
The availability of the Haemophilus genome offered several deep insights into the microbe's game plan, including the crucial mechanism by which it keeps shifting the composition of its coat to evade its host's immune system. News of the sequence had particular impact because few had believed a bacterium could be sequenced so easily; on that advice, the National Institutes of Health had refused to finance the project. Showing that bacterial genomes now lay within the sequencer's reach set off something of a researchers' gold rush.
At a conference on small genomes held this week at Hilton Head, S.C., Dr. John Stephenson, a senior official of the Wellcome Trust, said: ''It is incredible to realize that two years ago, everyone was very skeptical that Craig Venter could do what he did. The world of microbial genomics was changed overnight.''
The trust, which has built a $13 billion endowment through the recent sale of its shares in the Burroughs Wellcome company, decided within a few months of the publication of the Haemophilus genome to set aside $25 million for work on pathogenic genomes, Dr. Stephenson said. Dr. Anne Ginsberg, of the National Institutes of Allergy and Infectious Diseases, said the Haemophilus genome success had caused a ''change in the landscape.'' Her agency is paying for the sequencing of several pathogenic genomes.
Dr. Venter noted that 2 genomes had been completed in 1995 and 4 last year and that as many as 8 of the 35 genomes now being sequenced might be finished this year. He said that with sufficient financing, the genomes of all the major human pathogens could be sequenced by the end of the decade and that small genomes would be the major source of the half-million new genes he predicts will be discovered by then. The human genome has far fewer genes per length of DNA than the very compact genomes of bacteria, Dr. Venter and others said, but it is likely to prove to be far harder to interpret.
In a telephone interview, Dr. Harold E. Varmus, director of the National Institutes of Health, commented that both kinds of genome work would have significant impact. ''I don't think it is fair to say one will be bigger than the other,'' he said.
The speakers at the conference reported progress with a wide range of small genomes, mostly with enthusiasm, although one exhausted participant declared that he would never sequence a genome again.
Dr. Fred R. Blattner of the University of Wisconsin announced a long-awaited triumph: the completion on Jan. 16 of the sequence of Escherichia coli, the standard laboratory bacterium of molecular biology. While Haemophilus has just over one million units, or pairs of chemical bases, the E. coli genome is 4,638,858 base pairs, which contains the instructions for 4,286 genes.
The probable roles of 1,817 of these genes have been identified by comparing them with genes of known function in data bases. Even though biologists have studied the minutest parts of E. coli for decades, the roles of its other 2,469 genes are unknown. ''That shows the limitations of bottom-up genetic approaches,'' Dr. Blattner said, ''even when applied over extended periods.''
For much of his five-year struggle -- the National Institutes of Health nearly lost confidence in the project at one point -- Dr. Blattner and his team were competing with a Japanese team now led by Dr. Hirotada Mori, of the Nara Institute of Science and Technology. Dr. Mori said he had completed his E. coli sequence a week after Dr. Blattner. The teams sequenced slightly different strains, so their sequences would not be expected to match exactly. ''As a competition, it was perfectly dignified,'' Dr. Blattner said, ''but I'm glad that, like the Packers, we won.''
As work on one genome after another was described at the meeting, the scientists' mood was like that of people looking at newly discovered treasure maps, with the treasure not yet in hand but with wonderfully tantalizing clues all about.
For example, the order of genes in a genome seems to vary widely, even between closely related species of microbes, as if evolution were constantly shuffling the deck..
A major goal of those studying pathogenic organisms is to understand the microbes' ability to evade attack by the immune system. Dr. Moxon has made considerable progress with Haemophilus, finding that it weaves its coat from a material made of fat and different sugars. The core of the sugar assemblies stays the same, but different kinds and lengths of sugars can be tacked onto it, depending on which subset of the 25 coat-making genes is active.
Because the sugar coats of an invading Haemophilus army keep shifting, the body's immune system never has a fixed target. The unchanging sugar core seems like a good target for a vaccine. Although Dr. Moxon started this work with conventional methods, he said, the availability of the genome sequence was a ''wonderful gift'' that allowed him to proceed much faster.
In April last year, at a cost of $40 million, a consortium of laboratories, most of them European, completed the genetic sequence of yeast, a 12 million base-pair genome of high interest because it belongs to the realm of plants and animals and was the first such genome to be sequenced. Despite the many years yeast has been studied, more than 30 percent of its 5,885 genes turned out to be of unknown function. Laboratories in both the United States and Europe have begun major programs to identify the role of those genes.
Once there were only two ways of doing biology: in vivo, with a live organism, and in vitro, inside laboratory glassware. Biologists who now use computers to romp through DNA data bases and analyze genes believe that they have struck on a third kind: biology in silico, referring to the computer's silicon chips.
New techniques sometimes turn out to be a little less sparkling than the dreams in their proponents' eyes, and traditional microbiologists expect to see a gap or two opening between the in silico discoveries and the in vivo reality. Still, attacking pathogens through study of their genomes is likely to offer a new and fundamental way to design drugs and vaccines. Dr. Waclaw Szybalski, of the University of Wisconsin, said the current methods, based a lot on trial and error, ''are like trying to repair a TV set without a blueprint.''