By David N. Leff

As anti-missile tests ¿ ¿hit a bullet with a bullet¿ ¿ go on, skeptics in Congress have made the point that rogue nations and individual terrorists pose a greater threat with weapons of mass destruction delivered in automobiles, suitcases or small packages.

Among the smallest of such delivery systems is a smooth, spheroidal object with a diameter of 0.5 to 1.25 microns. It¿s a bacterium named Streptococcus pneumoniae. Besides pneumonia, this bioweapon bug inflicts fatal bacteremia and meningitis, not to mention chronic ear infections in small children.

Before the advent of antibiotics, pneumonia was called ¿friend of the aged,¿ because that disease brought swift and relatively painless death to people of advanced years. Today, despite medical progress, 3 million children a year die of S. pneumoniae infection, while the number of victims over 60 is much greater.

On the flip side, the world owes a debt of gratitude to this horrendous microbe, for ushering in the New Age of DNA. Its human author was bacteriologist Oswald Avery (1887-1955), who served at the then Rockefeller Institute in New York in the 1940s.

Molecular biologist and bioinformatics expert Hervi Tettelin, of The Institute for Genomic Research (TIGR) in Rockville, Md., picks up the story: ¿Using Streptococcus pneumoniae,¿ Tettelin recalled, ¿Avery was able to prove that DNA contains the organism¿s hereditary material. It was in the old days; there was this thing called DNA. No one knew its structure or function. Watson and Crick came a decade later.

¿What Avery did was take the DNA from an S. pneumoniae strain known to be virulent. That is, it had a capsule surrounding its cell body. He inserted this DNA into a related S. pneumoniae bacterium, which had no capsule, so was avirulent. By just transferring this DNA, nothing else from the cell,¿ Tettelin continued, ¿Avery was able to confer virulence on this avirulent strain. It produced a capsule and caused infection. As he reported in 1944, that meant the information acquired to confer capsule synthesis and virulence was present in the DNA, and therefore it was DNA that carried the hereditary material. That led to the beginnings of molecular biology.¿

Tettelin is lead author of a paper in today¿s Science, dated July 20, 2001. Its title: ¿Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.¿ Its senior author is Claire Fraser, president of TIGR. The Gram-positive pathogen¿s genome, they report, numbers 2,160,837 nucleotide base pairs. These contain 2,236 predicted gene coding regions, of which 1,440 (64 percent) were assigned biological roles. Many of these presumed gene functions, Tettelin told BioWorld Today, hold practical promise for developing new vaccines and therapeutic drugs against the bacterium.

Classical¿ Methods Bow To Genomic Approaches

¿Through classical discovery methods,¿ he pointed out, ¿you only gain access to the tip of the iceberg with regard to vaccine research or candidate drug targets. You need to mutate the bug, find its genotypes, then work on a couple of genes that turn out, after some years of work, to be unsuitable candidates.

¿With access to all of the genome,¿ Tettelin went on, ¿you can predict by bioinformatics which genes should be exposed on the organism¿s surface, and accessible to antibodies. So what we are doing right now is characterizing all the new predicted genes that we have identified through this genome sequence across 14 strains, to see if they are really conserved. If so, they¿ll be the best candidates for vaccine development.

¿Alternatively,¿ Tettelin continued, we can predict all the genes that are conserved across many strains involved in a pathway essential for the life of the bug ¿ which would make them ideal drug targets. Although you have failures in some, you have good ones, too. So you¿re really jump-starting the science.

¿What you need to do with this in mind,¿ he suggested, ¿is characterize essential genes without which the bug would be dead. In addition, make sure that those genes are present in all the strains that you would like to clear, using this drug.

¿Right now classical drug discovery approaches give you access only to that iceberg tip. You get a few candidates; you mutate a series of genes, and find that one is more sensitive to certain compounds. Then you pursue it and eventually realize that it¿s not very suitable, because of how to administer the drug, clear it fast enough to prevent disease ¿ whatever.¿

Pitch To Firms Holding Genes Close To Vest

Streptococcus pneumoniae holds two wild hole cards in its poker game with the immunologists and biochemists. One card plays wily ways of trumping the body¿s immune defenses; the other, special genes for mounting resistance to antibiotics.

¿The main way of evading the immune system is to have a good capsule,¿ Tettelin observed. ¿We have found here all the pieces that code for construction of this sugar-coated envelope. Typically, in pathogens that are capsulated, all the genes are in one cluster. In this sequence, we found such a cluster.

¿There is increased resistance to antibiotics now,¿ he pointed out, ¿which is one of the major problems with S. pneumoniae. In the old days, you would give penicillin, the antibiotic of choice, and that would quickly clear the pathogen from the patient. Right now, S. pneumoniae has acquired resistance that either prevents the antibiotic from entering, or degrades it once it¿s penetrated. And the bug survives.

¿Even worse,¿ he added, ¿some strains are resistant to many antibiotics that are commonly used in hospitals. If you don¿t have an antibiotic to clear the infection, you¿re helpless. We need to find new antibiotics to target the genes that have not been used before, so the organism can¿t build resistance to it ¿ yet.¿

Tettelin and his co-authors have an urgent message for the biotech community:

¿It¿s going to be extremely important to do comparative genomics with this organism, to compare the sequence of a certain strain to many other strains.

¿GlaxoSmithKline has published the draft sequence of another capsular strain, and Eli Lilly is about to publish the complete genome of a nonvirulent laboratory strain. A lot of pharmaceutical companies have draft sequences of many other strains,¿ he pointed out. ¿I would propose that they release their own sequences, so we can do extensive comparative genomics, and really draw the meat out of the combined data.¿

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