By David N. Leff
Babies born today with cystic fibrosis can look forward to life spans averaging 32 years of age. Last year, that prospect was 31 years, and a decade ago 28. Back in 1960, the outlook ranged from 15 to 20 years of life, whereas in earlier decades, death from the lung failure of cystic fibrosis (CF) struck in the very earliest years of childhood. CF now afflicts 30,000 people in the U.S.
This stingy improvement in life expectancy - due to intensive medical care, but no cure - reflects the tight grip by which the bacterium Pseudomonas aeruginosa (P.a.) holds the lungs of CF victims hostage.
But the ubiquitous pathogen doesn't stop there in its war against Homo sapiens. Swimming in a pond or pool polluted with P.a. can cause one's outer ear to turn red, painful and grossly swollen with perichondritis - another Pseudomonas specialty. It's an opportunistic pathogen, which means it can infect only a person with immune defenses weakened by disease, burn injury or chemotherapy. And besides that hit-'em-while-they're-down policy, P.a. is also a nosocomial bug.
"It's one of the leading causes of nosocomial - hospital-acquired - infections," observed microbiologist C. Kendall Stover, senior director of research biology at Seattle-based PathoGenesis Corp. "And," he added, "it's the leading cause of respirator-associated pneumonia in hospitals. That's probably a bigger patient market than CF - approximately 230,000 such pneumonias in critically ill patients, which are due to P.a. infection. The bug likes to lurk in warm, damp places and on indoor plumbing. Typical disinfectants are not effective at eradicating it, so P. aeruginosa can be found on nearly every shower curtain and drain pipe around the world."
The microbe even stoops so low as to reduce fixed nitrogen in swampy, waterlogged soil, thus removing up to half of that element's useful fertilizer properties. On its meagre plus side, Stover pointed out, "You've got pseudomonads - not P.a. - that eat oil; that can metabolize nasty organic chemicals, and they're used in industry for bioremedial purposes like that."
Right now, Pseudomonas aeruginosa has made it big time in the scientific news - accent on the "big." Today's issue of Nature, dated Aug. 31, 2000, reports: "Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen." Its lead author is Stover, and senior author is genomicist Maynard Olson, director of the University of Washington Genome Center, in Seattle. In all, the paper's co-authors number 31.
Of the 25 microorganisms that have had their genomes sequenced so far, P. aeruginosa's is by far the largest. (See adjacent box score.)
The Haemophilus influenzae gene is less than one-third its size, Stover pointed out. "P.a.," he went on, "is obviously more highly evolved than other bacteria. It's got a larger genome, and that isn't just due to duplicated genes and junk DNA. It's extra information. And the other thing is that a larger part of its genome is dedicated to command and control systems. Whereas maybe 3 percent of the Mycobacterium tuberculosis genome is dedicated to regulatory genes, and maybe 5 to 6 percent of Escherichia coli, almost 10 percent of the genes in Pseudomonas are focused on regulating other genes and other systems.
"This P.a. bug seems to be very efficient and effective at doing what it does. As a bacterial genome gets larger, it takes an increasingly larger proportion, apparently, of that genome to coordinate all its command and control systems. It controls the expression of its own genes. It switches genes on and off. It regulates biosynthetic pathways and motility - when it's going to move about and try to find another location. When it's going to dig in and form a biofilm."
Biofilm formation is a key activity in the life of Pseudomonas aeruginosa. "It's kind of communities of organized bacteria of one type," Stover explained. "It forms a slimy layer that can't move, of organized bacteria that operate together and interconnect. Biofilms help it dig in. They form a protective layer around the pathogens colonizing a CF lung to shield themselves from antibiotics and the host body's natural defenses. Biofilms make the bug more resistant to antibiotics for one thing.
"This new insight into the genome sequence," Stover observed, "now allows us to get the information to try to identify the essential mechanisms in this bacterium." When we got into this, we thought we would see more redundancy and junk DNA, that less of the genes would actually be essential, and all this extra information was just gingerbread. But it turns out," he continued, "that so far in initial studies that aren't published yet, it looks as if about a third of the genome is probably essential.
"The trick then is to identify some of these genes and mechanisms essential for maintenance of infection, isolate them, perform high-throughput screens and identify compounds from combinatorial libraries that can knock these mechanisms out. There are new targets that we're looking at in screening efforts to identify new drugs, for example - compounds that might be companion drugs, that work with existing antibiotics.
"PathoGenesis was interested in the Pseudomonas genome," Stover recounted, "because we have an antibiotic product - aerosol tobramycin - which is used to treat Pseudomonas infections in the lungs of CF patients. So we wanted to do the genome sequencing project, and we initiated discussions with Maynard Olson at the University of Washington, and then with the Cystic Fibrosis Foundation, in Bethesda, Md., as to whether or not they'd be interested in co-funding this project with us. They were."
The Foundation's president and CEO, biochemist Robert Beall, told BioWorld Today: "With the University of Washington and PathoGenesis, we put up the first million dollars of this genome sequencing. Also, we were the ones who demanded it be web-available every 90 days during the project. So it's really being used a lot.
"As a follow-up to the genome sequencing," Beall continued, "we are providing $1.2 million to PathoGenesis for high-throughput screening of their new drug candidates."
Pseudomonas Box Score
Its total genome size numbers 6,284,403 base pairs, of which 89.4 percent (5,618,256 bp) are gene-coding regions. Of its total 5,570 genes, 372 have demonstrated function, and 1,059 show strong homology with demonstrated function from other organisms. Another 1,590 genes discovered have proposed functions, and 2,549 unknown function. Web site: www.pseudomonas.com.n