April 18, 2003
An Unexplored Genomic Terrain in a Handful of Dirt
Howard Hughes Medical Institute researchers and their colleagues
have literally unearthed a treasure trove of genomic information from
ten newly identified viruses found in the monkey pit at the Bronx Zoo
and other locations. The viruses are called mycobacteriophages and they
infect a range of bacteria, including those that cause tuberculosis and
leprosy.
The studies, which were undertaken with the aid of high school
students from Pennsylvania and New York, have also uncovered evidence
supporting the theory that mycobacteriophages undergo constant random
genetic mixing in the wild. These free-flowing associations produce a
mélange of recombinant viruses, with the weaker strains weeded
out in survival-of-the-fittest competitions.
“Before, we were tempted to group microbial genes into those that are bacterial and those that are phage genes. Now, we might rethink that classification as a continuum of genes that are predominantly bacterial or phage.”
Graham Hatfull
The researchers reported their findings in the April 18, 2003, issue
of the journal Cell. The research team included HHMI Professor
Graham
Hatfull at the University of Pittsburgh and HHMI investigator William
Jacobs at the Albert Einstein College of Medicine.
The ten soil-dwelling mycobacteriophages selected for genomic
sequencing came from zoos, backyards, and even the soil outside a
tuberculosis sanitarium in India. Despite their humble surroundings,
the phages may have quite a story to tell. “Phages represent the
most abundant life form in the biosphere, with an estimated
1031 phage particles in the world,” said Hatfull.
“Our data indicate not only that this amazingly diverse
population constitutes the largest unexplored reservoir of sequence
information, but one that is extremely dynamic, swapping genes with
many other organisms.”
Hatfull and his colleagues enlisted the help of high school biology
students taught by Jacobs's sister, Debbie Jacobs-Sera, who is a
co-author of the article in Cell. “One student isolated a
phage from the rosebush in her front yard and from a nearby barnyard;
and another student found a phage in soil from the Bronx Zoo monkey
pit,” Jacobs said. Jacob Falbo and Joseph Gross, two students
from Jacobs-Sera's high school class in Latrobe, Pennsylvania, worked
with Hatfull's group in Pittsburgh, while Lauren Keenan, a high school
student from Pelham, New York, worked with Jacobs. Vanaja Kumar of the
Tuberculosis Research Center in Chennai, India also collaborated on the
work. All are listed as co-authors on the article in Cell.
Until now, scientists had only characterized the complete genomes of
four mycobacteriophages. The genomic sequences of the ten newly
isolated phages may offer important information to researchers, said
Hatfull. “Of those phages that we had genomic sequence
information for, the morphologies were rather similar to those that
we'd seen previously,” he said. “However, when viewed under
the electron microscope, the morphologies of these newly isolated
phages were quite a bit more varied than we had imagined. These
surprising findings should give us new information about the
relationship between genomic information and viral
morphologies.”
Hatfull's team turned up some interesting information when comparing
the genomes of the ten phages. “We were somewhat surprised by the
variety of genome lengths,” he said. “The previously
sequenced mycobacteriophage genomes were about in the same range, but
these new ones varied as much as threefold, and they didn't appear to
fall into any discrete groups.” His group also found that the
length of the phage genomes appeared to be statistically correlated
with the percentage of the DNA bases guanine and cytosine — a mystery
that will take some time to figure out.
The new phages exhibited an extraordinary genomic diversity, said
Hatfull. “Some of these new phages are clearly very different in
terms of their sequence information from any of the other phages that
we've isolated,” said Hatfull. “That suggests that if we
extrapolate to the huge group of phages as a whole, they are more
diverse than we ever imagined they could be.”
The genetic diversity of the more than 1600 phage genes the
researchers identified is just as eye-opening to Jacobs. “What's
amazing is that we now have 14 phages sequenced, and there is only one
gene that is common between two of the phages. And fifty percent of the
genes in this total dataset aren't in any genomic database,” he
said.
Hatfull added that the known genes they identified in the phages
also presented surprises. “We found a significant number of genes
that are related to genes previously seen in bacterial genomes or in
other genomes, that hadn't previously been seen in phages,” he
said. “Before, we were tempted to group microbial genes into
those that are bacterial and those that are phage genes. Now, we might
rethink that classification as a continuum of genes that are
predominantly bacterial or phage.”
The researchers' findings also suggest how phages mix their genes to
produce the widely varied “mosaic” structure of their
genomes. One theory posits that the genomes possess specific
“linker” sequences at which genes are snipped apart for
recombination. However Jacobs, Hatfull and their colleagues found more
persuasive genomic evidence for the “illegitimate
recombination” theory, in which the phage genes undergo nearly
random cutting and splicing, with the resulting phage genomes
succeeding or failing based on their competitive evolutionary
advantage.
“Most of the time you get genomic trash, garbage that is
destined to go nowhere,” Hatfull said. “But natural
selection can choose the small number of recombinant genomes that are
viable, that have the genes required for growth and give the phage a
genome of appropriate size.”
According to Jacobs, the phages may be able to teach scientists a
thing or two about evolution. “Typically, in cells of higher
organisms, cell division involves recombination of similar, or
homologous, chromosomes. But phages just put genes together randomly,
which makes them a fascinating model of evolution,” he said.
The studies also raise intriguing questions about the influence that
bacteriophages have on their bacterial hosts. “We had known that
bacteriophages can be intimately involved in the pathogenesis of their
bacterial hosts, such as the infamous pathogenic E. coli,”
said Hatfull. “But in these phages, a number of genes cropped up
that raise the question of phage involvement with mycobacterial
pathogenesis.” Such genes include those that code for proteins
that trigger immune responses in tuberculosis and leprosy, he said.
Another phage gene identified by the researchers resembles a human
gene called Ro that is involved in the autoimmune disease lupus.
The scientists detected sequences in one of the phages that resemble
“alarm clock” sequences that phages can use to activate
dormant bacteria, increasing the phage's chance of reproduction. The
presence of alarm clock sequences raises the question of whether these
phages are mimicking mechanisms usually involved in the control and
activation of tuberculosis latency, said Hatfull.
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