By Margrit McIntosh - University of Arizona
Many bacteria
take a short cut to evolution by picking up or dropping whole
genes or groups of genes, according to two University of Arizona
researchers.
In a review
to appear in the May 11 issue of the journal Science Howard Ochman
and Nancy A. Moran summarize recent advances in the study of bacterial
genomics, including their own original contributions to the field.
Their focus is on bacteria that live inside other organisms; both
those that are harmful, and those that are beneficial to their
host.
Genomics -
the sequencing and study of entire genomes of organisms - is opening
new windows into the lives of these specialized microbes. By comparing
the genomes of beneficial bacteria with those of harmful ones,
researchers are beginning to unravel how harmfulness or beneficiality
evolves.
In traditional
models of evolution, organisms are thought to change slowly over
time through small changes in their genes, or mutations. While
this may hold true for eukaryotic (non-bacterial) organisms, many
bacteria may evolve primarily by acquiring genes from each other,
or by dropping whole genes that are no longer needed.
Bacteria can
easily swap genes by direct transfer of genetic material from
one cell to another, even between bacteria that are only distantly
related. This well-known phenomenon allows harmful bacteria to
react quickly to new host defenses, and to share their new counter-defenses
with each other - witness for example the rapid spread of antibiotic
resistance among bacteria.
"If you
want to move into a new environment, it's much easier to get a
gene from someone else in that environment... than trying to evolve
it yourself - which is going to take a lot more time," explains
Ochman.
A more recently
discovered and less well-known aspect of genome evolution in bacteria
is gene loss, in which entire chunks of the genome are deleted.
"A region of a hundred genes or ten genes may have been lost
[at a time]... these big deletions occur all the time," Ochman
states.
Whereas gene
acquisition can be beneficial, gene loss is usually catastrophic.
However, in host-inhabiting bacteria, the protection of the host
environment may allow the bacteria to survive such a loss.
"If you're
a free-living organism, you lose a certain gene, if it's essential,
you're dead. But if it's something that's not essential,"
for example a gene for the production of a nutrient you can get
from your host, bacteria can keep living and reproducing after
the loss, but they can never perform that function again. Further,
because they are imprisoned within the host, they may have little
opportunity to gain the genes back from other bacteria by swapping
genes.
"Most
people think that bacteria only have tiny genomes so they can
replicate faster," Ochman says. Instead, a reduced genome
may be a negative side effect in bacteria living as obligate insiders.
Such bacteria have small populations, and because natural selection
is weaker in small populations that in large ones, harmful mutations
leading to gene loss can accumulate, whereas such mutations would
be weeded out in a larger, free-living population. "You're
not getting smaller because it helps you replicate faster, you're
getting smaller because things get knocked out, and are eroded
away, due to your population structure," Ochman emphasizes.
These microbes
with tiny genomes belong to large and ancient groups of bacteria
consisting of only pathogens or symbionts, underlining that genome
reduction in such circumstances is a one-way path.
"Once
you're a symbiont, and you've deleted [large parts of] your genome,
you're at a dead end - you can't go backwards," Ochman points
out.
"Bacteria
evolve in a different manner than eukaryotes [all non-bacterial
organisms]. Eukaryotes evolve by point mutations [changes in singe
base-pairs in the DNA], whereas bacteria evolve by getting these
large chunks of DNA. And they can get into a new niche then and
they become new species. But... you can lose genes, [and] that
make you into a new species also, because you can no longer go
into that niche that you could previously get into. So we wanted
to show that these big chunks of DNA, which are both gained and
lost, can dictate bacterial speciation, and the lifestyle that
the bacteria can have," Ochman says.
The ability
of bacteria to evolve rapidly, by gaining and losing whole chunks
of DNA, instead of by gradual genetic change, may perhaps be one
of their keys to success. After all, bacteria have been around
for 3.5 billion years, a good 2.5 billion years longer than any
other group of organisms, and they show no signs of giving way
to the late-comers. They must be doing something right.
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