Why Gene-Spliced Bacteria Are Inherently Hazardous

Posted 12/9/04

Dear Friends and Colleagues,

To let you know of our efforts to counterbalance one-sided genocentrism, we
send you this article illustrating how genes can only be understood within
the dynamic context of the living organism and its interaction with the
environment.

Ann-Elizabeth Barnes, Outreach Coordinator,

The Nature Institute

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Genes Are Not Immune to Context: Examples from Bacteria
Craig Holdrege (HYPERLINK
"mailto:craig@natureinstitute.org"craig@natureinstitute.org)

>From In Context #12 (Fall, 2004, pp. 11-12); copyright 2004 by
The Nature Institute. This article may be distributed; please
include this source information. Available online at:

http://www.natureinstitute.org/pub/ic/ic12/genes.htm

One of the most widespread misconceptions concerning the nature of
genes is that they have a defined and fixed function that allows them
to operate the same in all organisms and environments. We have the
picture of the robust gene determining all the characteristics an
organism has. And this gene will do the same thing in a bacterium as
in a corn plant or human being. It doesn't care where it is. The gene
carries its set of instructions with it wherever it goes and strictly
carries out its duty.

This picture informs genetic engineering. Take a gene from bacteria
and put it into a plant and the plant will produce its own pesticide
or become resistant to a herbicide. Since such transgenic plants
exist, the proof is evidently in the pudding. Genetic manipulation
works; genes are faithful workhorses. But does genetic manipulation
work the way we imagine with our schematic pictures? What else may be
occurring that doesn't fit into a neat mechanistic scheme?

It's somewhat ironic that precisely within the last ten to fifteen
years--the period in which genetically modified crops have been
developed and commercialized in the U.S. and some other countries--a
wealth of research on genes in relation to environmental effects has
been carried out, showing that genes are anything but automatic
instruction programs immune to their context. This research has
significant implications for the way we assess genetic engineering.
Unfortunately, it often seems that the results of this basic research
have little effect on the minds and pocket books supporting the global
drive to manipulate organisms genetically. In this article I'll
discuss some examples of the contextual gene in bacteria.

The Interactive Gene

With the widespread use of antibiotics in our culture, many bacteria
have become resistant. They thrive even when subjected to high doses
of antibiotics. As a rule, the resistance comes at a cost, since the
resistant bacteria tend to grow slowly. But when they are grown in
laboratory cultures, some of these resistant bacteria will experience
so-called compensatory mutations--they stay resistant, but change
genetically in a way that allows them to grow fast like wild,
nonresistant strains. Others mutate back to the wild form and lose
their resistance altogether.

The question arises whether such mutations (changes in genes or in
higher-order genetic structures) are in any way dependent on the
environment. The traditional view, rooted deeply in the Neodarwinian
theory of evolution, holds that genes mutate spontaneously and
independently of the environment. The classical experiment with
bacteria by Luria and Delbrück in the 1940s gave clear evidence that
such spontaneous, milieu independent mutations exist (Luria and
Delbrück 1943). For decades this experiment (along with other
evidence) served as the rock solid "proof" that genetic mutations,
except for extreme cases involving irradiation or exposure to chemical
toxins, are not influenced by their environment. But more recent
research shows that mutations do in fact arise in response to changing
environmental conditions.

A group of biologists in Sweden investigated whether the
above-mentioned compensatory mutations and the reversion to the wild
form in bacteria are influenced by the environment (Björkman et al.
2000). They grew antibiotic-resistant bacteria--in the absence of
antibiotics--as laboratory cultures (in petri dishes) and also
inoculated mice with the same bacteria. The researchers monitored the
mutations that occurred in the bacteria in these two different
habitats. They found that compensatory mutations occurred in both
habitats, but, to their surprise, they discovered that the way the
genetic material changed differed significantly depending upon the
environment. In the case of streptomycin-resistant bacteria in mice,
they found ten cases of identical compensatory mutations within the
resistance gene. In contrast, this gene never mutated in the
lab-cultured bacteria, where they found fourteen compensatory
mutations in genes outside the resistance gene. Evidently, the
environment had everything to do with what kind of mutations occurred.
"Mice are not furry petri dishes," as the title of a commentary
article put it (Bull and Levin 2000).

The authors conclude that the mutations are "condition-dependent" and
suggest that some unknown "mutational mechanism" limited the mutations
in the mice to a specific part of the resistance gene while also
increasing its mutation rate. Whatever the details of cell physiology
turn out to be, it is clear that the genome of the bacteria changes in
relation to a specific kind of environment. The bacteria--down into
their genes--interact with and evolve in relation to their
environment.

Adaptive Mutations

In another recent study (Bjedov et al. 2003), a research group in
France gathered wild strains of the bacterium E. coli from a wide
variety of environments--the large intestines of humans and different
animals, soil, air, and water. In the end they collected 787 different
strains. These strains were given optimal conditions in lab cultures
and began to grow and multiply rapidly, mimicking ideal conditions in
nature where bacteria reproduce quickly. But in nature, bacteria are
also exposed to times of dearth, where the substrate they live upon,
for example, is suddenly used up. To mimic these conditions, the
researchers withheld nutrients for a seven-day period. Most bacteria
survive under these conditions, but they no longer grow and divide.

The scientists measured the rate of mutations occurring in the
cultures the first day after withholding nutrients and then again at
the end of the seven-day period. During this time the mutation rate
increased on average sevenfold. In other words, the mutation rate
increased dramatically when the bacteria no longer received adequate
nutrition. The bacteria switch, in the words of the authors, "between
high and low mutation rates depending on environmental conditions" (p.
1409).

Such a stress-induced increase in mutation rate has been discovered in
many laboratory strains of bacteria. Does this increase in mutation
rate serve the bacteria, or is it a kind of last gasp, a dissolution
of the bacteria before they die of starvation? The answer is clear:
the bacteria produce unique kinds of mutations during such periods of
physiological stress, some of which help the bacteria survive under
specifically those conditions. One speaks of "adaptive mutations."
(See Wirz 1998 and Rosenberg 2001 for good overviews of the research
and literature.)

For example, there are strains of E. coli that have lost the capacity
to utilize the sugar lactose as a source of energy. If such a strain
is cultured in a starvation medium with lactose as the only energy
source, most of the bacteria remain in a stationary phase until they
die. But under these conditions some of the bacteria begin to
hypermutate, which means they rapidly create a large number of
mutations and among these are ones that allow them to live from
lactose. The bacteria with this ability survive, multiply and form new
colonies. In at least some cases such adaptive mutations arise only in
the specific medium--that is, the mutations allowing bacteria to
utilize lactose don't occur when bacteria are grown in a medium with
sugars other than lactose.

In other instances, E. coli bacteria do not hypermutate, but find
another way to deal with the environmental challenge. Some of the
bacteria in the medium with lactose produce multiple copies of the
gene related to their inability to live from lactose. This gene
amplification seems at first absurd. But scientists found that E. coli
strains unable to grow when they only receive lactose as a nutrient do
form enzymes that break down lactose, but in inadequate amounts. When
the bacteria amplify the defective lactose enzyme gene, the cumulative
effect is that they produce enough enzymes to break down a sufficient
amount of lactose to grow slowly and survive - a remarkably active and
meaningful genetic adaptation. This amplification occurs in no other
genes in the bacteria. It is specific to the lactose enzyme gene and
clearly induced by the environment.

Transfer of Resistance

Bacteria have a further way of adapting to new conditions. I have
already mentioned antibiotic-resistant bacteria. Cholera bacteria, for
example, are normally susceptible to different antibiotics. After 1993
antibiotic-resistant cholera bacteria rapidly spread around the globe.
How could this occur? Scientists discovered that these bacteria are
simultaneously resistant to at least five different antibiotics. They
found that the genes related to this resistance were all grouped
together and formed a "packet" of genes that can move from bacterium
to bacterium.

A research group at Tufts University in Boston recently discovered
conditions that facilitate this movement and uptake of genes (Beaber
et al. 2004). When bacteria are grown in cultures with concentrations
of antibiotics that are not sufficient to kill them, they go through
physiological changes similar to what happens to bacteria in a
starvation medium. Part of this transformation is called an SOS
response. It comes about when DNA is damaged and involves DNA repair
and duplication. The Tufts scientists found that during the SOS
response the bacteria also increased the transfer of the resistance
gene clusters to other bacteria. Evidently, the use of antibiotics
promotes the spread of antibiotic resistance among bacteria. In this
way, once resistance is anchored in mobile genetic elements, it can
spread rapidly.

The examples I have described show how strongly the environment
influences the activity of genes, induces changes within genetic
structures (mutations), and stimulates the movement of genes between
bacteria. Bacteria are in continual interplay with their environment,
actively responding to changing conditions. And this responsiveness
and flexibility includes genes. If we release genetically engineered
bacteria into the environment, there is little doubt that in time they
will be passing their genes to other bacteria, as well as receiving
genes from other bacteria and mutating according to changing
circumstances. Whether the manipulated foreign genes they carry will
be exchanged, or how they may affect or be affected by the dynamics of
genetic responses to changing environments is completely open. But two
things we can know for sure: these genes will not function immune to
the changing circumstances and things will happen that no one expects
or can foresee. I'm not saying this to promote fear, but to dissolve
the illusion that we can keep under control what we have released into
the world in this way. Genes are robust, but they are also part of the
world.

References

Beaber, John W. et al. (2004). "SOS Response Promotes Horizontal
Dissemination of Antibiotic Resistance Genes." Nature vol. 427, pp.
72-74.

Bjedov, Ivana et al. (2003). "Stress-Induced Mutagenesis in Bacteria."
Science vol. 300, pp. 1404-1409.

Björkman, J. et al. (2000). "Effects of Environment on Compensatory
Mutations to Ameliorate Costs of Antibiotic Resistance." Science vol.
287, pp. 1479-1482.

Bull, James and Bruce Levin (2000). "Mice Are Not Furry Petri Dishes."
Science vol. 287, pp. 1409-1410.

Luria, S.E. and M. Delbrück (1943). "Mutations of Bacteria from Virus
Sensitivity to Virus Resistance." Genetics vol. 28, pp. 491-511.

Rosenberg, Susan M. (2001). "Evolving Responsively: Adaptive
Mutation." Nature Reviews Genetics vol. 2, pp. 504-515.

Wirz, Johannes (1998). "Progress Towards Complementarity in Genetics."
Archetype Sept (No. 4), pp. 21-36. Available online:
http://www.ifgene.org/wirzcomp.htm.

Original source: In Context #12 (Fall, 2004, pp. 11-12); copyright
2004 by The Nature Institute

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