The appearance of antibiotic resistant bacteria has long been used as a classic example of Darwinian evolution in action. The general story works like this: take any population and there will be a certain amount of accumulated genetic variability as a consequence of a steady stream of random mutations. When the antibiotic is supplied, it interferes with some aspect of cell biology (cell wall synthesis, translation, transcription, etc.) Those few members of the population that just happen to possess a variation that makes them immune to the action of the antibiotic will survive and be favored by selection. Or at the very least, while the bacteria are exposed to the antibiotic, every new mutation that just happens to occur will become another opportunity to escape the insult.
A study by Floyd Romesberg and colleagues  has thrown a new and subtle twist into the story. The twist is this: in this case, mutations don’t “just happen” – bacteria make sure they happen. That is, the evolution of antibiotic resistance is not simply the passive process of selection screening through the available variability. On the contrary, bacteria respond to the insult by making sure there is a plentiful source of variability to screen.
In this study, it was determined that bacterial input was essential to the evolution of antibiotic resistance. In other words, the cellular process of “making sure there is a plentiful source of variability to screen” is exactly what is needed to evolve antibiotic resistance.
The researchers tested two antibiotics: ciprofloxacin, which targets the gyrase and topoisomerase (proteins involved in untangling DNA) and rifampicin, which targets the bacterial RNA polymerase. They found that after 72 hours of continual exposure to ciproflaxin, 3% of the recovered bacteria had acquired resistance to the antibiotic. With 72 hours of exposure to rifampicin, 100% of the bacteria were resistant. However, when they similarly tested a strain that lacked LexA, no antibiotic resistance has found. This led them to conclude “that LexA cleavage is absolutely required for the evolution of resistance to both ciprofloxacin and rifampicin during therapy in vivo.”
So what’s the deal with LexA? LexA is a DNA binding protein that normally represses the activity of over 20 different genes. When the DNA is damaged by a chemical or physical agent, it is often detected by a tread-milling protein cylinder that forms around the DNA known as RecA. Once the cylinder is formed, it interacts with LexA and causes it to split apart, releasing it from the DNA, thus releasing the repression. The various genes that are now expressed at much higher levels are involved in DNA repair and recombination. There is a certain hierarchy of expression, as explained in the press release associated with the study :
Take the bacterium Escherichia coli for instance. When E. coli cells are subjected to damage, they upregulate repair enzymes, which then go to work trying to fix the problem. If the damage persists, the cell upregulates recombination enzymes, which are tasked with recombining the DNA — another way to repair it. And, says Romesberg, if the damage still persists, the cells upregulate enzymes whose sole task is to make mutations.
In other words, LexA normally suppresses an “emergency repair kit” known as the SOS response. Yet as Andrei Kuzminov, of the Institute of Molecular Biology at the University of Oregon, explains:
The SOS response is by no means a desperate attempt to stay alive, as its name inaccurately implies, but, rather, an orderly and measured reaction of the cell to DNA synthesis inhibition. 
The mutators are actually error-prone DNA polymerases – Pol II, Pol IV, and PolV. And all three of the polymerases were needed to supply antibiotic resistance.
The researchers note:
In this study we have shown, in vivo, that preventing LexA cleavage renders bacteria unable to evolve resistance to either ciprofloxacin or rifampicin in a mouse thigh infection model. In vitro, the ability of bacteria to induce mutation and evolve resistance to ciprofloxacin is also dramatically reduced by rendering LexA uncleavable. Thus, our results indicate that the mutations that confer resistance to ciprofloxacin and rifampicin are not simply the result of unavoidable errors accumulated during genome replication, but rather are induced via the derepression of genes whose protein products act to significantly increase mutation rates.
This study does not in any way indicate a fundamental flaw in Darwin’s Theory. Nor does it demonstrate that bacteria can target the specific genes needed to survive the environmental insult. What it does do is help us understand that life takes control of its fate. Living things are not passive participants of the interplay between stochastic events and environmental pressures, where mutations that just happened to exist are favored in an environment that just happened to exist. Instead, environmental challenges are met with a truly biotic response. First, the cells try to repair themselves. But if this fails, then they seek out an adaptation by maximizing their chances of finding an adaptation. Evolution is, at least, partially controlled by properties intrinsic to life.
While the teleological echo is faint, it is nevertheless there. We can begin to catch a glimpse of evolution as homeostasis. The integrity of the genome is threatened. Standard small scale feedback responses ensue as the cell attempts to reverse the change through repair and recombination mechanisms. But if the insult is too severe or too common, the next level of feedback response is…..evolution itself. The antibiotic is the stress that perturbs the homeostasis of the cells and evolution is the effector that reverses the effects of the change. Life fights back.
A good designer will turn a problem into an opportunity. In this case, mutations are commonly viewed as “mistakes,” explaining why so much machinery is devoted to proof-reading and repair. But at some point, a phase shift occurs, where the mistakes becomes the solution, as they provide the response to a population threatened with extinction. Life is programmed to survive.
That evolution may be under some form of intrinsic control is only a piece of the teleological puzzle. But it is a significant piece, in that the ability to adapt, at least to these two antibiotics, is under control. So much so, that removal of a control gene (LexA) robs the cells of their ability to adapt. If the mere ability to adapt can be placed under control, one wonders what other aspects of adaptation can likewise be influenced by life itself.
Finally, the researchers raise an intriguing speculation.
The key signal that links the cellular response to the antibiotic with the evolution of resistance appears to be the RecA-ssDNA filaments that are formed to facilitate the repair of antibiotic-mediated DNA damage. These RecA-ssDNAfilaments also induce LexA cleavage and derepression of the mutagenic polymerases. We suggest that a similar mechanism might also serve to induce mutation and evolution in response to other antibiotics, or other forms of cellular stress, where DNA damage per se is not involved. For example, the ratio of ATP to ADP determines the level of supercoiling in the bacterial genome, and both increased and decreased levels of supercoiling inhibit replication fork progression . Thus, different stresses that perturb metabolism (i.e., alter ATP/ADP ratios) might also alter DNA topology and result in stalled replisomes; recombination-based rescue and RecA-ssDNA filament formation; and the induction of mutations required to reestablish a normal cellular environment. Interestingly, it has recently been shown that beta-lactams can induce the SOS response via a two component signal transduction system .
Not only does this speak to the importance of structure/form, but it again raises the theme of homeostasis – DNA may be more than a repository of sequence – it may be plugged into an elaborate system that allows it act as sensor for its own continued perpetuation.
2. Kuzminov, A. 1999. Recombination repair of DNA damage in Escherichia coli and bacteriophage ?. Micro and Mol Bio Rev 63: 751-813.