Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria

The primary function of Restriction Modification  systems is to restrict the foreign DNA and protect the host bacterium from potent invading life forms, such as bacteriophages.  Type II R-M system is often considered to be highly specific for the foreign DNA. However, bacteria harboring a promiscuous REN (Restriction endonuclease) compared to the one which carries high fidelity REN confers more fitness advantage when challenged with bacteriophages, says a recent study carried by a group of scientists at IISC and JNCASR, Bangalore.

The authors prove that the  ability of the R.KpnI to recognize and cleave noncanonical sequences in vivo confers additional protection to the host against the modified (methylated) infectious genome elements. At the same time they also prove that the self Vs nonself is taken care by the topological state of the naive DNA.

Even though the RM system in bacteria is stringent, the phages evade the defense statergy employed by the bacterium, by various means. In order to cope up with the phages defense mechanism, the bacterium has to counteract  these antirestriction strategies by acquiring additional R-M systems with distinct recognition specificities or by acquiring restriction activity with broader specificity through mutation.

The study says that

The retention of the promiscuous cleavage characteristicsof a type II REase that is normally expected to possess exquisite sequence specificity provides a selective advantage for the bacterial genome in the coevolutionary arms race between phages and bacteria.

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Bacteria Cooperate to Survive Overcrowding

For any bacterium, whether living deep in the ground or infecting a human body, overcrowding is one of the greatest threats it faces. A tightly packed environment means a shortage of food, competition for the best spaces, and the accumulation of toxic wastes excreted by its neighbors. And since many species of bacteria multiply very fast – a well-fed Escherichia coli cell can split in two every twenty minutes – overcrowding is almost inevitable.

Nevertheless, bacteria exist all around us, often packed to densities of billions in a single gram of soil. It’s hardly surprising that many scientists have wondered how these creatures manage to survive in such crowded conditions.

Now a joint study by Korean and American biologists has shown that not only do bacteria sense when their surroundings become severely congested, but that the bacterial community works together to help every bacterial cell survive the resultant stress. This involves a process named quorum sensing, by which bacteria can detect and respond to others of their kind.

Imagine every bacterial cell slowly releasing a chemical signal into its surroundings – a cell’s way of declaring ‘I am here’. As the environment grows steadily more crowded, more and more cells pump out their signal into a small space. When the amount of chemical signal present in the surroundings exceeds a certain level, indicating that a large number of cells are present, the quorum sensing system detects this change and directs all the cells to switch certain genes on or off, leading to a coordinated change in their behavior.

Glow-in-the-dark bacteria provide a classic example of the value of quorum sensing. Since a lone bacterium would not glow brightly enough to be noticeable, it keeps its light-producing apparatus switched off most of the time. But as soon as many such bacteria get together, all of them are simultaneously activated, producing a glow that is visible from afar.

In this case and others, bacteria use quorum sensing to avoid wasting energy. Though scientists guessed that quorum sensing might also help bacteria survive the stress of living in a crowded environment, this had not been demonstrated until now.

The study, published in the October issue of the Proceedings of the National Academy of Sciences, tested this idea and found it to be true. Researchers grew three species of bacteria under conditions that forced them to excrete ammonia as a waste product. Ammonia is toxic, and as the bacteria multiplied, the ammonia around them accumulated to potentially lethal levels.

However, as soon as the environment grew dangerously crowded, the quorum sensing system triggered all the bacteria to produce an acid called oxalate. This oxalate was released into the environment where it reacted with ammonia to form a harmless product, allowing the bacterial population to survive far longer than it would otherwise have.

This finding is particularly intriguing to scientists interested in social behavior, for it raises the possibility of interesting community dynamics among these bacteria. Would some bacteria cheat the rest by not producing any oxalate, instead surviving on the efforts of others? Over time, would the community evolve ways to punish these cheaters?

Even more interestingly, some of the bacteria used in this experiment are agents of disease in plants and humans, and the authors suspect that producing oxalate may help them survive the defenses of their hosts. If this is true, it might open the doors to a new strategy for treatment: one based not on killing bacteria, but on allowing them to crowd themselves to death.