Bacteria Provide Example of One of Nature's First Immune Systems, Research Shows

His findings, which appear in Nature Communications, a multidisciplinary publication dedicated to research in all areas of the biological, physical and chemical sciences, shed light on how bacteria have throughout the course of millions of years developed resistance to antibiotics by co-opting the DNA of their natural enemies -- viruses.

The battle between bacteria and bacteria-eating viruses, Wood explains, has been going on for millions of years, with viruses attempting to replicate themselves by -- in one approach -- invading bacteria cells and integrating themselves into the chromosomes of the bacteria. When this happens a bacterium makes a copy of its chromosome, which includes the virus particle. The virus then can choose at a later time to replicate itself, killing the bacterium -- similar to a ticking time bomb, Wood says.

However, things can go radically wrong for the virus because of random but abundant mutations that occur within the chromosome of the bacterium. Having already integrated itself into the bacterium's chromosome, the virus is subject to mutation as well, and some of these mutations, Wood explains, render the virus unable to replicate and kill the bacterium.

With this new diverse blend of genetic material, Wood says, a bacterium not only overcomes the virus' lethal intentions but also flourishes at a greater rate than similar bacteria that have not incorporated viral DNA.
"Over millions of years, this virus becomes a normal part of the bacterium," Wood says. "It brings in new tricks, new genes, new proteins, new enzymes, new things that it can do. The bacterium learns how to do things from this.
"What we have found is that with this new viral DNA that has been trapped over millions of years in the chromosome, the cell has created a new immune system," Wood notes. "It has developed new proteins that have enabled it to resists antibiotics and other harmful things that attempt to oxidize cells, such as hydrogen peroxide. These cells that have the new viral set of tricks don't die or don't die as rapidly."

Understanding the significance of viral DNA to bacteria required Wood's research team to delete all of the viral DNA on the chromosome of a bacterium, in this case bacteria from a strain of E. coli. Wood's team, led by postdoctoral researcher Xiaoxue Wang, used what in a sense could be described as "enzymatic scissors" to "cut out" the nine viral patches, which amounted to precisely removing 166,000 nucleotides. Once the viral patches were successfully removed, the team examined how the bacterium cell changed. What they found was a dramatically increased sensitivity to antibiotics by the bacterium.

While Wood studied this effect in E. coli bacteria, he says similar processes have taken place on a massive, widespread scale, noting that viral DNA can be found in nearly all bacteria, with some strains possessing as much as 20 percent viral DNA within their chromosome.

"To put this into perspective, for some bacteria, one-fifth of their chromosome came from their enemy, and until our study, people had largely neglected to study that 20 percent of the chromosome," Wood says. "This viral DNA had been believed to be silent and unimportant, not having much impact on the cell.
"Our study is the first to show that we need to look at all bacteria and look at their old viral particles to see how they are affecting the bacteria's current ability to withstand things like antibiotics. If we can figure out how the cells are more resistant to antibiotics because of this additional DNA, we can perhaps make new, effective antibiotics."

Single gram-negative Escherichia coli bacterium. Studying how bacteria incorporate foreign DNA from invading viruses into their own regulatory processes, Thomas Wood, professor in the Artie McFerrin Department of Chemical Engineering at Texas A&M University, is uncovering the secrets of one of nature's most primitive immune systems. (Credit: Janice Haney Carr)

Purple bacteria were among the first life forms on Earth. They are single celled microscopic organisms that play a vital role in sustaining the tree of life. This tiny organism lives in aquatic environments like the bottom of lakes and the colorful corals under the sea, using sunlight as their source of energy. Its natural design seems the best structural solution for harvesting solar energy. Neil Johnson, a physicist and head of the inter-disciplinary research group in complexity in the College of Arts and Sciences at the University of Miami, thinks its cellular arrangement could be adapted for use in solar panels and other energy conversion devices to offer a more efficient way to garner energy from the sun.

"These bacteria have been around for billions of years, you would think they are really simple organisms and that everything is understood about them. However, purple bacteria were recently found to adopt different cell designs depending on light intensity," says Johnson. "Our study develops a mathematical model to describe the designs it adopts and why, which could help direct design of future photoelectric devices."

Johnson and his collaborators from the Universidad de los Andes in Colombia share their findings in a study entitled "Light-harvesting in bacteria exploits a critical interplay between transport and trapping dynamics," published in the current edition of Physical Review Letters.
Solar energy arrives at the cell in "drops" of light called photons, which are captured by the light-gathering mechanism of bacteria present within a special structure called the photosynthetic membrane. Inside this membrane, light energy is converted into chemical energy to power all the functions of the cell. The photosynthetic apparatus has two light harvesting complexes. The first captures the photons and funnels them to the second, called the reaction center (RC), where the solar energy is converted to chemical energy. When the light reaches the RCs, they close for the time it takes the energy to be converted.
According to the study, purple bacteria adapt to different light intensities by changing the arrangement of the light harvesting mechanism, but not in the way one would think by intuition.


"One might assume that the more light the cell receives, the more open reaction centers it has," says Johnson. "However, that is not always the case, because with each new generation, purple bacteria create a design that balances the need to maximize the number of photons trapped and converted to chemical energy, and the need to protect the cell from an oversupply of energy that could damage it."


To explain this phenomenon, Johnson uses an analogy comparing it to what happens in a typical supermarket, where the shoppers represent the photons, and the cashiers represent the reaction centers.


"Imagine a really busy day at the supermarket, if the reaction center is busy it's like the cashier is busy, somebody is doing the bagging," Johnson says. "The shopper wonders around to find an open checkout and some of the shoppers may get fed up and leave…The bacteria are like a very responsible supermarket," he says. "They would rather lose some shoppers than have congestion on the way out, but it is still getting enough profit for it to survive."


The study develops the first analytical model that explains this observation and predicts the "critical light intensity," below which the cell enhances the creation of RCs. That is the point of highest efficiency for the cell, because it contains the greatest number and best location of opened RCs, and the least amount of energy loss.
Because these bacteria grow and repair themselves, the researchers hope this discovery can contribute to the work of scientists attempting to coat electronic devices with especially adapted photosynthetic bacteria, whose energy output could become part of the conventional electrical circuit, and guide the development of solar panels that can adapt to different light intensities.
Currently, the researchers are using their mathematical model and the help of supercomputers, to try to find a photosynthetic design even better than the one they found in purple bacteria, although outsmarting nature is proving to be a difficult task