Single Gene Lets Bacteria Jump From Host To Host

All life — plants, animals, people — depends on peaceful coexistence with a swarm of microbial life that performs vital services from helping to convert food to energy to protection from disease.Now, with the help of a squid that uses a luminescent bacterium to create a predator-fooling light organ and a fish that uses a different strain of the same species of bacteria like a flashlight to illuminate the dark nooks of the reefs where it lives, scientists have found that gaining a single gene is enough for the microbe to switch host animals.

The finding, reported this week (Feb. 1) in the journal Nature by a team of scientists from the University of Wisconsin-Madison, is important not only because it peels back some of the mystery of how bacteria evolved to colonize different animals, but also because it reveals a genetic pressure point that could be manipulated to thwart the germs that make us sick.

"It seems that every animal we know about has microbes associated with it," says Mark J. Mandel, the lead author of the study and a postdoctoral fellow in the UW-Madison School of Medicine and Public Health. "We pick up our microbial partners from the environment and they provide us with a raft of services from helping digestion to protection from disease."

In the Pacific, a species of bacteria known as Vibrio fischeri lives in luminescent harmony with two distinct hosts: the diminutive nocturnal bobtail squid and the reef-dwelling pinecone fish. In the squid, which feeds at night near the ocean surface, one strain of the bacterium forms a light organ that mimics moonlight and acts like a cloaking device to shield the squid from hungry predators below. In the pinecone fish, another strain of the bacterium colonizes a light organ within the animal's jaw and helps illuminate the dark reefs in which it forages at night. The fish light organ may also play a role in attracting the zooplankton that make up the pinecone fish's menu.

But how did a single species of bacteria come to terms with such different hosts?

Working in the UW-Madison laboratory of microbiologist Ned Ruby, Mandel and his colleagues scoured the genomes of the two different strains of V. fischeri and found that most of the bacterium's genetic architecture was conserved over the course of millions of years of evolutionary history, but with a key difference: The strain that colonizes the squid has a regulatory gene that controls other genes that lay down a biofilm that allows the microbe to colonize the animal's light organ.

"During squid colonization, this regulatory gene turns on a suite of genes that allow bacteria to colonize the squid through mucus produced by the animal," Mandel explains. "The mucus is the pathway to the light organ, but it also helps keep out the bad guys."

Both strains of bacteria, Mandel explains, have the same genes that produce the biofilms the bacterium needs to get established in its host. But the regulatory gene that sets the other biofilm genes in motion is absent in the strain that lives in the pinecone fish, the animal scientists believe was first colonized by V. fischeri before it moved in to the squid light organ when the squid family came onto the scene in the Pacific Ocean at least 30 million years ago.

"The regulatory gene entered the bacterium's lineage and allowed it to expand its host range into the squid," according to Mandel. "The bottom-line message of the paper is that bacteria can shift host range by modifying their capabilities with small regulatory changes."

The regulatory gene acquired by the bacterium, notes Ruby, is essentially a switch the organism uses to activate a set of genes that had been residing quietly in the V. fischeri genome. Such mechanisms, he says, are very likely at play in many other species of bacteria, including those that infect humans and cause illness.

"This is going to inform a question that has been around a long time in the area of pathogenesis," says Ruby. One line of thought is that "in order to become a pathogen, a whole suite of genes needs to be imported to a bacterium."

The new finding by his group, however, suggests that nature is far more parsimonious: Instead of requiring organisms to acquire many new genes to occupy a new host, the combination of a new regulatory gene and genes that already reside in a bacterium is enough to do the trick.

"Together, they can do something neither of them could do before. They can mix and match and open up new niches," says Ruby.

Knowing that a regulatory gene plays a key role in allowing an organism to fit a new host may prove useful in human medicine as many bacterial pathogens arose first in other animals before infecting humans. A single gene can be a much easier target for a drug or other intervention to prevent or mitigate infection, the Wisconsin scientists say.

In addition to Ruby and Mandel, authors of the new Nature report include Michael S. Wollenberg, also of UW-Madison; Eric V. Stabb of the University of Georgia; and Karen L. Visick of Loyola University Chicago. The study was supported by grants from the Betty and Gordon Moore Foundation, the National Institutes of Health and the National Science Foundation.

DNA Component Can Stimulate And Suppress Immune Response

A component of DNA that can both stimulate and suppress the immune system, depending on the dosage, may hold hope for treating cancer and infection, Medical College of Georgia researchers say.Low levels of CpG increase inflammation, part of the body's way of eliminating invaders. But high doses block inflammation by increasing expression of the enzyme indoleamine 2,3 dioxygenase, or IDO, an immunosuppressor, the researchers say.

"The same therapy can have two different effects," says Rusty Johnson, a fifth-year M.D./Ph.D. student in the MCG Schools of Medicine and Graduate Studies. "It was assumed that giving this treatment at higher doses would cause more stimulation, but it has the opposite effect."

The researchers hope that manipulating the dosage can help them optimize the role of inflammation in fighting invaders such as tumors and harmful bacteria. Mr. Johnson presented the findings at the Midwinter Conference of Immunologists this month in Asilomar, Calif. He is working with Drs. Andrew Mellor and David Munn, co-directors of the School of Medicine Immuno Discovery Institute, who discovered IDO's immunosuppressive capabilities more than a decade ago.

With the help of Drs. Babak Baban and Phillip Chandler, scientists in MCG's Immunotherapy Center, they've also learned IDO inhibits inflammation by blocking production of interleukin 6, a secreted factor that causes inflammation.

"This suggests that IDO is a counter-regulatory mechanism that serves as a balance to prevent too much inflammation," Mr. Johnson says. "Too much inflammation leads to destruction of normal body tissue, and this shows IDO's importance in preventing this from occurring."

The researchers already knew that IDO protects tumors from the immune system. While working with collaborators Drs. Alex Muller and George Prendergast at the Lankenau Institute in Philadelphia, they learned its role in tumor formation.

"Without it, a mouse becomes resistant to skin tumor formation, and tumors that do form are smaller and less malignant," Mr. Johnson says.

They've also learned that the cells IDO uses to suppress the immune system – IDO-competent dendritic cells – originate from B cells, which produce antibodies to fight infection.

Mr. Johnson was in his second year of medical school when he heard Dr. Munn lecture about his and Dr. Mellor's groundbreaking discovery of IDO's role in protecting a fetus from the mother's immune system. It was at that point that the Augusta native decided to pursue a career in immunology. Mr. Johnson earned a bachelor's degree in chemistry from the Georgia Institute of Technology and studied piano and voice at Augusta State University prior to coming to MCG.

Breakdown Of Barriers In Old Cells May Hold Clues To Aging Process

Like guards controlling access to a gated community, nuclear pore complexes are communication channels that regulate the passage of proteins and RNA to and from a cell's nucleus. Recent studies by researchers at the Salk Institute for Biological Studies offer new insights about the pores' lifespan and how their longevity affects their function.

Their findings, reported in the Jan. 23 issue of Cell, may provide clues to one of the most enduring questions of biology: how and why cells age. They also offer a new, promising avenue of investigation for scientists pursuing intervention strategies for neurodegenerative diseases.

"We still have a very poor understanding of the mechanisms behind cell aging. It has been known for some time that the gene expression profile of an aging cell changes and somehow is linked to age-related diseases, but no one really knows why. Our work could provide an explanation for why we observe age-dependent defects in cells," says Martin Hetzer, Ph.D., an assistant professor in the Salk's Molecular and Cell Biology Laboratory.

Made up of 30 different proteins, nuclear pore complexes assemble during cell division and penetrate the membrane separating the nucleus from the cytoplasm. Their job is traffic control on the world's busiest thoroughfare: Each one mediates approximately 1,000 transport events a second. Since nuclear pore complexes are as essential to nondividing cells as they are to dividing ones, the Salk team wanted to determine what happens to them over time. Do they turn over in nondividing cells, or do they remain in place for the life of the cell?

Because most of the cells in our body are not actively dividing, the answer would have implications for aging and age-related diseases. "Many of the neurons in the cortex area of the brain are as old as we are; they are nondividing for a very long time," explains Hetzer.

Approximately half the proteins in the nuclear pore complex make up the central scaffold, or core, while the other, peripheral proteins attach to the scaffold. Using C. elegans, a tiny roundworm that as an adult consists entirely of nondividing cells, Hetzer and his group found that while the peripheral proteins are continually exchanged, the proteins comprising the scaffold remain in place for the life of the cell.

Although the scaffold proteins are detectable, their genes are no longer active. The same held true in nondividing rat neurons. "If proteins are there, but transcripts of the information making the protein are no longer there, they have to be very stable," says Hetzer, noting that whereas most proteins turn over in minutes or hours, the ones comprising the scaffold in the nuclear pore complex remained intact for the entire lifespan of an organism. "We discovered one of the most stable structures in our cells."

"It's a novel concept," adds first author Maximiliano A. D'Angelo, Ph.D., a research associate in the Hetzer lab. "No one really saw a structure that would last for the entire life of the cell."

Hetzer and his group then set out to ascertain how these stable proteins hold up over time. Since one of the functions of the nuclear pore complex is to set a permeability barrier between the nucleus and cytoplasm, the researchers developed a reporting system that would scrutinize the barriers to see how efficient they were at excluding inappropriate molecules, much as security auditors keep tabs on airport baggage screeners' ability to detect and block contraband.

What they found was that in aging cells, one of the proteins composing the scaffold structure becomes damaged, and the permeability barrier deteriorates; molecules that should be restricted to the cytoplasm invade the nucleus.

"Because some cells live for a long time, the accumulation of damage in the long-lived nuclear pore complexes can impair their function and have important consequences for cell homeostasis and survival," says D'Angelo. "It may also play a significant role in the aging process."

In particular, a protein called tubulin, which is strictly a cytoplasmic protein, shows up as long filaments that co-opt a large part of the nucleus. For more than 100 years, pathologists had been aware of these filaments, but their origins were unknown. Associated with several neurodegenerative diseases, including Parkinson's, the filaments are found particularly in the substantia nigra of many Parkinson's patients, the part of the brain that is involved in dopamine production and that is affected by the condition.

Hetzer's team hypothesizes that it is the age-dependent defects in the scaffold proteins that undermine the nuclear permeability barrier. "We predict that when the permeability barrier is impaired, molecules are either lost from the nucleus or can leak into the nucleus and thereby change gene expression profiles," says Hetzer. "This could be a general aging mechanism, and it provides an explanation for the origin of these filaments, which have been known by pathologists for a long time."

By finding ways to prevent or reverse the leakage, the Salk researchers may be on course to identify novel approaches to treating these perplexing, devastating, and costly conditions.

In addition to Hetzer and D'Angelo, postdoctoral researcher Marcela Raices, Ph.D., and doctoral candidate Siler H. Panowski of Dr. Andrew Dillin's laboratory at the Salk Institute contributed to this study. The research was carried out with funding from the NIH.