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DR. SHILADITYA DASSARMA - University of Maryland, Center of Marine Biotechnology (COMB)

The Research: Salt-loving Microorganisms

Halophiles are a class of extremophiles (extreme-tolerant microbes) with a higher than normal tolerance for salt. Many of the known halophiles, and for that matter extremophiles in general, are known as Archaea, which are microorganisms that form a third branch of life which is distinct from the Bacteria and the Eukaryota. Only recognized since the 1970s, Archaea have characteristics that place them between bacteria and eukaryotes, or higher organisms. For over 20 years now, Shil DasSarma has been studying the halophiles, which are ubiquitous around the planet. Halophiles with varying degrees of salt tolerance can be found in salt marshes, on coasts, and anywhere else salt might concentrate, such as the Dead Sea and the Great Salt Lake. There they are so concentrated that their reddish color can be seen from planes and even space. Some, called extreme halophiles, can thrive in salt concentrations up to five times that of ocean water. DasSarma says the halophiles are especially useful as model organisms in part because, unlike some other extremophiles, which are commonly adapted to a single extreme condition, halophiles are typically adapted to a number of different extreme conditions.

"There is so much diversity on this planet about which we know very, very little and we think that halophilic Archaea are representative of that diversity," says DasSarma. His group is interested in the organisms mainly as a model for life in general, because they have a moderately sized genome that can be studied as a whole. Because they are relatively easy to grow in the laboratory, and their genes can be manipulated, DasSarma compares them in value for research to E. coli, the commonly used model bacterial organism. DasSarma and his team are also interested in potential applications derived from halophilic Archaea studies, such as using them to aid in the development of new vaccines and as indicators of environmental conditions.

Salty Characters

Many of the samples DasSarma's lab works with are provided to them by colleagues that work at sites such as the Dead Sea and the Great Salt Lake. However, the group is transitioning toward doing more field collection work, mainly at sites around the Chesapeake Bay.

DasSarma's research to date has focused most heavily on a strain of Halobacterium known as NRC1. "We're really trying to elevate this species to a model system and I think we're pretty far along in doing so," says DasSarma, who points out that the strain is being studied by more and more laboratories and is now readily available to researchers from a number of commercial sources. Of the organism's 2,500 or so genes, some 40% have predictable roles, but little work has been done to demonstrate the function of specific genes. In working toward correcting this deficiency, he and his team have developed a novel and reliable method for inactivating, or "knocking out," specific genes, which is allowing them to conduct a number of gene function studies. The DasSarma team has, for instance, identified and studied a number of genes responsible for arsenic resistance, and has shown one of these genes to be highly related to an analogous gene in mammals that is involved in arsenic resistance. With so many genes yet unstudied, though, says DasSarma, "There are really an unlimited number of projects."

Two other key species the group works with are Haloarcula marismortui, from the Dead Sea, and Halorubrum lacusprofundi, collected from a hypersaline lake in Antarctica whose temperature is -15 °C for half of the year but doesn't freeze because of a high salt content.

Using Gas Vesicles For Vaccines

The DasSarma lab's primary focus is on basic halophilic Archaea research, however, the work has also identified some potential practical applications. These include the possible development of a new type of vaccine based on the organisms' gas vesicles. Gas vesicles are organelles found within bacterial or Archaeal cells that act as primitive flotation devices. DasSarma's group has moved beyond basic studies of these organelles to exploring the possibility of manipulating Archaea genetically so that they produce gas vesicles with specific proteins on their surfaces. The team could, for instance, insert genes for proteins found in a particular virus into the Archaeal genome. The theory is that injecting such gas vesicles into humans would elicit the same immune response, namely the production of antibodies to attack the virus proteins called antigens, which would be triggered by the virus itself.

This is the basic concept of all vaccines, but the gas vesicle delivery system would be unlike anything currently in use and far more versatile. DasSarma says that in theory, the organisms could be induced to produce vesicles with any protein on their surface, opening the possibility of vaccine creation for almost any disease, even an emerging one. "It's really an enabling technology," he says. One specific application the team is currently working on is developing a vesicle vaccine for AIDS by working with SIV, or Simian Immunodeficiency Virus, a disease in monkeys that closely approximates the human condition.

Probing the Purple Membrane

The purple membrane is a specialized region of the cell membrane of halobacteria that pumps protons across the membrane in response to light, giving the organisms the ability to perform photosynthesis for limited periods of time. The purple membrane is a two-dimensional crystallized lattice composed of a colored protein called bacteriorhodopsin. It contains retinal, which is analogous to vitamin A. In the membrane, these two components are bound in a precise one-to-one ratio. Halobacterial pigments give a reddish hue to large blooms of halobacteria, such as are sometimes seen in the Great Salt Lake.

First discovered in 1969, the purple membrane was for 30 years considered unique to halobacteria. However, in the past decade, researchers have discovered a protein similar to bacteriorhodopsin in marine organisms, and the genes for its production are now known to be common in the sea.

DasSarma's group has worked for many years to understand how the purple membrane system is regulated. A single regulator controls production of both the bacteriorhodopsin and the chromophores in their correct proportion. The research group has focused much attention on how this works, in part by selectively knocking out genes to determine those responsible for purple membrane components and the regulation of their production. Though DasSarma's interest in the purple membrane remains basic, other groups have been pursuing applications for it, such as exploiting the crystallized lattice for use in biocomputing.

Close to Home: Halophiles in the Chesapeake Bay

One of the DasSarma group's newer pursuits is the study of halophiles in the Chesapeake Bay, work that has attracted interest and funding from both the National Park Service and the Chesapeake Bay Trust. The work is in its early stages, but could have a number of potential environmental applications. The group is also using the work as a tool for teaching.

DasSarma says that most people, when they think of pollution in a system such as the Chesapeake Bay, think of fish kills or declining crab populations. However, as in so many ecosystems, microoroganisms form the foundation of the Chesapeake Bay food web. If pollution affects them, all levels of the system are affected. Often in conjunction with student groups, the DasSarma team has extensively sampled portions of the bay in search of novel halophiles and also to study the impacts of pollution on known species. As the work progresses, DasSarma says a number of research directions are possible. Changes in the diversity of organisms in a given location could, for instance, be an indicator of environmental changes, possibly harmful changes. A good baseline understanding of this diversity is therefore needed so that impacts can be assessed.

Another route for environmental analysis is to study the impacts of pollutants on microbial species in the laboratory to determine effects that might ultimately be discernible in the environment as clues to problems. A final potential outcome of the work might ultimately be the discovery of species able to bioremediate pollution, which could take any number of forms such as the breakdown of oil or other pollutants.

Educational Background: A Chemical Transition

DasSarma did his undergraduate work at Indiana University in Bloomington. Though he was in the chemistry department, he became fascinated there with genetics. He did his graduate work at the Massachusetts Institute of Technology, where he first began working with halophiles and the purple membrane. One of his advisers was H. Gobind Khorana, who received the Nobel Prize for his work on cracking the genetic code. With Ph.D. in hand, DasSarma crossed the river to Harvard Medical School, where he worked as a postdoctoral fellow for two years with Howard Goodman, who is well known for cloning the human growth hormone and whose students founded biotech star Genentech. After Harvard, DasSarma spent a summer at the Pasteur Institute in Paris. He next took a position at the University of Massachusetts in Amherst where he spent 15 years before taking his current position at the University of Maryland in 2001.

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