University of Wisconsin–Milwaukee

Laura L. Hunt

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Dec 2, 2008 
UWM graduate student co-authors a paper in Nature
John Berges and Chang Jae Choi
Chang Jae Choi in John Berges's lab

University of Wisconsin-Milwaukee graduate student Chang Jae Choi already has something on his résumé very few researchers can claim: He has co-authored a paper published in the prestigious journal Nature.

The paper, which appeared in the Oct. 15 issue, offers findings of a comparative study of the genes of two diatoms – one-celled aquatic organisms that are so numerous and dissimilar, they are more easily defined by what they are not – bacteria, animals, plants or fungi.

Co-authored by a large group of academics and their graduate students – including John Berges, UWM associate professor of biological sciences and Choi’s thesis adviser – the study offers genetic confirmation that diatoms, which appeared early in the evolutionary time scale, are not easily categorized.

New insights into diatomsDiatoms

What in the world is a diatom? That question is at the center of a paper published in the Oct. 15 issue of the journal Nature, which is co-authored a group of academics and graduate students, including UWM Associate Professor John Berges and his graduate student, Chang Jae Choi. 

In the comparative study of the genes of two diatoms – an extremely diverse group of one-celled aquatic organisms – the researchers hoped they would gain better insights into what makes a diatom.

“We expected to find these two more similar,” says Berges. “But after looking at the genomes, they’re not even in the same universe.”

Diatoms are loosely classified with a huge group called protists, which include both algae and protozoa forms that live in water and make their food through photosynthesis – like a plant. In fact, they are so numerous that they are major ecological players affecting global levels of atmospheric carbon dioxide.

But these microorganisms are not plants.

They are examples of what life may have looked like before living things diverged into separate groups such as plants and animals, says Berges. And the two diatoms compared in the study share only 57 percent of their genes.

“Humans are more like oak trees than these two diatoms are like one another,” says Berges.

The study also found that the diatoms have a relatively large number of genes that have been transferred from bacteria.

One of the big differences between protists and bacteria is how each stores its DNA. While both are single-celled, in protists, DNA is housed within a nucleus; in bacteria, the DNA is less tightly bound. For this reason, bacteria have always been good at exchanging DNA, and this has been exploited by genetic engineers and molecular biologists.

The research indicates that bacterial genes are able to somehow pass through diatoms’ rigid cell walls and nuclear membranes to become incorporated in the diatom genome, a process called lateral gene transfer, says Berges.

Lateral gene transfer has important implications for the evolution of organisms, but it also has practical value. Understanding the process may allow genetic engineering of organisms for many purposes, including drug development.

– Laura L. Hunt

But the paper also gives new insights into the origins – and functions – of certain genes shared by both diatoms and higher, more complex organisms. These functions, including the ones Choi investigated, have potential applications in medicine and nanotechnology.

Explaining cell suicide

Choi’s role in the study was to analyze a set of genes that are responsible for a trait, common to both diatoms, called “programmed cell death.” Such genes are found in diatoms and other one-celled organisms, but also in animals and plants.

Programmed cell death often occurs as a normal step in the development of multi-celled organisms. For example, as tadpoles turn into frogs, new cells are made and other cells are “deleted.” The same thing happens to human fetuses as the fingers and toes form.

But in diatoms and other protists, it amounts to suicide.

“For one-celled organisms, like diatoms and phytoplankton, there is no clear reason for them to kill themselves,” says Choi. “We have an idea of how it is happening, but not the ‘why.’”

After the comparative study, however, Choi believes the ability to carry out programmed cell death is related to the diatom’s environmental stress response.

“It keeps the number of cells in a community in balance,” he says. For example, it may be used to keep the community of cells safe from a threat, such as the spread of a virus.

Because of their early origins, diatoms are useful in trying to determine the function and nature of genes, he adds.

“To unravel a complicated picture, you start with an ancient organism,” he says. “It gives you a general picture that can contribute to what’s going on in the more complex organism.”

Cell death in other organisms
The next step is to compare the stress-relief genes with those of organisms in a completely different classification, such as bacteria and yeast, says Choi. “That is one way I can get ideas on the functions of these genes.”

After earning a bachelor’s degree in life sciences from Korea University, Choi came to UWM specifically to work with Berges. Choi believes some of the discoveries made with the diatom study will not only shed light on why diatoms use the gene, but also how phytoplankton – and all plants – use it.

He is interested in applying the research to understanding why large populations of single- celled phytoplankton sometimes spontaneously “die off” in nature.

The results have implications for human use, too. Understanding an ability to signal intentional cell death can help reveal what happens during stages of diseases like cancer and Alzheimer’s.