Pack-MULEs are toting a new look at plant evolution

09/28/04

EAST LANSING, Mich. It's not too often you pick up a scientific journal to dig into a good mystery.

Ning Jiang et al. admittedly aren't going to give Agatha Christie a run for her money, yet in the Sept. 30 edition of the British science journal Nature, the article explores some surprising unexplored territory in the world of evolutionary biology.

"Pack-MULEs: transposable elements mediate gene evolution in plants" may sound like a western lost in the science fiction section, but it elevates a little-considered group of elements in the genome sequence to potentially major players in the process of evolution. It also throws out tantalizing possibilities that could turn some standard methodology on its ear.

"Even a lot of my colleagues say they don't understand my article," says Jiang, who one month ago left a post doc at the University of Georgia to take a faculty position at Michigan State University's horticulture department. "I'm looking at something people don't pay much attention to."

But not only did Jiang find a new way to look at genomic sequences a scientist's treasure map but she's also provided a refreshing testament to how personal and creative even the most dense and high-tech sciences can be.

Jiang is a native of China who entered science with a personal link to her area of study the genomic sequence of rice. Rice isn't just a plant with a sequenced genome that's comparatively manageable. Rice also has been a strong thread which runs through her life.

"Rice is the most important food for me; nothing else can replace it," Jiang said. "In the first 15 years of my life, the rice straw was the major fuel for us to cook our food."

Jiang studies transposable elements the "jumping genes" of plants. The genome sequence is in a certain order. Change the order of the genetic material and a function can be changed. Transposable elements are sort of the rowdy kids in a classroom their insertion may disrupt an orderly gene.

Jiang offers Indian corn as an example. An ear of Indian corn can be mostly row after row of purple kernels. Then a yellow kernel can show up. That's courtesy of the disruptive transposable element, an element that inserts itself into the gene that is responsible for the purple color. The transposable element jumps out and purple spots appear.

Some elements are mutator-like transposable elements called MULEs. Of those, Jiang has found that some carry fragments of cellular genes with them and were dubbed Pack-MULEs. No one can say scientists don't have a bit of poet in them.

Genome sequences are long it takes 430 MB (that's 430 million base pairs) to hold the genome sequence for rice so most of the time scientists examine them in chunks. Since the examination of genomes is a fairly new study (rice, for example, was sequenced in 2002) much attention is given to identifying different genes and their functions, or how a gene copies itself.

In comparison, Jiang explained, although Pack-MULEs were initially reported about 20 years ago, they didn't seem too significant. It just seemed like in a given chunk, there weren't too many of them.

Except Jiang was in the lab of Susan Wessler at the University of Georgia, a distinguished research professor who studies transposable elements. Jiang said Wessler directs the research of the lab, but meanwhile encourages people to develop their own interests and approaches. In this way, students and post docs can explore their maximum potential.

So Jiang allowed herself to get a little sentimental. The first Pack-MULE she found in a piece of rice sequence was lugging around the gene that triggers cold responses in a plant.

In 1998, MSU molecular geneticist Michael Thomashow and his associate found that increasing a plant's expression of a specific regulatory gene helps throw the plant into cold-coping mode, beefing up its defenses against freezing.

Her familiarity with Thomashow's work raised a flag. What, she wondered, was that supposedly insignificant element doing carrying around such an important gene?

That led Jiang and another team at Washington University, Zhirong Bao and Sean Eddy, to adopt a novel genomewide approach, using computers to examine the whole genome sequence of rice.

"This shows the power of collaboration," Jiang said.

They've found that indeed the Pack-MULEs are numerous. They appear to copy themselves prolifically some 3,000 times throughout the sequence, carrying various types of genes. And not only do they copy, but they rearrange a gene an instigator of variation which likely makes them newly discovered players in evolution.

At MSU, Jiang will continue to look at Pack-MULEs to try to better understand what their role is in evolution. She also will explore other questions such as the common use of MULEs in gene tagging the process of interrupting a gene to understand its function.

The research is funded by the National Science Foundation Plant Genome Program.

Source: Eurekalert & others

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