Plant Peroxisome Study Offers New Insights Into Conserved Cellular Functions

For most of their lives, plants get their energy from photosynthesis. But during the seed to seedling stage when they can't absorb light just yet, they rely on other sources, like fatty acids. To process the fatty acids, plant cells, like human cells, rely on a membrane-bound compartment called the peroxisome. For people interested in studying the peroxisome, plant cells are an excellent model to use. 

The plant we use, Arabidopsis, has large cells and peroxisomes so large that we can see inside them with a light microscope. The peroxisome gets even larger during the seed to seedling stage, when the plant is relying on fatty acids for energy, before shrinking back down to its normal size once the plant can photosynthesize." 

Bonnie Bartel, the Ralph and Dorothy Looney Professor of Biosciences

Bartel's research team studies these large peroxisomes, including a protein called PEX11, which has long been known to help peroxisomes divide. Their work, published in Nature Communications, showed that PEX11 also helps regulate the peroxisome's size changes observed during the seed to seedling stage. 

"Peroxisomes are implicated in some human diseases and used in bioengineering," said Nathan Tharp, first author of the paper and a Rice graduate student. "They can, however, be rather tricky to study." 

The classic way to find out what a protein does is pretty simple: break the gene coding for the protein and watch what happens. But PEX11 was coded for by five different genes, and breaking just one of the genes didn't seem to impact its function, while breaking all of them was lethal to the plant. To study PEX11, Tharp needed very fine control over the protein's five genes. 

"I was able to use recent advances in CRISPR to go in and break specific combinations of the five genes," said Tharp, who recently defended his thesis. "It was only then that we were able to see that PEX11 is clearly involved in controlling the growth of the peroxisome during the seed to seedling stage." 

Tharp created two mutants, each lacking a specific set of the PEX11 genes. In both of the mutants, the peroxisomes grew during the seed to seeding stage. And in both mutants, instead of shrinking back down to their normal size, some peroxisomes kept on growing. Some of them grew until they touched the top and bottom of the cell. 

The mutants were also missing vesicles, membrane-bound subcompartments that formed inside the peroxisome as the fatty acids were being processed. In a normal cell, the vesicles form as the peroxisome grows, taking pieces of the outer membrane of the peroxisome. 

"The vesicles taking pieces of membrane as they form may help control the peroxisome's growth," Tharp said. "In our PEX11 mutants, these vesicles either don't form or are abnormally small and rare, and so we see these massive peroxisomes, way larger than normal." 

While Tharp studied these peroxisomes in plants, he was curious to see if his findings could apply to other organisms, like yeast. So he tried another classic molecular biology experiment: fixing what he had broken. To do this, he reached for the yeast version of the protein, called Pex11 instead of PEX11. 

"We put yeast Pex11 into our mutant plant cells to see if it could return the peroxisomes back to normal," Tharp said. "And it did." 

This means, Tharp explained, that Pex11 could play the same role in yeast that it does in plants, even though plants and yeast are separated by over a billion years of evolution. And if it plays the same role in yeast as it does in plants, it may play the same role in other cells, like human cells. 

"Finding that this protein fills the same role in yeast and plant cells suggests that it may be a highly conserved protein," Bartel said. "Our findings in plants, in this relatively easy-to-study model, may thus be applicable to human cells and cells used for bioengineering."