New Faculty: Chan Yul Yoo Greening of the Globe …and Mars?

Chan Yul Yoo Seeing the Light

You may have heard that trees communicate, but did you know that plants have eyes?

“Just as we see the world by our eyes, plants see light with photoreceptors to control growth and development throughout their entire life cycle,” says Assistant Professor Chan Yul Yoo who arrived at the School of Biological Sciences this year. (His wife Heejin Yoo is also a new assistant professor at SBS with her own lab. You can read a research profile of her in our Spring 2022 issue of Our DNA.)

This and the banner photo together: The eye of green plants: phytochrome B photobodies fused with green fluorescent protein in every nucleus (blue, DAPI staining.

Chan Yul Yoo

“Our lab is interested in understanding fundamental functions of photobodies in reprogramming plant growth, development, and chloroplast biogenesis,” Yoo says. As our planet continues to encounter global climate changes including warming and drought, the greening of the earth through plant life is critical for cooling the atmosphere by transpiration and holding ground water in the soil. Yoo’s lab focuses, in particular, on the role of photobodies as developmental and environmental sensors in nucleus-chloroplast communication to orchestrate transcriptional regulation in nuclear and chloroplast (green plastid) genomes.

While you may be familiar with Charles Darwin’s work on evolution, he together with his son Francis Darwin also studied that plants can sense and bend towards the light from a book called The Power of Movement in Plants in 1880. Since then, molecular genetics and cell biology approaches have led to the identification of a suite of photoreceptors in plants and the discovery of photobody in the nucleus. Photobodies are plant-specific biomolecular condensates that contain photoreceptors for sensing light and regulating almost every facet of plant growth and development including chloroplast biogenesis. Phase separation behavior of photobodies have become an urgent field of scientific inquiry to help the earth continue to green through photosynthesis and to augment crop species for a hungry world.

That may be a mouthful of plant biology vocabulary, but Yoo has, since his arrival in SBS, been here to help us understand his work. The backstory to that work lies in evolution when the earliest photosynthetic organisms were single cell cyanobacterium containing chlorophyll, the green pigment used to absorb light energy

Chan Yul Yoo

and turning sunlight into food while expelling oxygen as a waste product and creating our breathable atmosphere for all living organisms including human. For billions of years these organisms remained under water in their colonies… and then, 500 million years ago, algae emerged. Algae featured chloroplasts where photosynthesis takes place.

Fast forward to the emergence of genomics when scientists learned that it requires two discrete sets of genomes—one found in the chloroplast of a plant cell, the other in its nucleus—to fix the CO2 in a way to produce sugar and oxygen, the magic of photosynthesis.

“Plant biologists have known this for a while,” says Yoo about the symbiotic genomes. As a post-doctoral researcher he sometimes despaired that “all things” in plant biology had already “been discussed, found, and otherwise saturated.” So what’s a post-doc to do?

It turns out that Yoo had despaired prematurely.

Seeing the Light

Plants like Arabidopsis, a well-established model species, feature chloroplasts that have evolved over time with territorial stressors: drought, high irradiance sunlight, fresh vs. salt water. Over time many genes of the plant have been lost or have migrated from the chloroplast to the cell’s nucleus.

We know that light triggers photosynthesis through photoreceptors which control growth and development in a plant. “Phytochromes,” for example, are photoreceptors that sense the red/far-red in the spectrum of light. Without these receptors, plants do not turn green and show the photomorphogenic phenotypes.

Once phytochromes sense red light, one of the earliest cellular events is the relocation of phytochromes from the cytoplasm of the cell to the nucleus whereby they form membrane-less organelles called photobodies, the “eyes” of the plant. These subnuclear foci “see” the light which in turn triggers the growth of a plant toward that those life-sustaining waves and the greening we relate to a healthy plant.

The greening (chloroplast biogenesis) requires coordinated nuclear and plastidial (chloroplast) gene expression. After all, the two sets of genes are each held within their own respective membranes. Clearly, communication of some kind is happening between the two organelles. But how? And what exactly is it?

It turns out that light-activated photobodies in the nucleus activate the assembly of bacterial-like multi-subunit RNA polymerase called PEP in chloroplasts. Using forward genetic screening, Yoo discovered albino mutants with defects of photobody and PEP assembly.

This was the research space the young scientist pivoted to during his post-doc malaise, and his research led to exciting discoveries about a novel framework of anterograde or nucleus-to-chloroplast signaling pathway. That pathway, again, through some kind of communication, is still under investigation. It’s what links photoreceptors-containing biomolecular condensates—the photobody eyes—in the nucleus to the chloroplast biogenesis.

Yoo lab’s current research is trying to identify this mysterious signaling molecule in nucleus-chloroplast communication. In addition, the lab is interested in uncovering mechanisms by which plants regulate the formation of photobodies via phase separation in response to environmental changes. Ultimately, Yoo lab expects to develop climate-resilient greener plants to make our planet green.

A Global Journey with Dr. “House”

The research journey for Dr. Yoo was a globe-trotting one. After securing his bachelor’s degree in his native South Korea, he earned his PhD in Horticultural Science at Purdue University in 2011. There he worked on plant molecular genetics involved in abiotic stress adaptation. His research was focused on understanding the molecular, developmental, and physiological mechanisms of acclimation and adaptation in various environmental stresses including high temperature and drought stresses. Then, Chan Yul joined to Dr. Meng Chen’s lab at Duke University as a postdoctoral associate and followed the lab’s move to the University of California Riverside to study light, one of the most important environmental signals for the life of plants.

Along the way he also picked up research tactics from popular culture, specifically the TV series House, and his use of what the good doctor (albeit, one with a notoriously scabrous bedside manner) calls “differential diagnosis:” when a patient’s symptoms match more than one condition and additional tests are necessary before making an accurate diagnosis. For Yoo, the “patient” is the tall and albino plant that is unable to green and eventually dies, and he wants to cure that. “There are possible reasons for that in many directions,” he explains. “You have to look at many different possibilities at the same time.”

For a plant biologist concerned with reprogramming plant growth and development, gene-editing has proved useful in “knocking out” multiple Phytochrome-Interacting transcription Factors (PIFs). Can we cure albino plants by removing of PIFs in the nucleus? The answer it turns out is yes. But the point is, you can’t just focus on the chloroplast since it’s also a nuclear event.

It’s also an event that requires communication between the two genomes, one each in the nucleus of the plant cell and in the chloroplast. This communication is what is still partially eluding Yoo and his team, but in the lab, differential diagnosis continues. Their work discovered another mutant at the same time as the publication of a paper in 2019. “We thought at the time, ‘let’s cure this mutant as well!’” says Yoo. But that didn’t work as there are two separate functions in the same signaling pathway.

It’s all part of the recursive and provisional conclusions of inquiry in Chan Yul Yoo’s new lab to help make plants—from the grass on a PGA golf course to crop plants like dwarf maize—“see” better, develop better, and keep our planet green.