Ph.D. Student Studies Effectors for Emerging Bacterial and Fungal Pathogens

It all started with the Four O’clock flowers young Egem Özbudak would study as a toddler growing up in Izmir, Turkey. The bursts of velvety purple and periwinkle-colored flowers studded with long red asterisks or yellow buttons in their middles were common near his home.

Özbudak’s friends played in the schoolyard and went to the beach with their families. But, he was, as a 5-year-old, collecting seeds in his pockets. Once home, he would germinate the seeds in damp white paper napkins. He observed the tiny seeds each day as they softened and the plant shoot split the seed body. As the new plants emerged, curled out from the seed pod, he would study them several times a day. The stems would reach toward light sources, flower, advance through senescence, and then push seeds.

As an elementary school student, Özbudak’s interest in science continued. His parents noticed his fascination and gave him science magazines published by the Scientific and Technological Research Council of Turkey.

“Those magazines helped me find my path,” said Özbudak. “I wanted to learn everything I could about living organisms—about how they grow—their diversity –shapes and colors.”

Along with his family, Özbudak grew flowers and plants in pots on the terrace of their multifamily apartment home. There were cloud-white and lilac and deep purple periwinkles. Fluted pink, white, red and yellow petunias waved from a crayon-box full of painted colors on ceramic and plastic pots.

The plants and the pots always changed. He grew vines, tried new flower species, and some vegetables. He watered, fertilized and replanted the many pots, needing no supervision from his parents. The family remarked on the pots, the plants, and Özbudak’s unwavering—joyous–interest in the plants.

“To me, the plants were like patients,” he said. “When I was in high school, my friends were interested in biology and medical studies, and I was interested in plants because they were living organisms that needed proper care to evolve.”

As Özbudak grew from a young boy into a young man, he realized that his home in Izmir was an inspiration. Its diversity, history, and connectedness to multiple cultures showed him interdependence and the value of people sharing work as a team, as with agricultural production. From such collaborations, civilization can advance, he said.

“Turkey is a bridge country,” he said. “Asians would say Turkey is in Europe; Europeans would say Turkey is in Asia.”

Özbudak completed a Bachelor of Science degree in Molecular Biology and Genetics at Izmir Institute of Technology under the supervision of Professor Anne Frary and Professor Sami Doganlar, working in marker-assisted selection for stress resistance in Solanum species.

“My studies until this time were abiotic, or observing and tabulating the way plants react to the environment, or changes in temperature, water, and nutrients,” said Özbudak.

His graduate work involved glycosylation or the expression of proteins in plants. It was during this work that he realized the interface of agriculture and the environment. He developed a desire to protect natural resources alongside food production. Özbudak found an exchange opportunity with the European Union and received the 2014 Erasmus Students Program Scholarship. The award was an academic bridge, a summer internship in The Sainsbury Laboratory in Norwich, United Kingdom, under the auspices of Professor Sophien Kamoun. Professor Kamoun was recently named a Fellow of the Royal Society whose famous Fellows include Isaac Newton, Charles Darwin, and Stephen Hawking. It was in the Kamoun laboratory that he met his direct supervisors, Dr. Yasin Dagdas, currently working at The Gregor Mendel Institute, and Dr. Liliana Cano, the University of Florida’s Institute of Food and Agricultural Science’s plant pathologist at the UF Indian River Research and Education Center (IRREC).

“Dr. Yasin Dagdas and Dr. Cano taught me how to engineer protein-protein interaction affinity to manipulate athophagy processes triggered by effectors in plants,” said Özbudak. “This is the moment when I realized the area where I want to work in my career. It is so dynamic.”

The summer internship experience in the Kamoun Laboratory was a pivotal moment for Özbudak. In Turkey, he learned how to follow experimental design. In the United Kingdom, he realized he could design his experiments by pursuing a doctorate program.

In the fall of 2016, he was recognized with a second Erasmus Students Program Scholarship Award. The new experience bridged him to Katowice, Poland, at the University of Silesia under the supervision of Dr. Hab Katarzyna Hupert-Kocurek. In Poland, his graduate studies involved work with biodegradation using endobacteria originally isolated from sewage water. These bacteria could be potentially used in the future for phytoremediation to clear contaminants from water bodies.

Before completion of the master’s degree, he secured an opportunity with the University of Florida. Dr. Cano helped Özbudak apply for a doctorate program to study at IRREC. He completed a Master of Science degree in Biology and Environmental Protection and then bridged to Florida.

“Learning and introducing new topics in science is important to a new scientist,” said Özbudak. “Networking is important because scientists do work together in collaborations, and meeting Dr. Cano was critical to my next step. I am grateful to her.”

In Dr. Cano’s laboratory at IRREC, Özbudak works with effectors from emerging bacterial and fungal pathogens. Cano said effectors are genes encoded by pathogens that function inside plant cells. She uses bioinformatics tools to identify these pathogen effector genes in the genomes of bacterial, fungal and oomycete pathogens found in citrus crops.

Özbudak believes that major diseases in Florida, like the citrus greening issue, may be resolved with advances in plant pathology. He said that there is hope for a solution to this problem by modifying citrus trees to resist the disease.

“During my career, I would like to improve plants worldwide so that food production will be more robust,” he said. “Increasingly, scientists will edit more genes in food crops, a technique which is getting accepted by the public.”

Özbudak is working on two additional emerging fungal pathogens in the Cano Laboratory. The projects are with Colletotrichum acutatum, the causal agent of post-bloom fruit drop disease in citrus and crown/fruit rot disease in strawberry, and, Diplodia natalensis, the causal agent of stem end rot in citrus.

“There is so much work to do in using science to make plants stronger to produce food more abundantly,” said Özbudak.

Özbudak’s long term goal is to contribute to the understanding of how effectors evolve to suppress the defense mechanisms of plants. He said the technique will help plant pathologists understand how disease and epidemics may be better managed.