When Adam J. Bogdanove, School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology, was an undergraduate student, he already cared deeply about the environment. But by his senior year, he didn’t care much about being a student.
“When I graduated, I knew I wanted out of academia,” he says. He set off to Japan to teach English, but his concerns and interests followed him. “After four years, I had this realization that if I wanted to do something about the things I cared about, I should be a scientist after all, and damn it, I would have to go back to school,” he says. “Luckily, it turns out, I’m very happy doing what I do.”
From Japan, Bogdanove moved to Cornell for his graduate work, beginning a career that has had the overarching goal of improving the health of crops and ultimately reducing world hunger. His research program now focuses particularly on diseases caused by bacteria in the genus Xanthomonas, which affect approximately 400 different plant species, including rice varieties, a primary focus of Bogdanove’s group. “Rice is the main source of carbohydrates for about 60 percent of the population,” says Bogdanove. “And it is a genetic and genomic model for all cereals.”
Bogdanove’s main aim of understanding the mechanisms for how bacteria perpetuate disease in their hosts—and finding ways to interfere with that mechanism—has broad implications. The outcomes can increase crop yields and improve the lives of farmers and consumers, especially in areas where over-population and food shortages threaten public health.
How TAL Effectors Win, until Scientists Step in
When a Xanthomonas pathogen attacks a host cell, it attaches to the outside of the cell and injects molecules inside. The injected molecules that Bogdanove studies are proteins called transcription activator-like effectors, or TAL effectors. After entering the cell, these TAL effectors go directly to the nucleus, attach to the DNA, and initiate transcription.
“TAL effectors in the leaf tissue take genes that are not expressed at all, or expressed at moderate levels, and they’ll ramp those expression levels up,” says Bogdanove. “When that upregulation of a gene contributes to disease progression, we call that gene an S gene, or a susceptibility gene.”
So TAL effectors just have to find the S genes on the DNA, bind there, and the battle is over—bacteria win. Of course, it’s not so simple: because the host has evolved various ways of combating and confusing TAL effectors, sometimes slightly changing the DNA sequence so that the TAL effector can’t bind. Another trick includes mutations that place binding sites next to a gene whose expression actually triggers an immune response. “It’s sort of an activation trap,” Bogdanove says.
“This sets up a really interesting, almost paradoxical set of selective pressures on TAL effectors,” he continues. “On the one hand they need to have some flexibility in their specificity to small changes in the target sequences in S genes, but they also need to have stringent enough specificity to avoid activation traps.”
To combat disease, Bogdanove and his team have to understand exactly how TAL effectors have solved this problem over the course of host and pathogen co-evolution. “The puzzle of what nature has come up with is what we chew on every day in the lab,” Bogdanove says.
“A key to reducing world hunger is not just producing more food,” says Bogdanove. “But producing more food where it’s consumed.
A related inquiry is figuring out what the S genes express and how that contributes to disease. Bogdanove’s lab has characterized one such S gene as crucial to sulfate transport. Other S genes have been found to code for sugar transporters, but the mechanisms of how these excesses aid the bacteria are still mysterious. Another frontier, Bogdanove says, is to understand the noncanonical impacts of TAL effectors. “We think that TAL effectors do things other than turn on genes,” he says. “They might also repress genes or activate expression of non-coding RNAs. We’re hot on the trail of these effects.”
Attacking TAL Effectors through Genome Editing
In 2009, Bogdanove and his team at Iowa State University made a breakthrough discovery—they were able to characterize how TAL effectors bind to DNA. Most significantly, they discovered that they do so modularly. TAL effector proteins have projections that Bogdanove likens to Lego blocks, with each Lego color binding to a specific amino acid in the DNA. This makes the TAL effector Legos a kind of reverse DNA code. “It’s so modular, that we can actually pull the TAL effector blocks apart and reassemble them to make proteins that will target whatever sequence we like,” Bogdanove says.
This finding, in addition to advancing fundamental understanding, led to a genome-editing technology. Bogdanove, with collaborators at the University of Minnesota, was able to design TAL effectors and attach DNA-cutting enzymes called nucleases to create TALENs, the first modular, engineerable DNA targeting reagents. “Our TAL effector work energized that field, and within a few years, the CRISPR-Cas9 system was described, which really democratized the process, making it faster and easier,” he says.
Creating Robust Rice Crops
Genome editing has burst open the possibilities for progress all across the biological sciences, and Bogdanove’s work on rice crops is one example. Using these technologies, Bogdanove and collaborators at Cornell and elsewhere were able to embark on a new project to create more robust varieties of rice.
Imagine a strain of rice that is drought resistant, pest and disease resistant, can tolerate acidic soil, and has S gene variants that can fool TAL effectors—those agents of bacteria—and prevent them from binding. If plant breeders could have easily selected for these traits, they would have done so already. “These traits are quantitative, and often the genetic determinants are pretty complex,” says Bogdanove. “One trait might depend on a sequence on the short arm of chromosome four and another sequence on the long arm of chromosome 11. For breeders, trying to get those bits into the same individual is challenging at best and often impossible, in addition to being totally time-consuming.”
Instead, Bogdanove and his collaborators, including Susan R. McCouch, Plant Breeding and Genetics, are going straight to editing the genome. “If you find wording in one variety that spells out drought tolerance, then you take that wording and change it in the test variety to match,” Bogdanove says.
The group will watch to see whether or not the desired phenotype is expressed with the edited genotype. “One characteristic of quantitative trait loci is that how they behave depends very much on the rest of the genome,” Bogdanove says. “So we’re able to take these loci and put them into a new genome and ask if they behave as expected.”
Funded by a $5.5 million grant from the National Science Foundation, the project has the potential to greatly change the lives of people who live in areas where crops struggle to survive. “A key to reducing world hunger is not just producing more food,” says Bogdanove. “But producing more food where it’s consumed. What’s really gratifying is that the discoveries we’re making have real meaning in addressing a critical problem that’s facing the planet.”