The sprouting of a seed is clearly a crucial stage in a plant’s life. Yet one part of the process has long been shrouded in mystery: How do seeds know when there’s enough water to germinate?
Researchers recently reported the discovery of a new, prion-like protein in seeds that might kick-start the process. The protein, named FLOE1, is usually dispersed throughout a seed. But when exposed to water, FLOE1 molecules rapidly condense to form blobs, essentially acting as water sensors; such protein characteristics are reminiscent of prions, which are known for their capacity to fold into multiple conformations. These blob structures are the result of a process called phase separation, which is critical to many cellular processes in plants and animals.
“Germination is a really critical stage in a plant’s life cycle. But we don’t totally understand why some seeds germinate under ideal conditions and others don’t,” says plant biologist Lucia Strader of Duke University, who was not involved with the study. “This may be part of the answer.”
Researchers studying seed germination have previously focused on the metabolic pathways involved, the role of different plant hormones, and other variables. But few had examined the physical properties of the proteins inside seeds—in part because a seed is notoriously tough to study in its dry state, says postdoctoral researcher and study coauthor Steven Boeynaems of Stanford University.
Boeynaems studies neurodegenerative diseases, not plants. But his lab teamed up with that of study coauthor and plant biologist Yanniv Dorone, a postdoc at the Carnegie Institution for Science at Stanford, because of the strange proteins at work: a group of floppy shape-shifting molecules known as intrinsically disordered proteins. In the last decade, researchers have found mammalian and yeast genomes littered with sequences for these molecules. Many are implicated in forming problematic insoluble structures in neurodegenerative diseases, particularly if they carry prion-like domains that seed protein clumps. “These proteins are disordered and floppy, but they’re also very sticky, which makes them prone to aggregate,” Boeynaems explains.
When trying to understand seeds, Dorone found a surprisingly high number of RNA sequences for intrinsically disordered proteins in the transcriptome of model plant species Arabidopsis thaliana. Of the 449 such proteins he identified, 14 had regions that allow them to clump up, much like oil droplets condensing on the surface of water. All but one of the 14 were linked to nucleic acid metabolism. Dorone created mutants of the outlier, a gene they named FLOE1, to test its role in germination and found that knocking out the gene allowed seeds to germinate with less water present. “It was intriguing, and we didn’t know how to make sense of it at first,” he says.
Most enzymatic methods, microscopy, or chemical reactions tend to require water-based buffers or reagents, hence studying the protein in the absence of water was difficult. As an alternative, Dorone and Boeynaems turned to glycerin as a medium to study embryos in seeds under the microscope. They found that in glycerin, FLOE1 was scattered throughout seed tissues. But in water, the protein instantly clumped up to form droplets. “That was the first hint that this switch from being diffuse to condensing when water is present could be a way for seeds to sense water,” Boeynaems says.
Pretreating seeds with a chemical that blocks protein synthesis didn’t alter the process; the FLOE1 protein appeared to accumulate during embryo formation, and its levels peaked in the mature, desiccated state of seeds. That a protein undergoes this sort of dry-to-wet transition and retains its function is “inconceivable for mammals,” Boeynaems says, though plants do this routinely. “If you let some egg white dry on your kitchen counter, you can’t just throw some water on it and get egg whites again,” adds Boeynaems. “But here, entire embryos dry out and then germinate once they sense water.”
FLOE1’s function depends on specific regions of the protein that allow it to shift between its diffused and condensed forms. When the team deleted certain domains, they created a version of the protein that stayed in the condensed form and “germination rates were through the roof,” Dorone says. In another set of seeds, they removed FLOE1 domains required for condensation, so the protein remained dispersed through seeds. These strains, as well as knockout mutants that lacked the FLOE1 protein altogether, appeared no different from wild-type seeds in terms of weight, size, or shape.
But when the team decreased water levels available to cells, both kinds of mutants showed higher germination rates than wild-type cells—suggesting that the protein prevents seeds from sprouting in unfavorable conditions. By doing so, the protein likely ensures plants have a better chance of survival, the researchers suspect.
Looking across plant genomes, the team also found two variants of the protein: a long, dominant form and a truncated version that tends to form larger condensates and can recruit the longer version to clump with it. “This second variant fine-tunes the properties of the first one,” Dorone says. “This interplay between two versions of this protein formed by the same gene could have helped plants adapt to different climate conditions.”
“Regulating this protein could potentially have applications in agriculture,” notes cell biologist Danfeng Cai of Johns Hopkins University, who studies phase separation in mammalian cells and was not involved with this study. “You could envision designing crops that respond to different environmental conditions.”
But such applications will require further studies of how a switch in FLOE1’s physical state triggers germination, Dorone and others say. For now, precisely how the protein might cause downstream effects is unclear. The protein might also have additional roles independent of phase separation, especially in its dry, dispersed form in desiccated seeds.
Understanding how plants benefit from the use of intrinsically disordered proteins could shed light on the role of these molecules in other arenas, including human disease, Boeynaems adds. “If we can figure out how other organisms make these sticky proteins work to their advantage, maybe we can make these proteins well behaved in the human brain too.”