How plants quickly adapt to shifting environmental conditions: Salk scientists find that canopy shade from competing plants triggers cellular changes in as little as five minutes

Scientists and gardeners have known for a long time that plants flower faster and grow taller when they are shaded from their neighbors. Researchers at the Salk Institute have now revealed the inner workings of this process for the first-time.Nature Genetics published the study on June 17th, 2021. It provides new insight into how gene activity affects plant growth and how fast plants react to changing light conditions. This can trigger molecular changes in just five minutes. These findings offer insight into how to increase food production and protect the environment from climate change."This paper shows in high resolution how plants react to subtle environmental changes at the cellular level," said Joanne Chory (co-corresponding author), director of Salk’s Plant Molecular and Cellular Biology Laboratory and Howard Hughes Medical Institute investigator and holder the Howard H. and Maryam R. Newman chair in Plant Biology. As climate change continues to intensify, it will be crucial that we discover how plants adapt to increased environmental stressors.Shaded plants grow taller and faster to reach greater light. In order to compete with other plants, they also flower earlier and produce more seeds in shaded conditions. While these responses may be beneficial for wildflowers in a meadow setting, they can also reduce the production of plants on farms and produce low-quality, bitter crops. Any gardener who has seen lettuce bolting knows this.Researchers examined the role of transcription factors in activating the growth response in the new study. Transcription factors, proteins that bind to DNA and turn genes on/off, are proteins that regulate gene expression.The team used mutant seedlings that were deficient in transcription factors, called PIFs (PHYTOCHROME INTERACTING FACTORS). The team grew the plants in simulated shade and found that they did not grow faster or longer than normal. The Chory lab previously demonstrated that PIF7 is the most important factor in controlling shade-induced growth.AdvertisementThe researchers looked at the role of histones, specifically H2A.Z. Histones, proteins that act as spools for DNA strands, are called proteins. Histones can be used to activate or suppress specific genes by being modified or exchanged.Scientists discovered that canopy shade caused the release of H2A.Z from growth-regulating genes via the DNA binding of PIF7. This in turn activated their expression.Researchers used very short time intervals to conduct their experiments and found that PIF7 activates, binds its target gene, and initiates H2A.Z removal within 5 minutes of plants being under canopy shade."Our study is another step in a mechanistic understanding how plants alter gene expression in response a changing environment," said Joseph Ecker, co-corresponding author and investigator at Howard Hughes Medical Institute. He's also a professor in Salk’s Genomic Analysis Laboratory.Previous studies had shown that H2A.Z and PIFs were important in plants' responses to high temperatures. However, timing was unknown, says co-author Bjrn Wilige, a Howard Hughes Medical Institute researcher in the Chory laboratory."Our study provides a detailed look at the mechanism and demonstrates the speed of the response. PIF7 binds with DNA when it is active. Our data show that this results in the removal of H2A.Z. Willige says that genes are then activated and this in turn induces growth to outcompete neighboring plants."Mark Zander, assistant professor at Rutgers University's Waksman Institute of Microbiology, said that the speed of the process was surprising. He observed that the histone landscape recovered quickly after being shaded, and the stress response was triggered within five minutes.He says, "When we removed the shade, the levels H2A.Z at PIF7 targets genes returned to normal in 30 minutes." "I was amazed at how dynamic the process was, which is the foundation of the elegance of our research."The growth, development, and protection of plants are all affected by PIFs. The team hopes to translate their findings to other important plant responses for farmers, particularly in relation to making plants more resilient to climate changes. Harnessing Plants Initiative at the Salk Institute aims to solve climate change by optimising plants' natural ability of storing and capturing carbon.