A new molecular mechanism reveals how plants keep their cool

How do plants adjust their body plan to cope with high-temperature stress?

When it gets hot, plants cannot stroll into the shade to cool down. Instead, they use thermomorphogenesis, they change their shape to improve their cooling. Martijn van Zanten and colleagues have found how they do this, opening up possibilities for new research. The molecule is called HISTONE DEACETYLASE 9 (HDA9), and new research published in PNAS shows how it signals other hormones to change the plant architecture when it gets too warm. It’s interesting because HDA9 is already known to have some functions in germination, and also it doesn’t seem to be connected to another molecule called PIF4.

Crops under the sun

PIF4 (PHYTOCHROME-INTERACTING FACTOR 4, to give it its full name) is a thermosensor. It helps a plant know how warm it is. PIF4 is connected to light responses in plants. So when you start interfering with how PIF4 works, there’s a risk you’ll also have unintended consequences in how the plant reacts to light and shade. HDA9 responds to heat without connecting to PIF4. At increasing temperatures, the abundance of the enzyme rises, which results in the removal of epigenetic modifications of DNA-bound Histone proteins that have an inhibiting effect on the synthesis of the well-known plant growth hormone auxin. As a result, auxin levels increase and the plant adjusts its stature.

“This new mechanism is scientifically very interesting, because it shows that a Histone Deacetylase 9 has an indirect positive effect on transcription, while Histone Deacetylases are generally accepted as suppressors of this process,” said Van Zanten. 

Quite how HDA9 itself is triggered is a bit of a puzzle van Zanten said. “We don’t know whether or not HDA9 is a direct thermosensor, only we show that HDA9 at least acts independent of the only confirmed thermosensor in plants; Phytochrome B (and so is part of a novel thermosignaling pathway). The intrinsic problem with studies on thermosensors is that in principle every biological molecule has thermosensing capacities by nature, due to passive thermodynamic effects. This makes studies into direct/active thermosensory events very difficult. In addition, HDA9 is an enzyme, so temperature signals are definitely passively mediated by the protein to its substrate. So, the question here is whether that occurs via non-typical temperature kinetics (probably a sensor) or via a normal (passive thermodynamic effects) temperature kinetics (may or may not be a sensor).”

Arabidopsis under IR light.
A thermal image of a plant that is able to keep its leaves cooler than its surroundings through perspiration and airflow. Stretching under high temperature leads to further cooling.

“We conducted some experiments on enzymatic activity of HDA9 at different temperatures, but this did not reveal an unusual ‘Q10 kinetics’ value, meaning that the temperature responsiveness of the enzyme is probably explained by a ‘normal’ passive thermodynamic effect. This however does not exclude the possibility of being a direct thermosensor as activity is only one aspect (protein folding could also be temperature-dependent for instance, to give an example). On the other hand, we observed that HDA9 protein levels stabilize at high temperatures and given the nature of the protein as an enzyme, it is not likely that HDA9 mediates its own stability. So, that would indicate that an upstream regulator of HDA9 is required and that regulator can be (part of) the thermosensory event. HDA9 is prone to proteasomal degradation, so we suspect that an upstream thermosensing effect could be a factor in the proteasome degrading HDA9 under control conditions, but stabilizes HDA9 at high temperatures.”

This isn’t the first time van Zanten has studied HDA9. He had earlier looked at its role in germination. It was plants from this earlier research that unexpectedly led to the new findings said van Zanten. “I started testing the mutants that I brought from my old institute and found the role of HDA9 in thermomorphogenesis in fact by coincidence. Later a group in Australia (one of the coauthors on my current paper) found a role for the factor Powerdress (PWR) in temperature signalling and that factor by then was just found to interact with HDA9 by others, and the data we collected at that point independently fitted entirely.”

“In the current paper in PNAS we elucidate the underlying mechanisms. We never tested the role of HDA9 in temperature-dependent germination (we should actually…), but we do know HDA9 has a role in seedling establishment and starting-up the vegetative program of the plants and switching off the embryonic program after germination. This matches our current conclusion that HDA9 is important for thermosensing in the early life of the plant (seedling). So, there is a spatial/temporal relation between HDA9’s role in seed biology and seedling establishment and thermomorphogenesis that we are currently following up on, by testing whether known HDA9 target genes in seeds also have a role in temperature acclimation.”

In his Nature Plants review, van Zanten notes that much plant temperature work has been between 20-29 °C. While this is a window that is important for agriculture, van Zanten thinks there may be more to find in how HDA9 reacts with physiology outside this range. “We only tested the role HDA9 in the ‘thermomorphogenesis’ range (20-29 °C), but I wouldn’t be surprised if it would also affect responses to heat or cold stress. Do note however, that we consider ‘thermomorphogenesis’ an physiological acclimation response (‘to live optimally under non optimal conditions’); i.e. no typical stress signalling is involved that is required for tolerance (to live or die), like ROS accumulation or induction cellular protection mechanisms, that are induced in cold and heat stress.”

“From a more historical perspective, the cold signalling and heat signalling fields are different communities and later the thermomorphogenesis community came in between, that has its roots in photobiology. We now start to realize that actually some of the key factors involved in cold signalling also have a role in thermomorphogenesis and likely vice versa the same is true. The problem with temperature experiments is that each ‘temperature’ studied requires a growth room set at that temperature, greatly complicating studies on temperature gradients in a controlled manner. We now developed a thermogradient table in which we can provide different temperatures from 5°C-40°C on the same time, with the aim to actually check whether temperature signalling is a continuum, involving the same factors, or that each temperature range depends on ‘its own’ genetic program. So, I hope I can provide a more conclusive answer in a few years from now.”

While crops may be better adapted with thermomorphogenesis, van Zanten says there are some trade-offs, with water use. But there could also be other benefits. “Water use will increase when plants transpire more, so yes thermomorphogenesis is typically also increasing water use, and this is not always wanted. However, in many cases the applied goal is not to make plants elongate, but retain them compact (think of ornamental plants). We can also apply the information on HDA9 there. Moreover, if plants are adapted optimally to a certain temperature, the benefits could lie in less requirement for heating or cooling the greenhouses; so saving energy.”

The key finding is that because HDA9 is independent of PIF4, it is now possible to pull apart light and heat response in plants. “Shade avoidance and thermomorphogenesis are phenotypically similar and most -if not all- genetic factors currently associated with thermomorphogenesis have a role in shade avoidance as well,” van Zanten said. “With HDA9 at hand, we can now separate the pathways and this may be of use to steer temperature responsiveness independent of light responses. Also, in the green revolution, selection of field crops was among other traits against shade avoidance (to allow dense stands in the field, with compact high yielding plants) and this has occurred at the expense of temperature sensitivity as well. Using HDA9 signalling, we can now start working on bringing back/tuning temperature responsiveness and light responsiveness to the need.”

As a result the research offers new targets for plant breeding to improve the climate-tolerance of crops. Given that currently each degree Celsius temperature increase can lead to up to 10 percent crop loss, this could be an important aid in feeding people in the future.