Oxygen is foundational for much of life, but relying on it means coping with fluctuating oxygen levels. New research has revealed that a molecular pathway that is involved in plants’ response to low oxygen is essential and independently self-sufficient – and feedback loops are an important factor in the strength of the response.
Plants face hypoxic (low oxygen) conditions either chronically within their tissues or acutely when flooded. Plants deal with this via transcription factors – proteins that control whether genes are turned on or off. Specifically, they use transcription factors called Ethylene Response Factors VII (ERFs); when oxygen is present, enzymes called plant cysteine oxidases (PCOs) bind the oxygen to ERFs. This turns off the ERFs so that they can’t induce genes related to switching from aerobic (oxygen-reliant) to anaerobic (not oxygen-reliant) respiration. However, this relatively simple mechanism interacts with other signalling cues and pathways in plants that are also prompted by hypoxia.
The researchers wanted to understand how much this mechanism is responsible for plants’ overall response to hypoxia. To do this, they isolated it from the other interactions taking place in plants by taking the mechanism from a plant and using it to engineer a ‘plantified’ yeast strain. They then monitored the speed and amplitude of response to hypoxia.
Dr Mikel Lavilla Puerta says:
“By looking at the ERF circuit in yeast, we were able to uncover how effective it is in responding to hypoxia independently of the many extra processes that affect gene regulation in plant cells. This is a unique way of teasing apart the different strands that form the overall response.”
They discovered that hypoxia triggered the ERF function in both the plant and yeast quickly – in just five minutes – but the initial similarity did not continue over time: while the response continued for two hours in plants, it stabilised within only a few minutes in yeast. This led to a huge difference in the overall level of response. In yeast, there was 2.5 times more gene expression from start to end, while in plants there was 200 times more.
The results indicate that the ERFs can trigger an initial reaction, but they can’t achieve the best outcome on their own. However, by prompting a feedback loop in the yeast, the researchers then managed to improve the result to 40 times more gene expression at the end – demonstrating that feedback is critical to a prolonged and effective response. This is a significant impact for just one circuit, though there are clearly still other factors at play in plants.
Professor Antonis Papachristodoulou (Department of Engineering Science) says:
“Our study unveiled the secret of timely responses to hypoxia in plant cells, combining mathematical modelling with experimental work. Among the many molecular components that operate on this pathway, our results indicate that the PCO enzymes that control ERFs’ stability are key. Modifying their activity and abundance would allow us to adjust the activation of responses to hypoxia according to the needs dictated by crop species and farming conditions.”
Professor Francesco Licausi says:
“This is the first time we have applied the ‘build to understand’ approach of synthetic biology to plant hypoxic research. The success of transferring signalling pathways from plants to yeast shows us that stripping a molecular circuit to its essential components can uncover important information on their operation and contribution to the overall plant response to hypoxia.”
As for next steps, there are two ways to go: yeast or plants. For yeast, the researchers can now insert oxygen-dependent genetic circuits and carefully control them, for example for metabolic engineering or bioproduction – increasing cells’ production of certain substances. For plants, this study suggests that the best and easiest way to make plants respond faster to hypoxia is by improving these specific types of PCOs that are induced by low oxygen, by making them either more ERF- or oxygen-sensitive. While they don’t have as large an effect overall, these PCOs are critical in securing a smooth transition from aerobic to anaerobic conditions. The first minutes of hypoxia are essential in how plants respond to this stress, so by making them respond faster we can improve their chances at surviving floods.
To read more about this research, published in PNAS, visit: https://www.pnas.org/doi/10.1073/pnas.2524358123
