Imitating to understand: a synthetic biology approach to studying oxygen sensing

Creating a novel oxygen sensing system for plants will help us to identify the features needed to enable effective oxygen homeostasis in multicellular organisms. Francesco Licausi explains how his research is helping shed new light on this for the Trinity Term 2021 Alumni Newsletter.

 Approximately one fifth of the Earth’s atmosphere is made up of oxygen. This is the result of billions of years of photosynthesis, a light-driven biochemical process where oxygen is released from water as a by-product. While nowadays oxygen is essential for most organisms, at the dawn of life it posed a serious threat, because several intermediates of oxygen metabolism can damage biological macromolecules such as DNA, proteins and lipids. Therefore, ancestral cells resorted to oxygen avoidance or detoxification strategies until the advent of oxidative phosphorylation, a biochemical mechanism that exploited oxygen for energy production.

As a consequence of this, aerobic organisms need to sense oxygen availability and adjust their metabolism accordingly. So far, numerous research initiatives have unveiled distinct molecular mechanisms adopted by prokaryotes and eukaryotes to perform this task. Remarkably, animals and plants, which represent the apex of evolutionary complexity, rely on very similar oxygen sensing strategies. These are based on the constant production and degradation of signalling proteins. Degradation is promoted under aerobic conditions since oxygen is required by specific enzymes to label them for destruction by the cell machinery. Conversely, low oxygen conditions lead to the stabilisation and consequent accumulation of these signalling proteins, which control the hypoxic adaptive response. However, while the overall mechanism is comparable, the biochemical factors involved differ between animals and plants.

Current models for oxygen signalling pathways have been deduced from experiments that addressed one feature of the system at a time in their original biological context. These studies led to the award of the Nobel Prize in Physiology or Medicine in 2019 for the discovery of the HIF system in animal cells. However, the full range of functions that oxygen signalling pathways have assumed in plants and animals is still unknown, and their manipulation for therapeutic and agricultural purposes requires additional investigation. Although mathematical models have been generated to predict the outcome of chemical or genetic interference of pathway components, the gap in our knowledge prevents us from precisely predicting the outcome of interfering with the oxygen-sensing pathway. The field is now ready for a step change in the experimental study of oxygen sensing systems by considering all their components together. The synthetic biology framework is perfectly suited for this task.

With the ERC-funded SynOxyS project, we aim to engineer new solutions inspired by metazoans for oxygen signalling and transport to control hypoxia homeostasis in plants. We will generate genetic circuits made from animal, bacterial, fungal and plant components. The molecular components will undergo rational design and directed evolution before being assembled into sensing systems which will reveal the mechanisms that operate oxygen sensing in higher plants and metazoans to an unprecedented level of detail. This information is essential to safely manipulate these systems for therapeutic and farming applications. It can be applied to address fundamental questions about oxygen perception and its contribution to plant development, as well as to drive adaptive responses to ambient oxygen limitation, such as flooding, and thus improve plant fitness under submergence. Moreover, successful completion of the planned activities will also serve to demonstrate feasibility and advantages of this novel strategy for the study of other signalling mechanisms.