How does PAP, a stress-induced metabolite, regulate gene expression?

Plants are commonly exposed to environmental fluctuations (such as high light or insufficient water) which are sufficient to limit crop yield in both field-grown and glasshouse-grown contexts. Damage induced by such stresses is typically first observed within the chloroplast and mitochondria, where perturbations in metabolism rapidly induce oxidative stress. These perturbations are communicated from organelles to the nucleus via multiple retrograde signaling pathways that alter nuclear gene expression, allowing plants to adjust their metabolism and development to tolerate environmental stress. However, the extent to which retrograde signals can regulate plant homeostasis, and by what mechanism(s), remain enigmatic.

Many abiotic and biotic are predominantly associated with specific times of day, driving the evolution of biological timing mechanisms that enable anticipation of biotic and abiotic stresses associated with either day or night. These biological timers (commonly referred to as the circadian system) have subsequently been co-opted to modulate many physiological processes including growth, photosynthesis, and flowering time. In addition to providing an endogenous timing reference, seasonal changes in daylength require that the circadian system is synchronized with environmental factors such as dusk and dawn. This induces a complex interplay between environmental signals, endogenous biological timers, and metabolic changes induced by sub-optimal environmental conditions. If we are to fully exploit the potential yield of crops it is vital that we understand how plants interact with their environment during daily environmental fluctuations.

Recently, it has been suggested that the circadian system acts as a metabolic governor (as found on steam engines), slowing metabolism and consequently improving survival during periods of stress. In agreement with this concept we have demonstrated that application of osmotic stress slows the circadian system. This results in repression of genes normally expressed during the evening. We have demonstrated that a signaling metabolite that accumulates in response to osmotic stress is sufficient to induce a comparable delay in the circadian system. Such data demonstrates how changes in metabolism arising from the application of stress can induce changes in gene expression, ultimately altering plant behavior.

The circadian system induces rhythmic expression of approximately one third of a plants genome but we do not have a precise understanding of how changes in metabolism alter the pace of the endogenous biological timer. Importantly, circadian timing components originally identified in the experimental workhorse Arabidopsis thaliana have been found to be conserved throughout the plant kingdom, with naturally-occurring alleles of known clock components being historically introduced into commercially grown varieties of barley and tomato. This study will take advantage of the genetic resources available in Arabidopsis. This will allow for rapid progress before our understanding is transferred into crops such as barley and wheat. Such work will advance our understanding of plants responses to osmotic stress and directly inform BBSRC's priorities to design crops with greater drought resilience that make more efficient use of available water resources.

Drought confers a multifaceted stress upon plants, but one of the first metabolic consequences is the perturbation of photosynthesis, leading to increased accumulation of ROS and the subsequent development of redox stress within the chloroplast. 3'-PhosphoAdenosine 5'-Phosphate (PAP) is a redox stress-induced metabolite that accumulates in response to drought and osmotic stress. The accumulation of PAP inhibits the activity of exoribonucleases (XRNs), leading to the accumulation of microRNAs (miRNAs). The PAP/XRN pathway is therefore able to induce changes in nuclear transcript stability in response to redox stress in the chloroplast.

Daily fluctuations in light and temperature have driven the evolution of the circadian system, a pervasive endogenous timing mechanism that coordinates gene expression and metabolism with prevailing environmental conditions. Recently, it has been proposed that the circadian system acts as a metabolic governor to slow plant metabolism during sub-optimal growth conditions, although it is not apparent how metabolic changes alter circadian timing.

This proposal will examine how the accumulation of PAP (arising from redox stress within the chloroplast) alters daily patterns of gene expression, and subsequently plant behaviour. We have shown that the accumulation of PAP represses expression of genes during the evening. In this proposal we seek to understand how stress-induced changes in metabolism alter nuclear gene expression. This will improve our understanding of how plants respond to environmental change and facilitate the development of stress-resistant crops in the future.

Agriculture and horticulture currently use over 50% of drinkable water and these demands will only rise as irrigation increases due to greater variability of rainfall during the growing season. In response to this, a key challenge for both agriculture and horticulture is maintaining crop yield and quality whilst reducing inputs such as irrigation. The work outlined in this proposal will address this by improving understanding of how plants respond to osmotic stress so that we can optimize crop yield.

INDUSTRIAL AND AGRONOMIC BENEFITS
This project will further define how plants respond to water deficit, enabling the optimization of irrigation schemes and informing the design of drought-tolerant crops. Beneficiaries will include agronomists and horticulturalists with an interest in improving commercially grown crops, as well as industry researchers. Our established partners, such as KWS UK Ltd (a company developing innovative seed stocks to serve farmers) will benefit from the application of our research to maintain crop yield whilst reducing water use. Their stakeholders - merchants, farmers, processors and end-user customers will also benefit from these improved varieties. Likewise, Gee Vee Enterprises, with whom we are currently collaborating to improve pepper fruit quality, will benefit from application of our findings which will assist their aims of growing high quality peppers at the lowest possible input cost whilst reducing environmental impact.

We are members of AgriTech East and the AgriFood Charities Partnership and attend relevant industry-facing events organized by the Agriculture and Horticulture Development Board (AHDB) to publicise our work and understand the challenges facing industry. We shall continue these engagements during the project to create new partnerships with industry. Once we have gathered our experimental data we will work closely with the Research and Enterprise Office at the University of Essex to patent and exploit commercialization opportunities.

OUTREACH IMPACT
Our work will also contribute towards developing the next generation of plant scientists. We will use this project to illustrate the wider applications of understanding how organisms perceive environmental change, and the benefits of altering drought-responsive pathways in crops. We will work with local schools (including Colchester County High School for Girls, Colchester Sixth Form College, Belfairs Academy, Maltings Academy) to enhance students' immediate education by supplementing the curriculum- for example we have recently presented seminar series at these schools discussing our work in relation to the control of gene expression, a central part of the A-level curriculum. These efforts will re-iterate the importance of plant biology to students and encourage them to complete plant biology-related courses at university, as well as ultimately pursuing careers in plant science.

We will also allow the interested public to engage with our research (via general science events such as Café Scientifique) and plant-themed events such as Fascination of Plants day (held in conjunction with Beth Chatto Gardens). This will improve the public perception of plant biology and enhance public understanding of transgenic crops.