A biological rationale for NMD in plants

Animals, fungi and plants split a long time ago and have evolved very different life strategies. Nevertheless, clues to their common origin can be found in the form of conserved processes carried out using many of the same components in all eukaryotes. Gene expression is one such process and the ability to turn genes on and off, up and down is fundamental to life. There are many ways to regulate gene activity. One of the least studied involves regulating the stability of molecules known as mRNA; the messenger signals that move from the genes in the nucleus to where the proteins are made in the cytoplasm. Recently, it has been discovered that a mechanism called NMD, that used to be considered as a sort of quality control sift for mRNA, destroying 'bad' mRNA before it ordered the production of the wrong proteins, actually oversees lots of different mRNAs, including many that appear to be normal. A working estimate of the total number of genes that could typically be inspected by NMD could be as many as 5% - perhaps 1500 genes. Why would a cell go to the expense of copying lots of genes into mRNA only to quickly destroy the mRNA again before its instructions could be acted upon? We have been looking at mutant plants where NMD is not working properly, both by studying the consequences for the plant as a whole and by looking at the effect on all of the plant's mRNA levels. These analyses have identified a potential biological rationale for what appears to be an energetically wasteful arrangement. Our work indicates that plants use NMD to suppress the levels of mRNAs that they will need quickly if they find themselves exposed to an environmental challenge, such as a change in the climate of a pathogen attack. This makes sense because by stopping NMD from destroying specific mRNA the plant can make those mRNAs stable, so that they can be translated many times over to make the necessary proteins to deal with the challenge the plant faces. Presently we have a list of both indirect and direct NMD targets in the plant cell. To dissect the interaction between the environment and co-ordinated gene regulation via mRNA stability we first need to identify both the direct targets and which of the conserved components are required to specify which target. At that point we can make artificial targets so that we can study how the environment signals to NMD and we can tease out the full range of responses mediated by this ancient process. This research could have applied benefits in terms of understanding plant interactions with pathogens and the environment and also by providing the tools to artificially conditionally regulate the stability and hence translatability of mRNA messages.

NMD is an evolutionarily conserved process, used by all eukaryotes to selectively target particular mRNA transcripts for destruction. It has been known for some time that this process helps the cell to survive the potentially damaging effects of repeatedly translating an aberrant mRNA to generate truncated or incorrect proteins. Over the last few years it has become recognised that NMD also targets many apparently normal mRNAs, that it can be regulated and that it comprises several overlapping subsets with respect to the components required. This raises the possibility the cells make and rapidly degrade specific mRNAs for a reason and that under certain circumstances the stability of particular mRNAs can be changed by NMD. Increasing the halflife of NMD-targeted mRNAs will result in an increase in steady state and multiple rounds of translation, making this an effective and rapid means to modulate gene expression. Despite its mechanistic conservation through evolution, common targets of NMD are rare at the level of individual genes and are rather confined to processes. Overall, a compelling biological rationale for what appears to be an energetically wasteful mode of gene regulation is lacking. We believe that we have such a rationale for NMD in plants, where our molecular genetic background work leads us to hypothesise that NMD helps plants respond to biotic and abiotic challenges. To test this and to investigate the potential to use this discovery as a tool to manipulate plant response to stimuli, we need to answer three questions, each addressed by a specific objective: What are the target transcripts on which NMD acts directly? Are the direct targets differentially regulated by NMD in response to distinct environmental conditions, are distinct subsets of NMD used and are distinct signals in the mRNA associated with particular subsets. What is the full range of downstream pathways under NMD control?

NMD is a process that selectively targets specific physiological mRNAs for destruction in the cell, thereby supressing the expression of a wide range of genes in the genome. Work from our group, relying on extensive background research funded by the BBSRC, has shown that the set of NMD regulated genes in plants largely coincides with genes induced on pathogen infection. This suggests that NMD acts to coordinate the host response to pathogens by suppressing response gene transcripts until they are required. Genetic analysis of NMD mutants indicates that NMD could be part of a wider host response network. In this project we propose to explore the potential for manipulating this novel form of gene regulation to enable plants to deal more effectively with biotic and abiotic environmental challenges. Understanding and utilising this mechanism would provide a means for mitigating the effects of changing environmental conditions on crop plants and thereby enhancing food security. Four primary potential outcomes are envisaged that could form the basis for future exploitation of this work: understanding the host pathogen response to allow improved resistance, exploring the links and interactions between multiple challenges, clarifying a high level regulation of amino acid metabolism to improve future resource utilisation and defining the requirements for conditionally stable and unstable transcripts as a means of gene regulation. Impact will be delivered according to the attached impact plan, largely in the following ways: Engagement with the wider scientific establishment through publications, online resources and presentations at meeting and seminars. Engagement with the plant pathogen field in the same way, facilitated by our collaboration with the Grant laboratory. Interaction, translation and dissemination to those concerned with crop security in the developing world by our formal, established links in China, India and Africa. Interaction with industry and commercialisation of our research through the action of our dedicated office of Enterprise and Innovation. Engagement with the wider public through a range of individual activities in schools, higher education and popular science initiatives and also via the specific activities of a dedicated publicity company, CampusPR. Training of several PhD students for future employment in academic and commercial environments. Continuing and broadening the training of the appointed fellow, Dr. Rayson, to equip her with a range of skills to ready her for independent research.