Genomics and Epigenomics of Plant-Plant and Plant-Environment Interactions

Plants rarely grow as solitary individuals but instead as a community of organisms. This can be a natural ecosystem with a diverse mixture of plant species, or an agricultural monoculture composed of many genetically similar individuals. Independent of the habitat, every plant strives to secure optimal access to resources by outcompeting others in direct proximity. During evolution, plants have developed diverse strategies to gain advantage over their neighbors. To secure access to light for example, bamboo grows faster than any other plant, while trees instead play the long game and grow slow but tall, eventually towering over the surrounding species.

Some plant species employ a quite different strategy: they engage in chemical warfare by producing chemical compounds that they release into the soil. Some species directly release these substances from their roots, while others store them in the above-ground tissues and release them when the leaves fall to ground and decompose. In either case, these compounds enter the roots of nearby plants and interfere with molecular and cellular processes to prevent growth or development, leaving the ‘donor’ plant with a competitive advantage.

This process of chemical interference between organisms is called “allelopathy” and has been known to farmers and gardeners for centuries. Many species that use allelopathy to suppress their neighbors have been identified; they range from trees (e.g. walnut) to shrubs and grasses, and include many of today’s major crops, e.g. wheat, rye, and maize. Even though many of the chemicals involved (“allelochemicals”) have been identified, it remains unclear how most of them act in the plant and why these chemicals are toxic to some plants and not to others.

Fig. 1 Model of aminophenoxazinone activity. Adapted from Venturelli et al., Plant Sig Behav 2016.

Our laboratory studies allelochemicals that are produced in horticultural and agricultural crops. Upon release from the roots, some of them, such as benzoxazinones, are only mildly toxic but are quickly converted to more toxic compounds in soil (Fig. 1). We recently found that once these degradation products enter the cells of plants, they bind to and inhibit the activity of a particular class of enzymes called histone deacetylases (HDA). The role of HDAs is to remove acetyl groups from proteins, particularly from histones. Histones contribute to the organization of the DNA in the nucleus, and the addition and removal of acetyl groups regulates the level of compaction of this DNA-protein complex (also known as chromatin). HDAs thus ultimately contribute to regulating the “openness” of DNA and consequently the accessibility of the genes in a certain region of the genome (Fig. 1). We were able to show that by inhibiting HDA activity, aminophenoxazinones change the overall organization of the chromatin and thereby interfere with basic cellular functions.

Currently, our group is working on solving the enzymatic specificity of aminophenoxazinones and the mechanisms of allelochemicals from other plant species, including those of barley and rice. To this end, we analyse global changes over time at the protein and gene expression levels, coupled with biochemical assays using purified proteins. To determine the potency of allelochemicals, we use the model plant Arabidopsis thaliana as a readout. For example, aminophenoxazinones inhibit root growth of this species in a dose-dependent manner (Fig. 2).

Fig. 2 Arabidopsis thaliana seedlings show a concentration-dependent inhibition of root growth when exposed to the allelochemical APO. Scale bar = 10 mm; adapted from Venturelli et al., Plant Sig Behav 2016.
Fig. 3 Different lines of Arabidopsis thaliana show different behavior in response to allelochemicals.

We also use A. thaliana for another approach in which we want to identify genes that allow some plants to tolerate allelochemicals. More specifically, we make use of the vast genetic diversity that exists in this species: the GMI is home to a vast collection of more than 1,100 A. thaliana plants that were collected from across the Northern Hemisphere (1001genomes.org) and whose genomes have been fully sequenced. We have screened approximately half of this collection and have identified a dozen genotypes that are resistant to aminophenoxazinones (Fig. 3). Using statistical analysis, we are searching for associations between specific genetic variants and increased resistance to the allelochemical to identify genes that are responsible for the resistance.

Our analyses are not limited to the plants involved in allelopathy: because the soil space surrounding plant roots is populated by thousands of bacterial and fungal species, some of which are tightly associated with the plant, we furthermore ask if and to what extent the presence of allelochemicals affects – negatively or positively – the microbial community, and how microbes in turn might contribute to the chemical dynamics in soil (Fig. 4). Using high-throughput, automated culture handling, we are screening approximately 200 bacterial strains, individually as well as in different combinations, for resistance to different allelochemicals (Fig. 5). Our goal is to identify bacteria that are able to metabolize and chemically convert the compounds, and that might play a role in detoxifying them in soil.

Fig. 4 In allelopathy, the donor plant releases secondary metabolites (red) into the soil. In “true” allelopathy (A), these metabolites act as toxic allelochemicals and inhibit the growth of neighboring plants. In contrast, “functional” allelopathy (B) requires microorganisms in the soil that convert non-toxic or mildly toxic metabolites into potent allelochemicals (blue). Conversely, allelochemicals can potentially influence the growth and proliferation of soil-dwelling microorganisms, thus generating a complex inter-dependence between plants, bacteria, and fungi.
Fig. 5 The phylogeny represents the relationship of 200 bacterial strains known to live on and around the roots of the model plant Arabidopsis thaliana; each point in the outer circle represents one strain.

Altogether, our research aims at resolving, at a molecular and genetic level, the intricate relationship between plants that grow in close proximity to each other. We hope that our work will contribute to a better understanding of the dynamics of natural ecosystems and agricultural plant communities, and that it will prepare the ground for the development of sustainable plant protection strategies.