Gene discovery suggests that plant breeders may be able to produce nitrogen-fixing crops more easily than previously thought

Scientists at the Sainsbury Laboratory (SL)[1], Norwich, have today reported the discovery of a plant gene that is essential in controlling the interactions between plants and microorganisms that enable them to establish intimate associations, which are of benefit to both partners. Published in the international science journal Nature, the report’s findings suggest that it may be easier than previously imagined to design plants that are able to make their own nitrogen fertiliser.

The roots of many plants are able to form intimate relationships with particular fungi living in the soil. These so-called arbuscular mycorrhizal associations[3] are a symbiosis – a partnership of benefit to both partners. The fungi are very efficient at absorbing nutrients, especially phosphate, from the soil. This is exchanged with the plant in return for plant sugars that are absorbed and used by the fungus.

In addition to mycorrhiza the roots of legume plants (members of the pea and bean family) form an unusual and highly specialized symbiosis with bacteria of the genus Rhizobium[4]. This symbiosis enables the bacteria to take nitrogen gas from the atmosphere and convert it into nitrate and ammonia, which are absorbed and used by the plant. The plants are effectively able to make their own fertilizer as a result of this partnership. In return the bacteria are able to absorb and use sugars produced by the plant.

“Scientists had always imagined that the nitrogen-fixing symbiosis between legumes and rhizobia bacteria was a unique relationship, so the discovery that it actually uses some of the same genes that control the very common mycorrhizal association of plant roots with fungi, is really exciting” said Dr Martin Parniske (Project leader in the SL). “This suggests that evolution of the nitrogen-fixing symbiosis used some of the genes that were controlling the plant-fungal partnerships that are widespread in the plant kingdom. So we now know that part of the genetic blueprint needed to establish a symbiotic relationship with nitrogen-fixing bacteria is present in all major plant types, including important crop species such as wheat and rice. Consequently, relatively few genetic changes might enable breeders to produce a wide range of plants that can establish symbiotic relationships with nitrogen fixing bacteria, and perhaps manufacture their own nitrogen fertiliser.”

The report describes the gene that controls a critical step in establishing a symbiosis, which is also the point at which the genetic blueprints for the two types of symbiosis overlap. Lotus plants, which were unable to form a symbiosis, either with mycorrhiza fungi or with nitrogen-fixing bacteria, because of a gene mutation, were compared with normal plants that could form both kinds of partnership. In the mutant lines the relationships failed in their early stages. Analysis at the DNA level enabled the scientists to find the gene involved, so called ‘SYMRK’ (symbiosis receptor-like kinase)[4]. This gene produces a molecule that is an essential early link in the chain of events that enables the Lotus plant to recognize, and respond to, mycorrhizal fungi and nitrogen-fixing bacteria living in the soil around its roots.

The chemical structure of the SYMRK molecule suggests it may itself be the receptor that recognizes and binds to molecules specifically produced by mycorrhizal fungi and nitrogen-fixing bacteria. More research is required but the researchers think it likely that the SYMRK molecule sits in the outer membrane of the cells of the plant’s roots where it is able to bind to chemicals produced by potential fungal and bacterial partners. The binding process changes the structure of the SYMRK molecule and triggers a cascade of reactions that activate genes involved in establishing a successful symbiosis.

[1] The Sainsbury Laboratory has a worldwide reputation for research on molecular plant-microbe interactions. The major aim of the Laboratory is to pursue the fundamental processes involved in the interactions of plants and their microbial pathogens and symbionts. Funding for the Laboratory is primarily through grants from a charitable foundation. In addition grants are obtained from research councils, the European Union and other organizations. The laboratory is located at the John Innes Centre, Norwich, UK, which is an independent, world-leading research centre in plant and microbial science.

[2] Arbuscular mycorrhiza are associations between roots and specific soil-living fungi, which are commonly found among many higher plants, including major crops. This is an ancient symbiosis (a relationship in which both partners benefit), having been found in fossils of early land plants.

Typically, the hyphae of a mycorrhizal fungus that come into contact with the root surface of a compatible plant, will penetrate the root epidermal cells and enter the root cortical cells. Here a specialised structure within the cell develops that accommodates the invading hypha of the fungal partner and a stable long-term symbiosis is established.

In Lotus plants, with the mutant SYMRK gene, the penetration of the majority of fungal hyphae is arrested in the epidermal cells. The hyphae show strange swellings and deformations indicating that the plant is resisting the fungal invasion. Consequently, a stable symbiosis is not established.

[3] The nitrogen-fixing symbiosis between legumes and Rhizobium bacteria is thought to be a relatively recent evolutionary development. Infected plants develop nodules on their roots that accommodate the bacteria. Root nodules can be thought of as the natural bio-reactors in which the conditions for nitrogen fixation are maintained. In response to the presence of compatible bacteria the root hairs of the legume host start to curl. In these curled regions infection threads form that allow the bacteria to enter the cells of the root hairs, These threads give rise to the root nodules in which the bacteria undergo physical and biological changes that enable them to fix atmospheric nitrogen.

The manufacture of ammonium fertilizer is an energy intensive process while the application of manufactured, and natural, nitrogen fertilizers can have adverse environmental impacts (eg. run-off to ground water). The ability of legumes to fix atmospheric nitrogen is the reason they are included in farm rotations – as a means to return nitrogen to the soil.

Rhizobia bacteria are known to produce so called Nod (nodulating) factors that stimulate the initial root hair curling response that precedes infection and nodulation. In Lotus plants with the mutant SYMRK gene treatment with Nod factors did not induce root hair curling.

[4] SYMRK was isolated by map-based cloning and is located on the bottom arm of Lotus chromosome 2. The gene sequence is 2,769 nucleotides long, coding for a protein of 923 amino acids with a predicted mass of 103,000. The protein consists of a signal peptide, an extracellular domain, a trans-membrane domain and an intracellular protein kinase domain.