Prof. Edward (Ted) Farmer

Plants underpin the major life processes in our biosphere. Much of our research uses the techniques of molecular biology, biochemistry and genetics to understand how organisms in the second trophic level (herbivores) try to sequester the carbon in plant tissues. The research has shown that a signal transduction pathway, the jasmonate pathway, intervenes to control carbon flow to this higher trophic level. The plant immune system provides direct protection against invaders and can also attract bodyguards in the form of predatory insects. Both these facets of the defense response ('direct' and 'indirect' defense) are controlled exquistitely by lipid signals: jasmonates. 

Our contribution to the field was to show that enzyme-controlled fatty acid oxidation leading to jasmonate production and signalling underlies much of the response to herbivory and wounding. We have also helped to define the structure of the JA biosynthesis pathway by discovering a hexadecanoid branch and we have worked on jasmonate signaling itself where we co-discovered JAZ proteins. We explored how jasmonates may control growth processes related to defense and provided evidence that attack not only slows growth but alters the architecture of new leaves thus improving their defense capacity against non-specialised attackers. We have offered a possible explanation for the evolutionary origin of the JA pathway and have tried to extend our knowledge of its large-scale role in nature. We have also worked on a variety of other oxylipins (oxygenated fatty acids) in plants.

Most recently we have established that JA synthesis in plants is extremely rapid (Glauser et al., 2008; 2009). We were then able to estimate the speed of the long distance signal travelling from wounded to unwounded leaves. The signal speed (conservative estimate) is 3.4 to 4.5 cm per min. Our finding of the fast jasmonate accumulation near the wound site and in distal tissues has opened up new possibilities to investigate the activation of JA synthesis and to study long-distance signalling itself. This new work is supported by SystemsX.ch (the Swiss systems biology programme) and the National Science Foundation and is now involves a collaborative effort with two leading physics laboratories (Prof. M. Chergui and Prof. T. Lasser, both at the EPFL Lausanne) to develop new non-invasive optical tools with which to image wound responses in real time.

The laboratory has a second line of research in an area of general biology : the genetics of nonenzymatic oxidation. A longterm effort to use genetics to investigate the potential biological importance of nonenzymatic oxidation in our lab has shown that the excess oxidation of alpha-linolenic acid is harmful to plants. This is not surprising and fits in well with the dogma that non-enzymatic oxidation and its products are damaging. But things may be very different when this fatty acid is oxidised slowly under more physiological conditions. Based on evidence, we have recently proposed that the slow nonenzymatic oxidation of highly unsaturated fatty acids may actually benefit organisms by providing a sink for reactive oxygen species (ROS). That is, some common omega-3 fatty acids might act as a new class of antioxidants. We focus on malondialdehyde (MDA) as a marker for fatty acid oxidation and have also investigated its potential biological activity as a cell survival signal.
 

Remorin: a new family of proteins

Discovered the remorin group of proteins. 'Remorins may be associated with the cytoskeleton or membrane skeleton i.e., in superstructures that help determine cell integrity and/or act as scaffolds for signaling in defense or development' (Plant Mol. Biol. 55, 579).

Antioxidant mechanisms

Antioxidants (such as tocopherols) and ROS-metabolising enzymes (such as catalase and SOD) are well established as controlling the overoxidation of cellular consituents. We propose a new and still hypothetical mechanism whereby polyunsaturated fatty acids are used as 'ROS sinks' to literally soak up ROS (J. Biol. Chem. 2009, 284, 1702).

Reactive Electrophile Species.

Proposed that 'reactive electrophile species' (RES) could play roles in abiotic stress responses and in the 'abiotic component' of biotic attack in plants (Plant J. 24, 467; Nature 411, 854). Developed a model for their beneficial and harmful actions in cells (Curr. Opin Plant Biol. 10, 380).

Demonstrated the origin and powerful biological activity in the ubiquitous and highly studied lipid peroxidation marker malondialdehyde (MDA) (Plant J. 37, 877) and shown that linolenic acid is the major source of damaging reactive molecules produced by non-enzymatic oxidation in plants (J. Biol. Chem. 202, 35749).

Developed a whole-body malodialdehyde mapping technique for the in situ visualization of MDA in complex organisms (J. Biol. Chem. 2007, 202, 35749).

Jasmonates

Proposed (with C.A. Ryan) a central role of jasmonates in the plant immune system (PNAS 87, 7713; Plant Cell 4, 129).

Co-discovered (in parallel with the goups of J. Browse and R. Solano) members of the 'JAZ' family of repressor proteins and shown that a natural transcript from JAS1/JAZ10 plays a role in wound-induced growth inhbition. Also descibed the 'JAS' motif as a functional element in this protein (Plant Cell 19, 2470).

Discovered a new jasmonate (dnOPDA) and revealed a novel 'hexadecanoid' branch of the jasmonate biosynthetic pathway (PNAS 94, 10473).

We proposed that rather than jasmonates moving through tissues to stimulate gene expression distal to wounds a very different mobile signal is involved (J. Biol. Chem. 284, 34506). We made the first constrained (minimum and maximum) velocity estimates for the speed of the long distance signal: 3.4 to 4.5 cm per min. These estimates are conservative (Glauser et al., 2009).

Shown that strong resistance to an insect and a pathogen can occur in the absence of wild-type jasmonic acid levels implying that another jasmonate is a key signal in vivo; cyclopentenone jasmonates (OPDA & dnOPDA) are candidates (PNAS 98, 12837).

Proposed an integrative model for ethylene, salicylate and jasmonate action (Curr. Opin Plant Biol. 1, 404).

Quantitated (using microarrays and statistical analysis) the number of chewing insect-inducible genes that are regulated throught the jasmonate signal pathway (an estimated 67-84%) (Plant Cell 16, 3132) and shown that a specialist and a generalist insect activate this pathway almost equally.

Isolated and characterized the 'fou2' mutant that now implicates cation flux (possibly K⁺ or Ca²⁺) in the control over jasmonate biosynthesis (Plant J. 49, 889; Plant Cell Physiol. 2007, 48, 1775). Another mutant we isolated recently (fou8) suggests that phosphoadenosine phosphosulphate (PAPS) helps control JA levels in resting leaves.

Jasmonates: Achille's Heels in the plant defense system

It is conventional to use co-evolved herbivore-plant combinations to study plant defenses. We starved isopod crustaceans that have never evolved to be herbivores and let them lose on Arabidopsis and rice. The isopods identified and attacked weak spots in the plants, cutting tissues to essentially convert the living into the dead. Perhaps the jasmonate pathway first evolved to stop ancient detritivores becoming herbivores (PNAS 2009, 106, 935).

Why do herbivores often cut round holes in leaves?

Now and again some of the things one finds changes the way one looks at nature. Herbivores often cut highly regular circles and semi-circles of leaf tissue. Birds often use the light coming through these holes to help them find caterpillars. In part the fact that insects often cut clean circles in leaves can be explained because it is simple and 'mechanically economic' (the insect doesn't have to move much) to do this. But there is more to the story. In carefully analysing microarray data we saw that some herbivores probably try to extract the maximum area of leaf tissue while leaving the minimal length of cut edge, so as to minimise stimulating plant defenses Plant Cell 12, 707). Insects understand calculus.

Missing phytoalexins from potato

Good candidates for low molecular mass antibiotics (phytoalexins) from the leaves of the historically and commercially important plant potato were unknown. They turned out to be relatively unstable molecules that had been described in vitro but that had previously escaped detection in living organisms. We identified divinyl ether fatty acids for the first time in nature in these leaves and proposed a role as antimicrobial compounds (Plant Cell 11, 485). They are still the best candidates for the long-lost phytoalexins in potato leaves, the primary infection site for potato blight.

Community resources

Our laboratory has strongly supported the development of central, shared community resources in molecular biolgy and played a role in the establishment of the Lausanne DNA Array Facility.

Outreach

EEF participates actively in the current debate about GMOs.