Prof. Edward (Ted) Farmer

Plants underpin the major life processes in our biosphere. Our research is aimed at understanding how organisms in the second trophic level (herbivores) try to sequester the carbon in plant tissues. We discovered that a signal transduction pathway, the jasmonate pathway, controls basal and inducible defense responses and this is now thought to limit 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 and mites. Both these facets of the defense response ('direct' and 'indirect' defenses) are controlled by lipid signals: jasmonates.

Research in the laboratory is organized around the question of how plant cells defend themselves from being eaten. This has broad relevance in agriculture but the laboratory focusses on basic research aimed at understanding the regulation and evolution of plant defense mechanisms.

Three areas in which we have published recently:

1. Initiation of jasmonate synthesis. We found that jasmonates are made surprisingly rapidly following attack and that vascular architectures determines where this occurs (J. Biol. Chem. (2008) 283, 16400; J. Biol. Chem. (2009) 284, 34506).

2. Leaf defense against vertebrates. We found that the jasmonate pathway increases plant resistance to a vertebrate herbivore (Mol. Ecol. (2012) 21, 2534).

3. Defense in regions of cell proliferation containing stem cells. We found that a small reactive aldehyde malondialdehyde (MDA) is highly inducible in proliferation zones (meristems) and might act as a defense compound (J. Biol. Chem. (2012) 287, 8954).

This latter project is part of a second line of research in the group: the genetics of nonenzymatic oxidation. We study the biology of lipid peroxidation catalyzed by lipoxygenases and occuring through nonenzymatic events. A main finding is that common omega-3 fatty acids such as linolenic acid might have a natural role as sinks for reactive oxygen species (ROS). That is they can be regarded as a new class of antioxidants (J. Biol. Chem. (2009) 284, 1702).

Jasmonates

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

Performed the first experiments to investigate the effects of a signal transduction pathway on the feeding behavior of a vertebrate herbivore (Mol. Ecol. 2012 in press).

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 (J. Biol. Chem. 284, 34506).

Showed that resistance to an insect can occur in the absence of wild-type jasmonic acid levels implicating cyclopentenone jasmonates (OPDA & dnOPDA) as signals (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.

Showed that jasmonate signalling promotes the establishment of a relatively oxidising environment near a wound (Plant Physiol. 156, 1797).

We isolated and characterized the 'fou2' mutant in the voltage-gated cation channel TPC1 from a genetic screen for plants with a constitutively active jasmonate pathway. This implicates cation flux (K+ and/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 sulphonucleotides (PAPS or PAP) help control JA levels in resting leaves.

Oxylipins control a major biological transition: from detritivory to herbivory

Evolution from detritivory (feeding on dead tissues) to herbivory (feeding on living plants) is one of the major transitions in biology. We starved isopod crustaceans (detritivores) and let them loose on Arabidopsis and rice mutants in jasmonate synthesis. The isopods started to feed on the living mutant plants but rarely damaged the WT (PNAS 2009, 106, 935). This shows that the absence of a signal pathway (the jasmonate pathway) in one organism causes a profound (transitional) effect on feeding in another.

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 the best candidates for the long-lost phytoalexins in potato leaves, the primary infection site for potato blight.

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 that polyunsaturated fatty acids are used as 'ROS sinks' to literally soak up ROS (J. Biol. Chem. 2009, 284, 1702).

Reactive Electrophile Species (RES)

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 powerful biological activity in the ubiquitous and highly studied lipid peroxidation marker malondialdehyde (MDA) (Plant J. 37, 877) and showed 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) and discovered inducible pools of MDA in stem cell-rich tissues including the pericycle (J. Biol. Chem. 2012 in press).

Remorin: a new family of proteins

Discovered the remorin group of plasma membrane 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).

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.