Selective control of Egyptian broomrape is extremely difficult because the close association between host crop and parasite limits the use of most mechanical and herbicidal approaches. However, this host–parasite interaction can also form the basis of the simplest control strategy: parasite-resistant crops. Although much work has been conducted to identify and characterize mechanisms of parasite resistance, varieties with stable resistance are still unavailable for most affected crops. The development of resistant crops can be accelerated by genetic engineering to the extent that important aspects of the host–parasite interaction are understood. In this study, we characterize a variety of gene promoter elements with respect to parasite induction and expression pattern. Studies were conducted using transgenic plants expressing fusions of the β-glucuronidase reporter gene with promoter elements from several genes. Promoters from genes known to have increased expression in response to pathogen attack or wounding showed localized, induced expression after parasitism. These included phenylalanine ammonia lyase, chalcone synthase, sesquiterpene cyclase, and HMG1 (3-hydroxy-3-methylglutaryl CoA reductase). In contrast, the systemic acquired resistance–associated gene PR-1a was not induced by parasitism. Non–defense-related genes varied in response, with squalene synthase being repressed, whereas farnesyltransferase was highly expressed in the region of parasite attachment. These results demonstrate a range of expression, both in intensity and tissue specificity, in response to parasitism.

Farnesyltransferase (FT) inhibitors can suppress tumor cell proliferation without substantially interfering with normal cell growth, thus holding promise for cancer treatment. A structure-based approach to the design of improved FT inhibitors relies on knowledge of the conformational flexibility of the zinc-containing active site of FT. Although several X-ray structures of FT have been reported, detailed information regarding the active site conformational flexibility of the enzyme is still not available. Molecular dynamics (MD) simulations of FT can offer the requisite information, but have not been applied due to a lack of effective methods for simulating the four-ligand coordination of zinc in proteins. Here, we report in detail the problems that occurred in the conventional MD simulations of the zinc-bound FT and a solution to these problems by employing a simple method that uses cationic dummy atoms to impose orientational requirement for zinc ligands. A successful 1.0 ns (1.0 fs time step) MD simulation of zinc-bound FT suggests that nine conserved residues (Asn127α, Gln162α, Asn165α, Gln195α, His248β, Lys294β, Leu295β, Lys353β, and Ser357β) in the active site of mammalian FT are relatively mobile. Some of these residues might be involved in the ligand-induced active site conformational rearrangement upon binding and deserve attention in screening and design of improved FT inhibitors for cancer chemotherapy.