BMC Genomics 2009, 10(Suppl 3):S19 http://www.biomedcentral.com/1471-2164/10/S3/S19 Background Plants are under constant threat of infections caused by pathogens that range from viruses, bacteria, fungi to nematodes and insects. The efficacy of plant defense depends on its ability to recognize a pathogen and mount the appropriate defense response. Plants often employ cell surface and intracellular receptors to detect a pathogen associated molecular pattern (PAMP) and trigger immune response against the invader. PolyGalac- turonase-Inhibiting Protein (PGIP) is one among the pathogenesis-related (PR) proteins that is found at the cell surface of plant cells. It binds and inhibits the enzyme PolyGalacturonase (PG) from the invading pathogen which could be fungus, insect or bacterium, thus preventing its colonization in the host cell and hence the progress of the disease [1,2]. PolyGalacturonases (PG) are a class of pectinolytic enzyme secreted by the pathogen at the early stages of infection to depolymerize homogalacturonan (HGA), the main component of pectin in the plant cell wall [3]. HGA is the 1, 4 linked alpha-D-galactosyluronic acid polymer found in the plant cell which forms the first line of barrier and thereby plays a critical role in controlling pathogen invasion [4-7]. The interaction of the plant protein PGIP with the fungal or insect PG limits the destructive potential of the PG and leads to the accumulation of elicitor active oligoga- lacturonides as shown by in vitro studies [8]. Hence PGIP seems to exert a dual role during fungal attack. It limits pathogen penetration and tissue colonization by inhibiting PG activity, this in turn, favours the accumu- lation of oligogalacturonides, which activate a prompt defense response [9]. PGIPs belong to the Leucine-rich Repeat (LRR) super family of proteins [10] containing tandem repeats of a 20-30 amino acid stretch of the extracytoplasmic type with a consensus that bear a con served par t [LxxLxLxxNxL or LxxLxLxxCxxL (L = I, L, V, F; N = N, T, S, C; C = C, S; x = any amino acid)] and a variable part [11,12]. The LRR-fold (Figure 1) which is believed to be specialized in protein-protein interaction is quite exten- sively used for the immune functions and for the recognition of non-self molecules by plants. The crystal structure of the only PGIP (PGIP2 from Phaseolus vulgaris) as well as the first LRR protein belonging to the plant-specific subfamily [13] ([ILVF]xx[ILVF]xx[ILVF] x[ILVF]xx[NTSC]x[ILVF] [TS]GxIPxx[ILVF]Gx) reveals a typical curved and elongated shape. Eight b strands (with one long b strand, B1, at the N-terminal end) comprise the inner concave face of the curved surface. On the opposite side of the b sheet, there are nine 310 helices that are almost parallel to the b sheet. The concave surface is known to bear residues necessary for binding and recognition specificity in this class of protein [14]. Figure 1 Ribbon representation of Crystal structure of PvPGIP2 (1OGQ). The protein is composed of tandemly repeating units called LRRs. The N-terminal and C-terminal cysteine-rich domains are shown in green. Three structural elements characterize this fold. The b-sheet B1 occupies the concave face of the scaffold (blue), a regular array of 310 helices characterizes the convex face (red), and a second non-regular b-sheet (B2; cyan) is found between the two faces. PGIPs function as very specific inhibitors [15]. PGIP from a particular plant that is able to inhibit the PG from a certain pathogen might not be able to inhibit PGs from other pathogens. Besides, for cases when a PGIP is able to inhibit PGs from different pathogens, the percent inhibition differs. Thus in plants, small gene families encode PGIP isoforms that differ in affinity and Page 2 of 12 (page number not for citation purposes)