The hypersensitive response (HR) in plants is often controlled by gene-for-gene systems where an avirulence gene in the pathogen matches the allelic form of a particular resistance gene in the plant. Downstream of this recognition event, signalling transduction pathways controlled by regulator genes are activated and lead to differential expression of defence-related genes (Dangl & Jones, 2001; Van Loon et al., 2006). Thus three types of genes are involved in the HR response: resistance genes, regulator genes and defence genes. Pathogenesis-related (PR) proteins fall into the latter class of defence genes (Van Loon et al., 2006). Our current picture of which genes are involved in disease resistance in monocotyledons is rather poor. By contrast, extensive studies in the plant model Arabidopsis have demonstrated that between 11% (Schenk et al., 2000) and 22% (Tao et al., 2003) of the genes are differentially regulated in a single situation (for review, see Eulgem, 2005). Most importantly, using Pseudomonas syringae pv. tomato, Tao et al. (2003) demonstrated that late compatible and early incompatible interactions show similar responses. Considering regulator genes that were identified in Arabidopsis by a forward genetic approach, most of the time they were shown to be differentially expressed upon infection. For example, the EDS5 gene was shown to be induced by virulent and avirulent strains of Pseudomonas syringae pv. tomato in Arabidopsis (Nawrath et al., 2002).
With the completion of rice and Magnaporthe grisea genomes, rice blast disease has become a model of choice to study host reactions in monocotyledons (Dean et al., 2005). Several large-scale approaches have been used to identify genes and proteins that are differentially expressed upon infection by M. grisea, other pathogens and related stresses. This led to the identification of genes that are potentially differentially regulated upon infection by M. grisea (Kim et al., 2001; Rauyaree et al., 2001; Jantasuriyarat et al., 2005) or related conditions (Xanthomonas oryzae pv. oryzae: Chu et al., 2004; Rice Yellow Mottle Virus: Ventelon-Debout et al., 2003). Differential cDNA libraries (SSH: Xiong et al., 2001; Lu et al., 2004; Shim et al., 2004; differential display: Kim et al., 2000) combined with reverse northern were also used. Although it is always difficult to compare such different studies, some common elements emerge:
- • As in other systems, incompatible and compatible interactions seem to differ mainly quantitatively (Wen et al., 2003; Lu et al., 2004).
- • Except for classical defence genes such as PR1, PR3 (chitinases), PBZ1 and metallothionein, there are few overlaps between the differentially expressed genes isolated in these studies. From reports on genes differentially expressed upon infection, it appears that only 18% were found in at least two independent studies (Droc et al., 2006; this study). This suggests that our knowledge of defence response in rice is far from complete.
- • Among the common patterns of gene expression emerging from those studies, several found repression of genes involved in photosynthesis (Zhou et al., 2002; Lu et al., 2004; Shim et al., 2004).
- • Many of the genes identified appear to belong to multigene families, and appropriate tools, such as quantitative RT-PCR, are needed to study their specific expression.
- • Besides transcriptional factors, such as WRKYs (Zhou et al., 2002) and MYBs (Xiong et al., 2001), and with the exception of the Mlo gene (Zhou et al., 2002), no major regulator gene known to be required for disease resistance in Arabidopsis or monocotyledons was found in the thousands of genes differentially expressed upon infection.
We are currently studying the interaction between rice resistance gene Pi33 (Berruyer et al., 2003) and M. grisea avirulence gene ACE1 (Böhnert et al., 2004). In rice cultivar IR64, the Pi33 gene belongs to a 5 Mb introgression from O. rufipogon located on the small arm of O. sativa chromosome 8 (E. Ballini et al., unpublished). Pi33 is also found in some wild rice species, suggesting an ancient origin (E. Ballini et al., unpublished). However, the Pi33 resistance gene is probably a classical resistance gene as it maps to a small interval from the rice chromosome 8 containing several classical resistance gene analogues (Berruyer et al., 2003; E. Ballini et al., unpublished). Avirulence gene ACE1 encodes a putative hybrid protein between a polyketide synthase and a nonribosomal peptide synthase. Mutagenesis studies strongly support the hypothesis that the metabolite produced by this enzyme, rather than the enzyme itself, is the avirulence molecule (Böhnert et al., 2004). Such an interaction between a fungal metabolite and a disease resistance gene is unique among known avirulence/resistance interactions in fungi (Böhnert et al., 2004). As this interaction is original, this avirulence gene may induce plant defence mechanisms that differ from other avirulence/resistance interactions, at least during the early phases of recognition. Therefore we decided to explore rice defence reactions in this particular avirulence/resistance interaction. Nontargeted differential gene expression was performed using DNA chips to identify genes up- or down-regulated during early stages in this interaction. Additionally, the expression of genes known to be required for disease resistance in rice or other plants was monitored during ACE1/Pi33 interaction. Whereas more than 50 regulator genes required for disease resistance are known in dicots (Hammond-Kosack & Parker, 2003), only 14 have been described in cereals, mostly in barley (Ayliffe & Lagudah, 2004), and rice, including rice genes SPL11 (Zeng et al., 2004), OsMT2b (Wong et al., 2004), OsRac1 (Ono et al., 2001), NRR (Chern et al., 2005), SPL7 (Yamanouchi et al., 2002), OsEDR1 (Kim et al., 2003), OsEREBP (Kim et al., 2000), OsLSD1 (Wang et al., 2005) and OsMAPK6 (Lieberherr et al., 2005). Some of these disease resistance regulator genes are differentially expressed upon infection. The corresponding rice genes are probably involved in the control of disease resistance and as such have been used as putative markers of disease resistance induction in rice. Finally, there is a need for the identification of novel genes in rice that are differentially expressed during infection. Our strategy towards this goal involves a combination of DNA chip-based differential screening and an expression survey of selected disease resistance regulator genes. This first screening was followed by the monitoring of the expression of a selected number of differentially expressed genes during different compatible/incompatible interactions to identify patterns specific of Pi33/ACE1 interaction.