Molecular cloning, expression and mapping of the translational initiation factor eIF1 gene in Oryza sativa

Protein translation is very sensitive to salt stress and the proteins involved in this process may be an important determinant of salt tolerance. We isolated a rice cDNA clone (OseIF1) from a salt-tolerant indica cultivar (Pokkali) subjected to 150 mm NaCl, the deduced amino acid sequence of which had homology with the Sui1 suppressor locus in Saccharomyces cerevisiaei Hansen. The sequence contains 753 bp with an open-reading frame of 345 bp and shares similarity with the sequences of Sui1 and eIF1 in plants and mammals. Southern analysis indicates that the gene is present in more than a single copy per haploid genome and mapped to chromosome 1 of rice. Expression of the gene was increased by salt stress and also upregulated after exogenous ABA and mannitol treatments, suggesting that its induction is related to the water-deficit effect of high salt.

SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation

Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches were performed in a database containing 28 469 nonredundant rice cDNA sequences.

Identification of oxalate oxidase in rice defence system against rice blast

A rice cDNA library was screened using OSK3 protein kinase as bait in a yeast two-hybrid system. The gene encoding oxalate oxidase was one of the positive clones interacting with OSK3 protein kinase. The interactions were verified by detecting expression of the reporter gene lacZ. The results suggest that oxalate oxidase is a downstream element in the disease resistance signal cascade mediated by OSK3 protein kinase in rice.

Rice cDNA Microarray-Based Gene Expression Profiling of the Response to Flagellin Perception in Cultured Rice Cells

Incompatible strains of Acidovorax avenae elicit an immune response in cultured rice cells, with immunity specifically induced by the flagellin of the incompatible strain. To identify genes regulated by flagellin perception signaling in cultured rice cells, gene expression patterns were analyzed with rice cDNA microarrays, including 3,353 independent rice cDNA clones. In all, 131 genes were differentially expressed between incompatible and compatible interactions. K-means clustering showed that 94 genes were upregulated and 32 genes were downregulated during incompatible interactions, whereas only 5 genes were upregulated during compatible interactions. Among the 126 genes that were up- or downregulated during incompatible interactions, expression of 46 genes was decreased when cultured rice cells were inoculated with a flagellin-deficient incompatible strain (Δfla1141-2), indicating that approximately 37% of the 126 genes were directly controlled by flagellin perception. Real-time reverse-transcription polymerase chain reaction analysis using flagellins purified from incompatible or compatible strains was performed to confirm flagellin-regulated expression of candidate genes selected by microarray analysis. Results showed that induction of some genes involved in the immune response is regulated not only by the flagellin perception pathway, but also by another recognition molecule-perception pathway.