Towards establishment of a rice stress response interactome.

Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%-60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein-protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance.

Strategies for Efficient RNAi-Based Gene Silencing of Viral Genes for Disease Resistance in Plants.

RNA interference (RNAi) is an evolutionarily conserved gene silencing mechanism in eukaryotes including fungi, plants, and animals. In plants, gene silencing regulates gene expression, provides genome stability, and protect against invading viruses. During plant virus interaction, viral genome derived siRNAs (vsiRNA) are produced to mediate gene silencing of viral genes to prevent virus multiplication. After the discovery of RNAi phenomenon in eukaryotes, it is used as a powerful tool to engineer plant viral disease resistance against both RNA and DNA viruses. Despite several successful reports on employing RNA silencing methods to engineer plant for viral disease resistance, only a few of them have reached the commercial stage owing to lack of complete protection against the intended virus. Based on the knowledge accumulated over the years on genetic engineering for viral disease resistance, there is scope for effective viral disease control through careful design of RNAi gene construct. The selection of target viral gene(s) for developing the hairpin RNAi (hp-RNAi) construct is very critical for effective protection against the viral disease. Different approaches and bioinformatics tools which can be employed for effective target selection are discussed. The selection of suitable target regions for RNAi vector construction can help to achieve a high level of transgenic virus resistance.

Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management.

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the devastating diseases of rice worldwide. The pathogen reported to cause 70% crop loss in some of the susceptible genotypes under disease favoring environments, viz., temperature ranging between 25 to 34°C and relative humidity more than 70%. In Xoo, about 245 genes govern the pathogenicity and host specificity. The hypersensitive response and pathogenicity (hrp) genes responsible for disease occurrence were clustered in the pathogenicity island of 31.3 Kb. The protein secreted through type three secretory system and type one secretory system mediates infection and establishment of the pathogen inside the host. However, elicitor molecules from Xoo triggered the resistant response in rice against the pathogen. An array of resistant genes (R genes) was known to be invoked by the host to combat the bacterial infection. To date, of the 45 Xa genes in rice, nine were cloned and characterized. The evolution of new races has made the task of developing resistant rice genotypes more challenging as it demands a comprehensive breeding strategy involving the best use of R genes from the existing gene pool. Thus, to combat the infection from the existing races and to slow down the emergence of new Xoo races, pyramiding two or more R genes was found to be effective against bacterial blight disease. In India, the successfully commercialized example includes the development of rice genotypes, viz., Improved Pusa Basmati- 1, Improved Samba Mahsuri, PR106, Type 3 Basmati, and Mahsuri with selected R genes, viz., xa5, Xa4, xa13 and Xa21 against bacterial blight resistance. This review primarily portray Xoo-rice interactions and provides opportunities for its effective management through sustainable technologies.

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.

WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.

ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements.

UNLABELLED: Detailed structural analysis of protein necessitates investigation at primary, secondary and tertiary levels, respectively. Insight into protein secondary structures pave way for understanding the type of secondary structural elements involved (α-helices, ß-strands etc.), the amino acid sequence that encode the secondary structural elements, number of residues, length and, percentage composition of the respective elements in the protein. Here we present a standalone tool entitled "ExSer" which facilitate an automated extraction of the amino acid sequence that encode for the secondary structural regions of a protein from the protein data bank (PDB) file. AVAILABILITY: ExSer is freely downloadable from http://code.google.com/p/tool-exser/

Functional insight for beta-glucuronidase in Escherichia coli and Staphylococcus sp. RLH1.

Glycosyl hydrolases hydrolyze the glycosidic bond either in carbohydrates or between carbohydrate and non-carbohydrate moiety. The beta-glucuronidase (beta D-glucuronoside glucuronosohydrolase; EC 3.2.1.31) enzyme belongs to the family-2 glycosyl hydrolase. The E. coli borne beta-glucuronidase gene (uidA) was devised as a gene fusion marker in plant genetic transformation experiments. Recent plant transformation vectors contain a novel beta-glucuronidase (gusA) derived from Staphylococcus sp. RLH1 for E. coli uidA. It is known to have a ten fold higher sensitivity compared to E. coli beta-glucuronidase. The functional superiority of Staphylococcus (gusA) over E. coli (uidA) activity is not fully known. The comparison of secondary structural elements among them revealed an increased percentage of random coils in Staphylococcus beta-glucuronidase. The 3D model of gusA shows catalytic site residues 396Glu, 508Glu and 471Tyr of gusA in loop regions. Accessible surface area (ASA) calculations on the 3D model showed increased ASA for active site residues in Staphylococcus beta-glucuronidase. Increased random coil, the presence of catalytic residues in loops, greater solvent accessibility of active residues and increased charged residues in gusA of Staphylococcus might facilitate interaction with the solvent. This hypothesizes the enhanced catalytic activity of beta-glucuronidase in Staphylococcus sp. RLH1 compared to that in E. coli.

Beta-glucuronidase of family-2 glycosyl hydrolase: a missing member in plants.

Glycosyl hydrolases hydrolyze the glycosidic bond in carbohydrates or between a carbohydrate and a non-carbohydrate moiety. beta-glucuronidase (GUS) is classified under two glycosyl hydrolase families (2 and 79) and the family-2 beta-glucuronidase is reported in a wide range of organisms, but not in plants. The family-79 endo-beta-glucuronidase (heparanase) is reported in microorganisms, vertebrates and plants. The E. coli family-2 beta-glucuronidase (uidA) had been successfully devised as a reporter gene in plant transformation on the basis that plants do not have homologous GUS activity. On the contrary, histochemical staining with X-Gluc was reported in wild type (non-transgenic) plants. Data shows that, family-2 beta-glucuronidase homologous sequence is not found in plants. Further, beta-glucuronidases of family-2 and 79 lack appreciable sequence similarity. However, the catalytic site residues, glutamic acid and tyrosine of the family-2 beta-glucuronidase are found to be conserved in family-79 beta-glucuronidase of plants. This led to propose that the GUS staining reported in wild type plants is largely because of the broad substrate specificity of family-79 beta-glucuronidase on X-Gluc and not due to the family-2 beta-glucuronidase, as the latter has been found to be missing in plants.