Characterization of the rice pathogen-related protein Rir1a and regulation of the corresponding gene

Improving Nitrogen Use Efficiency Through Overexpression of Alanine Aminotransferase in Rice, Wheat, and Barley

Nitrogen is an essential nutrient for plants, but crop plants are inefficient in the acquisition and utilization of applied nitrogen. This often results in producers over applying nitrogen fertilizers, which can negatively impact the environment. The development of crop plants with more efficient nitrogen usage is, therefore, an important research goal in achieving greater agricultural sustainability. We utilized genetically modified rice lines over-expressing a barley alanine aminotransferase (HvAlaAT) to help characterize pathways which lead to more efficient use of nitrogen. Under the control of a stress-inducible promoter OsAnt1, OsAnt1:HvAlaAT lines have increased above-ground biomass with little change to both nitrate and ammonium uptake rates. Based on metabolic profiles, carbon metabolites, particularly those involved in glycolysis and the tricarboxylic acid (TCA) cycle, were significantly altered in roots of OsAnt1:HvAlaAT lines, suggesting higher metabolic turnover. Moreover, transcriptomic data revealed that genes involved in glycolysis and TCA cycle were upregulated. These observations suggest that higher activity of these two processes could result in higher energy production, driving higher nitrogen assimilation, consequently increasing biomass production. Other potential mechanisms contributing to a nitrogen-use efficient phenotype include involvements of phytohormonal responses and an alteration in secondary metabolism. We also conducted basic growth studies to evaluate the effect of the OsAnt1:HvAlaAT transgene in barley and wheat, which the transgenic crop plants increased seed production under controlled environmental conditions. This study provides comprehensive profiling of genetic and metabolic responses to the over-expression of AlaAT and unravels several components and pathways which contribute to its nitrogen-use efficient phenotype.

Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice

The "Green Revolution" that dramatically reduced cultivar heights and sharply boosted rice production mid-century was achieved in large part through introgression of defective alleles of Semi-Dwarf 1 (SD1), which encodes a GA20ox oxidase involved in the final steps of the synthesis of bioactive gibberellin in rice. Here, we ask whether converting the defective sd1 version in a modern semi-dwarf cultivar back to wild-type SD1 in situ recovers ancestral plant traits, and more broadly, what it reveals about pleiotropic effects of this gene. We assess these effects of SD1 restoration in three independent recombinant lines recovered from F₂ progeny of a cross between 93-11 and PA64s. We then used RNA-seq to dissect gene network changes that accompanied SD1 restoration. We report that this in situ restoration of wild-type SD1 nearly doubles plant height, increases total grain yield per panicle, and elongates the second-leaf length. Comparison of expression profiles reveals changes in key nodes of the gibberellin pathway, such as OsKO1 and OsGA2ox3, and more broadly in genes related to metabolic networks, defense response, and catabolic processes. Two JA-induced genes, RIR1b and OsPR1b, are extremely down-regulated after SD1 restoration, suggesting that SD1 restoration alters the balance between GA and JA to plant growth, at the cost of degrading the defense response. This in situ approach at the SD1 locus also provides a model example that is applicable to other systems and will further understanding of gene networks underlying high-yield traits in crops.

TaWIR1 contributes to post-penetration resistance to Magnaporthe oryzae, but not Blumeria graminis f. sp. tritici, in wheat

Members of the Wheat-Induced Resistance 1 (TaWIR1) gene family are highly induced in response to a wide range of pathogens. Homologues have been identified in barley, but not in Brachypodium, whereas, in rice, only distant WIR1 candidates are known. Phylogenetic analysis placed TaWIR1a and TaWIR1b within a distinct clade of wheat transcripts, whereas TaWIR1c clustered with HvWIR1 genes. Transcripts of all three TaWIR1 genes were strongly induced by a wheat-adapted isolate of Magnaporthe oryzae. Virus-induced gene silencing of the TaWIR1 gene family had no effect on the initial penetration of epidermal cells by M. oryzae. However, following the establishment of an infection site, the fungus was able to grow more extensively within the leaf tissue, relative to control leaves, indicating a role for the TaWIR1 gene family in the cell-to-cell movement of M. oryzae. In contrast, the silencing of TaWIR1 transcripts had no effect on epidermal cell penetration by a wheat-adapted isolate of Blumeria graminis, or on the subsequent growth of hyphae. Differential transcription of TaWIR1 genes was also seen in epidermal peels, relative to the remaining leaf tissue, following inoculation with M. oryzae.

Convergent evidence for a role of WIR1 proteins during the interaction of barley with the powdery mildew fungus Blumeria graminis

Pathogen attack triggers a multifaceted defence response in plants that includes the accumulation of pathogenesis-related proteins and their corresponding transcripts. One of these transcripts encodes for WIR1, a small glycine- and proline-rich protein of unknown function that appears to be specific to grass species. Here we describe members of the HvWIR1 multigene family of barley with respect to phylogenetic relationship, transcript regulation, co-localization with quantitative trait loci for resistance to the barley powdery mildew fungus Blumeria graminis (DC.) E.O. Speer f.sp. hordei, the association of single nucleotide polymorphisms or gene haplotypes with resistance, as well as phenotypic effects of gene silencing by RNAi. HvWIR1 is encoded by a multigene family of moderate complexity that splits up into two major clades, one of those being also represented by previously described cDNA sequences from wheat. All analysed WIR1 transcripts accumulated in response to powdery mildew attack in leaves and all mapped WIR1 genes were associated with quantitative trait loci for resistance to B. graminis. Moreover, single nucleotide polymorphisms or haplotypes of WIR1 members were associated with quantitative resistance of barley to B. graminis, and transient WIR1 gene silencing affected the interaction of epidermal cells with the pathogen. The presented data provide convergent evidence for a role of the HvWIR1a gene and possibly other family members, during the interaction of barley with B. graminis.

A novel cold-regulated gene from Camellia sinensis, CsCOR1, enhances salt- and dehydration-tolerance in tobacco

In present research, the full-length cDNA and the genomic sequence of a novel cold-regulated gene, CsCOR1, were isolated from Camellia sinensis L. The deduced protein CsCOR1 contains a hydrophobic N-terminus as a signal peptide and a hydrophilic C-terminal domain that is rich in glycine, arginine and proline. Two internal repetitive tridecapeptide fragments (HSVTAGRGGYNRG) exist in the middle of the C-terminal domain and the two nucleotide sequences encoding them are identical. CsCOR1 was localized in the cell walls of transgenic-tobaccos via CsCOR1::GFP fusion approach. The expression of CsCOR1 in tea leaves was enhanced dramatically by both cold- and dehydration-stress. And overexpression of CsCOR1 in transgenic-tobaccos improved obviously the tolerance to salinity and dehydration.

Recent advances in rice biotechnology--towards genetically superior transgenic rice

Rice biotechnology has made rapid advances since the first transgenic rice plants were produced 15 years ago. Over the past decade, this progress has resulted in the development of high frequency, routine and reproducible genetic transformation protocols for rice. This technology has been applied to produce rice plants that withstand several abiotic stresses, as well as to gain tolerance against various pests and diseases. In addition, quality improving and increased nutritional value traits have also been introduced into rice. Most of these gains were not possible through conventional breeding technologies. Transgenic rice system has been used to understand the process of transformation itself, the integration pattern of transgene as well as to modulate gene expression. Field trials of transgenic rice, especially insect-resistant rice, have recently been performed and several other studies that are prerequisite for safe release of transgenic crops have been initiated. New molecular improvisations such as inducible expression of transgene and selectable marker-free technology will help in producing superior transgenic product. It is also a step towards alleviating public concerns relating to issues of transgenic technology and to gain regulatory approval. Knowledge gained from rice can also be applied to improve other cereals. The completion of the rice genome sequencing together with a rich collection of full-length cDNA resources has opened up a plethora of opportunities, paving the way to integrate data from the large-scale projects to solve specific biological problems.

Isolation and characterization of novel defense response genes involved in compatible and incompatible interactions between rice and Magnaporthe grisea

To identify early-induced defense genes involved in broad-spectrum resistance to rice blast, suppression subtractive hybridization was used to generate two cDNA libraries enriched for transcripts differentially expressed in Pi9(t)-resistant and -susceptible plants. After differential screening by membrane-based hybridization and subsequent confirmation by reverse Northern blot analysis, selected clones were sequenced and analyzed. Forty-seven unique cDNA clones were found and assigned to eight different groups according to the putative function of their homologous genes in the database. These genes may be involved in pathogen or stress response, signal transduction, transcription, cell transport, metabolism, energy or protein destination. Northern blot analysis showed that most of these genes were induced or suppressed after blast infection, and that half of them showed differential expression patterns between compatible and incompatible interactions. Interestingly, all but one of the identified genes are reported here for the first time to be involved in defense response to rice blast. In addition, hybridization of these clones with cDNAs synthesized from RNA samples from bacterial blight-infected leaves showed that few of them are induced or repressed in Xa21- or Xa7-resistant plants, suggesting a minimum overlap of defense responses mediated by different resistance genes to fungal and bacterial pathogens at an early stage of infection. Further characterization and functional analysis of these genes will enhance our understanding of the molecular mechanism of broad-spectrum resistance in rice.

Isolation and characterization of a novel rice gene encoding a putative insect-inducible protein homologous to wheat Wir1

A full-length cDNA, designated BpHi008A, was cloned representing a rice (Oryza sativa) mRNA that accumulates after brown planthopper (BPH) Nilapar vata lugens Stål feeding. The cDNA encodes a putative 82 amino acid protein (BpHi008A) exhibiting about 37% amino acid sequence identity to Wir1 family of proteins that are encoded by pathogen-induced transcripts in wheat. Like Wir1 proteins, it consists of a hydrophobic N-terminal half and a hydrophilic C-terminal half relatively rich in glycine and proline. These proteins are predicted to be integrated into the membrane, with the C-terminus being extracytoplastic. Genomic Southern analysis indicated that the BpHi008A gene was present as a single-copy sequence in the rice genome. Temporal and spatial studies showed that BpHi008A were systemically induced in rice when 2nd and 3rd-instars were feeding. The BpHi008A transcripts level was also increased in seedlings damaged by mechanical wounding. These data indicated that BphHi008A was implicated in the response of rice plants to BPH feeding and wounding.

Cytological and molecular analysis of the Hordeum vulgare-Puccinia triticina nonhost interaction

Cultivated barley, Hordeum vulgare L., is considered to be a nonhost or intermediate host species for the wheat leaf rust fungus Puccinia triticina. Here, we have investigated, at the microscopic and molecular levels, the reaction of barley cultivars to wheat leaf rust infection. In the nonhost resistant cultivar Cebada Capa, abortion of fungal growth occurred at both pre- and posthaustorial stages, suggesting that defense genes are expressed throughout the development of the inappropriate fungus during the nonhost resistance reaction. In the two barley lines L94 and Bowman, a low level of prehaustorial resistance to P. triticina was observed and susceptibility was comparable to that of wheat control plants. Suppression subtractive hybridization was used to identify genes that are differentially expressed during the nonhost resistance reaction in Cebada Capa as well as during the successful establishment of the inappropriate wheat leaf rust fungus in L94. Northern analysis indicated that two candidate genes, including a barley ortholog of the rice resistance gene Xa21, are putatively involved in nonhost and non-race-specific resistance reactions. In addition, a new gene that is specifically induced during the successful development of the inappropriate fungus P. triticina in barley has been identified.

Tourist C transposable elements are closely associated with genes expressed in flowers of rice (Oryza sativa)

Tourist elements comprise a group of transposable elements in plants. One of these elements, Tourist-OsaCatA(a Tourist C element), has been found in the 5; flanking region of a catalase gene, CatA, in rice (Oryza sativa). Using reverse transcriptase-PCR (RT-PCR) analyses of leaves, roots, flowers and developing seeds of rice, we assessed the transcription levels of ten known genes containing Tourist C elements, and of three additional putative genes for which expressed sequence tags (ESTs) including Tourist C elements have been isolated. We found that nine of the ten known genes and two of the three represented by ESTs were expressed in at least one of the organs we analyzed, and all of the genes detected were expressed in flowers, usually in stamens or pistils. We also assessed the expression of the 29 Tourist C-containing hypothetical coding sequences (CDSs) obtained so far by high-throughput genomic sequencing. We found that CDSs of all 11 genes whose transcripts were detectable by RT-PCR were expressed in flowers, especially in stamens or pistils. In contrast, RT-PCR analyses of genes or CDSs associated with other miniature inverted-repeat transposable elements (MITEs), such as Tourist D, Gaijin, Explorer, and Castaway, showed that some of them were expressed only minimally or not at all in flowers. Therefore, compared with other MITEs, Tourist C elements seem to show a strong association with genes that are expressed in the flowers of rice.

Characterization of RCI-1, a chloroplastic rice lipoxygenase whose synthesis is induced by chemical plant resistance activators

A full-length lipoxygenase cDNA (RCI-1) has been cloned from rice (Oryza sativa) whose corresponding transcripts accumulate in response to treatment of the plants with chemical inducers of acquired resistance such as benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester (BTH), 2,6-dichloroisonicotinic acid (INA), and probenazole. In contrast, RCI-1 transcript levels did not increase after inoculation with compatible and incompatible races of the rice blast fungus Magnaporthe grisea and the nonhost pathogen Pseudomonas syringae pv. syringae. RCI-1 transcript levels also increased after exogenous application of jasmonic acid, but not upon wounding. Dose-response and time course experiments revealed a similar pattern of transcript accumulation and lipoxygenase activity in BTH-treated rice leaves. Enzymatic analysis of recombinant RCI-1 protein produced in Escherichia coli revealed that 13-hydroperoxy-octadecanoic acids were the predominant reaction products when either linoleic or linolenic acid used as a substrate. The RCI-1 sequence features a putative chloroplast targeting sequence at its N-terminus. Indeed, a protein consisting of the putative chloroplast transit peptide fused to green fluorescent protein was exclusively localized in chloroplasts, indicating that RCI-1 is a chloroplastic enzyme.

Syringolin-mediated activation of the Pir7b esterase gene in rice cells is suppressed by phosphatase inhibitors

Inoculation of rice plants (Oryza sativa) with the nonhost pathogen Pseudomonas syringae pv. syringae leads to the activation of defense-related genes and ultimately to induced resistance against the rice blast fungus Pyricularia oryzae. One of the molecular determinants of P. syringae pv. syringae that is recognized by the plant cells and evokes these defense responses is syringolin A, an elicitor that is secreted by the bacteria under appropriate conditions. In order to investigate signal transduction events elicited by syringolin A, the response of cultured rice cells to syringolin A application was analyzed. Cultured rice cells were able to sense syringolin A at concentrations in the nanomolar range as observed by the transient accumulation of Pir7b esterase transcripts. Syringolin A-mediated Pir7b transcript accumulation was inhibited by cycloheximide, indicating that de novo protein synthesis was required. Calyculin and okadaic acid, two protein phosphatase inhibitors, blocked Pir7b gene induction, whereas the serine/threonine protein kinase inhibitors staurosporine and K-252a had no effect on Pir7b transcript levels. Actin transcript levels were essentially not affected by inhibitor treatments over the experimental time span. These results imply that dephosphorylation of a phosphoprotein is an important step in the syringolin A-triggered signal transduction pathway.