Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice

In this study, we used a cross-species network approach to uncover nitrogen-regulated network modules conserved across a model and a crop species. By translating gene “network knowledge” from the data-rich model Arabidopsis (Arabidopsis thaliana) to a crop (Oryza sativa), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N-use efficiency in transgenic plants. To uncover such conserved N-regulatory network modules, we first generated a N-regulatory network based solely on rice (O. sativa) transcriptome and gene interaction data. Next, we enhanced the “network knowledge” in the rice N-regulatory network using transcriptome and gene interaction data from Arabidopsis and new data from Arabidopsis and rice plants exposed to the same N-treatment conditions. This cross-species network analysis uncovered a set of N-regulated transcription factors (TFs) predicted to target the same genes and network modules in both species. Supernode analysis of the TFs and their targets in these conserved network modules uncovered genes directly related to nitrogen use (e.g. N-assimilation) and to other shared biological processes indirectly related to nitrogen. This cross-species network approach was validated with members of two TF families in the supernode network, bZIP-TGA and HRS1/HHO family, have recently been experimentally validated to mediate the N-response in Arabidopsis.Fil: Obertello, Mariana. University of New York; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular ; ArgentinaFil: Shrivastava, Stuti. University of New York; Estados UnidosFil: Katari, Manpreet S.. University of New York; Estados UnidosFil: Coruzzi, Gloria M.. University of New York; Estados Unido

Modeling the global effect of the basic-leucine zipper transcription factor 1 (bZIP1) on nitrogen and light regulation in Arabidopsis

Background: Nitrogen and light are two major regulators of plant metabolism and development. While genes involved in the control of each of these signals have begun to be identified, regulators that integrate gene responses to nitrogen and light signals have yet to be determined. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of nitrogen (N) and light (L) treatment conditions and performing transcriptome analysis. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide. Results: This transcriptome analysis demonstrates that a mutation in the bZIP1 gene can alter the L and/or N-regulation of several gene clusters. More surprisingly, the bZIP1 mutation can also trigger N and/or L regulation of genes that are not normally controlled by these signals in WT plants. This analysis also reveals that bZIP1 can, to a large extent, invert gene regulation (e. g., several genes induced by N in WT plants are repressed by N in the bZIP1 mutant). Conclusion: These findings demonstrate that the bZIP1 mutation triggers a genome-wide de-regulation in response to L and/or N signals that range from i) a reduction of the L signal effect, to ii) unlocking gene regulation in response to L and N combinations. This systems biology approach demonstrates that bZIP1 tunes L and N signaling relationships genome-wide, and can suppress regulatory mechanisms hypothesized to be needed at different developmental stages and/or environmental conditions

Interaction between Trichoderma pseudokoningii strains and the arbuscular mycorrhizal fungi Glomus mosseae and Gigaspora rosea

The interaction between Trichoderma pseudokoningii (Rifai) 511, 2212, 741A, 741B and 453 and the arbuscular mycorrhizal fungi Glomus mosseae (Nicol. & Gerd.) Gerdemann & Trappe BEG12 and Gigaspora rosea Nicolson & Schenck BEG9 were studied in vitro and in greenhouse experiments. All T. pseudokoningii strains inhibited the germination of G. mosseae and Gi. rosea except the strain 453, which did not affect the germination of Gi. rosea. Soluble exudates and volatile substances produced by all T. pseudokoningii strains inhibited the spore germination of G. mosseae. The germination of Gi. rosea spores was inhibited by the soluble exudates produced by T. pseudokoningii 2212 and 511, whereas T. pseudokoningii 714A and 714B inhibited the germination of Gi. rosea spores by the production of volatile substances. The strains of T. pseudokoningii did not affect dry matter and percentage of root length colonization of soybean inoculated with G. mosseae, except T. pseudokoningii 2212, which inhibited both parameters. However, all T. pseudokoningii strains decreased the shoot dry matter and the percentage of AM root length colonization of soybean inoculated with Gi. rosea. The saprotrophic fungi tested seem to affect AM colonization of root by effects on the presymbiotic phase of the AM fungi. No influence of AM fungi on the number of CPUs of T. pseudokoningii was found. The effect of saprotrophic fungi on AM fungal development and function varied with the strain of the saprotrophic species tested.Fil: Martinez, Alicia Elba. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Buenos Aires; ArgentinaFil: Obertello, Mariana. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pardo, Alejandro Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Ocampo, Juan A.. Consejo Superior de Investigaciones Científicas. Estación Experimental del Zaidín; EspañaFil: Godeas, Alicia Margarita. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Actinorhizal nitrogen fixing nodules: infection process, molecular biology and genomics

Actinorhizal hosts are non-leguminous perennial plants belonging to 8 angiosperm families. They are capable of forming root nodules as a result of infection by a nitrogen-fixing actinomycete called Frankia. Actinorhizal nodules consist of multiple lobes, each of which represents a modified lateral root with infected cells in the expanded cortex. This article summarizes the most recent knowledge about this original symbiotic process. The infection process is described both at cytological and molecular levels. The use of transgenic Casuarinaceae for studying in actinorhizal nodules the regulation of several symbiotic promoters from legumes is also discussed. With progress in plant genome sequencing, comparative genomics in legumes and actinorhizal plants should contribute to the understanding of the evolutionary history of nitrogen-fixing symbioses. Key words : Nitrogen-fixation, actinorhizal nodules, Frankia, Casuarina, symbiotic gene. African Journal of Biotechnology Vol. 2 (12), pp. 528-538, December 200

Interactions between Frankia BCU110501 (actinorhiza) and Gigaspora rosea (arbuscular mycorrhiza) with Discaria trinervis studied by spot inoculation

Root endosymbioses are associations between plants and soil microorganisms which contribute worldwide to plant nutrition and fitness. The most common associations is with arbuscular mycorrhizal fungi (AMF) and this is formed by the majority of land plants with fungi belonging to the Glomeromycota. Another important association is that formed by the Gram-positive actinobacteria, Frankia, and actinorhizal plants such as Discaria trinervis. In this paper we studied the effect of dual symbioses resulting from spot inoculation. This method was developed and tested to ensure actinorhizal nodule development only at the site of inoculation. Our results show that both symbioses can coexist and that AMF and Frankia can stimulate plant growth both as a single inoculum and in combination. Moreover, we suggest that there is no interference between the regulation of actinorhizal and arbuscular mycorrhizal symbiosis in D. trinervis, and that there is a synergistic effect on plant growth following the development of both symbioses.Fil: Obertello, Mariana. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnologia; ArgentinaFil: Wall, Luis Gabriel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnologia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular; Argentin