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Developmental gene expression in Gaspe in response to nitrate

ABSTRACT: Elucidation of the gene networks underlying the response to N supply and demand should facilitate the improvement of the N uptake efficiency of plants. We undertook a transcriptomic analysis of maize to identify genes responding to both NO3- provision and to development-based N demand changes across the entire lifecycle. Gene co-expression networks were derived by cluster analysis of the transcript profiles. The majority of NO3--responsive transcription occurred at 11 (D11), 18 (D18) and 29 (D29) days after emergence, with differential expression predominating in the root at D11 and D29 and in the leaf at D18. A cluster of 98 probe sets was identified, the expression pattern of which is similar to that of the high-affinity NO3- transporter (NRT2) genes across the lifecycle. The cluster is enriched with genes encoding enzymes and proteins of lipid metabolism and transport, respectively. These are candidate genes for the response of maize to N supply and demand. Only a few patterns of differential gene expression were observed over the entire lifecycle, however the composition of the classes of the genes differentially regulated at individual time points was unique, suggesting tightly controlled regulation of NO3- responsive gene expression.

ORGANISM(S): Zea mays

PROVIDER: GSE61820 | GEO | 2014/09/27

SECONDARY ACCESSION(S): PRJNA262444

REPOSITORIES: GEO

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Project description:Arable soils are extremely heterogeneous in spatial nutrient distribution. It is well documented that lateral roots (LRs) proliferate in nitrate-rich patch. Yet less information is available as to which genes are involved in this process, in particular in cereals. To understand the molecular mechanism for local nitrate induced LR growth in maize (Zea mays L.), we analyzed the gene expression profiling in maize root in early response (1 hour) to local nitrate stimulation by using Maize Oligonucleotide Array (http://www.maizearray.org) and a split-root system. Selected differentially expressed genes were further confirmed by semi-quantitative RT-PCR. The results showed that reception and/or transduction of local NO3- signal involve some important protein kinases and protein phosphatases (histidine kinases, serine/threonine kinases, protein phosphatase 2A etc.) and transcription factors (F-box, Zinc finger, Myb and bZIP transcription factors and response regulator). Increasing expression of genes encoding auxin response factor 7b, ethylene receptor, and cytokinin oxidase suggests strong interaction among hormonal pathways and local NO3- signaling pathways. Genes involving NO3- uptake and assimilation (NRT2.1, NR, etc.), sugar transport (a sugar transporter) and utilization (a sucrose synthase) were enhanced in the N-fed root. Furthermore, local NO3- induces rapid expression of genes related to cell division and expansion such as alpha-expansin, celluose synthase, kinesin, plasma membrane and tonoplast aquaporins. Based on the differentially expressed genes, a putative model which combines both the 'NO3- signal' and 'metabolic sink' theories is proposed to explain the molecular mechanism controlling local nitrate induced LR elongation in maize. plants were pre-cultured in solution containing 0.5 mmol L-1 NO3- for 6 days and then transferred to N-free solution to grow for another 2 days. Then these plants were transferred to a two-compartment split-root system with only half root supplied with 1.0 mmol L-1 NO3-. Supply of Ca2+ in the N-free half was compensated by adding 1.0 mmol L-1 CaCl2. One hour after the local nitrate treatment, root segments (15cm from root tip to lateral root elongation zone) were sampled for RNA extraction. Two biological replicates were performed for each treatment.

Project description:Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to cluster 19A mutants and individual sub-deletions for the cluster 19A genes tin1, tin3, tin4 and tin5. We found plant responses to the mutants were significantly different although the macroscopic phenotypes of the individual mutants were very similar. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200∆19A, SG200∆tin1, SG200∆tin3, SG200∆tin4 and SG200∆tin5, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023). These data served as controls for this experiment.

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Developmental gene expression in Gaspe in response to nitrate

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