BackgroundSugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N2-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins.ResultsAdopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases.ConclusionAn extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties.

The mammalian BiP is regulated by phosphorylation, and it is generally accepted that its unmodified form constitutes the biologically active species. In fact, the glycosylation inhibitor tunicamycin induces dephosphorylation of mammalian BiP. The stress-induced phosphorylation state of plant BiP has not been examined. Here, we demonstrated that soybean BiP exists in interconvertible phosphorylated and nonphosphorylated forms, and the equilibrium can be shift to either direction in response to different stimuli. In contrast to tunicamycin treatment, water stress condition stimulated phosphorylation of BiP species in soybean cultured cells and stressed leaves. Despite their phosphorylation state, we demonstrated that BiP isoforms from water-stressed leaves exhibit protein binding activity, suggesting that plant BiP functional regulation may differ from other eukaryotic BiPs. We also compared the induction of the soybean BiP gene family, which consists of at least four members designated soyBiPA, soyBiPB, soyBiPC, and soyBiPD, by tunicamycin and osmotic stress. Although all soybean BiP genes were induced by tunicamycin, just the soyBiPA RNA was upregulated by osmotic stress. In addition, these stresses promoted BiP induction with different kinetics and acted synergistically to increase BiP accumulation. These results suggest that the soybean BiP gene family is differentially regulated by abiotic stresses through distinct signaling pathways.

The hyperhydricity in eggplant (Solanum melongena L.) plants was monitored by the induction of the ER-luminal resident protein BiP. Although tissue culture conditions may induce BiP synthesis, the accumulation of BiP in hyperhydric shoots was consistently higher than in non-hyperhydric shoots. The leaf and stem anatomy in non-hyperhydric and hyperhydric eggplant was investigated aiming to identify structural changes associated with this phenomenon. In non-hyperhydric organs there were smaller and more organized cells, besides a more differentiated vascular system when compared with its hyperhydric counterpart. Scanning electron microscopy of leaves showed that leaf surface and stomata differentiation were also affected in hyperhydric plants.

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Plant nutrient uptake is an active process, requiring energy to accumulate essential elements at higher levels in plant tissues than in the soil solution, while the presence of toxic metals or excess of nutrients requires mechanisms to modulate the accumulation of ions. Genes encoding ion transporters isolated from plants and yeast were used to identify sugarcane putative homologues in the sugarcane expressed sequence tag (SUCEST) database. Five cluster consensi with sequence homology to plant high-affinity phosphate transporter genes were identified. One cluster consensus allowed the prediction of a full-length protein containing 541 amino acids, with 81% amino acid identity to the Nicotiana tabacum NtPT1 gene, consisting of 12 membrane-spanning domains divided by a large hydrophilic charged region. Putative homologues to Arabidopsis thaliana micronutrient transporter genes were also detected in some of the SUCEST libraries. Iron uptake in grasses involves the release of the phytosiderophore mugeneic acid (MA) which chelate Fe 3+ which is then absorbed by a specific transporter. Sugarcane expressed sequence tag (EST) homologous to genes coding for three enzymes of the mugeneic acid biosynthetic pathway [nicotianamine synthase; nicotianamine transferase; and putative mugeneic acid synthetase (ids3)] and a putative Fe 3+ -phytosiderophore transporter were detected. Seven sugarcane sequence clusters were identified with strong homology to members of the ZIP gene family (ZIP1, ZIP3, ZIP4, IRT1 and ZNT1), while four clusters homologous to ZIP2 and three to ZAT were found. Homologues to members of another gene family, Nramp, which code for broad-specificity transition metal transporters were also detected with constitutive expression. Partial transcripts homologous to genes encoding γ-glutamylcysteine synthetase, glutathione synthetase, and phytochelatin synthase (responsible for biosynthesis of the metal chelator phytochelatin) and all four types of the major plant metal-chelator peptide metallothionein (MT) were identified: Type I MT being the most abundant (>1% of seed-library reads), followed by Type II which had a similar pattern of expression as that described for Arabidopsis MT. Identifying and understanding the expression of genes associated with nutrient uptake and metal tolerance could lead to the development of more nutrient-efficient sugarcane cultivars, or might allow the use of sugarcane as a hyper-accumulator plant for the restoration of contaminated areas in phytoremediation programs.

The soybean binding protein (BiP) gene family consists of at least four members designated soyBiPA, soyBiPB, soyBiPC and soyBiPD. We have performed immunoblotting of two-dimensional (2D) gels and RT-PCR assays with gene-specific primers to analyze the differential expression of this gene family in various soybean organs. The 2D gel profiles of the BiP forms from different organs were distinct and suggested that the BiP genes are under organ-specific regulation. In fact, while all four BiP transcripts were detected in leaves by gene-specific reverse transcriptase-polymerase chain reaction (RT-PCR) assays, different subsets were detected in the other organs. The soyBiPD was expressed in all organs, whereas the expression of the soyBiPB was restricted to leaves. The soyBiPA transcripts were detected in leaves, roots and seeds and soyBiPC RNA was confined to leaves, seeds and pods. Our data are consistent with organ-specific expression of the soybean BiP gene family.

The binding protein BiP is an endoplasmic reticulum (ER)-resident member of the HSP70 stress-related protein family, which is essential for the constitutive function of the ER. In addition to responding to a variety of environmental stimuli, plant BiP exhibits a tissue-specific regulation. We have isolated two soybean BiP genomic clones, designated gsBiP6 and gsBiP9, and different extensions of their 5' flanking sequences were fused to beta-glucuronidase (GUS) reporter gene and introduced into Nicotiana tabacum by Agrobacterium tumefaciens-mediated transformation. Transgenic plants displayed prominent GUS activity in the vascular bundles of roots and shoots as well as in regions of intense cell division, such as procambial region and apical meristems. Promoter deletion analyses identified two cis-regulatory functional domains that are important for the spatially-regulated activation of BiP expression under normal plant development. While an AT-rich enhancer-like sequence, designated cis-acting regulatory domain 1, CRD1 (-358 to -211, on gsBiP6), activated expression of the BiP minimal promoter in all organs analyzed, BiP promoter activity in meristematic tissues and phloem cells required the presence of a second activating domain, CRD2 (-211 to -80). Apparently, the CRD2 sequence also harbors negative cis-acting elements, because removal of this region caused activation of gsBiP6 promoter in parenchymatic xylem rays. These results suggest that the tissue-specific control of BiP gene expression requires a complex integration of multiple cis-acting regulatory elements on the promoter.

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