Transcriptomic adaptations in rice suspension cells under sucrose starvation

Abstract

Sugar is an important resource for energy generation and developmental regulation in plants, and sucrose starvation causes enormous changes in cellular morphology, enzyme activities and gene expression. Genome-wide gene expression profiling provides a comprehensive knowledge of gene expression under nutrient depletion and senescence; however, that of a monocot model plant, rice, under sucrose depletion is still under investigation. Here, the time-course monitoring of gene expression profiles in sucrose-starved rice (Oryza sativa cv Tainung67) suspension cells was investigated by 21495 probes contained in Agilent rice chip. In sucrose-starved cells, the induced vacuolar biogenesis coincided with significantly upregulated transcripts of H+-pyrophosphatase, delta-TIP, one putative alpha-TIP, several vacuolar proteases and proteinase inhibitors, and one OsATG3. To survey the overall metabolic adaptations under sucrose depletion, the genes with significantly altered expression level were incorporated into multiple metabolic pathways. Most genes encoding enzymes involved in biosynthesis and degradation pathways of various macromolecules were comprehensively down-and upregulated, respectively, with sucrose starvation. Transcriptional regulation of gene expression is important for physiological adaptations to environmental stress, and many transcription factors, including bZIPs, NACs, and WRKY, showed significant increase in transcriptional level under sucrose starvation. Concurrently, statistical analysis revealed that their corresponding consensus cis-elements, such as ABA-responsive element, CACG, ACI, ACII and CTTATCC, were frequently found in the promoter regions of many sucrose starvation-upregulated genes. Particle bombardment-mediated and luciferase activity-based transient promoter assays revealed the CTTATCC, derived form TATCCA, and the AC motifs to be promising sucrose-starvation responsive activators in rice suspension cells.

Differential Anoxic Expression of Sugar-Regulated Genes Reveals Diverse Interactions between Sugar and Anaerobic Signaling Systems in Rice

“…Currently, genome-wide scale data for glucose response is not available in rice. Therefore, we have checked the potential sugar responsiveness of those selected genes by examining their occurrence in genomic profiling data for sucrose starvation in rice suspension cells (Wang, 2007). More than 32% of anoxia-responding genes (848/2648) were found to be sugar-responsive in rice, too ( Supplementary Fig.…”

Transcriptional dynamics during cell wall removal and regeneration reveals key genes involved in cell wall development in rice

“…The data was compared with the genes induced in response to sucrose starvation in rice suspension cells (Wang et al 2007) and cellulase treatment to rice leaves (Jha et al 2010). Microarray analysis has also been reported to identify genes induced during cell elongation (Kwon et al 2005) and cell wall regeneration using suspension cells in Arabidopsis (Irshad et al 2008).…”

“…The datasets used for comparison include sucrose starvation in suspension cells (Wang et al 2007); cellulase treatment to leaves (Jha et al 2010); Xanthomonas oryzae pv. oryzae (XOO) and Xanthomonas oryzae pv.…”

“…Because of their ability to regenerate cell walls and their homogenous nature, protoplasts have emerged as a versatile investigative tool for understanding the physiological and genetic aspects of plants in response to experimental treatments and cell wall perturbations (Burgess 1983;Cazale et al 1998;Manfield et al 2004;Pojnar and Cocking 1967;Shea et al 1989;Skopelitis et al 2006;Wang et al 2007;Bart et al 2010). Cell wall regeneration around protoplasts varies in different species ranging from as soon as 10 min following transfer of cells to regeneration medium to *5 days (Amstel and Kengen 1996; Burgess and Fleming 1974;Kwon et al 2005;Yang et al 2008).…”

Convergent Starvation Signals and Hormone Crosstalk in Regulating Nutrient Mobilization upon Germination in Cereals

“…The TA box is the most highly conserved motif and controls the promoter activity of at least 20 genes upregulated by sugar starvation in rice suspension cells (Wang et al, 2007). The a-amylase promoter is also activated by GA through the gibberellin response complex (GARC), in which the adjacent gibberellin response element (GARE) and the TA/ Amy box are key elements and act synergistically (Lanahan et al, 1992;Rogers et al, 1994;Gubler et al, 1999;Gómez-Cadenas et al, 2001).…”