Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings

Abstract

To understand the transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings, genome-wide changes in gene expression were analyzed using a soybean microarray chip containing 42,034 60-mer oligonucleotide probes. More than 6,000 of flooding-responsive genes in the roots including hypocotyl of soybean seedlings were identified. The transcriptional analysis showed that genes related to photosynthesis, glycolysis, Ser-Gly-Cys group amino acid synthesis, regulation of transcription, ubiquitin-mediated protein degradation and cell death were significantly up-regulated by flooding. Meanwhile, genes related to cell wall synthesis, secondary metabolism, metabolite transport, cell organization, chromatin structure synthesis, and degradation of aspartate family amino acid were significantly down-regulated. Comparison of the responses with other plants showed that genes encoding pyrophosphate dependent phosphofructokinase were down-regulated in flooded soybean seedlings, however, those in tolerant plants were up-regulated. Additionally, genes related to RNA processing and initiation of protein synthesis were not up-regulated in soybean, however, those in tolerant plants were up-regulated. Furthermore, we found that flooding-specific up-regulation of genes encoding small proteins which might have roles in acclimation to flooding. These results suggest that functional disorder of acclimative responses to flooding through transcriptional and post-transcriptional regulations is involved in occurring flooding injury to soybean seedlings.

Evaluation of Metabolite Alteration under Flooding Stress in Soybeans

“…Furthermore, Komatsu et al 20 suggested that flooding stress directly affects plasma membrane proteins. Recently, in a transcriptome study 39 , the expression of many genes related to photosynthesis, glycolysis, amino acid metabolism, hormone metabolism, protein degradation, metabolite transport, and cell wall metabolism was significantly affected by flooding stress, which suggested that the latter affects many areas of metabolism. However, it is unclear which metabolic pathways were strongly affected, although there was an impact on many biological processes.…”

“…However, the influence of flooding stress on metabolites related to fermentation and glycolysis remains unclear, although the expression of these proteins was affected by flooding stress. Recently, transcriptome studies revealed that hypoxia and flooding stress affected the expression of genes related to carbon metabolism, nitrogen metabolism, cell wall formation, and signal transduction, as well as transcription factors 1,19,23,39 . These reports suggested that many metabolites are affected by flooding stress, making it necessary to elucidate the changes in numerous metabolites using a metabolomics technique which may enable a comprehensive understanding of plant response to flooding.…”

Waterproofing Crops: Effective Flooding Survival Strategies

“…Lee et al, 2011;Nanjo et al, 2011). The strong down-regulation of protein synthesis and highly selective mRNA translation during low-oxygen stress has been investigated by comparative profiling of the total cellular mRNA content with the mRNAs engaged in translation (translatomes) during hypoxia (Branco-Price et al, 2005, 2008.…”

A Co-Opted Hormonal Cascade Activates Dormant Adventitious Root Primordia upon Flooding in Solanum dulcamara

“…This results in detrimental effects on cellular metabolic homeostasis, but at the same time these changes in gas concentrations are used as cues to alter gene expression leading to acclimation. In many plant species, genes involved in (hormonal) signaling, photosynthesis, anaerobic metabolism, and secondary metabolism are rapidly modulated in response to flooding (Zhang et al, 2006;Lee et al, 2007;Christianson et al, 2010;Lee et al, 2011;Nanjo et al, 2011;Qi et al, 2012). To prevent or shorten the imminent energy crisis, plant species from wetland habitats show morphological adaptations such as elongation of the shoot, formation of aerenchyma in existing tissues, or development of new, aerenchymatous adventitious roots (ARs), all of which are aimed at improving gas exchange between plant tissues and the atmosphere (Bailey-Serres and Voesenek, 2008).…”