Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery.

The rice (Oryza sativa L.) ethylene-responsive transcription factor gene SUB1A-1 confers tolerance to prolonged, complete submergence by limiting underwater elongation growth. Upon desubmergence, SUB1A-1 genotypes rapidly recover photosynthetic function and recommence development towards flowering. The underpinnings of the transition from stress amelioration to the return to homeostasis are not well known. Here, transcriptomic and metabolomic analyses were conducted to identify mechanisms by which SUB1A improves physiological function over the 24 hr following a sublethal submergence event. Evaluation of near-isogenic genotypes after submergence and over a day of reaeration demonstrated that SUB1A transiently constrains the remodelling of cellular activities associated with growth. SUB1A influenced the abundance of ca. 1,400 transcripts and had a continued impact on metabolite content, particularly free amino acids, glucose, and sucrose, throughout the recovery period. SUB1A promoted recovery of metabolic homeostasis but had limited influence on mRNAs associated with growth processes and photosynthesis. The involvement of low energy sensing during submergence and recovery was supported by dynamics in trehalose-6-phosphate and mRNAs encoding key enzymes and signalling proteins, which were modulated by SUB1A. This study provides new evidence of convergent signalling pathways critical to the rapidly reversible management of carbon and nitrogen metabolism in submergence resilient rice.

VIZR--an automated chemometric technique for metabolic profiling.

A chemometric technique, visual interpretation of z-score ratios (VIZR), written in the open source code R, has been developed to identify metabolic differences between individual biosamples and a control group. To demonstrate the capabilities of VIZR, 49 urine samples were collected from healthy volunteers: 41 samples were collected randomly following a normal dietary routine and 7 test samples were collected after dietary supplementation with either ibuprofen or alcoholic beverages. An eighth test sample was prepared by 50% dilution of a control sample. Sample analysis was conducted by (1)H nuclear magnetic resonance (NMR) spectroscopy and the collected data were subjected to VIZR analysis, which successfully discriminated each of the 8 test samples from the 41 control samples. In addition, VIZR analysis revealed the NMR spectral regions responsible for the disparity between the individual test samples and the control group. The self-normalizing nature of the VIZR calculation provides a robust analysis independent of dilution effects, which is especially important in urine analyses. Potential applications of VIZR include high-throughput data analysis for toxicological profiling, disease diagnosis, and biomarker identification in any type of biosample for which a control dataset can be established. Although demonstrated herein for the statistical analysis of (1)H NMR data, the VIZR program is platform independent and could be applied to digitized metabolic datasets acquired using other techniques including hyphenated mass spectrometry measurements.