Molecular insights into plant desiccation tolerance: transcriptomics, proteomics and targeted metabolite profiling in Craterostigma plantagineum

Abstract

Summary The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long‐term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and targeted metabolite profiling was carried out on leaves collected from different stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 39 metabolites were differentially abundant across the different sampling points. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post‐transcriptional modification in metabolic reprogramming to prepare plants for desiccation and recovery. The integrative analysis of all three data sets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of precise changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. The maintenance of cyclic electron flow and photorespiration, and the switch from C3 to crassulacean acid metabolism photosynthesis, may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration. Transcripts with a delayed translation, ATP‐independent bypasses, alternative respiratory pathway and 4‐aminobutyric acid shunt may all play a role in energy management, together conferring bioenergetic advantages to meet energy demands upon rehydration. This study provides a high‐resolution map of the changes occurring in primary metabolism during dehydration and rehydration and enriches our understanding of the molecular mechanisms underpinning plant desiccation tolerance. The data sets provided here will ultimately inspire biotechnological strategies for drought tolerance improvement in crops.

Systems biology of resurrection plants

“…In barley etioplasts, detection of ELIP proteins in the thylakoid membranes occurs after transcript abundance has decreased considerably [ 87 ]. The possible disconcordance between transcript and protein abundance in desiccating tissues has been highlighted previously in relation to resurrection species [ 1 , 5 , 88 ].…”

“…A recent combined transcriptomic, metabolomic and proteomics analysis of dehydrating C. plantagineum provides a more detailed snapshot of protein changes during desiccation [ 88 ]. The authors identified over 1400 proteins, of which 43% showed significant changes in abundance during VDT.…”

The Cell Wall Proteome of Craterostigma plantagineum Cell Cultures Habituated to Dichlobenil and Isoxaben

“…Proteins were quantified with the RC DC™ kit (BioRad, Temse, Belgium). The steps of gel-free proteomics were performed exactly as recently published [37].…”

“…MS analyses were performed as previously reported [36]. MS and MS/MS spectra were submitted for database-dependent identification against the in-house transcript database (containing 288,270 sequences [37]), using Mascot. The parameters used were the following: mass tolerance MS 100 ppm, mass tolerance MS/MS 0.5 Da, maximum 2 missed cleavages, fixed modification carbamidomethyl-cysteine, variable modifications oxidation of methionine, oxidation of tryptophan to kynurenine, double oxidation of tryptophan and the loss of 2Da from phenylalanine to didehydrophenylalanine.…”

“…After querying the in-house C. plantagineum transcriptome [37], the shotgun approach based on LC-MS identified 310, 254 and 33 significant ID proteins passing the filters [p-value < 0.05, maximum fold change (max FC) > 1.5] in the CaCl 2 , EGTA and LiCl fractions, respectively. Of these proteins, 62, 75, and 4 were predicted to be extracellular, corresponding to 20%, 29.5%, and 12% of the total proteins in the 3 fractions (Figure S3 and Supplementary File S1 where the % values appear in the subfolders for each fraction).…”