Messenger RNA is conserved during drying of the drought-tolerant moss Tortula ruralis

Stability investigation of air-dried olive ribo nucleic acids for metavirome studies

BACKGROUND

The application of ribo nucleic acids for molecular studies requires high integrity and quality of extracted total RNA samples. In addition, the need to transfer RNA samples at room temperature without special treatments such as ice and liquid nitrogen storage according to international transport laws highlights the importance of low cost alternative methods such as RNA air-drying, lyophilisation and transportable agents. In this study, the quality and quantity of air-dried RNA samples from leaf, petiole and bark tissues of different olive genotypes using several RNA extraction methods were compared with lyophilized ground leaves and RNAlater-stored tissue samples before precipitation. The quality of RNA and prepared libraries were checked by several techniques including agarose and polyacrylamide gel electrophoresis, Agilent quality control, RT-PCR amplification of housekeeping and viral genes and high throughput sequencing.

RESULTS

Although RNA value varied amongst cultivars, RNA extraction with TRIzol™ Reagent in fresh extractions and samples stored in RNAlater before RNA extraction resulted in 455.26 ng/µL and 63.46 ng/µL (mean value of cultivars) as the highest RNA concentration averages, respectively. RNA samples extracted by TRIzol™ Reagents and stored for a short term at - 80 °C before air-drying showed the third highest concentration (44.87 ng/µL). The synthesized cDNAs quality for PCR amplification of housekeeping genes (Rbc 1 and Nad 5) and partial genomes of Arabis mosaic virus and Cucumber mosaic virus showed satisfactory results in RNA samples extracted by TRIzol™ Reagents despite its variation amongst cultivars.

CONCLUSIONS

Considering the difficulties in the extraction of high quality and quantity RNA in olive for molecular analyses, this study demonstrated that RNA extraction method based on TRIzol™ Reagent can be considered for virobiome studies of both fresh and air-dried samples.

Cloning of a novel trypsin inhibitor from the Traditional Chinese medicine decoction pieces, Radix Trichosanthis

Most herbs of traditional Chinese medicine (TCM) are used as air-dried decoction pieces that are manufactured and kept at ambient temperature for long periods. Given the ability of some desiccation-tolerant plants to conserve RNA, it could be worthwhile to isolate mRNA from TCM decoction pieces as part of a transcriptomic strategy to identify new substances with potential pharmaceutical application. Here, we report the molecular cloning of a novel trypsin inhibitor (as the probable alleleic variants TKTI-2 and TKTI-3) from the decoction piece of Radix Trichosanthis, representing the dried root of Trichosanthes kirilowii. From this material, the total RNA was extracted and a cDNA library was constructed from the isolated mRNA from which the cDNAs of two precursors were successfully cloned and sequenced. TKTI-3 showed an amino-acid substitution in the otherwise highly-conserved P1-P1' reaction site of the mature peptide, which we confirmed to not be an artefact. Subsequent analysis using LC-MS/MS detected the presence of specific tryptic peptides expected from TKTI-3, confirming the presence and expression of this locus in Radix Trichosanthis. More generally, this study indicates that mRNA can persist in decoction pieces and so could present a viable option for the molecular cloning from other TCMs.

Proteomic analysis of leaf proteins during dehydration of the resurrection plant Xerophyta viscosa

The desiccation-tolerant phenotype of angiosperm resurrection plants is thought to rely on the induction of protective mechanisms that maintain cellular integrity during water loss. Two-dimensional (2D) sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the Xerophyta viscosa Baker proteome was carried out during dehydration to identify proteins that may play a role in such mechanisms. Quantitative analysis revealed a greater number of changes in protein expression levels at 35% than at 65% relative water content (RWC) compared to fully hydrated plants, and 17 dehydration-responsive proteins were identified by tandem mass spectrometry (MS). Proteins showing increased abundance during drying included an RNA-binding protein, chloroplast FtsH protease, glycolytic enzymes and antioxidants. A number of photosynthetic proteins declined sharply in abundance in X. viscosa at RWC below 65%, including four components of photosystem II (PSII), and Western blot analysis confirmed that two of these (psbP and Lhcb2) were not detectable at 30% RWC. These data confirm that poikilochlorophylly in X. viscosa involves the breakdown of photosynthetic proteins during dismantling of the thylakoid membranes. In contrast, levels of these photosynthetic proteins were largely maintained during dehydration in the homoiochlorophyllous species Craterostigma plantagineum Hochst, which does not dismantle thylakoid membranes on drying.

Glutathione Status and Protein Synthesis during Drought and Subsequent Rehydration in Tortula ruralis

Glutathione status and its relationship to protein synthesis during water deficit and subsequent rehydration have been examined in the drought-tolerant moss, Tortula ruralis. During slow drying there is a small decrease in total glutathione but the percentage of oxidized glutathione (GSSG) increases. During rapid drying there is little change in total glutathione but a small increase in GSSG. On rehydration of slowly dried moss, GSSG rapidly declines to normal level. But when rapidly dried moss is rehydrated, there is an immediate, sharp increase in GSSG as a percentage of total glutathione. After 2 hours of rehydration GSSG starts declining and reaches a normal level in about 6 hours. When an increasing degree of steady state water deficit is imposed on the moss tissue with polyethylene glycol 6000, there is a progressive decrease in protein synthesis but an increase in oxidized glutathione. When 5 millimolar GSSG is supplied exogenously during rehydration of rapidly dried or slowly dried moss, protein synthesis is strongly inhibited. In vitro protein synthesis supported by moss mRNA is also inhibited by more than 85% by 150 micromolar GSSG. The role of glutathione status in water deficit-induced inhibition of protein synthesis is discussed.

Enzyme Dynamics of the Resurrection Plant Selaginella lepidophylla (Hook. & Grev.) Spring during Rehydration

The activities of 10 enzymes involved in carbohydrate metabolism were measured in both desiccated and rehydrated fronds of the desiccation-tolerant pteridophyte Selaginella lepidophylla (Hook. & Grev.) Spring. Enzyme conservation was defined as the ratio of desiccated to hydrated frond enzyme activity. The mean level of conservation was 74%, with nine of the 10 enzymes showing significant activity increases (P<0.05) during hydration. The mean of photosynthetic enzyme conservation was significantly lower (P=0.05) than the mean for glycolytic and respiratory enzymes combined. Chloramphenicol inhibited the normal activity increase in ribulose bisphosphate carboxylase and (NADPH)triose-P dehydrogenase but not pyruvate kinase upon rehydration. Cycloheximide did not affect the normal activity increase for these three enzymes. It is concluded that substantial enzyme conservation is beneficial for rapid resumption of metabolic activity in resurrection plants.

Proteins Associated with Adaptation of Cultured Tobacco Cells to NaCl

Cultured tobacco cells (Nicotiana tabacum L. cv Wisconsin 38) adapted to grow in medium containing high levels of NaCl or polyethylene glycol (PEG) produce several new or enhanced polypeptide bands on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The intensities of some of the polypeptide bands (molecular weights of 58, 37, 35.5, 34, 26, 21, 19.5, and 18 kilodaltons) increase with increasing levels of NaCl adaptation, while the intensities of other polypeptide bands (54, 52, 17.5, and 16.5 kilodaltons) are reduced. Enhanced levels of 43- and 26-kilodalton polypeptides are present in both NaCl and PEG-induced water stress adapted cells but are not detectable in unadapted cells. In addition, PEG adapted cells have enhanced levels of 29-, 17.5-, 16.5-, and 11-kilodalton polypeptides and reduced levels of 58-, 54-, 52-, 37-, 35.5-, 34-, 21-, 19.5-, and 18-kilodalton polypeptide bands.Synthesis of 26-kilodalton polypeptide(s) occurs at two different periods during culture growth of NaCl adapted cells. Unadapted cells also incorporate (35)S into a 26-kilodalton polypeptide during the later stage of culture growth beginning at midlog phase. The 26-kilodalton polypeptides from adapted and unadapted cells have similar partial proteolysis peptide maps and are immunologically cross-reactive. During adaptation to NaCl, unadapted cells synthesize and accumulate a major 26-kilodalton polypeptide, and the beginning of synthesis corresponds to the period of osmotic adjustment and culture growth. From our results, we suggest an involvement of the 26-kilodalton polypeptide in the adaptation of cultured tobacco cells to NaCl and water stress.

Plant Desiccation and Protein Synthesis : V. Stability of Poly (A) and Poly (A) RNA during Desiccation and Their Synthesis upon Rehydration in the Desiccation-Tolerant Moss Tortula ruralis and the Intolerant Moss Cratoneuron filicinum

Upon desiccation of gametophytes of the desiccation-tolerant moss Tortula ruralis preexisting pools of poly(A)(-) RNA (rRNA) remain inact, regardless of the speed at which desiccation is achieved. Preexisting poly(A)(+) RNA pools (mRNA) are unaffected by slow desiccation but are substantially reduced during rapid desiccation. Poly(A)(-) RNA involved in protein synthesis is also unaffected by desiccation, whereas the levels of polysomal poly(A)(+) RNA in rapid- and slow-dried moss closely reflect the state of the protein synthetic complex in these dried samples.Poly(A)(-) RNA pools, both total and polysomal, are also stable during the rehydration of both rapid- and slow-dried moss. The total poly(A)(+) RNA pool decreases upon rehydration, but this reduction is simply an expression of the normal turnover of poly(A)(+) RNA in this moss. Analysis of polysomal fractions during rehydration reveals the continued use of conserved poly(A)(+) RNA for protein synthesis. The rate of synthesis of poly(A)(+) RNA upon rehydration appears to depend upon the speed at which prior desiccation is administered. Rapidly dried moss synthesizes poly(A)(+) RNA at a faster rate, 60 to 120 minutes after the addition of water, than does rehydrated slowly dried moss. Recruitment of this RNA into the protein synthetic complex also follows this pattern. Comparative studies involving the aquatic moss Cratoneuron filicinum are used to gain an insight into the relevance of these findings with respect to the cellular mechanisms associated with desiccation tolerance.

Plant Desiccation and Protein Synthesis. IV. RNA Synthesis, Stability, and Recruitment of RNA into Protein Synthesis during Desiccation and Rehydration of the Desiccation-Tolerant Moss, Tortula ruralis

Upon rehydration of desiccated Tortula ruralis, RNA synthesis is immediately resumed; this resumption is quicker in moss recovering from slow drying than from rapid drying. Newly synthesized RNA enters the protein synthetic complex almost immediately upon rehydration, reaching control steady state levels within 2 hours after slow drying and 6 hours after rapid drying. RNA synthesized in the 1st hour following the readdition of water enters into polysomes much earlier after slow drying than after rapid drying. The RNA components of the protein synthetic complex are stable to desiccation at either slow or rapid speeds, although more so following the former drying regime. Immediately upon rehydration, these conserved RNA are readily utilized for protein synthesis, and continue to be so at least 4 hours thereafter. Hence, the speed of desiccation affects the rate at which RNA is synthesized upon subsequent rehydration, as well as the mode of utilization of that RNA.

Stability and Synthesis of Phospholipids during Desiccation and Rehydration of a Desiccation-Tolerant and a Desiccation-Intolerant Moss

The fatty acid composition of the phospholipids from the desiccation-tolerant moss Tortula ruralis (Hedw.) Gaertn, Meyer and Scherb and the desiccation-intolerant moss Cratoneuron filicinum has been determined. No changes in composition occur in either moss as a consequence of rapid drying, but, after slow drying, there is a decline in some unsaturated fatty acids. Upon rehydration of T. ruralis after slow drying, these acids decline further; however, within 105 minutes, they regain the same levels as those in undesiccated controls. A smaller and more transient decline occurs after rapid desiccation. Most phospholipid unsaturated fatty acids decrease during rehydration of C. filicinum, and their levels are not recovered. After both rapid and slow drying of T. ruralis, acetate and glycerol are incorporated into the phospholipid fraction, although de novo synthesis, alone, might not account for the increase in unsaturated fatty acids upon rehydration. Very little acetate or glycerol is incorporated during rehydration of C. filicinum. Loss of unsaturated fatty acids from the phospholipids of T. ruralis does not appear to be associated with increased lipoxygenase activity. Furthermore, there is little correlation between the extent of peroxidation of fatty acids due to desiccation and changes in the phospholipid fraction.

Protein Synthesis and Photosynthetic Recovery in the Resurrection Plant, Selaginella lepidophylla

The effects of inhibition of protein synthesis on whole-plant CO(2) exchange and on protein synthesis during hydration of the resurrection plant Selaginella lepidophylla (Hook and Grev.) were examined. Both chloramphenicol and cycloheximide inhibited the redevelopment of photosynthetic capacity which normally occurs within 24 hours of hydration in the light. The inhibitory effect of chloramphenicol was greater than that of cycloheximide. The onset of chloramphenicol inhibition of net photosynthesis occurred only after 12 hours of hydration. Cycloheximide stimulated net CO(2) influx early after rehydration and inhibited net CO(2) influx after 14 hours of hydration. Total protein synthesis, as measured by l-[(35)S]methionine incorporation, increased through 24 hours of hydration. Based upon the results obtained with the protein synthesis inhibitors, most protein synthesis within the first 12 hours of hydration was cytoplasm-directed, whereas the rate of organelle-directed protein synthesis remained low until 12 hours of hydration and increased rapidly thereafter. These data suggest that both organelle- and cytoplasm-directed protein synthesis are necessary for full photosynthetic recovery during rehydration of S. lepidophylla.