Integrated Metabolomic and Transcriptomic Analyses to Understand the Effects of Hydrogen Water on the Roots of Ficus hirta Vahl.

Wuzhimaotao (Ficus hirta Vahl) is an important medicinal and edible plant in China. The extract from the roots of Ficus hirta Vahl contains phenylpropanoid compounds, such as coumarins and flavonoids, which are the main active components of this Chinese herbal medicine. In this study, we analyzed the transcriptomic and metabolomic data of the hydrogen-water-treated roots of Ficus hirta Vahl and a control group. The results showed that many genes and metabolites were regulated in the roots of Ficus hirta Vahl that were treated with hydrogen water. Compared with the control group, 173 genes were downregulated and 138 genes were upregulated in the hydrogen-rich water treatment group. Differential metabolite analysis through LC-MS showed that 168 and 109 metabolites had significant differences in positive and negative ion mode, respectively. In the upregulated metabolites, the main active components of Wuzhimaotao, such as the phenylpropane compounds naringin, bergaptol, hesperidin, and benzofuran, were found. Integrated transcriptomic and metabolomic data analysis showed that four and one of the most relevant pathways were over enriched in positive and negative ion mode, respectively. In the relationship between metabolites and DEGs, phenylpropanoid biosynthesis and metabolism play an important role. This indicates that phenylpropanoid biosynthesis and metabolism may be the main metabolic pathways regulated by hydrogen water. Our transcriptome analysis showed that most of the DEGs with |log2FC| ≥ 1 are transcription factor genes, and most of them are related to plant hormone signal transduction, stress resistance, and secondary metabolism, mainly phenylpropanoid biosynthesis and metabolism. This study provides important evidence and clues for revealing the botanical effect mechanism of hydrogen and a theoretical basis for the application of hydrogen agriculture in the cultivation of Chinese herbal medicine.

Progress in the study of biological effects of hydrogen on higher plants and its promising application in agriculture.

While the medical effects of hydrogen have been broadly analyzed, research into the effects of hydrogen on higher plants has often been of lesser concern. Recent studies on the botanical effects of hydrogen have shown that it is involved in signal transduction pathways of plant hormones and can improve the resistance of plants to stressors, such as drought, salinity, cold and heavy metals. In addition, hydrogen could delay postharvest ripening and senescence of fruits. Observational evidence has also shown that hydrogen can regulate the flowering time of plants. These results indicate that hydrogen may have great potential applications within agricultural production, indicating that there may be a new 'hydrogen agricultural era' to come.

Molecular hydrogen is involved in phytohormone signaling and stress responses in plants.

Molecular hydrogen (H2) metabolism in bacteria and algae has been well studied from an industrial perspective because H2 is viewed as a potential future energy source. A number of clinical trials have recently reported that H2 is a therapeutic antioxidant and signaling molecule. Although H2 metabolism in higher plants was reported in some early studies, its biological effects remain unclear. In this report, the biological effects of H2 and its involvement in plant hormone signaling pathways and stress responses were determined. Antioxidant enzyme activity was found to be increased and the transcription of corresponding genes altered when the effects of H2 on the germination of mung bean seeds treated with phytohormones was investigated. In addition, upregulation of several phytohormone receptor genes and genes that encode a few key factors involved in plant signaling pathways was detected in rice seedlings treated with HW. The transcription of putative rice hydrogenase genes, hydrogenase activity, and endogenous H2 production were also determined. H2 production was found to be induced by abscisic acid, ethylene, and jasmonate acid, salt, and drought stress and was consistent with hydrogenase activity and the expression of putative hydrogenase genes in rice seedlings. Together, these results suggest that H2 may have an effect on rice stress tolerance by modulating the output of hormone signaling pathways.

Evolutionary expansion and functional diversification of oligopeptide transporter gene family in rice.

BACKGROUND: Oligopeptide transporters (OPTs) play important roles in the mobilization of organic nitrogenous compounds and usually associate with tissues that show signs of rapid protein hydrolysis, such as germinating seeds and senescing leaves. This study is to investigate rice OPT genes. RESULTS: A total of sixteen OsOPT genes (Os for Oryza sative L.) were identified in the rice genome, which were then classified into six sections that belong to two subfamilies (the PT and YSL subfamily). The major mechanisms for evolutionary expansion of the sixteen genes during the rice genome evolution include segmental and tandem duplication. Calculation of the duplication event dates indicated that the sixteen genes originated from nine original OsOPT genes, and the duplication events could be classified into three evolutionary stages. The first evolutionary stage occurred approximately 50 million years ago (Mya) and involved the evolution of four new genes. The second evolutionary stage was approximately 20 Mya and was marked by the appearance of two new genes, and the third evolutionary stage was approximately 9 Mya when two new genes evolved. Mining of the expression database and RT-PCR analysis indicated that the expression of most duplicated OsOPT genes showed high tissue specificities. Diverse expression patterns for the sixteen genes were evaluated using both semi-quantitative RT-PCR and the MPSS data. Expression levels of some OsOPT genes were regulated by abiotic and biotic stresses suggesting the potential involvement of these gene products in rice stress adaptation. Five OsOPT gene mutants showed abnormal development and growth, the primary analysis of five OsOPT gene mutants suggested that they may be necessary for rice development. CONCLUSIONS: These results suggested that rice-specific OsOPT genes might be potentially useful in improving rice.

Slatkin's Paradox: when direct observation and realized gene flow disagree. A case study in Ficus.

In flying insects, there is frequently a lack of congruence between empirical estimates of local demographic parameters and the prediction that differentiation between populations should decrease with increasing dispersal, a puzzling phenomenon known as Slatkin's Paradox. Here, we generalize Slatkin's Paradox to other taxa, drawing from available information on dispersal to predict the relative importance of pollen vs. seed migration in structuring broad-scale patterns of genetic variation in Ficus hirta, a dioecious fig whose pollen is dispersed by minute, species-specific fig wasps and whose seeds are disseminated by a variety of vagile vertebrates (especially bats and birds). Local-scale observational and genetic studies of dioecious understory figs suggest comparable rates of pollen and seed migration. In contrast, we found unusually low nuclear differentiation (F(ST) =0.037, R(ST) =0.074) and high chloroplast differentiation (G(ST) =0.729, N(ST) =0.798) among populations separated by up to 2850km, leading us to reject the hypothesis of equal pollen and seed migration rates and to obtain an equilibrium estimate of the ratio of pollen to seed migration of r=16.2-36.3. We reconcile this example of Slatkin's Paradox with previously published data for dioecious figs and relate it to the picture of exceptionally long-distance wasp-mediated pollen dispersal that is emerging for large monoecious fig trees. More generally, we argue that Slatkin's Paradox is a general phenomenon and suggest it may be common in plants and animals.

Expression of the hypersensitive response-assisting protein in Arabidopsis results in harpin-dependent hypersensitive cell death in response to Erwinia carotovora.

Active defense mechanisms of plants against pathogens often include a rapid plant cell death known as the hypersensitive cell death (HCD). Hypersensitive response-assisting protein (HRAP) isolated from sweet pepper intensifies the harpin(Pss)-mediated HCD. Here we demonstrate that constitutive expression of the hrap gene in Arabidopsis results in an enhanced disease resistance towards soft rot pathogen, E. carotovora subsp. carotovora. This resistance was due to the induction of HCD since different HCD markers viz. Athsr3, Athsr4, ion leakage, H(2)O(2) and protein kinase were induced. One of the elicitor harpin proteins, HrpN, from Erwinia carotovora subsp. carotovora was able to induce a stronger HCD in hrap-Arabidopsis than non-transgenic controls. To elucidate the role of HrpN, we used E. carotovora subsp. carotovora defective in HrpN production. The hrpN(-) mutant did not induce disease resistance or HCD markers in hrap-Arabidopsis. These results imply that the disease resistance of hrap-Arabidopsis against a virulent pathogen is harpin dependent.