CwJAZ4/9 negatively regulates jasmonate-mediated biosynthesis of terpenoids through interacting with CwMYC2 and confers salt tolerance in Curcuma wenyujin.

Plant JASMONATE ZIM-DOMAIN (JAZ) genes play crucial roles in regulating the biosynthesis of specialized metabolites and stressful responses. However, understanding of JAZs controlling these biological processes lags due to numerous JAZ copies. Here, we found that two leaf-specific CwJAZ4/9 genes from Curcuma wenyujin are strongly induced by methyl-jasmonate (MeJA) and negatively correlated with terpenoid biosynthesis. Yeast two-hybrid, luciferase complementation imaging and in vitro pull-down assays confirmed that CwJAZ4/9 proteins interact with CwMYC2 to form the CwJAZ4/9-CwMYC2 regulatory cascade. Furthermore, transgenic hairy roots showed that CwJAZ4/9 acts as repressors of MeJA-induced terpenoid biosynthesis by inhibiting the terpenoid pathway and jasmonate response, thus reducing terpenoid accumulation. In addition, we revealed that CwJAZ4/9 decreases salt sensitivity and sustains the growth of hairy roots under salt stress by suppressing the salt-mediated jasmonate responses. Transcriptome analysis for MeJA-mediated transgenic hairy root lines further confirmed that CwJAZ4/9 negatively regulates the terpenoid pathway genes and massively alters the expression of genes related to salt stress signaling and responses, and crosstalks of multiple phytohormones. Altogether, our results establish a genetic framework to understand how CwJAZ4/9 inhibits terpenoid biosynthesis and confers salt tolerance, which provides a potential strategy for producing high-value pharmaceutical terpenoids and improving resistant C. wenyujin varieties by a genetic approach.

Gene coexpression networks allow the discovery of two strictosidine synthases underlying monoterpene indole alkaloid biosynthesis in Uncaria rhynchophylla.

Plant-derived monoterpene indole alkaloids (MIAs) from Uncaria rhynchophylla (UR) have huge medicinal properties in treating Alzheimer's disease, Parkinson's disease, and depression. Although many bioactive UR-MIA products have been isolated as drugs, their biosynthetic pathway remains largely unexplored. In this study, untargeted metabolome identified 79 MIA features in UR tissues (leaf, branch stem, hook stem, and stem), of which 30 MIAs were differentially accumulated among different tissues. Short time series expression analysis captured 58 pathway genes and 12 hub regulators responsible for UR-MIA biosynthesis and regulation, which were strong links with main UR-MIA features. Coexpression networks further pointed to two strictosidine synthases (UrSTR1/5) that were coregulated with multiple MIA-related genes and highly correlated with UR-MIA features (r > 0.7, P < 0.005). Both UrSTR1/5 catalyzed the formation of strictosidine with tryptamine and secologanin as substrates, highlighting the importance of key residues (UrSTR1: Glu309, Tyr155; UrSTR5: Glu295, Tyr141). Further, overexpression of UrSTR1/5 in UR hairy roots constitutively increased the biosynthesis of bioactive UR-MIAs (rhynchophylline, isorhynchophylline, corynoxeine, etc), whereas RNAi of UrSTR1/5 significantly decreased UR-MIA biosynthesis. Collectively, our work not only provides candidates for reconstituting the biosynthesis of bioactive UR-MIAs in heterologous hosts but also highlights a powerful strategy for mining natural product biosynthesis in medicinal plants.

Multiple anti-inflammatory mechanisms of Zedoary Turmeric Oil Injection against lipopolysaccharides-induced acute lung injury in rats elucidated by network pharmacology combined with transcriptomics.

BACKGROUND: Prospects for the drug treatment of acute lung injury (ALI) is unpromising. Managing inflammation can prevent ALI from progressing and minimize further deterioration. Zedoary turmeric oil injection (ZTOI), a patented traditional Chinese medicine (TCM) that has been used against ALI, has shown significant anti-inflammatory effects. However, the mechanisms underlying these effects remain unclear. PURPOSE: Elucidate the anti-inflammatory mechanism by which ZTOI acts against ALI in rats using an ingredients-targets-pathways (I-T-P) interaction network. STUDY DESIGN AND METHODS: The key ingredients of ZTOI were characterized using UPLC-MS/MS combined with literature mining. The target profiles of each ingredient were established using drug-target databases. The anti-inflammatory activity of ZTOI against lipopolysaccharides (LPS)-induced rat ALI was validated using histopathology and inflammatory factor assessments. The therapeutic targets of ZTOI were screened by integrating transcriptomic results of lung tissues with protein-protein interaction (PPI) expansion. Using KEGG pathway enrichment, an I-T-P network was established to determine the essential interactions among ingredients, targets, and pathways of ZTOI against lung inflammation in ALI. Molecular docking and immunofluorescence staining were utilized to confirm the accuracy of the I-T-P network. RESULTS: A total of 11 sesquiterpenes, whose target profiles may characterize the potential function of ZTOI, were identified as key ingredients. In the ALI rat model, ZTOI can alleviate lung inflammation by decreasing the levels of C-reactive protein, interleukin-6, interleukin-1ß, and tumor necrosis factor α both in serum and lung tissues. Based on our biological samples, transcriptomics, PPI network expansion, and KEGG pathway enrichment, 11 ingredients, 174 targets, and 8 signaling pathways were linked in the I-T-P networks. From these results, ZTOI could be inferred to exert multiple anti-inflammatory effects against ALI through Toll-like receptor, NF-kappa B, RIG-I-like receptor, TNF, NOD-like receptor, IL-17, MAPK, and the Toll and Imd signaling pathways. In addition, two significantly regulated targets in the transcriptome, Usp18 and Map3k7, could be the essential anti-inflammatory targets of ZTOI. CONCLUSION: By integrating network pharmacology with ingredient identification and transcriptomics, we show the multiple anti-inflammatory mechanisms by which ZTOI acts against ALI on an I-T-P level. This work also provides a methodological reference for related research into TCM.

Transcriptome profiling of red swamp crayfish (Procambarus clarkii) hepatopancreas in response to lipopolysaccharide (LPS) infection.

The RNA-sequencing followed by de novo assembly generated 61,912 unigene sequences of P. clarkii hepatopancreas. Comparison of gene expression between LPS challenged and PBS control samples revealed 2552 differentially expressed genes (DEGs). Of these sequences, 1162 DEGs were differentially up-regulated and 1360 DEGs differentially down-regulated. The DEGs were then annotated against gene ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Some immune-related pathways such as PPAR signaling pathway, lysosome, Chemical carcinogenesis, Peroxisome were predicted by canonical pathways analysis. The reliability of transcriptome data was validated by quantitative real time polymerase chain reaction (qRT-PCR) for the selected genes. The data presented here shed light into antibacterial immune responses of crayfish. In addition, these results suggest that transcriptomic data provides valuable sequence resource for immune-related gene identification and helps to understand P. clarkii immune functions.

Molecular structure and functional characterization of the peroxiredoxin 5 in Procambarus clarkii following LPS and Poly I:C challenge.

Peroxiredoxin (Prx) family members play a critical role in host defense against oxidative stress, and are also involved in immune responses following microbial infection. In the present study, we firstly cloned the cDNA of Peroxiredoxin 5 from Procambarus clarkii (denoted as PcPrx5) and investigated its immune functions towards LPS and Poly I:C exposure. The PcPrx5 cDNA was composed of 564 bp and consisting of 187 amino acid residues which included Prx5-like subfamily domain, AHP1 domain and Redoxin domain. The recombinant protein was expressed in Escherichia coli (Transetta DE3), and anti-Prx5 antibodies were prepared. Tissue specific expression analysis showed that PcPrx5 was ubiquitously expressed in all examined tissues. Further, its mRNA transcript was greatest in hepatopancrease, haemocyte followed by gut and stomach, and was weak in muscle. The LPS and Poly I:C exposure could both significantly up-regulate the transcript level of PcPrx5, however the expression trends were different following LPS and Poly I: C treatments. Further, we investigated the antioxidant role of recombinant PcPrx5 protein in vitro by mixed-function oxidase assay; the results demonstrated a dose-dependent inhibition of DNA damage by PcPrx5. Our results implicate PcPrx5 as an important defense against microbial pathogens and oxidants in P. clarkii.

Insights from the Cold Transcriptome and Metabolome of Dendrobium officinale: Global Reprogramming of Metabolic and Gene Regulation Networks during Cold Acclimation.

Plant cold acclimation (CA) is a genetically complex phenomenon involving gene regulation and expression. Little is known about the cascading pattern of gene regulatroy network and the link between genes and metabolites during CA. Dendrobium officinale (DOKM) is an important medicinal and ornamental plant and hypersensitive to low temperature. Here, we used the large scale metabolomic and transcriptomic technologies to reveal the response to CA in DOKM seedlings based on the physiological profile analyses. Lowering temperature from 4 to -2°C resulted in significant increase (P < 0.01) in antioxidant activities and electrolyte leakage (EL) during 24 h. The fitness CA piont of 0°C and control (20°C) during 20 h were firstly obtained according to physiological analyses. Subsequently, massive transcriptome and metabolome reprogramming occurred during CA. The gene to metabolite network demonstrated that the CA associated processes are highly energy demanding through activating hydrolysis of sugars, amino acids catabolism and citrate cycle. The expression levels of 2,767 genes were significantly affected by CA, including 153-fold upregulation of CBF transcription factor, 56-fold upregulation of MAPKKK16 protein kinase. Moreover, the gene interaction and regulation network analysis revealed that the CA as an active process, was regulated at the transcriptional, post-transcriptional, translational and post-translational levels. Our findings highligted a comprehensive regulatory mechanism including cold signal transduction, transcriptional regulation, and gene expression, which contributes a deeper understanding of the highly complex regulatory program during CA in DOKM. Some marker genes identified in DOKM seedlings will allow us to understand the role of each individual during CA by further functional analyses.

Hydrogen sulfide stimulates ß-amylase activity during early stages of wheat grain germination.

We recently reported that H 2S could significantly promote the germination of wheat grains subjected to aluminum (Al(3+)) stress.1 In these experiments seeds were pretreated with the H 2S donor NaHS for 12 h prior to Al(3+) stress. During this pre-incubation period we observed that H2S increased the activity of grain amylase in the absence of Al(3+). Using embryoless half grains of wheat we now show that H2S preferentially affects the activity of endosperm ß-amylase and that α-amylase synthesis and activity is unaffected by this treatment.

A user-friendly alternative to formaldehyde-based DNA silver-staining method on polyacrylamide gels.

We have developed a practical, cost-effective and user-friendly protocol to meet the needs of nucleic acids research, particularly in respect of DNA detection on polyacrylamide gels. In this method, the most commonly used alkaline formaldehyde developer in DNA silver stain, which does harm to operator, is first replaced by glucose in alkaline borate buffer. In addition, the effects of six reducing sugars on the quality of DNA visualization were investigated. Consequently, the optimal protocol using glucose takes about 45 min to complete all the procedures, with a detection limit of 5 pg of single DNA band on polyacrylamide gels, was developed. The results indicate that this user-friendly and economic protocol could be a good choice for routine use in DNA visualization on polyacrylamide gels.

A visible dye-based staining method for DNA in polyacrylamide gels by ethyl violet.

We describe a visible dye-based staining method for DNA in polyacrylamide gels using ethyl violet (EV). The novel method is a background-free, sensitive, economical, and simple procedure involving only staining and washing steps that can be completed within 30 min. As little as 0.8-1.6 ng of phiX174 DNA/HaeIII can be detected by EV, which is about eightfold more sensitive than Nile blue (NB) stain and twofold less sensitive than ethidium bromide (EB) stain.

[Study on genetic diversity of Curcuma wenyujin from various habitats by SRAP].

OBJECTIVE: The DNA fingerprints of Curcuma wenyujin from various habitats were generated by using SRAP markers to find the feasibility in analyzing their relationship. METHODS: The DNA polymorphism of Curcuma wenyujin from various habitats were detected by SRAP molecular markers. RESULTS: We had screened five pairs of primer combinations, and built the DNA fingerprints of Curcuma wenyujin from various habitats. The phylogenetic clustering results revealed that the genetic difference in Curcuma wenyujin from various habitats were little. CONCLUSION: SRAP markers may offer some evidence for protecting and exploiting of Curcuma wenyuji.

[Genetic diversity and recombination of soybean cultivar Suinong 14 and its pedigree].

In this study, 14 agronomic traits and 139 SSR loci, distributed on 20 linkage groups of soybean (Glycine max L.) cultivar Suinong 14 and its pedigree were analyzed to explain the genetic diversity and recombination of Suinong 14 and to provide useful information for breeding. The cluster analysis based on SSR makers agreed with the pedigree information. The Shannon-Weaver index of each SSR locus ranged from 0 to 1.677. The average genetic similarity coefficient among cultivars was 0.6380, ranged from 0.538 to 0.799. At least three SSR loci were needed to discriminate Suinong 14 from its pedigree, for example a combination of Satt543, Sat_130 and Satt218. These loci have more alleles. No significant difference was observed between the end portion and the mid-portion within a linkage group, which indicates that the distribution of recombination occurred randomly in each linkage group. No polymorphism was detected within 39 of 139 SSR loci between Suinong 14 and its 8 parents. It implys their importance during cultivar improvement. Satt168, a marker on LGB2, was the only locus transmitted from Zihua 4 to Suinong 14, which indicates that the genetic constitute of Suinong 14 is greatly changed compared with Zihua 4 through five generations of recombination.