Distribution, characterization, and evolution of heavy metal resistance genes and Tn7-like associated heavy metal resistance Gene Island of Burkholderia.

Introduction: Burkholderia is a rod-shaped aerobic Gram-negative bacteria with considerable genetic and metabolic diversity, which can beused for bioremediation and production applications, and has great biotechnology potential. However, there are few studies on the heavy metal resistance of the Burkholderia genus. Methods: In this paper, the distribution, characteristics and evolution of heavy metal resistance genes in Burkholderia and the gene island of Tn7-like transposable element associated with heavy metal resistance genes in Burkholderia were studied by comparative genomic method based on the characteristics of heavy metal resistance. Results and discussion: The classification status of some species of the Burkholderia genus was improved, and it was found that Burkholderia dabaoshanensis and Burkholderia novacaledonica do not belong to the Burkholderia genus.Secondly, comparative genomics studies and pan-genome analysis found that the core genome of Burkholderia has alarger proportion of heavy metal resistance genes and a greater variety of heavy metalresistance genes than the subsidiary genome and strain specific genes. Heavy metal resistance genes are mostly distributed in the genome in the form of various gene clusters (for example, mer clusters, ars clusters, czc/cusABC clusters). At the same time, transposase, recombinase, integrase and other genes were foundupstream and downstream of heavy metal gene clusters, indicating that heavy metal resistance genes may beobtained through horizontal transfer. The analysis of natural selection pressure of heavy metal resistance genes showed that heavy metal resistance genes experienced strong purification selection under purification selection pressure in the genome.The Tn7 like transposable element of Burkholderia was associated with the heavy metal resistance gene island, and there were a large number of Tn7 transposable element insertion events in genomes. At the same time, BGI metal gene islands related to heavy metal resistance genes of Tn7 like transposable element were found, and these gene islands were only distributed in Burkholderia cepacia, Burkholderia polyvora, and Burkholderia contaminant.

Phytochemical composition, isolation and hepatoprotective activity of active fraction from Veronica ciliata against acetaminophen-induced acute liver injury via p62-Keap1-Nrf2 signaling pathway.

ETHNOPHARMACOLOGICAL RELEVANCE: Veronica ciliata Fisch, a traditional Tibetan medicine, used to cure hepatitis and existed in lots of Tibetan medicine prescriptions owing to its hepatoprotective activity. AIMS OF THIS STUDY: In this study, we are aimed to systematically analysis and isolate the chemical constituents of the ethyl acetate fraction from V. ciliata (EAFVC), and test the hepatoprotective effect and mechanism of EAFVC and its compounds on attenuating the liver injury induced by acetaminophen (APAP) in vivo and vitro. MATERIALS AND METHODS: UPLC-PDA-ESI-MS method was established for the analysis of the components in EAFVC, which was further separated using multiple chromatographic techniques. The MS, 1H and 13C NMR were applied to elucidate their structures. UPLC-PDA method was applied for the simultaneous quantification of major compounds of EAFVC. Furthermore, the protective effect of the EAFVC was determined using APAP-induced acute hepatotoxicity in mice and BRL-3A cells model, respectively. In addition, the hepatoprotective activity of two main compounds in EAFVC on relieving APAP-induced liver injury was further evaluated. Finally, we have some concerns about the protective mechanism of EAFVC via enzyme-linked immunosorbent assay (ELISA), reactive oxygen species (ROS) detection, quantitative real-time PCR (qPCR), western blot analysis and molecular docking. RESULTS: Thirteen compounds were successfully identified using UPLC-PDA-ESI-MS for the first time. Meanwhile, other twelve compounds were separated from EAFVC. Eventually, twenty-five compounds were successfully identified from the EAFVC. Among these compounds, fourteen compounds (3, 8, 10, 14-17, 19-25) were separated from V.ciliata for the first time. In addition, UPLC-PDA analysis method was first to establish for simultaneous determination of the main compounds (1, 2, 4, 5, 7, 9, 12). Further assay indicated that the liver injury in mice induced by APAP showed a significant reversal by EAFVC, as evidenced by reducing the activities of liver function enzymes, suppressing the lipid peroxidation as well as increasing the serum total antioxidant capacity (T-AOC) and the activities of antioxidant enzymes. Pathological sections showed that the liver in the high dose has significant improvement in mice. In vitro experiment also showed that EAFVC elevate the viability, inhibiting the activities of liver function enzymes as well as the generation of ROS of BRL-3A cells. In addition, Catalposide and verproside could reverse the low cell viability of BRL-3A cells induced by APAP. The mechanism research in vitro demonstrated that EAFVC could promote the mRNA and protein expression of heme oxygenase-1 (HO-1), NAD(P) H dehydrogenase quinone 1 (NQO-1) and catalytic or modify subunit of glutamate-cysteine ligase (GCLC/GCLCM) via enhancing nuclear factor-E2-related factor 2 (Nrf2) and p62/SQSTM1 (p62) expression in protein level. Molecular docking results demonstrated that catalposide and verproside have strong affinity to the kelch-like ECH-associated protein-1(Keap1) Kelch domain. CONCLUSION: This research is the first to clarify the substance basis of the hepatoprotective activity of the EAFVC and provide the further scientific data for the traditional use of this Tibetan Medicine. EAFVC is valuable to be further investigated as active preparations for application in liver protection via activating p62- Keap1-Nrf2 pathway.

Downregulation of OsAGO17 by artificial microRNA causes pollen abortion resulting in the reduction of grain yield in rice

Background: Pollen development is an important reproductive process that directly affects pollen fertility and grain yield in rice. Argonaute (AGO) proteins, the core effectors of RNA-mediated silencing, play important roles in regulating plant growth and development. However, few AGO proteins in rice were reported to be involved in pollen development. In this study, artificial microRNA technology was used to assess the function of OsAGO17 in pollen development. Results: In this study, OsAGO17, a rice-specific gene, was specifically expressed in rice pollen grains, with the highest expression in uninucleate microspores. Downregulation of OsAGO17 by artificial microRNA technology based on the endogenous osa-miRNA319a precursor was successfully achieved. It is found that downregulation of OsAGO17 could significantly affect pollen fertility and cause pollen abortion, thus suggesting that OsAGO17 functions in rice pollen development. In addition, the downregulation of OsAGO17 mainly caused a low seed-setting rate, thereby resulting in the reduction of grain yield, whereas the downregulation of OsAGO17 did not significantly affect rice vegetative growth and other agricultural traits including number of florets per panicle, number of primary branch per panicle, and 100-grain weight. Furthermore, the result of subcellular localization analysis indicated that the OsAGO17 protein was localized to both the nucleus and the cytoplasm. Conclusion: These results represent the first report of the biological function for OsAGO17 in rice and indicate that OsAGO17 may possibly play crucial regulatory roles in rice pollen development. It helps us to better understand the mechanism of pollen development in rice.

Transcriptome analysis of female and male flower buds of Idesia polycarpa Maxim. var. vestita Diels

Background: Idesia polycarpa Maxim. var. vestita Diels, a dioecious plant, is widely used for biodiesel due to the high oil content of its fruits. However, it is hard to distinguish its sex in the seedling stage, which makes breeding and production problematic as only the female tree can produce fruits, and the mechanisms underlying sex determination and differentiation remain unknown due to the lack of available genomic and transcriptomic information. To begin addressing this issue, we performed the transcriptome analysis of its female and male flower. Results: 28,668,977 and 22,227,992 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 84,213 unigenes with an average length of 1179 bp were generated and 65,972 unigenes (78.34%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG and GO databases. Functional annotation of the unigenes uncovered diverse biological functions and processes, including reproduction and developmental process, which may play roles in sex determination and differentiation. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed many unigenes annotated as metabolic pathways, biosynthesis of secondary metabolites pathways, plant­ pathogen interaction, and plant hormone signal transduction. Moreover, 29,953 simple sequence repeats were identified using the microsatellite software. Conclusion: This work provides the first detailed transcriptome analysis of female and male flower of I. polycarpa and lays foundations for future studies on the molecular mechanisms underlying flower bud development of I. polycarpa.

Response of alternative splice isoforms of OsRad9 gene from Oryza sativa to environmental stress.

Rad9 protein plays an important role in cell-cycle checkpoint signal transduction in human and yeast cells, but knowledge about Rad9 in plants is limited. This study reports that the Rad9 gene of rice can generate the transcript products OsRad9.1 and OsRad9.2 through alternative splicing. OsRad9.1, with all nine exons, is the main cell-cycle checkpoint protein involved in the response of rice to genotoxic stresses (ultraviolet radiation and antibiotic stress), environmental stresses (drought, salt, and heavy metal stress), and auxin stimuli (2,4-D, IAA, and IBA). Meanwhile, transcript isoform OsRad9.2, which lost exon7 and exon8, showed different preferential stimulation effects on these stresses and pollen development duration. These results might indicat that besides the monitoring and repair of DNA damage, Rad9 might involve in the development of pollen.

Liquid Hybridization and Solid Phase Detection: A Highly Sensitive and Accurate Strategy for MicroRNA Detection in Plants and Animals.

MicroRNAs (miRNAs) play important roles in nearly every aspect of biology, including physiological, biochemical, developmental and pathological processes. Therefore, a highly sensitive and accurate method of detection of miRNAs has great potential in research on theory and application, such as the clinical approach to medicine, animal and plant production, as well as stress response. Here, we report a strategic method to detect miRNAs from multicellular organisms, which mainly includes liquid hybridization and solid phase detection (LHSPD); it has been verified in various species and is much more sensitive than traditional biotin-labeled Northern blots. By using this strategy and chemiluminescent detection with digoxigenin (DIG)-labeled or biotin-labeled oligonucleotide probes, as low as 0.01-0.25 fmol [for DIG-CDP Star (disodium2-chloro-5-(4-methoxyspiro{1,2-dioxetane-3,2'-(5'-chloro)tricyclo[3.3.1.13,7]decan}-4-yl)phenyl phosphate) system], 0.005-0.1 fmol (for biotin-CDP Star system), or 0.05-0.5 fmol (for biotin-luminol system) of miRNA can be detected and one-base difference can be distinguished between miRNA sequences. Moreover, LHSPD performed very well in the quantitative analysis of miRNAs, and the whole process can be completed within about 9 h. The strategy of LHSPD provides an effective solution for rapid, accurate, and sensitive detection and quantitative analysis of miRNAs in plants and animals.

Overexpression of a cysteine proteinase inhibitor gene from Jatropha curcas confers enhanced tolerance to salinity stress

Background Cysteine proteinase inhibitor (cystatin, CPI) is one of the most important molecules involved in plant development and defense, especially in the regulation of stress responses. However, it is still unclear whether the Jatropha curcas CPI (JcCPI) gene functions in salinity response and tolerance. In this study, the sequence of the JcCPI gene, its expression pattern, and the effects of overexpression in Escherichia coli and Nicotiana benthamiana were examined. The purpose of this study was to evaluate the regulatory role of JcCPI in salinity stress tolerance. Results The CPI gene, designated JcCPI, was cloned from J. curcas; its sequence shared conserved domains with other plant cystatins. Based on a transcription pattern analysis, JcCPI was expressed in all tissues examined, but its expression was highest in the petiole. Additionally, the expression of JcCPI was induced by salinity stress. A potential role of JcCPI was detected in transgenic E. coli, which exhibited strong CPI activity and high salinity tolerance. JcCPI was also transferred to tobacco plants. In comparison to wild-type plants, transgenic plants expressing JcCPI exhibited increased salinity resistance, better growth performance, lower malondialdehyde (MDA) contents, higher anti-oxidase activity, and higher cell viability under salinity stress. Conclusions Based on the results of this study, overexpression of JcCPI in E. coli and N. benthamiana conferred salinity stress tolerance by blocking cysteine proteinase activity. The JcCPI gene cloned in this study will be very useful for the development of stress-tolerant crops.