ERF4 interacts with and antagonizes TCP15 in regulating endoreduplication and cell growth in Arabidopsis.

Endoreduplication is prevalent during plant growth and development, and is often correlated with large cell and organ size. Despite its prevalence, the transcriptional regulatory mechanisms underlying the transition from mitotic cell division to endoreduplication remain elusive. Here, we characterize ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR 4 (ERF4) as a positive regulator of endoreduplication through its function as a transcriptional repressor. ERF4 was specifically expressed in mature tissues in which the cells were undergoing expansion, but was rarely expressed in young organs. Plants overexpressing ERF4 exhibited much larger cells and organs, while plants that lacked functional ERF4 displayed smaller organs than the wild-type. ERF4 was further shown to regulate cell size by controlling the endopolyploidy level in the nuclei. Moreover, ERF4 physically associates with the class I TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) protein TCP15, a transcription factor that inhibits endoreduplication by activating the expression of a key cell-cycle gene, CYCLIN A2;3 (CYCA2;3). A molecular and genetic analysis revealed that ERF4 promotes endoreduplication by directly suppressing the expression of CYCA2;3. Together, this study demonstrates that ERF4 and TCP15 function as a module to antagonistically regulate each other's activity in regulating downstream genes, thereby controlling the switch from the mitotic cell cycle to endoreduplication during leaf development. These findings expand our understanding of how the control of the cell cycle is fine-tuned by an ERF4-TCP15 transcriptional complex.

Genome-wide identification of the tobacco GDSL family and apical meristem-specific expression conferred by the GDSL promoter.

BACKGROUND: GDSL esterases/lipases are a large protein subfamily defined by the distinct GDSL motif, and play important roles in plant development and stress responses. However, few studies have reported on the role of GDSLs in the growth and development of axillary buds. This work aims to identify the GDSL family members in tobacco and explore whether the NtGDSL gene contributes to development of the axillary bud in tobacco. RESULTS: One hundred fifty-nine GDSL esterase/lipase genes from cultivated tobacco (Nicotiana tabacum) were identified, and the dynamic changes in the expression levels of 93 of these genes in response to topping, as assessed using transcriptome data of topping-induced axillary shoots, were analysed. In total, 13 GDSL esterase/lipase genes responded with changes in expression level. To identify genes and promoters that drive the tissue-specific expression in tobacco apical and axillary buds, the expression patterns of these 13 genes were verified using qRT-PCR. GUS activity and a lethal gene expression pattern driven by the NtGDSL127 promoter in transgenic tobacco demonstrated that NtGDSL127 is specifically expressed in apical buds, axillary buds, and flowers. Three separate deletions in the NtGDSL127 promoter demonstrated that a minimum upstream segment of 235 bp from the translation start site can drive the tissue-specific expression in the apical meristem. Additionally, NtGDSL127 responded to phytohormones, providing strategies for improving tobacco breeding and growth. CONCLUSION: We propose that in tobacco, the NtGDSL127 promoter directs expression specifically in the apical meristem and that expression is closely correlated with axillary bud development.

MapGene2Chrom, a tool to draw gene physical map based on Perl and SVG languages.

Genetic linkage map is helpful for analysis on heredity of some gene families and map-based gene cloning because of its simple and elegant manifestation. One software is in need to draw a gene physical map, which shows a manner similar to the genetic linkage map, based on the relative physical distance between genes. Although some tools like GBrowse and MapViewer etc. are available to draw gene physical map, there are obvious limitations for them: (1) the data need to be decorated in advance; (2) users can't modify results. Therefore, we developed a bio-assisted mapping software--MapGene2Chrom with PC and web versions, which is based on Perl and SVG languages. The software can be used to draw the corresponding physical map quickly in SVG format based on the input data. It will become a useful tool for drawing gene physical map with the advantages of simple input data format, easily modified output and very good portability.

[Genome-wide analysis of cytochrome P450 monooxygenase genes in the tobacco].

Plant cytochrome P450 monooxygenases (CYP) constitute a large superfamily of heme-thiolate proteins, which are involved in a wide range of metabolic pathways. In this study, comparative genomic approaches were used to analyze tobacco CYP genes and their expression patterns. Based on analysis of the tobacco genomic DNA sequences that are currently available, 263 P450 genes that belong to 44 distinct clans were identified. EST evidence from 173 of the CYPs suggested that these genes are transcribed. Sequence features and secondary structures of the tobacco P450 genes were further analyzed through comparison with known P450 proteins. The expression profiles of 73 P450 genes were subsequently investigated by analyses of tobacco microarray data and RT-PCR. The results showed a variety of expression patterns of these genes in different tissues with a number of genes expressed in a tissue-specific manner. This study has set a foundation for further studies on functions of P450 genes in tobacco.

A photochromic and scintillation Eu-MOF with visual X-ray detection in bright and dark environments.

The detection of X-rays has always been a frontier of scientific research. An Eu-MOF with both X-ray-induced photochromic and scintillation properties has been synthesized through the combination of a photochromism-active viologen ligand and rare earth Eu element with high-efficiency absorption of X-rays. In a bright environment, Eu-MOF exhibits different color changes under high-energy X-rays and low-energy X-rays, which can effectively distinguish X-rays. Eu-MOF can also be used for X-ray detection by scintillation properties in dark environments. This work provides a new perspective on the design of multifunctional materials that can perform simple X-ray detection in different environments.

[Bioinformatic prediction of conserved microRNAs and their target genes in eggplant (Solanum melongena L.)].

MicroRNAs (miRNAs), a recently discovered class of small (-21nt), non-coding, endogenous, single-stranded RNAs in eukaryotes, regulate gene expression negatively at the post-transcriptional levels depending on the extent of complementation between miRNA and mRNA. To date, a large number of miRNAs have been reported in many species, but none for eggplant (Solanum melongena L.). In this paper, a computational homology search approach based on the conservation of miRNA sequences and the stem-loop hairpin secondary structures of miRNAs was adopted. The search was started with the known plant miRNAs compared to eggplant expressed sequence tags (EST) databases to find potential miRNAs. Following a range of filtering criteria, a total of 16 potential miRNAs belonging to 12 families were identified. Three pairs of sense and antisense strand eggplant miRNAs belonging to three different miRNA families were also found. Furthermore, miR390 and miR399 sense/antisense pairs are identified for the first time in plants. Using online software psRNATarget, we further predicted the target genes of these 16 miRNAs and got 71 potential targets genes on base of 15 eggplant miRNAs. Most of these target genes were predicted to encode proteins that play key role in eggplant growth, development, metabolism, and stress responses.

Genome-wide identification of the ARRs gene family in tobacco (Nicotiana tabacum).

BACKGROUND: The growth of axillary buds determines the shoot branching and morphology of plants, and its initiation and development are regulated by a series of hormonal signals, such as cytokinin. Arabidopsis response regulators (ARRs) can regulate the growth and development, disease resistance and stress resistance of plants by participating in cytokinin signaling. OBJECTIVE: To explore the distribution and expression pattern of ARR members in tobacco. METHODS: The identification, isoelectric points, molecular weights, protein subcellular localization prediction, multiple sequence alignment, phylogenetic analysis, protein motifs and structures, chromosome distributions of deduced ARR proteins were conducted. The gene expression profiling of various tissues in response to topping, low temperature and drought were analyzed by RNA-seq and qRT-PCR. RESULTS: 59 ARR genes from cultivated tobacco (Nicotiana tabacum) were identified, namely NtARRs, including 21 type A NtARRs and 38 type B NtARRs. The 59 NtARRs were expressed mainly in all organs except the fruits. Some representative NtARRs may participate in axillary bud initiation and development, as well as in stress resistance through cytokinin signal transduction. CONCLUSION: Understanding the roles of NtARRs in the molecular mechanisms responsible for axillary bud growth and stress tolerance could aid in targeted breeding in crops.

Control of axillary bud growth in tobacco through toxin gene expression system.

The control of axillary bud development after removing the terminal buds (topping) of plants is a research hotspot, and the control of gene expression, like switching on and off, allows us to further study biological traits of interest, such as plant branching and fertility. In this study, a toxin gene control system for plants based on dexamethasone (DEX) induction was constructed, and the positive transgenic tobacco exhibited growth retardation in the application area (axillary bud). The expression level of the lethal Diphtheria toxin A (DTA) gene under different DEX concentrations at different application days was analyzed. The highest expression levels appeared at 5 days after the leaf injection of DEX. The DTA transcripts were induced by 5 µM DEX and peaked in response to 50 µM DEX at 5 days after leaf injection. Here, a chemical induction system, combined with a toxin gene, were used to successfully control the growth of tobacco axillary buds after topping. The DTA expression system under DEX induction was sensitive and efficient, therefore, can be used to control axillary bud growth and development in tobacco.

Induction of Male Sterility in Tobacco by Anther-Specific Expression of the Gene for Ricin Enzymatic Subunit A Chain RTA.

Targeted gene expression in plants allows us to further study biological traits of interest, such as reproductive and developmental processes. Here, the tobacco TA29 anther-specific promoter was used to direct the expression of the ricin enzymatic subunit A (RTA) in transgenic tobacco plants, phenotypic analysis of the resulting positive transgenic tobacco (Nicotiana tabacum L.) plants demonstrated that RTA expression led to a reduction in pistil length and shriveling of anthers, as well as the grayish-brown color of anthers, the reduced pollen viability and male sterility. For the first time, a plant-derived ricin gene enzymatic subunit A (RTA) expression system under the tissue-specific promoter was demonstrated to be sensitive and efficient in controlling plant sterility and creating male-sterile materials. Consequently, it could be used to control other agronomic traits and produce hybrid seeds in plants in the future.

Transcriptomic analysis of topping-induced axillary shoot outgrowth in Nicotiana tabacum.

Topping is an important agronomic practice that significantly impacts the yield of various crop plants. Topping and the regulation of axillary shoot outgrowth are common agronomic practices in tobacco. However, the effects of topping on gene expression in tobacco remain unknown. We applied the Illumina HiSeq™ 2000 platform and analyzed differentially expressed genes (DEGs) from untopped and topped plants to study the global changes in gene expression in response to topping. We found that the number of DEGs varied from 7609 to 18,770 based on the reads per kilobase per million mapped reads (RPKM) values. The Gene Ontology (GO) enrichment analysis revealed that the cellular carbohydrate metabolic process and the disaccharide metabolic process, which may contribute to starch accumulation and stress/defense, were overrepresented terms for the DEGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that many DEGs were involved in starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and plant hormone signal transduction, among other processes. The knowledge gained will improve our understanding of the processes of axillary shoot formation and enlargement at the transcriptional level. This study lays a solid foundation for future studies on molecular mechanisms underlying the growth of axillary shoots.

Absorption characteristics of the total alkaloids from Mahonia bealei in an in situ single-pass intestinal perfusion assay.

AIM: To investigate the absorption characteristics of the total alkaloids from Mahoniae Caulis (TAMC) through the administration of monterpene absorption enhancers or protein inhibitors. METHOD: The absorption behavior was investigated in an in situ single-pass intestinal perfusion (SPIP) assay in rats. RESULTS: The intestinal absorption of TAMC was much more than that of a single compound or a mixture of compounds (jatrorrhizine, palmatine, and berberine). Promotion of absorption by the bicyclic monoterpenoids (borneol or camphor) was higher than by the monocyclic monoterpenes (menthol or menthone), and promotion by compounds with a hydroxyl group (borneol or menthol) was higher than those with a carbonyl group (camphor or menthone). The apparent permeability coefficient (Papp) of TAMC was increased to 1.8-fold by verapamil, while it was reduced to one half by thiamine. The absorption rate constant (Ka) and Papp of TAMC were unchanged by probenecid and pantoprazole. CONCLUSION: The intestinal absorption characteristics of TAMC might be passive transport, and the intestinum tenue was the best absorptive site. In addition, TAMC might be likely a substrate of P-glycoprotein (P-gp) and organic cation transporters (OCT), rather than multidrug resistance protein (MRP) and breast cancer resistance protein (BCRP). Compared with a single compound and a mixture of compounds, TAMC was able to be absorbed in the blood circulation effectively.

Alkaloids from Mahonia bealei posses anti-H⁺/K⁺-ATPase and anti-gastrin effects on pyloric ligation-induced gastric ulcer in rats.

The purpose of this study was to investigate the underlying mechanism(s) of the total alkaloids (TA) from Mahonia bealei in treating pyloric ligation-induced gastric ulcers in rats. Animals were sacrificed after 19 h of the ligation. Gastric acid, peptic activities, mucin levels, H(+)/K(+)-ATPase activities and the gastrin level were analyzed. To improve the accuracy of the observations, IPP 6.0 software was introduced to measure the area of ulcer. TA (18.56 mg/kg/day, i.g.) showed an antiulcer effect by significantly decreasing the gastric ulcer areas (11.28 mm(2)) compared with model group (26.36 mm(2)). The TA ulcer inhibition ratio was 57.2%, compared with the effect of the positive control, omeprazole (62.96%). The results also showed that TA had a significant effect in inhibiting the release of H(+)/K(+)-ATPase, reducing the content of gastrin and decreasing gastric acidity on experimental animals. However, the TA had no significant effects on gastric mucus secretion and pepsin activity. Data indicated that TA had gastric ulcer protective effects by modulating the H(+)/K(+)-ATPase activity and gastrin level. TA has a potential to be developed as a pharmacological agent for the treatment of gastric ulcers.