Identification of the AP2/ERF transcription factor family of Eleutherococcus senticosus and its expression correlation with drought stress.

In this study, through analysis of the genome of Eleutherococcus senticosus (ES). 228 AP2/ERF genes were identified and classified into 5 groups AP2 (47 genes), ERF (108 genes), RAV (6 genes), DREB (64 genes), and soloist (3 genes). According to the AP2/ERF classification of Arabidopsis thaliana, the ES AP2/ERF proteins were subdivided into 15 groups. The gene structure and motifs of each group of AP2/ERF in ES were highly similar, which confirmed the conservation of AP2/ERF genes. The ES AP2/ERF genes were unevenly distributed on chromosomes, and a total of four pairs of tandem repeats, and 84 co-linear gene pairs were found, so the AP2/ERF genes expanded in a fragment replication manner, and dominated by pure selection during evolution. By analyzing the transcriptome data of ES under different drought stress conditions, 87 AP2/ERF genes with differential expression were obtained, of which 10 genes with highly significant differences were further analyzed and screened for qRT-PCR validation. To the best of our knowledge, this is the first report on the AP2/ERF gene of Eleutherococcus senticosus, and the bioinformatics analysis and experimental validation provided valuable information about them, which is of great significance for further research on the molecular mechanisms of ES in response to drought stress.

Genome-wide identification of MBD gene family members in Eleutherococcus senticosus with their expression motifs under drought stress and DNA demethylation.

BACKGROUND: Methyl-binding domain (MBD) is a class of methyl-CpG-binding domain proteins that affects the regulation of gene expression through epigenetic modifications. MBD genes are not only inseparable from DNA methylation but have also been identified and validated in various plants. Although MBD is involved in a group of physiological processes and stress regulation in these plants, MBD genes in Eleutherococcus senticosus remain largely unknown. RESULTS: Twenty EsMBD genes were identified in E. senticosus. Among the 24 chromosomes of E. senticosus, EsMBD genes were unevenly distributed on 12 chromosomes, and only one tandem repeat gene existed. Collinearity analysis showed that the fragment duplication was the main motif for EsMBD gene expansion. As the species of Araliaceae evolved, MBD genes also evolved and gradually exhibited different functional differentiation. Furthermore, cis-acting element analysis showed that there were numerous cis-acting elements in the EsMBD promoter region, among which light response elements and anaerobic induction elements were dominant. The expression motif analysis revealed that 60% of the EsMBDs were up-regulated in the 30% water content group. CONCLUSIONS: By comparing the transcriptome data of different saponin contents of E. senticosus and integrating them with the outcomes of molecular docking analysis, we hypothesized that EsMBD2 and EsMBD5 jointly affect the secondary metabolic processes of E. senticosus saponins by binding to methylated CpG under conditions of drought stress. The results of this study laid the foundation for subsequent research on the E. senticosus and MBD genes.

Metabolome and transcriptome analysis of eleutheroside B biosynthesis pathway in Eleutherococcus senticosus.

Eleutheroside B (syringin) is a medicinal active ingredient extracted from Eleutherococcus senticosus (Ruper. et Maxim.) Maxim with high clinical application value. However, its synthesis pathway remains unknown. Here, we analyzed the eleutheroside B biosynthesis pathway in E. senticosus. Consequently, metabolomic and transcriptomic analyses identified 461 differentially expressed genes (DEGs) and 425 metabolites. Further, we identified 7 DEGs and 67 metabolites involved in the eleutheroside B biosynthetic pathway in the eleutheroside B high and low plants. The correlation between the gene and metabolites was explored using the pearson correlation coefficient (PCC) analysis. Caffeoyl-CoA O-methyltransferase, caffeic acid-O-methyltransferase, ß-amyrin synthase (ß-AS) genes, NAC5, and HB5 transcription factors were identified as candidate genes and transcription factors related to the eleutheroside B synthesis. Eleutheroside B content was the highest at the young stage of the leaves both in the high and low eleutheroside B plants. Quantitative real-time polymerase chain reaction revealed that phenylalanine ammonia-lyase1, cinnamate 4-hydroxylase, ß-AS, and leucoanthocyanidin reductase gene had higher expression levels at the young stage of the leaves in the low eleutheroside B plants but lower expression levels in the high eleutheroside B plants. In the present study, we complemented the eleutheroside B biosynthetic pathway by analyzing the expression levels of relevant genes and metabolite accumulation patterns.

Genome-wide identification and expression analysis of glycosyltransferase gene family 1 in Quercus robur L.

Glycosyltransferase gene family 1, also known as uridine diphosphate glycosyltransferase (UGT), is the largest glycosyltransferase family in plants, playing a vital role in their growth and development. In this study, 244 UGT genes with conserved PSPG motifs were identified in the genome of Quercus robur L. The collinearity analysis results showed that tandem repeat was the main way of UGT genes expansion in Q. robur, with 21 groups of 55 tandem repeat genes. UGT genes were divided into 15 subgroups A-P; group K was lost, and the gene structure and conserved domain of the same subgroup were basically the same. Cis-element analysis showed that upstream 2,000 bp promoter sequence of UGT genes contained light response elements, plant hormone response elements, and stress-related cis-elements, which indicated that UGT genes of Q. robur might be regulated by various metabolic pathways. In particular, some UGTs in group L of Q. robur contained a conserved promoter structure. The expression pattern analysis results demonstrated that UGT genes of groups B, D, E, and I were differentially expressed under Tortrix viridana L. stress. The expression of UGTs in group E decreased under stress, the expression of group L increased, and that of genes in groups D and B were different. The functions of UGT genes in E and L groups are relatively conservative, and their functions may also conserve among species. The study results have a particular reference value for further research on the function of Q. robur UGT genes.

Adaptive Evolution of Chalcone Isomerase Superfamily in Fagaceae.

Chalcone Isomerase (CHI) catalyzes the biosynthesis of flavonoids and secondary metabolism in plants. Currently, there is no systematic analysis of CHIs gene family in Fagaceae which is available. In this study, twenty-two CHI proteins were identified in five species of the Fagaceae family. The CHI superfamily in Fagaceae can be classified into three subfamilies and five groups using phylogenetic analysis, analysis of physicochemical properties, and structural prediction. Results indicated that serine (Ser) and isoleucine (Ile) residues determine the substrate preferred by active Type I Fagaceae CHI, and the chalcone isomerase-like (CHIL) of Fagaceae had active site residues. Adaptive analysis of CHIs showed that CHIs are subject to selection pressure. The active CHI gene of Fagaceae was located in the cytoplasm, and it had the typical gene structure of CHI and contains four exons. All the twenty-two identified CHIs had the conserved domain motif 3, and the different groups had their own structural characteristics. In the process of fatty acid binding protein (FAP) evolution to CHIL and CHI, the physical and chemical properties of proteins also had significant differences in addition to changes in protein functions.

WSTF acetylation by MOF promotes WSTF activities and oncogenic functions.

Williams syndrome transcription factor (WSTF) is a transcription factor and tyrosine kinase. WSTF overexpression promotes migration and proliferation of various cancers, and Ser158 (WSTFS158) phosphorylation plays an important role in this process. However, the role of the other posttranslational modifications of WSTF is unknown. Here, we report that lysine (K) 426 on WSTF is acetylated by MOF and deacetylated by SIRT1. Mechanistically, male-specific lethal (MSL) 1v1 interaction with WSTF facilitates its interaction with MOF for WSTF acetylation, which in turn promotes WSTFS158 phosphorylation. The kinase and transcriptional regulatory activity of WSTF were enhanced by acetylation. WSTFK426ac levels positively and significantly correlated with tumor size, histological grade, and age. Moreover, we demonstrated that acetylated WSTF promotes cancer cell proliferation, migration, invasion, and tumor formation. In conclusion, we identified the enzymes regulating WSTF K426 acetylation, and demonstrated an acetylation-dependent mechanism that modulates the activities of WSTF and contributes to tumorigenesis. Our findings provide new clues to study WSTF-mediated normal development and disease.

JMJD6 regulates histone H2A.X phosphorylation and promotes autophagy in triple-negative breast cancer cells via a novel tyrosine kinase activity.

Overexpression of Jumonji domain-containing 6 (JMJD6) has been reported to be associated with more aggressive breast cancer characteristics. However, the precise role of JMJD6 in breast cancer development remains unclear. Here, we demonstrate that JMJD6 has intrinsic tyrosine kinase activity and can utilize ATP and GTP as phosphate donors to phosphorylate Y39 of histone H2A.X (H2A.XY39ph). High JMJD6 levels promoted autophagy in triple negative breast cancer (TNBC) cells by regulating the expression of autophagy-related genes. The JMJD6-H2A.XY39ph axis promoted TNBC cell growth via the autophagy pathway. We show that combined inhibition of JMJD6 kinase activity and autophagy efficiently decreases TNBC growth. Together, these findings suggest an effective strategy for TNBC treatment.

[Analysis of transicriptomes and exploring flavonoid biosynthetic pathway genes in Lithocarpus polystachyus].

The sweet taste and health effect of Lithocarpus polystachyus are mainly related flavonoid. To obtain Lithocarpus transcriptome database and flavonoid biosynthesis-related genes, the RNA-Seq techology (Illumina HiSeq 4000) was used to sequence its transcriptome. Six Gb database was assembled after assembly steps, and 41 043 of L. polystachyus unigenes were obtained. With blasting them with 7 data banks, all unigenes were involved in 51 GO-terms and 237 metabolic pathways. And furthermore 28 genes of the flavonoid biosynthesis-related were found. After using the MicroSatallite, 18 161 SSR were obtained, the single-nucleotide-repeated was the richest at 7 346. These data represent abundant messages about transcripts and provide valuable genome data sources in molecular biology of L. polystachyus.

Phosphorylation of H2A.XTyr39 positively regulates DNA damage response and is linked to cancer progression.

Double-stranded DNA breaks induce serine phosphorylation of histone H2A.X, producing γ-H2A.X foci that are then recognized by DNA damage response pathway proteins. Formation of γ-H2A.X is therefore critical for the repair of DNA double-stranded breaks and maintenance of genomic stability, and defects in the recognition or repair of double-stranded breaks can result in tumorigenesis. However, key details regarding the formation of γ-H2A.X and its possible role in tumorigenesis remain elusive. Here, we report a previously unknown phosphorylation site on H2A.X, Tyr39. Phosphorylation at this site is induced by ionizing radiation and is a prerequisite for γ-H2A.X formation. Increased phosphorylation of H2A.X at Tyr39 was observed in multiple cancer cell lines, and we found that H2AX Tyr39 phosphorylation positively correlated with histological grade, tumor size and tumor node metastasis stage, and negatively correlated with survival. We also identified a potential role for eyes absent 2 (EYA2) in regulating H2A.X Tyr39 phosphorylation. Our study supports an important role for H2AX Tyr39 phosphorylation in γ-H2A.X formation and cancer progression.

KRASG12 mutant induces the release of the WSTF/NRG3 complex, and contributes to an oncogenic paracrine signaling pathway.

It remains unclear how the signals of mutant KRASG12 in the transformed cells spread to the surrounding non-mutated cells and changes the microenvironment to promote tumor formation. We identified that Williams-Beuren syndrome transcription factor (WSTF), a non-secretory protein, was released in complex with secretory protein-neuregulin-3 (NRG3). The KRASG12 mutant activates the transcription of NRG3. The WSTF/NRG3 in extracellular space could activate oncogenic pathways in normal colon cells carrying wild type KRAS and endow them with the ability to express NRG3 and release WSTF/NRG3. Extracellular WSTF/NRG3 promotes the formation of colon tumors. Blockade of extracellular WSTF could restore cetuximab sensitivity of colon cancer cells with mutant KRAS. The appearance of WSTF/NRG3 in serum and urine correlates with a colon tumor carrying a KRASG12 mutant. In summary, our demonstration provides a new pathway to our understanding of the biological development of complex diseases.

[Expression profiles analysis of two member of squaleneepoxidase gene family from Eleutherococcus senticosus].

In order to find the characteristics of two members of gene family of squaleneexpoxidase (SE) , a quantitative real time PCR method was developed to analyze the expression of Eleutherococcus senticosus SE1 and SE2 gene from different growth periods and in different organs. The result indicated that all the expression of SE2 more than SE1 in the whole growth period and organs of E. senticosus. And in the whole growth period, expression of SE1 showed a low-high-low characteristic. Both expression of SE2 and growth period showed the same trend. The lowest content of the expression was in the roots. SE1 expression have been improved more than SE2 when treated with MeJA. The expression of E. senticosus SE1 and saponins content had significantly positive correlation (P < 0.05) and the correlation coefficients was 0. 858, while the correlation was not significant for SE2. That indicated that SE1 played a key enzyme gene in the biosynthesis of triterpenoidsaponins

WITHDRAWN: WSTF Phosphorylation Specifically Links H3K9ac with H4K16ac through PCAF/WSTF/MOF Complex.

This article has been withdrawn by the authors.

[Analyze on the expression differences of key genes in saponins biosynthesize in Eleutherococcus senticosus and its callus].

OBJECTIVE: To analyze the expression differences of SS, SE and bAS in leaf, petiole and callus from leaf and petiole of Eleutherococcus senticosus. METHODS: Calluses were induced from explants of E. senticosus leaf and petiole. The expression amount of SS, SE and bAS gene was detected by real time PCR. RESULTS: The expression amount of SS, SE and bAS genes in callus from leaf were 89.3%, 73.8% and 83.4% of that in leaf, respectively. The expression amount of SS, SE and bAS genes in callus from petiole were 80.2%, 87.7% and 70.9% of that in petiole, respectively. CONCLUSION: The expression amount of SS, SE and bAS gene in callus from E. senticosus are significantly lower than that in plant.