Genome-Wide Identification and Expression Analysis of Terpene Synthase Genes in Cymbidium faberi

Terpene synthases (TPSs) are essential for forming terpenes, which play numerous functional roles in attracting pollinators, defending plants, and moderating the interaction between plants. TPSs have been reported in some orchids, but genome-wide identification of terpenes in Cymbidium faberi is still lacking. In this study, 32 putative TPS genes were classified in C. faberi and divided into three subfamilies (TPS-a, TPS-b, and TPS-e/f). Motif and gene structure analysis revealed that most CfTPS genes had the conserved aspartate-rich DDxxD motif. TPS genes in the TPS-a and TPS-b subfamilies had variations in the RRX8W motif. Most cis-elements of CfTPS genes were found in the phytohormone responsiveness category, and MYC contained most of the numbers associated with MeJA responsiveness. The Ka/Ks ratios of 12/13 CfTPS gene pairs were less than one, indicated that most CfTPS genes have undergone negative selection. The tissue-specific expression patterns showed that 28 genes were expressed in at least one tissue in C. faberi, and TPS genes were most highly expressed in flowers, followed by leaves and pseudobulbs. In addition, four CfTPS genes were selected for the real-time reverse transcription quantitative PCR (RT-qPCR) experiment. The results revealed that CfTPS12, CfTPS18, CfTPS23, and CfTPS28 were mainly expressed in the full flowering stage. CfTPS18 could convert GPP to β-myrcene, geraniol, and α-pinene in vitro. These findings of CfTPS genes of C. faberi may provide valuable information for further studies on TPSs in orchids.

Molecular basis for SPIN·DOC-Spindlin1 engagement and its role in transcriptional inhibition

ABSTRACTSpindlin1 is a transcriptional coactivator with three Tudor-like domains, of which the first and second Tudors are engaged in histone methylation readout, while the function of the third Tudor is largely unknown. Recent studies revealed that the transcriptional co-activator activity of Spindlin1 could be attenuated by SPIN•DOC. Here we solved the crystal structure of SPIN•DOC-Spindlin1 complex, revealing that a hydrophobic motif, DOCpep3 (256-281), of SPIN•DOC interacts with Tudor 3 of Spindlin1 and completes its β-barrel fold. Massive hydrophobic contacts and hydrogen bonding interactions ensure a high affinity DOCpep3-Spindlin1 engagement with a binding Kd of 30 nM. Interestingly, we characterized two more K/R-rich motifs of SPIN•DOC, DOCpep1 (187-195) and DOCpep2 (228-239), which bind to Spindlin1 at lower affinities with Kd values of 78 μM and 31 μM, respectively. Structural and binding studies revealed that DOCpep1 and DOCpep2 competitively bind to the aromatic cage of Spindlin1 Tudor 2 that is responsible for H3K4me3 readout. Although DOCpep3-Spindlin1 engagement is compatible with histone readout, an extended SPIN•DOC fragment containing DOCpep1 and DOCpep2 inhibits histone or TCF4 binding by Spindin1 due to introduced competition. This inhibitory effect is more pronounced for weaker binding targets but not for strong ones such as H3 “K4me3-K9me3” bivalent mark. Our RT-qPCR experiment showed that the removal of the hydrophobic motif or the K/R-rich region compromised the inhibitory effects of SPIN•DOC on Spindlin1-mediated transcriptional activation. In sum, here we revealed multivalent engagement between SPIN•DOC and Spindlin1, in which a hydrophobic motif acts as the primary binding site for stable SPIN•DOC-Spindlin1 association, while two more neighboring K/R-rich motifs further modulate the target selectivity of Spindlin1 via competitive inhibition, therefore attenuating the transcriptional co-activator activities of Spindlin1 through affecting its chromatin association.

Integrated multivariate analysis of transcriptomic data reveals immunological mechanisms in mice after Leishmania infantum infection

ABSTRACTTranscriptional analysis of complex biological scenarios has been extensively used, even though sometimes results may prove imprecise or difficult-to interpret due to an overwhelming amount of information. In this study, a large-scale Real-time qPCR experiment was coupled to multivariate statistical analysis to describe the main immunological events underlying the early L. infantum infection in livers of BALB/c mice. High-throughput qPCR was used to evaluate the expression of 223 genes related to immunometabolism 1-, 3-, 5- and 10-days post infection. This integrative analysis showed strikingly different gene signatures at 1- and 10-days post infection, revealing progression of infection in the experimental model based on the upregulation of particular immunological response patterns and mediators. This approach addresses the challenge of integrating large collections of transcriptional data for the identification of candidate biomarkers in experimental models.

Long non coding RNA CCAT2 enhances the proliferation, migration, invasion and drug-resistances of non-small lung cancer via activating the miR-204-3p-suppresed IGFBP2/AKT/Bcl2 pathway

Background: To date, the treatment efficacy of NSCLC remains unsatisfactory mainly ascribed to the rapid progress, high rate of metastasis, and emerged drug-resistance. It has been demonstrated that aberrant expression of long non coding RNA colon cancer-associated transcript 2 (CCAT2) was closely related to tumorigenesis and development of drug-resistance of many cancer types. The present study was aimed to thoroughly investigate the effect of CCAT2 in the progress of NSCLC and the underlying mechanisms, so that provide valuable theoretical basis for efficient treatment of NSCLC.Methods: The expressions of CCAT2 were determined using the RT-qPCR experiment. Its target genes and downstream molecules were respectively evaluated by Western-blot assay and RT-qPCR experiment. Cell growth of NSCLC cells was investigated using the CCK-8 kit. The effect of CCAT2 on the progress of NSCLC and the underlying mechanisms in vivo was determined on the NSCLC-bearing mice models.Results: Higher expression of CCAT2 was detected in the lung cancer tissues and cells than the normal ones. Moreover, it was revealed that aberrant expression of CCAT2 in lung cancer signally contributed to proliferation, invasion, and migration of cancer cells and the progress of tumor tissues. Additionally, high level of CCAT2 dramatically down-regulated the cytotoxicity of cisplatin (DDP) to NSCLC cells and tissues by upregulation of the drug-resistance related proteins. Mechanisms studies displayed that upregulation of CCAT2 markedly decreased the miR-204-3p while contrary result was obtained when down-regulated the CCAT2 level. We further demonstrated that down-regulation of miR-204-3p level signally enhanced the activity of the insulin-like growth factor (IGF) signaling pathway.Conclusions: The CCAT2 promoted the progress and drug-resistance of NSCLC thorough activation of the miR-204-3p suppressed IGFBP2/AKT/Bcl2 pathway, and may provide theoretical basis for improvement of therapy of NSCLC.

Heterogenic Origin of Micro RNAs in Atlantic Salmon (Salmo salar) Seminal Plasma

The origin and contribution of seminal plasma RNAs into the whole semen RNA repertoire are poorly known, frequently being overlooked or neglected. In this study, we used high-throughput sequencing and RT-qPCR to profile microRNA (miRNA) constituents in the whole semen, as well as in fractionated spermatozoa and seminal plasma of Atlantic salmon (Salmo salar). We found 85 differentially accumulated miRNAs between spermatozoa and the seminal plasma. We identified a number of seminal plasma-enriched and spermatozoa-enriched miRNAs. We localized the expression of some miRNAs in juvenile and mature testes. Two abundant miRNAs, miR-92a-3p and miR-202-5p, localized to both spermatogonia and somatic supporting cells in immature testis, and they were also highly abundant in somatic cells in mature testis. miR-15c-5p, miR-30d-5p, miR-93a-5p, and miR-730-5p were detected only in mature testis. miRs 92a-3p, 202-5p, 15c-5p, and 30d-5p were also detected in a juvenile ovary. The RT-qPCR experiment demonstrated lack of correlation in miRNA transcript levels in seminal plasma versus blood plasma. Our results indicate that salmon semen is rich in miRNAs, which are present in both spermatozoa and seminal plasma. Testicular-supporting somatic cells are likely the source of seminal plasma enrichment, whereas blood plasma is unlikely to contribute to the seminal plasma miRNA repertoire.

LncRNA ADAMTS9-AS2 in osteosarcoma inhibits cell proliferation and enhances paclitaxel sensitivity by suppressing microRNA-130a-5p

Introduction: Long noncoding RNA ADAMTS9-AS2 (lncRNA ADAMTS9-AS2) has critical function in tumor growth and drug resistance of various cancers. However, the role and mechanism of lncRNA ADAMTS9-AS2 in osteosarcoma (OS) is still unclear. Methods: The expression of lncRNA ADAMTS9-AS2 and MicroRNAs-130a-5p (miR-130a-5p) was detected by real-time polymerase chain reaction (RT-qPCR) experiment. In addition, we used the plasmids transfection to construct the lncRNA ADAMTS9-AS2 overexpressed OS cell lines. Subsequently, the cell proliferation ability and the sensitivity to paclitaxel (PTX) in OS cells upon up-regulating lncRNA ADAMTS9-AS2 expression were analyzed via CCK-8 assay, while Western blotting experiment was performed to detect the regulatory mechanism. Results: We found that lncRNA ADAMTS9-AS2 was down-regulated in OS tissues, and the OS patients with lncRNA ADAMTS9-AS2 downexprssion were usually accompanied with a poor prognosis. Subsequently, we discovered that up-regulation of lncRNA ADAMTS9-AS2 inhibited cell proliferation and increased the sensitivity to PTX in OS cells. Interestingly, the Western blot results showed that overexpression of lncRNA ADAMTS9-AS2 could lead to PTEN expression increased, with PI3K and p-AKT expression decreased, indicating that lncRNA ADAMTS9-AS2 could increase the OS cell sensitivity to PTX via regulating PTEN-PI3K/AKT pathway. Furthermore, we identified MicroRNAs-130a-5p (miR-130a-5p) as the downstream target gene of lncRNA ADAMTS9-AS2, which was further confirmed by the luciferase reporter assay. More importantly, our data revealed that miR-130a-5p mimics could partly reverse the influence on cell proliferation and drug sensitivity induced by lncRNA ADAMTS9-AS2 overexpression. Conclusion: LncRNA ADAMTS9-AS2 exerts its anti-carcinogenesis function by sponging miR-130a-5p, which might be a new therapeutic target for OS treatment.