Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii).

Alpine plants remain the least studied plant communities in terrestrial ecosystems. However, how they adapt to high-altitude environments is far from clear. Here, we used RNA-seq to investigate a typical alpine plant maca (Lepidium meyenii) to understand its high-altitude adaptation at transcriptional and post-transcriptional level. At transcriptional level, we found that maca root significantly up-regulated plant immunity genes in day-time comparing to night-time, and up-regulated abiotic (cold/osmotic) stress response genes in Nov and Dec comparing to Oct. In addition, 17 positively selected genes were identified, which could be involved in mitochondrion. At post-transcriptional level, we found that maca had species-specific characterized alternative splicing (AS) profile which could be influenced by stress environments. For example, the alternative 3' splice site events (A3SS, 39.62%) were predominate AS events in maca, rather than intron retention (IR, 23.17%). Interestingly, besides serine/arginine-rich (SR) proteins and long non-coding RNAs (lncRNAs), a lot of components in nonsense-mediated mRNA decay (NMD) were identified under differential alternative splicing (DAS), supporting AS coupled to NMD as essential mechanisms for maca's stress responses and high-altitude adaptation. Taken together, we first attempted to unveil maca's high-altitude adaptation mechanisms based on transcriptome and post-transcriptome evidence. Our data provided valuable insights to understand the high-altitude adaptation of alpine plants.

Pharmacophore modeling, molecular docking and molecular dynamics simulations toward identifying lead compounds for Chk1.

Checkpoint kinase 1 (Chk1), a serine/threonine protein kinase, plays an important role in G2/M checkpoint, which is a key regulator in response to DNA damage. In this study, the structure-based drug design approach and molecular dynamics (MD) simulations were used to explore potent Chk1 inhibitors. A series of the best fitting candidates were picked out from the Specs database. Out of these, five candidates were submitted for MD simulations to explore the stability of complex. The result indicates that these five candidates could be considered potential Chk1 inhibitors and represents a promising starting point for developing potent inhibitors of Chk1 for the treatment of tumor.

Antibacterial and antifungal potentials of the solvents extracts from Eryngium caeruleum, Notholirion thomsonianum and Allium consanguineum.

BACKGROUND: Herbal medicines have long been used for various ailments in various societies and natural bioactive compounds are gaining more and more importance due to various factors. In this context, three plant species i.e., Eryngium caeruleum, Notholirion thomsonianum and Allium consanguineum have been aimed for the scientific verification of their purported traditional uses against various infectious diseases. METHODS: In this study, three plants were assayed for antibacterial and antifungal potentials. The antibacterial investigations were performed via well diffusion method and nutrient broth dilution method. The bacterial strains used in the study were Enterococcus faecalis, Proteus mirabilis, Escherichia coli, Salmonella typhi, Klebsiella pneumonia and Pseudomonas aeruginosa. The antifungal potential was investigated by dilution method of Muller-Hinton agar media of the plants' samples. The fungal strains used were Aspergillis fumigatus, Aspergillis flavus and Aspergillis niger. Ceftriaxone and nystatin were used as standard drugs in antibacterial and antifungal assays respectively. RESULTS: Different fractions from N. thomsonianum were tested against five bacterial strains while the samples from A. consanguineum and E. caeruleum were tested against six bacterial strains. All the samples exhibited prominent antibacterial activity against the tested strains. Overall, chloroform and ethyl acetate fractions were found most potent among the three plants' samples. N. thomsonianum excelled among the three plants in antibacterial activity. Similarly, in antifungal assay, N. thomsonianum exhibited strong antifungal activity against the fungal strains. The chloroform fraction displayed MFCs of 175.67 ± 5.20***, 29.33 ± 5.48*** and 63.00 ± 4.93*** µg/ml against Aspergillus fumigatus, Aspergillus flavus and Aspergillus niger respectively. The whole study demonstrates that all the three plant species were active against tested bacterial and fungal strains. CONCLUSION: It can be concluded from our findings that N. thomsonianum, A. consanguineum and E. caeruleum have broad antibacterial and antifungal potentials. In all of the plants' samples, chloroform and ethyl acetate fractions were more active. Furthermore, being the potent samples, the chloroform and ethyl acetate fractions of these plants can be subjected to column chromatography for the isolation of more effective antimicrobial drugs.

Targeted methylation and gene silencing of VEGF-A in human cells by using a designed Dnmt3a-Dnmt3L single-chain fusion protein with increased DNA methylation activity.

The C-terminal domain of the Dnmt3a de novo DNA methyltransferase (Dnmt3a-C) forms a complex with the C-terminal domain of Dnmt3L, which stimulates its catalytic activity. We generated and characterized single-chain (sc) fusion proteins of both these domains with linker lengths between 16 and 30 amino acid residues. The purified sc proteins showed about 10-fold higher DNA methylation activities than Dnmt3a-C in vitro and were more active in bacterial cells as well. After fusing the Dnmt3a-3L sc enzyme to an artificial zinc-finger protein targeting the vascular endothelial cell growth factor A (VEGF-A) promoter, we demonstrate successful targeting of DNA methylation to the VEGF-A promoter in human cells and observed that almost complete methylation of 12 CpG sites in the gene promoter could be achieved. Targeted methylation by the Dnmt3a-3L sc enzymes was about twofold higher than that of Dnmt3a-C, indicating that Dnmt3a-3L sc variants are more efficient as catalytic modules in chimeric DNA methyltransfeases than Dnmt3a-C. Targeted methylation of the VEGF-A promoter with the Dnmt3a-3L sc variant led to a strong silencing of VEGF-A expression, indicating that the artificial DNA methylation of an endogenous promoter is a powerful strategy to achieve silencing of the corresponding gene in human cells.

Auto-methylation of the mouse DNA-(cytosine C5)-methyltransferase Dnmt3a at its active site cysteine residue.

The Dnmt3a DNA methyltransferase is responsible for establishing DNA methylation patterns during mammalian development. We show here that the mouse Dnmt3a DNA methyltransferase is able to transfer the methyl group from S-adenosyl-l-methionine (AdoMet) to a cysteine residue in its catalytic center. This reaction is irreversible and relatively slow. The yield of auto-methylation is increased by addition of Dnmt3L, which functions as a stimulator of Dnmt3a and enhances its AdoMet binding. Auto-methylation was observed in binary Dnmt3a AdoMet complexes. In the presence of CpG containing dsDNA, which is the natural substrate for Dnmt3a, the transfer of the methyl group from AdoMet to the flipped target base was preferred and auto-methylation was not detected. Therefore, this reaction might constitute a regulatory mechanism which could inactivate unused DNA methyltransferases in the cell, or it could simply be an aberrant side reaction caused by the high methyl group transfer potential of AdoMet. ENZYMES: Dnmt3a is a DNA-(cytosine C5)-methyltransferase, EC 2.1.1.37. STRUCTURED DIGITAL ABSTRACT: • Dnmt3a methylates Dnmt3a by methyltransferase assay (View interaction) • Dnmt3a and DNMT3L methylate Dnmt3a by methyltransferase assay (View interaction).

Approaches to enzyme and substrate design of the murine Dnmt3a DNA methyltransferase.

Dnmt3a-C, the catalytic domain of the Dnmt3a DNA-(cytosine-C5)-methyltransferase, is active in an isolated form but, like the full-length Dnmt3a, shows only weak DNA methylation activity. To improve this activity by directed evolution, we set up a selection system in which Dnmt3a-C methylated its own expression plasmid in E. coli, and protected it from cleavage by methylation-sensitive restriction enzymes. However, despite screening about 400 clones that were selected in three rounds from a random mutagenesis library of 60 000 clones, we were not able to isolate a variant with improved activity, most likely because of a background of uncleaved plasmids and plasmids that had lost the restriction sites. To improve the catalytic activity of Dnmt3a-C by optimization of the sequence of the DNA substrate, we analyzed its flanking-sequence preference in detail by bisulfite DNA-methylation analysis and sequencing of individual clones. Based on the enrichment and depletion of certain bases in the positions flanking >1300 methylated CpG sites, we were able to define a sequence-preference profile for Dnmt3a-C from the -6 to the +6 position of the flanking sequence. This revealed preferences for T over a purine at position -2, A over G at -1, a pyrimidine at +1, and A and T over G at +3. We designed one "good" substrate optimized for methylation and one "bad" substrate designed not to be efficiently methylated, and showed that the optimized substrate is methylated >20 times more rapidly at its central CpG site. The optimized Dnmt3a-C substrate can be applied in enzymatic high-throughput assays with Dnmt3a-C (e.g., for inhibitor screening), because the increased activity provides an improved dynamic range and better signal/noise ratio.