Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids

Regulatory microRNAs and phasiRNAs of paclitaxel biosynthesis in Taxus chinensis

Paclitaxel (trade name Taxol) is a rare diterpenoid with anticancer activity isolated from Taxus. At present, paclitaxel is mainly produced by the semi-synthetic method using extract of Taxus tissues as raw materials. The studies of regulatory mechanisms in paclitaxel biosynthesis would promote the production of paclitaxel through tissue/cell culture approaches. Here, we systematically identified 990 transcription factors (TFs), 460 microRNAs (miRNAs), and 160 phased small interfering RNAs (phasiRNAs) in Taxus chinensis to explore their interactions and potential roles in regulation of paclitaxel synthesis. The expression levels of enzyme genes in cone and root were higher than those in leaf and bark. Nearly all enzyme genes in the paclitaxel synthesis pathway were significantly up-regulated after jasmonate treatment, except for GGPPS and CoA Ligase. The expression level of enzyme genes located in the latter steps of the synthesis pathway was significantly higher in female barks than in male. Regulatory TFs were inferred through co-expression network analysis, resulting in the identification of TFs from diverse families including MYB and AP2. Genes with ADP binding and copper ion binding functions were overrepresented in targets of miRNA genes. The miRNA targets were mainly enriched with genes in plant hormone signal transduction, mRNA surveillance pathway, cell cycle and DNA replication. Genes in oxidoreductase activity, protein-disulfide reductase activity were enriched in targets of phasiRNAs. Regulatory networks were further constructed including components of enzyme genes, TFs, miRNAs, and phasiRNAs. The hierarchical regulation of paclitaxel production by miRNAs and phasiRNAs indicates a robust regulation at post-transcriptional level. Our study on transcriptional and posttranscriptional regulation of paclitaxel synthesis provides clues for enhancing paclitaxel production using synthetic biology technology.

Epilepsy and the smell of fear

OBJECTIVE

In our canine scent detection research involving a specific volatile organic compound (VOC) associated with human epileptic seizure, we began to suspect involvement of the primitive neural networks associated with production of a previously undescribed human alarm pheromone as the origin of our seizure scent. We hypothesized that if we presented fear-scented sweat to our canine seizure scent detection team, and they identified the fear scent as their seizure scent, then that would suggest that they are identical compounds.

METHODS

Following consent and approval, sweat samples taken from volunteers associated with the Brooke Gordon Comprehensive Epilepsy Center at Denver Health were processed by the Canine Assistants (CA) service dog team that had been imprinted to recognize the unique seizure scent from our previous study. In part one, sweat samples were collected from subjects, who had no prior history of epilepsy or seizures, under two different testing environments: watching a scary movie (It) and a neutral/comedy movie (Airplane!). In part two, a larger follow-up study utilizing fear sweat, exercise sweat, epilepsy sweat, and other distractor scents were provided in a multiple choice paradigm to better understand the inter-rater reliability of the canine responses.

RESULTS

In part one, our canine seizure scent detection team identified fear-scented sweat samples as their seizure scent in 4 of 5 study participants. There was almost perfect agreement of seizure scent detection during fear scent trials between the canine seizure scent detectors with a kappa value of 0.814 (95% CI: 0.668-0.960). In part two, (utilizing eleven different subjects) our canine scent detection team identified samples of either fear or seizure sweat with a sensitivity of 82% and a specificity of 100% (no false positives) from among the multiple choices offered. Additionally, there was 92% agreement between the members of the canine scent detection team.

SIGNIFICANCE

While this hypothesis testing study is small and deserves replication, it confirms that the Canine Assistants seizure scent detection team consistently and accurately identified fear-scented sweat as their seizure scent, implying that the VOC, menthone, is common to both conditions. This further implies that human seizure propagation and fear network circuitry may share a common anatomy, and that menthone may not only be an early seizure biomarker, but a newly described human alarm pheromone.

Recent Research Progress in Taxol Biosynthetic Pathway and Acylation Reactions Mediated by Taxus Acyltransferases

Taxol is one of the most effective anticancer drugs in the world that is widely used in the treatments of breast, lung and ovarian cancer. The elucidation of the taxol biosynthetic pathway is the key to solve the problem of taxol supply. So far, the taxol biosynthetic pathway has been reported to require an estimated 20 steps of enzymatic reactions, and sixteen enzymes involved in the taxol pathway have been well characterized, including a novel taxane-10β-hydroxylase (T10βOH) and a newly putative β-phenylalanyl-CoA ligase (PCL). Moreover, the source and formation of the taxane core and the details of the downstream synthetic pathway have been basically depicted, while the modification of the core taxane skeleton has not been fully reported, mainly concerning the developments from diol intermediates to 2-debenzoyltaxane. The acylation reaction mediated by specialized Taxus BAHD family acyltransferases (ACTs) is recognized as one of the most important steps in the modification of core taxane skeleton that contribute to the increase of taxol yield. Recently, the influence of acylation on the functional and structural diversity of taxanes has also been continuously revealed. This review summarizes the latest research advances of the taxol biosynthetic pathway and systematically discusses the acylation reactions supported by Taxus ACTs. The underlying mechanism could improve the understanding of taxol biosynthesis, and provide a theoretical basis for the mass production of taxol.

Genetic resources for advanced biofuel production described with the Gene Ontology

Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology () project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.