Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

Author Manuscript February 6, 2011Taxol (paclitaxel) is a potent anticancer drug first isolated from the Taxus brevifolia Pacific yew tree. Currently, cost-efficient production of Taxol and its analogs remains limited. Here, we report a multivariate-modular approach to metabolic-pathway engineering that succeeded in increasing titers of taxadiene—the first committed Taxol intermediate—approximately 1 gram per liter (~15,000-fold) in an engineered Escherichia coli strain. Our approach partitioned the taxadiene metabolic pathway into two modules: a native upstream methylerythritol-phosphate (MEP) pathway forming isopentenyl pyrophosphate and a heterologous downstream terpenoid–forming pathway. Systematic multivariate search identified conditions that optimally balance the two pathway modules so as to maximize the taxadiene production with minimal accumulation of indole, which is an inhibitory compound found here. We also engineered the next step in Taxol biosynthesis, a P450-mediated 5α-oxidation of taxadiene to taxadien-5α-ol. More broadly, the modular pathway engineering approach helped to unlock the potential of the MEP pathway for the engineered production of terpenoid natural products

Влияние донации оксида азота на выраженность митохондриальной дисфункции почечной ткани при моделировании искусственного кровообращения: экспериментальное исследование

АКТУАЛЬНОСТЬ: Одним из наиболее частых осложнений при кардиохирургических операциях с искусственным кровообращением (ИК) является острое почечное повреждение. Ряд исследований показал, что донация экзогенного оксида азота (NO) уменьшает частоту острого почечного повреждения. Однако субклеточные механизмы реализации нефропротективных свойств NO остаются неизвестными. ЦЕЛЬ ИССЛЕДОВАНИЯ: Изучить безопасность технологии плазмохимического синтеза оксида азота и оценить влияние доставки полученного оксида азота на митохондриальное повреждение почечной ткани при моделировании искусственного кровообращения. МАТЕРИАЛЫ И МЕТОДЫ: В эксперимент включили 12 баранов алтайской породы. Животные были разделены на 2 группы: 6 животным моделировали ИК; 6 животным моделировали ИК с доставкой NO. Митохондриальное повреждение оценивалось по кальций-связывающей способности и по трансмембранному потенциалу митохондрий через 1 ч после отлучения от аппарата ИК. Безопасность метода доставки NO по предложенной методике оценивали по концентрации диоксида азота на вдохе, уровню метгемоглобина. Эффективность доставки NO по предложенной методике оценивали по уровню стабильных метаболитов NO: эндогенного нитрита, нитрата, общей концентрации метаболитов NO. РЕЗУЛЬТАТЫ: В группе животных, которым проводили доставку NO, статистически значимо выше средний уровень трансмембранного потенциала митохондрий (171,66 ± 20,41 vs 126,66 ± 18,61; p = 0,00256) и кальций-связывающей способности митохондрий (1466,66 ± 216,02 vs 866,66 ± 216,02; p = 0,000712) почечной паренхимы. Содержание метгемоглобина выше рекомендованных в клинической практике пороговых значений не было зарегистрировано в группе ИК+NO. Показатели общей концентрации метаболитов NO и нитратов статистически значимо выше в группе ИК+NO по сравнению с группой ИК, р = 0,00006; р = 0,0035 соответственно. ВЫВОДЫ: Плазмохимический синтез оксида азота является безопасной технологией, а применение полученного оксида азота на фоне искусственного кровообращения приводит к снижению выраженности митохондриальной дисфункции в паренхиме почек

Novel catalytically active pd/Ru bimetallic nanoparticles synthesized by Bacillus benzeovorans

This work was supported by a UK Commonwealth scholarship to JBO. BK was supported by the Petroleum Technology Development Funds (PTDF) of Nigeria. The project was funded by NERC grant NE/L014076/1 to LEM. The Science City Photoemission Facility used in this research was funded through the Science Cities Advanced Materials Project 1: Creating and Characterizing Next Generation of Advanced Materials with support from AWM and ERDF funds. The microscopy work was conducted in the “Laboratorio de Microscopias Avanzadas” at “Instituto de Nanociencia de Aragon - Universidad de Zaragoza” Spain. The authors acknowledge the LMA-INA for offering access to their instruments and expertise.Bacillus benzeovorans assisted and supported growth of ruthenium (bio-Ru) and palladium/ruthenium (bio-Pd@Ru) core@shell nanoparticles (NPs) as bio-derived catalysts. Characterization of the bio-NPs using various electron microscopy techniques and high-angle annular dark field (HAADF) analysis confirmed two NP populations (1–2 nm and 5–8 nm), with core@shells in the latter. The Pd/Ru NP lattice fringes, 0.231 nm, corresponded to the (110) plane of RuO2. While surface characterization using X-ray photoelectron spectroscopy (XPS) showed the presence of Pd(0), Pd(II), Ru(III) and Ru(VI), X-ray absorption (XAS) studies of the bulk material confirmed the Pd speciation (Pd(0) and Pd(II)- corresponding to PdO), and identified Ru as Ru(III) and Ru(IV). The absence of Ru–Ru or Ru–Pd peaks indicated Ru only exists in oxide forms (RuO2 and RuOH), which are surface-localized. X ray diffraction (XRD) patterns did not identify Pd-Ru alloying. Preliminary catalytic studies explored the conversion of 5-hydroxymethyl furfural (5-HMF) to the fuel precursor 2,5-dimethyl furan (2,5-DMF). Both high-loading (9.7 wt.% Pd, 6 wt.% Ru) and low-loading (2.4 wt.% Pd, 2 wt.% Ru) bio-derived catalysts demonstrated high conversion efficiencies (~95%) and selectivity of ~63% (~20% better than bio-Ru NPs) and 58%, respectively. These materials show promising future scope as efficient low-cost biofuel catalysts.Funded by NERC grant NE/L014076/

Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae

With the increasing demand for biopharmaceutical proteins and industrial enzymes, it is necessary to optimize the production by microbial fermentation or cell cultures. Yeasts are well established for the production of a wide range of recombinant proteins, but there are also some limitations; e.g., metabolic and cellular stresses have a strong impact on recombinant protein production. In this work, we investigated the effect of the specific growth rate on the production of two different recombinant proteins. Our results show that human insulin precursor is produced in a growth-associated manner, whereas alpha-amylase tends to have a higher yield on substrate at low specific growth rates. Based on transcriptional analysis, we found that the difference in the production of the two proteins as function of the specific growth rate is mainly due to differences in endoplasmic reticulum processing, protein turnover, cell cycle, and global stress response. We also found that there is a shift at a specific growth rate of 0.1 h(-1) that influences protein production. Thus, for lower specific growth rates, the alpha-amylase and insulin precursor-producing strains present similar cell responses and phenotypes, whereas for higher specific growth rates, the two strains respond differently to changes in the specific growth rate

Economic Impact of Dengue Illness and the Cost-Effectiveness of Future Vaccination Programs in Singapore

Dengue illness is a tropical disease transmitted by mosquitoes that threatens more than one third of the worldwide population. Dengue has important economic consequences because of the burden to hospitals, work absenteeism and risk of death of symptomatic cases. Governments attempt to reduce the disease burden using costly mosquito control strategies such as habitat reduction and spraying insecticide. Despite such efforts, the number of cases remains high. Dengue vaccines are expected to be available in the near future and there is an urgent need to evaluate their cost-effectiveness, i.e. whether their cost will be justified by the reduction in disease burden they bring. For such an evaluation, we estimated the economic impacts of dengue in Singapore and the expected vaccine costs for different prices. In this way we estimated price thresholds for which vaccination is not cost-effective. This research provides useful estimates that will contribute to informed decisions regarding the adoption of dengue vaccination programs

Statistical Analysis of Molecular Signal Recording

A molecular device that records time-varying signals would enable new approaches in neuroscience. We have recently proposed such a device, termed a “molecular ticker tape”, in which an engineered DNA polymerase (DNAP) writes time-varying signals into DNA in the form of nucleotide misincorporation patterns. Here, we define a theoretical framework quantifying the expected capabilities of molecular ticker tapes as a function of experimental parameters. We present a decoding algorithm for estimating time-dependent input signals, and DNAP kinetic parameters, directly from misincorporation rates as determined by sequencing. We explore the requirements for accurate signal decoding, particularly the constraints on (1) the polymerase biochemical parameters, and (2) the amplitude, temporal resolution, and duration of the time-varying input signals. Our results suggest that molecular recording devices with kinetic properties similar to natural polymerases could be used to perform experiments in which neural activity is compared across several experimental conditions, and that devices engineered by combining favorable biochemical properties from multiple known polymerases could potentially measure faster phenomena such as slow synchronization of neuronal oscillations. Sophisticated engineering of DNAPs is likely required to achieve molecular recording of neuronal activity with single-spike temporal resolution over experimentally relevant timescales.United States. Defense Advanced Research Projects Agency. Living Foundries ProgramGoogle (Firm)New York Stem Cell Foundation. Robertson Neuroscience Investigator AwardNational Institutes of Health (U.S.) (EUREKA Award 1R01NS075421)National Institutes of Health (U.S.) (Transformative R01 1R01GM104948)National Institutes of Health (U.S.) (Single Cell Grant 1 R01 EY023173)National Institutes of Health (U.S.) (Grant 1R01DA029639)National Institutes of Health (U.S.) (Grant 1R01NS067199)National Science Foundation (U.S.) (CAREER Award CBET 1053233)National Science Foundation (U.S.) (Grant EFRI0835878)National Science Foundation (U.S.) (Grant DMS1042134)Paul G. Allen Family Foundation (Distinguished Investigator in Neuroscience Award

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

<p>Abstract</p> <p>Background</p> <p>The need for rapid and efficient microbial cell factory design and construction are possible through the enabling technology, metabolic engineering, which is now being facilitated by systems biology approaches. Metabolic engineering is often complimented by directed evolution, where selective pressure is applied to a partially genetically engineered strain to confer a desirable phenotype. The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering.</p> <p>Results</p> <p>In this work we performed whole genome high-throughput sequencing and annotation can be used to identify single nucleotide polymorphisms (SNPs) between <it>Saccharomyces cerevisiae </it>strains S288c and CEN.PK113-7D. The yeast strain S288c was the first eukaryote sequenced, serving as the reference genome for the <it>Saccharomyces </it>Genome Database, while CEN.PK113-7D is a preferred laboratory strain for industrial biotechnology research. A total of 13,787 high-quality SNPs were detected between both strains (reference strain: S288c). Considering only metabolic genes (782 of 5,596 annotated genes), a total of 219 metabolism specific SNPs are distributed across 158 metabolic genes, with 85 of the SNPs being nonsynonymous (e.g., encoding amino acid modifications). Amongst metabolic SNPs detected, there was pathway enrichment in the galactose uptake pathway (<it>GAL1</it>, <it>GAL10</it>) and ergosterol biosynthetic pathway (<it>ERG8</it>, <it>ERG9</it>). Physiological characterization confirmed a strong deficiency in galactose uptake and metabolism in S288c compared to CEN.PK113-7D, and similarly, ergosterol content in CEN.PK113-7D was significantly higher in both glucose and galactose supplemented cultivations compared to S288c. Furthermore, DNA microarray profiling of S288c and CEN.PK113-7D in both glucose and galactose batch cultures did not provide a clear hypothesis for major phenotypes observed, suggesting that genotype to phenotype correlations are manifested post-transcriptionally or post-translationally either through protein concentration and/or function.</p> <p>Conclusions</p> <p>With an intensifying need for microbial cell factories that produce a wide array of target compounds, whole genome high-throughput sequencing and annotation for SNP detection can aid in better reducing and defining the metabolic landscape. This work demonstrates direct correlations between genotype and phenotype that provides clear and high-probability of success metabolic engineering targets. The genome sequence, annotation, and a SNP viewer of CEN.PK113-7D are deposited at <url>http://www.sysbio.se/cenpk</url>.</p