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1.  Statistical Experimental Design Guided Optimization of a One-Pot Biphasic Multienzyme Total Synthesis of Amorpha-4,11-diene 
PLoS ONE  2013;8(11):e79650.
In vitro synthesis of chemicals and pharmaceuticals using enzymes is of considerable interest as these biocatalysts facilitate a wide variety of reactions under mild conditions with excellent regio-, chemo- and stereoselectivities. A significant challenge in a multi-enzymatic reaction is the need to optimize the various steps involved simultaneously so as to obtain high-yield of a product. In this study, statistical experimental design was used to guide the optimization of a total synthesis of amorpha-4,11-diene (AD) using multienzymes in the mevalonate pathway. A combinatorial approach guided by Taguchi orthogonal array design identified the local optimum enzymatic activity ratio for Erg12:Erg8:Erg19:Idi:IspA to be 100∶100∶1∶25∶5, with a constant concentration of amorpha-4,11-diene synthase (Ads, 100 mg/L). The model also identified an unexpected inhibitory effect of farnesyl pyrophosphate synthase (IspA), where the activity was negatively correlated with AD yield. This was due to the precipitation of farnesyl pyrophosphate (FPP), the product of IspA. Response surface methodology was then used to optimize IspA and Ads activities simultaneously so as to minimize the accumulation of FPP and the result showed that Ads to be a critical factor. By increasing the concentration of Ads, a complete conversion (∼100%) of mevalonic acid (MVA) to AD was achieved. Monovalent ions and pH were effective means of enhancing the specific Ads activity and specific AD yield significantly. The results from this study represent the first in vitro reconstitution of the mevalonate pathway for the production of an isoprenoid and the approaches developed herein may be used to produce other isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP) based products.
doi:10.1371/journal.pone.0079650
PMCID: PMC3835790  PMID: 24278153
2.  Combinatorial Engineering of 1-Deoxy-D-Xylulose 5-Phosphate Pathway Using Cross-Lapping In Vitro Assembly (CLIVA) Method 
PLoS ONE  2013;8(11):e79557.
The ability to assemble multiple fragments of DNA into a plasmid in a single step is invaluable to studies in metabolic engineering and synthetic biology. Using phosphorothioate chemistry for high efficiency and site specific cleavage of sequences, a novel ligase independent cloning method (cross-lapping in vitro assembly, CLIVA) was systematically and rationally optimized in E. coli. A series of 16 constructs combinatorially expressing genes encoding enzymes in the 1-deoxy-D-xylulose 5-phosphate (DXP) pathway were assembled using multiple DNA modules. A plasmid (21.6 kb) containing 16 pathway genes, was successfully assembled from 7 modules with high efficiency (2.0 x 103 cfu/ µg input DNA) within 2 days. Overexpressions of these constructs revealed the unanticipated inhibitory effects of certain combinations of genes on the production of amorphadiene. Interestingly, the inhibitory effects were correlated to the increase in the accumulation of intracellular methylerythritol cyclodiphosphate (MEC), an intermediate metabolite in the DXP pathway. The overexpression of the iron sulfur cluster operon was found to modestly increase the production of amorphadiene. This study demonstrated the utility of CLIVA in the assembly of multiple fragments of DNA into a plasmid which enabled the rapid exploration of biological pathways.
doi:10.1371/journal.pone.0079557
PMCID: PMC3818232  PMID: 24223968
3.  Combining Genotype Improvement and Statistical Media Optimization for Isoprenoid Production in E. coli 
PLoS ONE  2013;8(10):e75164.
Isoprenoids are a large and diverse class of compounds that includes many high value natural products and are thus in great demand. To meet the increasing demand for isoprenoid compounds, metabolic engineering of microbes has been used to produce isoprenoids in an economical and sustainable manner. To achieve high isoprenoid yields using this technology, the availability of metabolic precursors feeding the deoxyxylulose phosphate (DXP) pathway, responsible for isoprenoid biosynthesis, has to be optimized. In this study, phosphoenolpyruvate, a vital DXP pathway precursor, was enriched by deleting the genes encoding the carbohydrate phosphotransferase system (PTS) in E. coli. Production of lycopene (a C40 isoprenoid) was maximized by optimizing growth medium and culture conditions. In optimized conditions, the lycopene yield from PTS mutant was seven fold higher than that obtained from the wild type strain. This resulted in the highest reported specific yield of lycopene produced from the DXP pathway in E. coli to date (20,000 µg/g dry cell weight). Both the copy number of the plasmid encoding the lycopene biosynthetic genes and the expression were found to be increased in the optimized media. Deletion of PTS together with a similar optimization strategy was also successful in enhancing the production of amorpha-1,4-diene, a distinct C15 isoprenoid, suggesting that the approaches developed herein can be generally applied to optimize production of other isoprenoids.
doi:10.1371/journal.pone.0075164
PMCID: PMC3790805  PMID: 24124471
4.  Draft Genome Sequence of the Sponge-Associated Strain Bacillus atrophaeus C89, a Potential Producer of Marine Drugs 
Journal of Bacteriology  2012;194(16):4454.
Bacillus atrophaeus C89, isolated from the marine sponge Dysidea avara, is a potential producer of bioactive compounds, such as neobacillamide A and bacillamide C. Here, we present a 4.2-Mb assembly of its genome. The nonribosomal peptide synthetases (NRPSs) make it possible to produce the bioactive compounds.
doi:10.1128/JB.00835-12
PMCID: PMC3416270  PMID: 22843588
5.  30-Day In-vivo Performance of a Wearable Artificial Pump-Lung for Ambulatory Respiratory Support 
The Annals of thoracic surgery  2011;93(1):274-281.
Background
The purpose of this study was to evaluate the long-term in-vivo hemodynamics, gas transfer and biocompatibility of an integrated artificial pump-lung (APL) developed for ambulatory respiratory support.
Methods
The study was conducted in an ovine model by surgically placing the APL between the right atrium and pulmonary artery. Nine sheep were implanted. Heparin was infused as an anticoagulant. The device flow, gas transfer and plasma free hemoglobin (PFH) were measured daily. Hematological data, platelet activation and blood biochemistry were assessed twice a week. After 30 days, the sheep were euthanized for necropsy. The explanted devices were examined for gross thrombosis.
Results
Five sheep survived for 29 to 31 days and were electively terminated. Four sheep expired or were terminated early due to mechanical failure of IV lines or device. The APL devices in the five long-term animals were capable of delivering an oxygen transfer rate of 148±18 ml/min at a flow rate of 2.99±0.46 l/min with blood oxygen saturation of 96.7±1.3%. The device flow and oxygen transfer were stable over 30 days. The animals had normal end-organ functions except for surgery-related transient alteration in kidney function, liver function, and cell and tissue injury. There was no hemolysis. The device flow path and membrane surface were free of gross thrombus.
Conclusions
The APL exhibited the capability of providing respiratory support with excellent biocompatibility, long-term reliability and the potential for bridging to lung transplant.
doi:10.1016/j.athoracsur.2011.08.076
PMCID: PMC3244576  PMID: 22115337
Artificial organs; Device; Extracorporeal membrane oxygenation, ECMO; Lung; Transplantation, Lung
6.  Enhancing solubility of deoxyxylulose phosphate pathway enzymes for microbial isoprenoid production 
Background
Recombinant proteins are routinely overexpressed in metabolic engineering. It is well known that some over-expressed heterologous recombinant enzymes are insoluble with little or no enzymatic activity. This study examined the solubility of over-expressed homologous enzymes of the deoxyxylulose phosphate pathway (DXP) and the impact of inclusion body formation on metabolic engineering of microbes.
Results
Four enzymes of this pathway (DXS, ISPG, ISPH and ISPA), but not all, were highly insoluble, regardless of the expression systems used. Insoluble dxs (the committed enzyme of DXP pathway) was found to be inactive. Expressions of fusion tags did not significantly improve the solubility of dxs. However, hypertonic media containing sorbitol, an osmolyte, successfully doubled the solubility of dxs, with the concomitant improvement in microbial production of the metabolite, DXP. Similarly, sorbitol significantly improved the production of soluble and functional ERG12, the committed enzyme in the mevalonate pathway.
Conclusion
This study demonstrated the unanticipated findings that some over-expressed homologous enzymes of the DXP pathway were highly insoluble, forming inclusion bodies, which affected metabolite formation. Sorbitol was found to increase both the solubility and function of some of these over-expressed enzymes, a strategy to increase the production of secondary metabolites.
doi:10.1186/1475-2859-11-148
PMCID: PMC3545872  PMID: 23148661
Isoprenoids; Protein solubility; Deoxyxylulose phosphate pathway; Activity analysis; Metabolic engineering
7.  Metabolite Profiling Identified Methylerythritol Cyclodiphosphate Efflux as a Limiting Step in Microbial Isoprenoid Production 
PLoS ONE  2012;7(11):e47513.
Isoprenoids are natural products that are all derived from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). These precursors are synthesized either by the mevalonate (MVA) pathway or the 1-Deoxy-D-Xylulose 5-Phosphate (DXP) pathway. Metabolic engineering of microbes has enabled overproduction of various isoprenoid products from the DXP pathway including lycopene, artemisinic acid, taxadiene and levopimaradiene. To date, there is no method to accurately measure all the DXP metabolic intermediates simultaneously so as to enable the identification of potential flux limiting steps. In this study, a solid phase extraction coupled with ultra performance liquid chromatography mass spectrometry (SPE UPLC-MS) method was developed. This method was used to measure the DXP intermediates in genetically engineered E. coli. Unexpectedly, methylerythritol cyclodiphosphate (MEC) was found to efflux when certain enzymes of the pathway were over-expressed, demonstrating the existence of a novel competing pathway branch in the DXP metabolism. Guided by these findings, ispG was overexpressed and was found to effectively reduce the efflux of MEC inside the cells, resulting in a significant increase in downstream isoprenoid production. This study demonstrated the necessity to quantify metabolites enabling the identification of a hitherto unrecognized pathway and provided useful insights into rational design in metabolic engineering.
doi:10.1371/journal.pone.0047513
PMCID: PMC3487848  PMID: 23133596
8.  Effect of combined function of temperature and water activity on the growth of Vibrio harveyi 
Brazilian Journal of Microbiology  2012;43(4):1365-1375.
Vibrio harveyi is considered as a causative agent of the systemic disease, vibriosis, which occurs in many biological fields. The effects of temperatures (12.9–27.1 °C) and water activity (NaCl% 0.6%-3.4%) on V. harveyi were investigated. The behavior and growth characteristics of V. harveyi was studied and modeled. Growth curves were fitted by using Gompertz and Baranyi models, and the Baranyi model showed a better fittness. Then, the maximum growth rates (μmax) and lag phase durations (LPD, λ) obtained from both Gompertz and Baranyi model were modeled as a combination function of temperature and water activity using the response surface and Arrhenius-Davey models for secondary model. The value of r2, MSE, bias and accuracy factor suggest Baranyi model has better fitness than Gompertz model. Furthermore, validation of the developed models with independent data from ComBase also shown better interrelationship between observed and predicted growth parameter when using Baranyi model.
doi:10.1590/S1517-838220120004000018
PMCID: PMC3769047  PMID: 24031965
Vibrio harveyi; modelling; temperature; water activity
9.  Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR 
BMC Molecular Biology  2011;12:18.
Background
Accurate interpretation of quantitative PCR (qPCR) data requires normalization using constitutively expressed reference genes. Ribosomal RNA is often used as a reference gene for transcriptional studies in E. coli. However, the choice of reliable reference genes has not been systematically validated. The objective of this study is to identify a set of reliable reference genes for transcription analysis in recombinant protein over-expression studies in E. coli.
Results
In this study, the meta-analysis of 240 sets of single-channel Affymetrix microarray data representing over-expressions of 63 distinct recombinant proteins in various E. coli strains identified twenty candidate reference genes that were stably expressed across all conditions. The expression of these twenty genes and two commonly used reference genes, rrsA encoding ribosomal RNA 16S and ihfB, was quantified by qPCR in E. coli cells over-expressing four genes of the 1-Deoxy-D-Xylulose 5-Phosphate pathway. From these results, two independent statistical algorithms identified three novel reference genes cysG, hcaT, and idnT but not rrsA and ihfB as highly invariant in two E. coli strains, across different growth temperatures and induction conditions. Transcriptomic data normalized by the geometric average of these three genes demonstrated that genes of the lycopene synthetic pathway maintained steady expression upon enzyme overexpression. In contrast, the use of rrsA or ihfB as reference genes led to the mis-interpretation that lycopene pathway genes were regulated during enzyme over-expression.
Conclusion
This study identified cysG/hcaT/idnT to be reliable novel reference genes for transcription analysis in recombinant protein producing E. coli.
doi:10.1186/1471-2199-12-18
PMCID: PMC3110127  PMID: 21513543
10.  A ZYG-12–dynein interaction at the nuclear envelope defines cytoskeletal architecture in the C. elegans gonad 
The Journal of Cell Biology  2009;186(2):229-241.
Changes in cellular microtubule organization often accompany developmental progression. In the Caenorhabditis elegans embryo, the centrosome, which is attached to the nucleus via ZYG-12, organizes the microtubule network. In this study, we investigate ZYG-12 function and microtubule organization before embryo formation in the gonad. Surprisingly, ZYG-12 is dispensable for centrosome attachment in the germline. However, ZYG-12–mediated recruitment of dynein to the nuclear envelope is required to maintain microtubule organization, membrane architecture, and nuclear positioning within the syncytial gonad. We examined γ-tubulin localization and microtubule regrowth after depolymerization to identify sites of nucleation in germ cells. γ-Tubulin localizes to the plasma membrane in addition to the centrosome, and regrowth initiates at both sites. Because we do not observe organized microtubules around zyg-12(ct350) mutant nuclei with attached centrosomes, we propose that gonad architecture, including membrane and nuclear positioning, is determined by microtubule nucleation at the plasma membrane combined with tension on the microtubules by dynein anchored at the nucleus by ZYG-12.
doi:10.1083/jcb.200902101
PMCID: PMC2717649  PMID: 19635841

Results 1-10 (10)