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Amorpha-4,11-diene (AMD4,11) is a precursor to artemisinin, a potent antimalarial drug that is traditionally extracted from the shrubs of Artemisia annua. Despite significant prior efforts to produce artemisinin and its precursors through biotechnology, there remains a dire need for more efficient biosynthetic routes for its production. Here, we describe the optimization of key process conditions for an Escherichia coli strain producing AMD4,11 via the native methylerythritol phosphate (MEP) pathway. By studying the interplay between glucose uptake rates and oxygen demand, we were able to identify optimal conditions for increasing carbon flux through the MEP pathway by manipulating the availability of NADPH required for terpenoid production. Installation of an optimal qO2 /qglucose led to a 6.7-fold increase in product titers and a 6.5-fold increase in carbon yield.

Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature’s use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications., Classic monodirectional promoters are of limited use for multiple gene co-expression. Here the authors generate a library of 168 bidirectional promoters for the yeast K. phaffii (syn. P. pastoris) with diverse expression profiles to optimize metabolic pathway design.

Taxadiene-5α-Hydroxylase (CYP725A4) is a membrane-bound plant cytochrome P450 that catalyzes the oxidation of taxadiene to taxadiene-5α-ol. This oxidation is a key step in the production of the valuable cancer therapeutic and natural plant product, taxol. In this work, we report the bacterial expression and purification of six different constructs of CYP725A4. All six of these constructs are N-terminally modified and three of them are fused to cytochrome P450 reductase to form a chimera construct. The construct with the highest yield of CYP725A4 protein was then selected for substrate binding and kinetic analysis. Taxadiene binding followed type-1 substrate patterns with an observed KD of 2.1 μM ± 0.4 μM. CYP725A4 was further incorporated into nanoscale lipid bilayers (nanodiscs) and taxadiene metabolism was measured. Taxadiene metabolism followed Michaelis-Menten kinetics with an observed Vmax of 30 ± 8 pmol/min/nmolCYP725A4 and a KM of 123 ± 52 μM. Additionally, molecular operating environment (MOE) modeling was performed in order to gain insight into the interactions of taxadiene with CYP725A4 active site. Taken together, we demonstrate the successful expression and purification of the functional membrane-bound plant CYP, CYP725A4, in E. coli.

Chemically inducible chromosomal evolution (CIChE) was developed for stable multicopy chromosomal integration of heterologous genes. In this technique, flanking an antibiotic selection marker and a gene of interest with identical regions of homology permits gene duplication via recA mediated homologous recombination. A strong selective pressure for gene duplication can be applied by increasing antibiotic concentration, and in a week's time one can create a set of strains with a wide range of cassette copy numbers (upward of 20×), which can be made stable by deletion of recA. Herein, we describe a generalized workflow for this methodology.

Recent advances in metabolic engineering have demonstrated the potential to exploit biological chemistry for the synthesis of complex molecules. Much of the progress to date has leveraged increasingly precise genetic tools to control the transcription and translation of enzymes for superior biosynthetic pathway performance. However, applying these approaches and principles to the synthesis of more complex natural products will require a new set of tools for enabling various classes of metabolic chemistries (i.e., cyclization, oxygenation, glycosylation, and halogenation) in vivo. Of these diverse chemistries, oxygenation is one of the most challenging and pivotal for the synthesis of complex natural products. Here, using Taxol as a model system, we use nature's favored oxygenase, the cytochrome P450, to perform high-level oxygenation chemistry in Escherichia coli. An unexpected coupling of P450 expression and the expression of upstream pathway enzymes was discovered and identified as a key obstacle for functional oxidative chemistry. By optimizing P450 expression, reductase partner interactions, and N-terminal modifications, we achieved the highest reported titer of oxygenated taxanes (∼570 ± 45 mg/L) in E. coli. Altogether, this study establishes E. coli as a tractable host for P450 chemistry, highlights the potential magnitude of protein interdependency in the context of synthetic biology and metabolic engineering, and points to a promising future for the microbial synthesis of complex chemical entities.

The increasing public awareness of adverse health impacts from excessive sugar consumption has created increasing interest in plant-derived, natural low-calorie or zero-calorie sweeteners. Two plant species which contain natural sweeteners, Stevia rebaudiana and Siraitia grosvenorii, have been extensively profiled to identify molecules with high intensity sweetening properties. However, sweetening ability does not necessarily make a product viable for commercial applications. Some criteria for product success are proposed to identify which targets are likely to be accepted by consumers. Limitations of plant-based production are discussed, and a case is put forward for the necessity of biotechnological production methods such as plant cell culture or microbial fermentation to meet needs for commercial-scale production of natural sweeteners.

Natural product metabolic engineering potentially offers sustainable and affordable access to numerous valuable molecules. However, challenges in characterizing and assembling complex biosynthetic pathways have prevented more rapid progress in this field. The anticancer agent Taxol represents an excellent case study. Assembly of a biosynthetic pathway for Taxol has long been stalled at its first functionalization, putatively an oxygenation performed by the cytochrome P450 CYP725A4, due to confounding characterizations. Here, through combined in vivo (Escherichia coli), in vitro (lipid nanodisc), and metabolite stability assays, we verify the presence and likely cause of this enzyme's inherent promiscuity. Thereby, we remove the possibility that promiscuity simply existed as an artifact of previous metabolic engineering approaches. Further, spontaneous rearrangement and the stabilizing effect of a hydrophobic overlay suggest a potential role for nonenzymatic chemistry in Taxol's biosynthesis. Taken together, this work confirms taxadiene-5α-ol as a primary enzymatic product of CYP725A4 and provides direction for future Taxol metabolic and protein engineering efforts.

Impressive advances in the field of synthetic biology go hand in hand with the discovery, design, and use of novel DNA and RNA elements. Efficient synthesis of large oligonucleotides and double-stranded DNA parts, chip-based synthesis of DNA libraries, and a detailed understanding of fundamental biological mechanisms and increased capacities in bioinformatics enable new findings and applications.

Transcription is a complex and dynamic process representing the first step in gene expression that can be readily controlled through current tools in molecular biology. Elucidating and subsequently controlling transcriptional processes in various prokaryotic and eukaryotic organisms have been a key element in translational research, yielding a variety of new opportunities for scientists and engineers. This chapter aims to give an overview of how the fields of molecular and synthetic biology have contributed both historically and presently to the state of the art in transcriptional engineering. The described tools and techniques, as well as the emerging genetic circuit engineering discipline, open the door to new advances in the fields of medical and industrial biotechnology.

Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as ‘multivariate modular metabolic engineering’ (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering., National Institutes of Health (U.S.) (1-R01-GM085323-01A1), Special Research Funds BOF (BOF08/PDO/014), Research Foundation Flanders (FWO-Vlaandern V.4.174.10.N.01)

Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature's use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications.

A common strategy of metabolic engineering is to increase the endogenous supply of precursor metabolites to improve pathway productivity. The ability to further enhance heterologous production of a desired compound may be limited by the inherent capacity of the imported pathway to accommodate high precursor supply. Here, we present engineered diterpenoid biosynthesis as a case where insufficient downstream pathway capacity limits high-level levopimaradiene production in Escherichia coli . To increase levopimaradiene synthesis, we amplified the flux toward isopentenyl diphosphate and dimethylallyl diphosphate precursors and reprogrammed the rate-limiting downstream pathway by generating combinatorial mutations in geranylgeranyl diphosphate synthase and levopimaradiene synthase. The mutant library contained pathway variants that not only increased diterpenoid production but also tuned the selectivity toward levopimaradiene. The most productive pathway, combining precursor flux amplification and mutant synthases, conferred approximately 2,600-fold increase in levopimaradiene levels. A maximum titer of approximately 700 mg/L was subsequently obtained by cultivation in a bench-scale bioreactor. The present study highlights the importance of engineering proteins along with pathways as a key strategy in achieving microbial biosynthesis and overproduction of pharmaceutical and chemical products.

Engineering robust microbes for the biotech industry typically requires high-level, genetically stable expression of heterologous genes and pathways. Although plasmids have been used for this task, fundamental issues concerning their genetic stability have not been adequately addressed. Here we describe chemically inducible chromosomal evolution (CIChE), a plasmid-free, high gene copy expression system for engineering Escherichia coli. CIChE uses E. coli recA homologous recombination to evolve a chromosome with approximately 40 consecutive copies of a recombinant pathway. Pathway copy number is stabilized by recA knockout, and the resulting engineered strain requires no selection markers and is unaffected by plasmid instabilities. Comparison of CIChE-engineered strains with equivalent plasmids revealed that CIChE improved genetic stability approximately tenfold and growth phase-specific productivity approximately fourfold for a strain producing the high metabolic burden-biopolymer poly-3-hydroxybutyrate. We also increased the yield of the nutraceutical lycopene by 60%. CIChE should be applicable in many organisms, as it only requires having targeted genomic integration methods and a recA homolog.

The present article reviews the self-assembly of oligopeptides to form nanostructures, both in solution and in solid state. The solution structures of the peptides were examined using circular dichroism and dynamic light scattering. The solid state assembly was examined by adsorbing the peptides onto a mica surface and analyzing it using atomic force microscopy. The role of pH and salt concentration on the peptide self-assembly was also examined. Nanostructures within a size range of 3–10 nm were obtained under different conditions.

Fabrication of two and three-dimensional nanostructures requires the development of new methodologies for the assembly of molecular/macromolecular objects on substrates in predetermined arrangements. Templated self-assembly approach is a powerful strategy for the creation of materials from assembly of molecular components or nanoparticles. The present study describes the development of a facile, template directed self-assembly of (metal/organic) nanomaterials into periodic micro- and nanostructures. The positioning and the organization of nanomaterials into spatially well-defined arrays were achieved using an amphiphilic conjugated polymer-aided, self-organization process. Arrays of honeycomb patterns formed from conjugated C 12 PPPOH film with homogenous distribution of metal/organic nanomaterials. Our approach offers a straightforward and inexpensive method of preparation for hybrid thin films without environmentally controlled chambers or sophisticated instruments as compared to multistep micro-fabrication techniques.

Molecular level alignment of components and optimum morphology of hybrid materials are of great interest in many applications. Morphology control has been extensively used as a direct tool in the evaluation of interactions and assemblies of components in thin films. It is believed that preparation method and composition are powerful tools to direct the morphology, particularly in self-assembled systems such as fullerene-based hybrid materials. The present report outlines a synergistic self-assembly of fullerenes (C(60)) and functionalized poly (p-phenylene) (PPP) to develop nanofibers with high aspect ratios. Nanostructured PPP-C(60) hybrids were prepared by direct casting of the dilute solution on solid substrates and on water under ambient conditions. The formation of whiskers with high aspect ratio and investigation of interesting photophysical properties are discussed. An amphiphilic PPP was used as a template for preparing nanohybrids of C(60) at ambient temperature and conditions.

Protein microarray offers a means for high-throughput profiling of cellular proteins to provide insights into the mechanisms of biological processes. This study describes the design and fabrication of a robust platform, spatially addressable protein array (SAPA), by exploring the specificity of ssDNA hybridization for self-assembly of semi-synthetic ssDNA-antibody conjugates which capture antigens from complex biological samples. This approach does not involve the direct immobilization of antibodies nor antigen, but instead captures the target antigens in the solution phase followed by self-directed assembly of the complex onto the surface. In an effort to optimize the platform, the effects of surface chemistry, nonspecific protein adsorption, facile preparation, and purification of ssDNA-conjugated antibody and capture of the antigen from a complex biological sample such as cell lysate were examined. This platform allowed antigen detection in cell lysate with high sensitivity (1 pM). The method described herein can be extended to the high-throughput detection of other interacting molecules in solution phase and their subsequent assembly onto any substrate.

Nature employs specialized macromolecules to produce highly complex structures and understanding the role of these macromolecules allows us to develop novel materials with interesting properties. Herein, we report the role of modified conjugated polymers in the nucleation, growth, and morphology of calcium carbonate (CaCO 3 ) crystals. In situ incorporation of sulfonated poly(p-phenylene) (s(PPP)) into a highly oriented calcium carbonate matrix is investigated along with the synthesis and patterning of luminescent CaCO 3 -PPP hybrid materials. Functionalized PPP with polar and nonpolar groups are used as additives in the mineralization medium. The polymer (P1) with polar groups give iso-oriented calcite crystals, whereas PPP with an additional alkyl chain (P2) results in vaterite crystals. The crystallization mechanism can be explained based on self-assembly and aggregation of polymers in an aqueous environment. Such light-emitting hybrid composites with tunable optical properties are excellent candidates for optoelectronics and biological applications.

Protein microarrays are promising tools that can potentially enable high throughput proteomic screening in areas such as disease diagnosis and drug discovery. A critical aspect in the development of protein microarrays is the optimization of the array's surface chemistry to achieve the high sensitivity required for detection of proteins in cell lysate and other complex biological mixtures. In the present study, a high-density antibody array with minimal nonspecific cellular protein adsorption was prepared using a glass surface coated with a poly(propyleneimine) dendrimer terminated with carboxyl group (PAMAM-COOH). The carboxyl-terminated dendrimer-modified surface has almost similar nonspecific cellular protein adsorption when compared to an inert PEG-modified surface. In addition, the multiple functional sites available for reaction on the dendrimer surface facilitated high-density immobilization of antibodies and efficient capture of bioanalytes. Various molecules were tested for their ability to block or deactivate the reactive carboxyl surface after antibody immobilization to further reduce the nonspecific binding. A short oligoethylene glycol (NH2-d4-PEG-COOH), was found to significantly improve the signal-to-noise ratio of the assay, resulting in higher sensitivity. The properties and functional qualities of the various surfaces were characterized by contact angle and AFM measurements. Nonspecific protein adsorption and protein immobilization as a function of dendrimer generations and sensitivity of antigen capturing from a buffer (1 pM) as well as from the complex cell lysate (10 pM) system were examined. Our detailed experimental studies demonstrated a facile method of preparing surfaces with high protein loading and low nonspecific protein binding for the development of high sensitivity protein microarrays.

Conversion of carbohydrates to lipids at high yield and productivity is essential for cost-effective production of renewable biodiesel. Although some microorganisms can convert sugars to oils, conversion yields and rates are typically low due primarily to allosteric inhibition of the lipid biosynthetic pathway by saturated fatty acids. By reverse engineering the mammalian cellular obese phenotypes, we identified the delta-9 stearoyl-CoA desaturase (SCD) as a rate limiting step and target for the metabolic engineering of the lipid synthesis pathway in Yarrowia lipolytica. Simultaneous overexpression of SCD, Acetyl-CoA carboxylase (ACC1), and Diacylglyceride acyl-transferase (DGA1) in Y. lipolytica yielded an engineered strain exhibiting highly desirable phenotypes of fast cell growth and lipid overproduction including high carbon to lipid conversion yield (84.7% of theoretical maximal yield), high lipid titers (~55g/L), enhanced tolerance to glucose and cellulose-derived sugars. Moreover, the engineered strain featured a three-fold growth advantage over the wild type strain. As a result, a maximal lipid productivity of ~1g/L/h is obtained during the stationary phase. Furthermore, we showed that the engineered yeast required cytoskeleton remodeling in eliciting the obesity phenotype. Altogether, our work describes the development of a microbial catalyst with the highest reported lipid yield, titer and productivity to date. This is an important step towards the development of an efficient and cost-effective process for biodiesel production from renewable resources.

Morphosynthesis of calcium-rich materials by tuning the chemical structure of organic matrices has tremendous potential in the preparation of functional mineralized materials. In this paper, we have demonstrated the deposition of thin films of CaCO3 by subtle modifications of the backbone of poly(methyl methacrylate) (PMMA) by the incorporation of many hydroxyl groups. The water-insoluble hydroxylated PMMA (HyPMMA) was used as a template along with poly(acrylic acid) (PA) as an additive for CaCO3 mineralization. Thin film deposition was controlled by the addition of an appropriate amount of PA to the crystallization medium. At lower concentrations (PA = 50 and 100 μg/mL), irregular aggregates of calcite crystallites were formed. As the concentration of PA was increased (500 μg/mL and 1 mg/mL), calcite thin films were deposited. Time-dependent crystallization showed that the precipitates obtained after 3 h were biphasic in structure, consisting of both amorphous and crystalline domains. Observations sugges...

Micro- and nanostructuring of conjugated polymers are of critical importance in the fabrication of molecular electronic devices as well as photonic and bandgap materials. The present report delineates the single-step self-organization of highly ordered structures of functionalized poly(p-phenylene)s without the aid of either a controlled environment or expensive fabrication methodologies. Microporous films of these polymers, with a honeycomb pattern, were prepared by direct spreading of the dilute polymer solution on various substrates, such as glass, quartz, silicon wafer, indium tin oxide, gold-coated mica, and water, under ambient conditions. The polymeric film obtained from C 12 PPPOH comprises highly periodic, defect-free structures with blue-light-emitting properties. It is expected that such microstructured, conjugated polymeric films will have interesting applications in photonic and optoelectronic devices. The ability of the polymer to template the facile micropatterning of nanomaterials gives rise to hybrid films with very good spatial dispersion of the carbon nanotubes.

Over the past two decades, considerable efforts have been devoted to the development of conjugated polymeric materials for electronic applications due to the tunability of their properties through variation of their chemical structure. The LB technique is one of the most effective and precise methods for controlling the organization and thereby the properties of polymer films at the nanoscale for device fabrication. A detailed study was performed on the Langmuir-Schaefer (LS) monolayer and Langmuir-Blodgett-Kuhn (LBK) multilayer formation of newly designed conjugated poly(p-phenylene)s (C(n)PPPOH), incorporated with alkoxy groups with different chain lengths (C(6)H(13)O-, C(12)H(25)O-, and C(18)H(37)O-) and hydroxyl groups on the polymer backbone. The monolayer formed at the air-water interface was characterized using surface pressure-area isotherms, including hysteresis measurements. The films were then transferred to different hydrophilic solid substrates and analyzed using surface plasmon resonance spectroscopy, UV-vis spectroscopy, fluorescence spectroscopy, and AFM measurements. The results showed that the polymer with a short alkoxy chain (C(6)PPPOH) forms uniform monolayers at the air-water interface and can be transferred as multilayer films compared to C(12)PPPOH and C(18)PPPOH. The observed film thicknesses measured by SPR and AFM studies were similar to the theoretical value obtained in the case of C(6)PPPOH, whereas this was not the case with the other two polymers. The present study shows that the polymer C(n)PPPOH with short alkoxy chain can be transferred onto different solid substrates for device fabrication with molecular level control.

A novel poly(p-phenylene) derivative (C12PPPC11OH) was synthesized and used as a template for silica polymerization under ambient conditions in the absence of added catalysts. A few polymers of analogous molecular structures were also simultaneously used in control experiments to derive a molecular mechanism for the observed catalytic activity of C12PPPC11OH. Silica spheres can be dispersed in both hydrophobic and hydrophilic solvents. The optical spectra of the solution-dispersed polymer−silica composite spheres indicated the presence of polymers incorporated in the silica matrix. The UV spectra of the silica−C12PPPC11OH composite dispersed in THF solution was similar to those of the polymer in THF, indicating no significant effect of solvent on the electronic structure of C12PPPC11OH in the composite. Moreover, confocal micrographs of the blue fluorescent spheres of the composites were also taken to show the presence of polymers in the composite. It is anticipated that, by appropriate modifications of t...

The emerging science of nanobiotechnology relies on the observation that, through evolution, nature has produced highly complex nanostructures using macromolecules, especially nucleic acids, polysaccharides and proteins. Understanding the molecular mechanism of how these macromolecules interact to produce nanostructures is the key to the biomimetic materials design and synthesis. Calcium carbonate (CaCO 3 )-based biominerals such as nacre of mollusk shells have complex and hierarchal architectures on submicrometer length scales. The fabrication of such composite materials with control over the shape and properties can be achieved by adopting the natural process of template-driven biomineralization. Our strategy is to obtain nanostructured thin films of CaCO 3 by tuning the chemical structures of organic matrices. Herein, we report the fabrication of functional thin films of aragonite, vaterite and calcite by a template-driven mineralization of calcium carbonate over a functionalized natural scaffold such as demineralized eggshell membrane. The functionalized templates were generated by the pre-adsorption of various soluble polymers such as polyaspartic acid (PAsp), polyglutamic acid (PGlu) and aspartic acid incorporated polyacrylic acid (PA-Asp). These biocompatible calcium carbonate coatings might be useful for tissue engineering applications and also for fundamental studies of cell–matrix interactions.

The isotropic property of amorphous calcium carbonate (ACC) is useful for the controlled synthesis of calcium carbonate based biomaterials. A simple and efficient strategy for the synthesis of monodispersed microspheres of ACC is reported using a low-temperature precipitation of calcium carbonate in the presence of magnesium ions. The room-temperature aging of this amorphous phase yielded superstructures of self-assembled calcite crystals. The stability of the precipitated ACC is proportional to an increase in the concentration of the magnesium ions and the precipitation time. The ACC with high magnesium content was stable for a one month period at room temperature under dry conditions. The ACC aged in solution was stable for up to 48 h. It is believed that the low temperature and the presence of magnesium ions facilitated the formation of stable monodispersed spheres of ACC. The morphological studies and characterizations were carried out using SEM, FTIR, XRD, electron diffraction, and Raman spectroscopy...

Transfer of a biosynthetic pathway between evolutionary distant organisms can create a metabolic shunt capable of bypassing the native regulation of the host organism, hereby improving the production of secondary metabolite precursor molecules for important natural products. Here, we report the engineering of Escherichia coli genes encoding the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway into the genome of Saccharomyces cerevisiae and the characterization of intermediate metabolites synthesized by the MEP pathway in yeast. Our UPLC-MS analysis of the MEP pathway metabolites from engineered yeast showed that the pathway is active until the synthesis of 2-C-methyl-d-erythritol-2,4-cyclodiphosphate, but appears to lack functionality of the last two steps of the MEP pathway, catalyzed by the [4Fe–4S] iron sulfur cluster proteins encoded by ispG and ispH. In order to functionalize the last two steps of the MEP pathway, we co-expressed the genes for the E. coli iron sulfur cluster (ISC) assembly machinery. By deleting ERG13, thereby incapacitating the mevalonate pathway, in conjunction with labeling experiments with U–[superscript 13]C[subscript 6] glucose and growth experiments, we found that the ISC assembly machinery was unable to functionalize ispG and ispH. However, we have found that leuC and leuD, encoding the heterodimeric iron–sulfur cluster protein, isopropylmalate isomerase, can complement the S. cerevisiae leu1 auxotrophy. To our knowledge, this is the first time a bacterial iron–sulfur cluster protein has been functionally expressed in the cytosol of S. cerevisiae under aerobic conditions and shows that S. cerevisiae has the capability to functionally express at least some bacterial iron–sulfur cluster proteins in its cytosol., National Institutes of Health (grant no. 1-R01-GM085323-01A1), Denmark. Technical University, Singapore-MIT Alliance

Thin films of calcium carbonate polymorphs were grown on natural and synthetic scaffolds in the presence of acidic polymers. Decalcified eggshell membrane and Nylon 66 fiber knits were used as 3D scaffolds, and acidic polymers such as polyaspartic acid, polyglutamic acid, and poly(acrylic acid) were used as control macromolecules. The Nylon 66 knits preadsorbed with acidic polymers produced thin films of calcite phase, whereas smooth vaterite or aragonite thin films were formed on the eggshell membrane. The preadsorption of the soluble macromolecules was characterized by the ATR-FTIR spectroscopy. The characterization of the mineral films was carried out using scanning electron microscope, X-ray diffraction, and energy-dispersive X-ray scattering investigations.

Ansocalcin is a novel goose eggshell matrix protein with 132 amino acid residues, which induces the formation of polycrystalline calcite aggregates in in vitro crystallization experiments. The central region of ansocalcin is characterized by the presence of multiplets of charged amino acids. To investigate the specific role of charged amino acid multiplets in the crystal nucleation, three short peptides REWD-16, REWDP-17 (containing charged doublets), and RADA-16 (alternating charged residues) were synthesized and characterized. The aggregation of these peptides in solution was investigated using circular dichroism, intrinsic tryptophan fluorescence, and dynamic light scattering experiments. The peptides REWD-16 and REWDP-17 induced the polycrystalline calcite crystal aggregates, whereas RADA-16 did not induce significant changes in calcite crystal morphology or aggregate formation in in vitro crystallization experiments. The lattice and morphology of the calcite crystals were characterized using X-ray diffraction and scanning electron microscope. The results discussed in this paper reveal the importance of multiplets of charged amino acid residues toward the nucleation of polycrystalline calcite crystal aggregates in solution.

Despite the potential in utilizing microbial fermentation for chemical production, the field of industrial biotechnology still lacks a standard, universally applicable principle for strain optimization. A key challenge has been in finding and applying effective ways to address metabolic flux imbalances. Strategies based on rational design require significant a priori knowledge and often fail to take a holistic view of cellular metabolism. Combinatorial approaches enable more global searches but require a high-throughput screen. Here, we present the recent advances and promises of a novel approach to metabolic pathway and strain optimization called multivariate modular metabolic engineering (MMME). In this technique, key enzymes are organized into distinct modules and simultaneously varied based on expression to balance flux through a pathway. Because of its simplicity and broad applicability, MMME has the potential to systematize and revolutionize the field of metabolic engineering and industrial biotechnology.

This article illustrates the application of a 2% ethyleneglycol dimethacrylate-cross-linked polystyrene support (EGDMA-PS) in manual solid phase peptide synthesis. This copolymer has been characterised and optimised for peptide synthesis by performing the synthesis of a few model peptides and two biologically important peptides. EGDMA-cross-linked polystyrene support was prepared by the suspension polymerisation of the monomers EGDMA and styrene. EGDMA-PS resin undergoes facile swelling in a variety of solvents, both polar and nonpolar, used in peptide synthesis. The polymer was functionalised by Friedel-Crafts chloromethylation reaction. Peptides were assembled on a 2% cross-linked chloromethyl polymer support of capacity 1.63 mmol Cl/g. The biological peptides synthesised are an 11-residue peptide ATP binding site of the CDC2 kinase and a difficult sequence-a nine-residue peptide β 34–42 corresponding to a portion of the hydrophobic terminus of the β-amyloid protein β 1–42. After synthesis, the peptides were cleaved from the support by treating with neat TFA. Purity of the peptides obtained in good yield was checked by TLC and HPLC methods and found to be fairly high.

Studies leading to optimization of butanediol dimethacrylate-crosslinked polystyrene supports (BDDMA-PS) for solid phase peptide synthesis are delineated. BDDMA-PS copolymers with different crosslink densities were prepared and functionalised with chloromethyl groups. The reactivity of the Lys(2-Cl−Z)−OH residue bound to these polymers through a benzyl ester linkage was investigated by following the kinetics of acylation by the HOBt active ester of Boc-Alanine. From the results it was observed that the rate of peptide bond formation was maximum for a 2% BDDMA crosslinked resin. This resin was compared with a 2% DVB-crosslinked polystyrene resin (DVB-PS). Synthesis of an extremely insoluble, hydrophobic, antiparallel β-sheeted difficult sequence peptide LMVGGVVIA (β 34–42), C-terminal fragment of β-amyloid protein, β (1–42), was carried out on both 2% DVB-PS and 2% BDDMA-crosslinked polystyrene supports. The synthesis of the peptide was carried out using Boc amino acid strategy. Greater extent of swelling of the resino peptide, increased coupling efficiency during the assembly of amino acids and relatively high purity of synthesised peptide were observed in the case of 2% BDDMA-PS polymer.

Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.

Taxa-4(5),11(12)-diene is the first dedicated intermediate in the metabolic pathway responsible for synthesizing the anticancer compound Taxol. In this study, the heterologous production of taxadiene was established in and analyzed between K- and B-derived Escherichia coli strains. First, recombinant parameters associated with precursor metabolism (the upstream methylerythritol phosphate (MEP) pathway) and taxadiene biosynthesis (the downstream pathway) were varied to probe the effect different promoters and cellular backgrounds have on taxadiene production. Specifically, upstream MEP pathway genes responsible for the taxadiene precursors, dimethylallyl diphosphate and isopentenyl diphosphate, were tested with an inducible T7 promoter system within K and B E. coli strains. Whereas, inducible T7, Trc, and T5 promoters were tested with the plasmid-borne geranylgeranyl diphosphate synthase and taxadiene synthase genes responsible for the downstream pathway. The K-derivative produced taxadiene roughly 2.5-fold higher than the B-derivative. A transcriptomics study revealed significant differences in pyruvate metabolism between the K and B strains, providing insight into the differences observed in taxadiene biosynthesis and targets for future metabolic engineering efforts. Next, the effect of temperature on cell growth and taxadiene production was analyzed in these two strains, revealing similar phenotypes between the two with 22°C as the optimal production temperature. Lastly, the effect of indole on cell growth was investigated between the two strains, showing that the K-derivative demonstrated greater growth inhibition compared to the B-derivative.

A robust high-throughput and high-fidelity screening platform for identifying and validating potential target molecules is the key for drug development. During the past decade, microarray platforms have demonstrated enormous potential for developing robust tools for small molecules as well as protein-based drug discovery and analysis. Recently, we developed a DNA-directed assembly microarray platform with improved screening and immobilization strategies. In contrast to conventional microarray platforms, our technique allows the solution phase interaction of the probes and analytes in a biological environment and further the detection through the directed assembly of specific DNA probes on a dendrimer-modified glass surface. Herein, we describe the detailed experimental protocols in performing the DNA-directed assembly platform for antibody microarray, a RNA polymerase-DNA binding microarray, and a drug-screening microarray.

A robust high-throughput and high-fidelity screening platform for identifying and validating potential target molecules is the key for drug development. During the past decade, microarray platforms have demonstrated enormous potential for developing robust tools for small molecules as well as protein-based drug discovery and analysis. Recently, we developed a DNA-directed assembly microarray platform with improved screening and immobilization strategies. In contrast to conventional microarray platforms, our technique allows the solution phase interaction of the probes and analytes in a biological environment and further the detection through the directed assembly of specific DNA probes on a dendrimer-modified glass surface. Herein, we describe the detailed experimental protocols in performing the DNA-directed assembly platform for antibody microarray, a RNA polymerase-DNA binding microarray, and a drug-screening microarray.

Author Manuscript February 6, 2011, Taxol (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.

Formation and characterization of nanocrystallite spheres from a hybrid of functionalized cross-conjugated poly(p-phenylene) and C(60) are reported.

Microarray technology has made it possible to simultaneously study the abundance, interactions, and functions of potentially tens of thousands of biological molecules. From its earliest use in DNA microarrays, where only nucleic acids were captured and detected on the arrays, applications of microarrays now extend to those involving biomolecules such as antibodies, proteins, peptides, and carbohydrates. In contrast to the relative robustness of DNA microarrays, the use of such chemically diverse biomolecules on microarray formats presents many challenges in their fabrication as well as application. Among the many methods that have been proposed to overcome these challenges, DNA-directed assembly (DDA) has emerged as a promising strategy for the high sensitivity and multiplexed capture and detection of various analytes. In this review, we explore the challenges faced during the design, fabrication, and utilization of protein microarrays and highlight how DDA strategies, together with other recent advances in the field, are accelerating the development of platforms available for protein microarray applications.

Terpenoids represent a diverse class of molecules that provide a wealth of opportunities to address many human health and societal issues. The expansive array of structures and functionalities that have been evolved in nature provide an excellent pool of molecules for use in human therapeutics. While this class of molecules has members with therapeutic properties including anticancer, antiparasitic, antimicrobial, antiallergenic, antispasmodic, antihyperglycemic, anti-inflammatory, and immunomodulatory properties, supply limitations prevent the large scale use of some molecules. Many of these molecules are only found in ppm levels in nature thus requiring massive harvesting to obtain sufficient amounts of the drug. Synthetic biology and metabolic engineering provide innovative approaches to increase the production of the desired molecule in the native organism, and most importantly, transfer the biosynthetic pathways to other hosts. Microbial systems are well studied, and genetic manipulations allow the optimization of microbial metabolisms for the production of common terpenoid precursors. Using a host of tools, unprecedented advancements in the large scale production of terpenoids have been achieved in recent years. Identification of limiting steps and pathway regulation, coupled with design strategies to minimize terpenoid byproducts wih a high flux to the desired biosynthetic pathways, have yielded greater than 100-fold improvements in the production of a range of terpenoids. This review focuses on the biodiversity of terpenoids, the biosynthetic pathways involved, and engineering efforts to maximize the production through these pathways.

Ultrathin films of a cross-linked and chemically distinct conjugated poly(p-phenylene) network via electropolymerization are described. The amphiphilic network precursor was synthesized by incorporating the alkoxy carbazole group (-O(CH2)5Cb) to a poly(p-phenylene) (C6PPPOH) backbone. In order to investigate the combined thin film electrochemical and photophysical properties of poly(p-phenylene)s and polycarbazole conjugated polymers, C6PPPC5Cb was deposited on substrates using the Langmuir Blodgett Kuhn (LBK) method. The monolayer isotherm of the polymer, C6PPPC5Cb, showed a liquid expanded region slightly different from the parent polymer C6PPPOH. Multilayers (up to 30 layers) were transferred to different substrates such as quartz, gold coated LaSFN9 and ITO substrates for analysis. For conversion to a conjugated polymer network (CPN) film, the electroactive carbazole group was electropolymerized using cyclic voltammetry (CV) resulting in polycarbazole linking units. The differences in the film properties and corresponding changes in the electrochemical behavior indicate the importance of film thickness and electron/ion transport process in cross linked network films. From the electrochemical studies, the scan rate was found to have a considerable effect on electropolymerization with higher oxidation and reduction peak values found for the rigid network polymer compared to the uncrosslinked polymers.

The isoprenoid superfamily of compounds holds great potential for delivering commercial therapeutics, neutraceuticals and fine chemicals. As such, it has attracted widespread attention and prompted research aimed at metabolic engineering of the pathway for isoprenoid overproduction. The carotenoids in particular, because of their convenient colorimetric screening properties, have facilitated the investigation of new tools for pathway optimization. Because all isoprenoids share common metabolic precursors, genetic platforms resulting from work with carotenoids can be applied to the biosynthesis of other valuable products. In this review we summarize the many tools and methods that have been developed for isoprenoid pathway engineering, and the potential of these technologies for producing other molecules of this family, especially terpenoids.