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PubMed2001

Carotenoid biosynthesis and biotechnological application.

A survey is given on the carotenoid biosynthetic pathway leading to beta-carotene and its oxidation products in bacteria and plants. This includes the synthesis of prenyl pyrophosphates via the mevalonate or the 1-deoxyxylulose-5-phosphate pathways as well as the reaction sequences of carotenoid formation and interconversion together with the properties of the enzymes involved. Biotechnological application of this knowledge resulted in the development of heterologous carotenoid production systems using bacteria and fungi with metabolic engineered precursor supply and crop plants with manipulated carotenoid biosynthesis. The recent developments in engineering crops with increased carotenoid contents are covered.

Bacterial Proteins↗
PubMed2001

The effects of feed and intracellular pyruvate levels on the redistribution of metabolic fluxes in Escherichia coli.

In a previous study, an Escherichia coli strain lacking the key enzymes (acetate kinase and phosphotransacetylase, ACK-PTA) of the major acetate synthesis pathways reduced acetate accumulation. The ackA-pta mutant strain also exhibits an increased lactate synthesis rate. Metabolic flux analysis suggested that the majority of excessive carbon flux was redirected through the lactate formation pathway rather than the ethanol synthesis pathway. This result indicated that lactate dehydrogenase may be competitive at the pyruvate node. However, a 10-fold overexpression of the fermentative lactate dehydrogenase (ldhA) gene in the wild-type parent GJT001 was not able to divert carbon flux from acetate. The carbon flux through pyruvate and all its end products increases at the expense of flux through biosynthesis and succinate. Intracellular pyruvate measurements showed that strains overexpressing lactate dehydrogenase (LDH) depleted the pyruvate pool. This observation along with the observed excretion of pyruvate in the ackA-pta strain indicates the significance of intracellular pyruvate pools. In the current study, we focus on the role of the intracellular pyruvate pool in the redirection of metabolic fluxes at this important node. An increasing level of extracellular pyruvate leads to an increase in the intracellular pyruvate pool. This increase in intracellular pyruvate affects carbon flux distribution at the pyruvate node. Partitioning of the carbon flux to acetate at the expense of ethanol occurs at the acetyl-CoA node while partitioning at the pyruvate node favors lactate formation. The increased competitiveness of the lactate pathway may be due to the allosteric activation of LDH as a result of increased pyruvate levels. The interaction between the reactions catalyzed by the enzymes PFL (pyruvate formate lyase) and LDH was examined.

Acetyltransferases↗
PubMed1996

Preproricin expressed in Nicotiana tabacum cells in vitro is fully processed and biologically active.

Ricin, the highly toxic glycoprotein expressed in the endosperm of castor seeds, is composed of a galactose-binding lectin B chain (RTB) disulfide linked to a RNA N-glycosidase A chain (RTA). Chemically modified ricin has been conjugated to monoclonal antibodies and used for targeted therapy of cancer and autoimmune diseases. Replacement of chemically coupled molecules with a genetically engineered targeted ricin would improve homogeneity and yield and permit structural changes in the fusion toxin to be introduced readily by oligonucleotide-directed mutagenesis. Previous methods of expression of ricin fusion proteins have been limited to expression of RTA or RTB moieties alone or expression of incompletely processed toxin in Xenopus laevis oocytes. In the present study, we introduced the cDNA encoding preproricin into cultured tobacco cells via Agrobacterium tumefaciens-mediated gene transfer. Yields of ricin in soluble cell extracts were 1 microg/g in cells or, approximately, 0.1% of the total soluble protein. The ricin was partially purified by P2 monoclonal antibody anti-RTB affinity chromatography. The RTA and RTB immunoreactive material migrated on SDS-PAGE at 65 kDa under nonreducing conditions and at 32-35 kDa under reducing conditions. The tobacco ricin bound to immobilized asialofetuin as avidly as castor bean ricin, suggesting intact sugar binding. Tobacco ricin inhibited rabbit reticulocyte lysate protein translation similar to castor bean ricin (IC50 of 3 x 10(-12) M for tobacco ricin and 1 x 10(-11) M for castor bean ricin). The human cutaneous T cell lymphoma cell line HUT102 showed similar sensitivity to tobacco ricin when compared to castor bean ricin (IC50 = 9 x 10(-13) and 2 x 10(-12) M, respectively). The efficiency of gene transfer, reasonable levels of expression, and full post-translational processing indicate that this expression system is suitable for production of ricin fusion toxins for therapeutic applications.

Agrobacterium tumefaciens↗
PubMed1996

Laundry performance of subtilisin proteases.

Effective laundry protease performance against susceptible stains depends upon both the enzyme itself and the environment in which it must work. In order to technically design superior laundry proteases, a model for protease's mechanism of action in detergents was developed which has been substantiated through-the-wash. While evaluation of this model and/or a given protease's effectiveness could be judged by a variety of methods, the utility of using visual wash performance comparisons, analytical, and stain characterization studies is described. Finally, data comparing the performance of wild type Subtilisin proteases with mutants designed via the projected model are given, demonstrating possible utility of the system.

Catalysis↗
PubMed1996

Estimating biodegradative gene numbers at a JP-5 contaminated site using PCR.

We have utilized a most-probable-number polymerase chain reaction (MPN-PCR) procedure to estimate gene numbers and biodegradative potential at a jet fuel (JP-5) contaminated site undergoing the first phase of bioremediation. Nucleic acid analysis was used to determine whether a lack of genetic potential for bioremediation was responsible for low levels of oxygen utilization at the site. Total community DNA was extracted and analyzed by PCR for genes (nahAc,alkB, and xylE) known to be involved in the degradation of certain JP-5 constituents. Results indicate that significant aromatic biodegradative potential exists at the site and outlying areas not subjected to engineered remediation, suggesting that physical and/or chemical factors are inhibiting oxygen delivery. xylE and nahAc were often present in significant portions of the microbial community, whereas alkB was rarely detected. This study illustrates the utility of molecular techniques in evaluating biodegradative potential in the field during active bioremediation.

Base Sequence↗
PubMed2006

Well-defined protein-polymer conjugates--synthesis and potential applications.

During the last decades, numerous studies have focused on combining the unique catalytic/functional properties and structural characteristics of proteins and enzymes with those of synthetic molecules and macromolecules. The aim of such multidisciplinary studies is to improve the properties of the natural component, combine them with those of the synthetic, and create novel biomaterials in the nanometer scale. The specific coupling of polymers onto the protein structures has proved to be one of the most straightforward and applicable approaches in that sense. In this article, we focus on the synthetic pathways that have or can be utilized to specifically couple proteins to polymers. The different categories of well-defined protein-polymer conjugates and the effect of the polymer on the protein function are discussed. Studies have shown that the specific conjugation of a synthetic polymer to a protein conveys its physico-chemical properties and, therefore, modifies the biodistribution and solubility of the protein, making it in certain cases soluble and active in organic solvents. An overview of the applications derived from such bioconjugates in the pharmaceutical industry, biocatalysis, and supramolecular nanobiotechnology is presented at the final part of the article.

Biocompatible Materials↗
PubMed1991

Functionally-stabilized proteins--a review.

The maintenance or stabilization of protein or enzyme function is of vital importance in Biotechnology. Investigations of thermophilic organisms, studies of denaturation and the use of enzymes in organic solvents have each contributed to an understanding of protein stability. Enzymes can reliably and reproducibly be stabilized by variety of means including immobilization, use of additives, chemical modification in solution and protein engineering. Examples of each of these are discussed. With these recent advances it appears that a rational strategy for achieving a particular stabilized enzyme or protein may be within reach.

Journal Article↗
PubMed2006

Functional interaction of nitrogenous organic bases with cytochrome P450: a critical assessment and update of substrate features and predicted key active-site elements steering the access, binding, and orientation of amines.

The widespread use of nitrogenous organic bases as environmental chemicals, food additives, and clinically important drugs necessitates precise knowledge about the molecular principles governing biotransformation of this category of substrates. In this regard, analysis of the topological background of complex formation between amines and P450s, acting as major catalysts in C- and N-oxidative attack, is of paramount importance. Thus, progress in collaborative investigations, combining physico-chemical techniques with chemical-modification as well as genetic engineering experiments, enables substantiation of hypothetical work resulting from the design of pharmacophores or homology modelling of P450s. Based on a general, CYP2D6-related construct, the majority of prospective amine-docking residues was found to cluster near the distal heme face in the six known SRSs, made up by the highly variant helices B', F and G as well as the N-terminal portion of helix C and certain beta-structures. Most of the contact sites examined show a frequency of conservation < 20%, hinting at the requirement of some degree of conformational versatility, while a limited number of amino acids exhibiting a higher level of conservation reside close to the heme core. Some key determinants may have a dual role in amine binding and/or maintenance of protein integrity. Importantly, a series of non-SRS elements are likely to be operative via long-range effects. While hydrophobic mechanisms appear to dominate orientation of the nitrogenous compounds toward the iron-oxene species, polar residues seem to foster binding events through H-bonding or salt-bridge formation. Careful uncovering of structure-function relationships in amine-enzyme association together with recently developed unsupervised machine learning approaches will be helpful in both tailoring of novel amine-type drugs and early elimination of potentially toxic or mutagenic candidates. Also, chimeragenesis might serve in the construction of more efficient P450s for activation of amine drugs and/or bioremediation.

Amines↗
PubMed2005

Role of poly(ADP-ribose) glycohydrolase (PARG) in shock, ischemia and reperfusion.

Poly(ADP-ribosyl)ation is regulated by the synthesizing enzyme poly(ADP-ribose) polymerase-1 (PARP-1) and the degrading enzyme poly(ADP-ribose) glycohydrolase (PARG). Homeostasis of poly(ADP-ribosyl)ation has been proposed to be an important regulator for pathogenesis in multi-cellular organisms. Although the role of PARP-1 in tissue damage, inflammation and ischemia has been extensively studied, the function of PARG in various cellular processes is largely unknown. Recent studies using chemical inhibitors of PARG and genetically engineered Drosophila and mouse models that carry a disrupted PARG gene have started to shed new light on the biological function of PARG in vivo. These animal models and cells isolated from them will be useful for further validation of PARG as a potential pharmaceutical target to intervene the pathogenesis induced by acute tissue injury, ischemia and inflammation.

Animals↗
PubMed2004

Introduction and overview. Perinatal carcinogenesis: growing a node for epidemiology, risk management, and animal studies.

Perinatal carcinogenesis as a cross-disciplinary concern is the subject of this special issue of Toxicology and Applied Pharmacology, which consists of a total of eight reviews or commentaries in the areas of epidemiology, risk assessment, and animal models. Some of the conclusions from these articles, and the Questions and Answers section that follows most of them, are summarized here. There is adequate reason to suspect that perinatal exposures contribute to human cancer risk, both childhood cancers, and those appearing later in life. The latter type of risk may actually be quantitatively the more important, and involve a wide range of types of effects, but has received only limited attention. With regard to childhood cancers, fetal irradiation and diethylstilbestrol exposure are known etiological agents, and it is likely, but not yet certain, there are additional external causes of a portion of these. Some current focal points of interest here include nitroso compounds, DNA topoisomerase inhibitors, viruses, anti-AIDS drugs, and endocrine disruptors. Regulatory agencies must rely heavily on animal data for estimation of human risk due to perinatal exposures to chemicals, and the quantity and quality of these data presently available for this purpose are greatly limiting. Correctly designed conventional animal studies with suspect chemicals are still needed. Furthermore, genetically engineered mouse models for childhood cancers, especially medulloblastoma, have become available, and could be used for screening of candidate causative agents for this cancer type, and for better understanding of gene-environment interactions.

Animals↗
PubMed2003

Structural determinants of the rate of protein folding.

To understand the mechanism of protein folding and to assist rational design of fast-folding, non-aggregating and stable artificial enzymes, it is essential to determine the structural parameters which govern the rate constants of folding, kf. It has been found that -logkf is a linear function of the so-called chain topology parameter (CTP) within the range of 10(-1)s(-1)< or = kf < or =10(8)s(-1). The correlation between -logkf and CTP is much improved than using previously published contact order (CO) method. It has been further suggested that short sequence separations may be preferred for the establishment of stable interactions for the design of novel artificial enzymes and the modification of slow-folding proteins with aggregating intermediates.

Animals↗
PubMed2001

DBP formation kinetics in a simulated distribution system.

Little is known about how the growth of halogenated disinfection by-products (DBPs) in drinking water is affected by time spent in a distribution system. Experiments were performed to compare the rate of trihalomethane and haloacetic acid production in a simulated pipe environment to that observed for the same water held in glass bottles. Results showed that although the rate of chlorine consumption in the pipe was much greater than in the bottle, there was no decrease in the amount of haloacetic acids produced and that trihalomethane levels actually increased by an average of 15%. Separate tests confirmed that this increase was due to a reservoir of organic precursor material associated with deposits on the pipe wall. This work suggests that the rate of DBP production in a distribution system will not necessarily be reduced by increased chlorine consumption due to non-DBP producing reactions with deposits on the pipe wall.

Bromides↗
PubMed2002

Solid-phase genetic engineering with DNA immobilized on a gold surface.

A novel method for immobilizing large DNA fragments on a solid surface was developed. A mixed self-assembled monolayer of thiolated single-stranded DNA with inert alkanethiol was generated on a gold (Au) surface through the Au-S reaction. Surface-tethered DNA generated by this method was compatible with various genetic engineering techniques, including hybridization, polymerization, restriction enzyme digestion and ligation. Kinetic control of surface coverage of immobilized DNA was critical for optimizing genetic engineering techniques on solid-phase. Multi-step reaction schemes utilizing various genetic engineering techniques described above were employed for solid-phase gene assembly. We were able to immobilize DNA fragments of up to 1180 bp on a solid surface. Furthermore, we showed that these immobilized genes can be regenerated by PCR. The present work suggests that these types of assembled genes can be used to store and regenerate genes on solid-phase.

Base Sequence↗
PubMed1996

Molecular mechanism of LH/CG receptor activation.

It is known that the N-terminal half of the LH/CG receptor is responsible for high hCG binding whereas the C-terminal half is capable of receptor activation. Our results suggest that initial hCG binding at the high affinity site in the N-half receptor induces conformational adjustments. This leads to low affinity secondary contacts of the complex of hCG/the N-half receptor with the C-half receptor. This low affinity secondary contact is responsible for activating the receptor. This is based on the following observations. The C-terminal tail of hCG alpha is known to be involved in activation of the LH/CG receptor. In addition to hCG, we examined the C-terminal three residues (His90-Lys91-Ser92) of the common alpha subunit of FSH and TSH. The results show their differential roles in the three hormones. Ser92 is important for binding and cAMP induction of TSH but not for hCG and FSH. Lys91 is important for binding and cAMP induction of hCG, and cAMP induction but not binding of FSH. It is not important for binding or cAMP induction of TSH. His90 is important for all three hormones. When all three residues were truncated, FSH and TSH lose their affinity for binding and cAMP induction, whereas hCG is still capable of binding but not cAMP induction. Therefore, the three amino acids contribute differently in receptor binding and cAMP induction of hCG, FSH and TSH. Our data also indicate that the evolution of the alpha subunit has been constrained in order not to impair any of the hormones. This suggests that each hormone can be independently engineered to improve the potency. To chemically identify the contact site of the alpha C-tail of hCG in the LH/CG receptor, a decamer peptide corresponding to the alpha subunit sequence from His83 to Ser92 (peptide alpha 81-92) was derivatized with UV sensitive reagent, ABG and radio-iodinated. The resulting ABG-125I-peptide alpha 83-92 was capable of binding and activating the LH/CG receptor. Furthermore, it specifically photoaffinity-labeled the LH/CG receptor. In addition, the amino group of alpha Lys91 of peptide alpha 83-92 is crosslinked to a carboxyl group of the receptor, an indication of close association. Reciprocal mutagenesis of alpha Lys91 and Asp397 in exoloop 1 of the LH/CG receptor suggests the complementary of this pair in receptor activation but not the high affinity interaction of hCG and the receptor. In addition, Lys583 of exoloop 3 is also crucial for receptor activation. To test the conformational adjustment, ABG was attached to hCG alpha and reassociated with untreated beta to produce ABG-125I-alpha/beta. The extent of inter-subunit crosslinking of ABG-125I-alpha/beta bound to the receptor was two to three fold less than unbound ABG-125I-alpha/beta. This result indicates structural change at the subunit interface in response to hCG binding to the receptor.

Affinity Labels↗
PubMed2001

Effects of system parameters on the physical characteristics of bubbles produced through air sparging.

Air sparging is a relatively new, cost-effective technology for the remediation of soil and groundwater contaminated with volatile organic compounds (VOCs). While the method has met with reasonable success at a large number of field sites, implementation of the technique is restricted to relatively coarse-grained soils with large values of air permeability, which significantly limits its applicability. An understanding of the fundamental parameters that control the formation and distribution of air in the sparging process is useful for optimizing the system implementation and extending its range of applicability. This work presents the results of an experimental investigation into the effect of process control parameters on the size and size distribution of air bubbles produced in aqueous and idealized saturated porous media systems. The experiments used digital image analysis to image and quantify the physical characteristics of the bubbles generated in a bench scale test cell. Results demonstrated that the average bubble size and range of size distribution increased as the injection pressure and size of the injection orifice were increased. Larger diameter bubbles with wider size distributions were produced in the presence of particles when compared to aqueous systems. As the particle size was decreased, the size of bubbles produced increased. Finally, the presence of trace quantities of the surfactant Triton X100 led to uniformly small diameter bubbles under all experimental conditions. The presence of the surfactant coating produced bubbles with physical characteristics that are more suited to in situ stripping of VOCs than the bubbles produced in the absence of a surfactant.

Air↗
PubMed1999

Novel optical methodologies in studying mechanical signal transduction in mammalian cells.

For the last 3 decades evidence has been accumulating that some types of mammalian cells respond to their mechanically active environment by altering their morphology, growth rate, and metabolism. The study of such responses is very important in understanding, physiological and pathological conditions ranging from bone formation to atherosclerosis. Obtaining this knowledge has been the goal for an active research area in bioengineering termed cell mechanotransduction. The advancement of optical methodologies used in cell biology research has given the tools to elucidate cellular mechanisms that would otherwise be impossible to visualize. Combined with molecular biology techniques, they give engineers invaluable tools in understanding the chemical pathways involved in mechanotransduction. Herein we briefly review the current knowledge on mechanical signal transduction in mammalian cells, focusing on the application of novel optical techniques in the ongoing research.

Animals↗