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PubMed2003

Coupling cell movement to multicellular development in myxobacteria.

The myxobacteria are Gram-negative organisms that are capable of multicellular, social behaviour. In the presence of nutrients, swarms of myxobacteria feed cooperatively by sharing extracellular digestive enzymes, and can prey on other bacteria. When the food supply runs low, they initiate a complex developmental programme that culminates in the production of a fruiting body. Myxobacteria move by gliding and have two, polarly positioned engines to control their motility. The two engines undergo coordinated reversals, and changes in the reversal frequency and speed are responsible for the different patterns of movement that are seen during development. The myxobacteria communicate with each other and coordinate their movements through a cell-contact-dependent signal. Here, the cell movements that culminate in the development of the multicellular fruiting body are reviewed.

Morphogenesis↗

PubMed1993

Recovery from changes in the blood and nasal cavity and/or lungs of rats caused by exposure to methanol-fueled engine exhaust.

One group of male, pathogen-free, Fischer 344 rats was exposed to about 17-fold diluted exhaust generated by an M85 methanol-fueled engine (methanol with 15% gasoline) without catalyst for 8 h, and then the rates of recovery from the resulting increased levels of plasma formaldehyde and carboxyhemoglobin in their erythrocytes were measured. The carboxyhemoglobin level in the erythrocytes was restored within 4 h, whereas the plasma formaldehyde level was still elevated after 4 h but was restored to the normal level within 8 h. No methanol or formic acid was detected in the plasma. Another group of rats was exposed to the same dilution of exhaust for 8 h/d for 7 d, and then the recovery from histopathological damage of the nasal cavity and lungs was also examined. Hyperplasia/squamous metaplasia and erosion of the respiratory epithelium lining the nasoturbinate, maxilloturbinate, or nasal septum, and infiltration of neutrophils into the submucosa at level 1 (level of the posterior edge of the upper incisor teeth) were observed immediately after the exposure period. Lesions of the respiratory epithelium at level 2 (incisive papilla) were less than those at level 1. Slight lesions at levels 1 or 2 were still noticed 1 wk after exposure, but not 4 wk after exposure. Just after exposure, decreases of Clara cells in the terminal bronchiolus and of cilia in the bronchial/bronchiolar epithelium were also observed. Moreover, focal hypertrophy of alveolar walls and increase of macrophages were observed in parts adjacent to respiratory bronchiolus. One week after the exposure period, these changes were no longer seen. These results indicate that changes in the blood and in the nasal cavity and lungs caused by methanol-fueled engine exhaust are reversible. However, complete recovery from damage of the nasal cavity caused by 7-d exposure to the exhaust takes 4 wk, and recovery from elevated plasma formaldehyde and erythrocyte carboxyhemoglobin levels caused by a single 8-h exposure takes 4-8 h.

Animals↗

PubMed2004

In vivo gene transfer to pancreatic beta cells by systemic delivery of adenoviral vectors.

Type 1 diabetes results from autoimmune destruction of pancreatic beta cells. This process might be reversed by genetically engineering the endocrine pancreas in vivo to express factors that induce beta cell replication and neogenesis and counteract the immune response. However, the pancreas is difficult to manipulate and pancreatitis is a serious concern, which has made effective gene transfer to this organ elusive. Thus, new approaches for gene delivery to the pancreas in vivo are required. Here we show that pancreatic beta cells were efficiently transduced to express beta-galactosidase after systemic injection of adenovirus into mice with clamped hepatic circulation. Seven days after vector administration about 70% of pancreatic islets showed beta-galactosidase expression, with an average of about 20% of the cells within positive islets being transduced. In addition, scattered acinar cells expressing beta-galactosidase were also observed. Thus, this approach may be used to transfer genes of interest to mouse islets and beta cells, both for the study of islet biology and gene therapy of diabetes and other pancreatic disorders.

Adenoviridae↗

PubMed1992

Cellulose-binding domains: potential for purification of complex proteins.

The endoglucanase CenA and the exoglucanase Cex from Cellulomonas fimi each contain a discrete cellulose-binding domain (CBD), at the amino-terminus or carboxyl-terminus respectively. The gene fragment encoding the CBD can be fused to the gene of a protein of interest. Using this approach hybrid proteins can be engineered which bind reversibly to cellulose and exhibit the biological activity of the protein partner. Alkaline phosphatase (PhoA) from Escherichia coli, and a beta-glucosidase (Abg) from an Agrobacterium sp. are dimeric proteins. The fusion polypeptides CenA-PhoA and Abg-CBC(Cex) are sensitive to proteolysis at the junctions between the fusion partners. Proteolysis results in a mixture of homo- and heterodimers; these bind to cellulose if one or both of the monomers carry a CBD, e.g. CenA-PhoA/CenA-PhoA and CenA-PhoA/PhoA. CBD fusion polypeptides could be used in this way to purify polypeptides which associate with the fusion partner.

Alkaline Phosphatase↗

PubMed1999

Exon shuffling by L1 retrotransposition.

Long interspersed nuclear elements (LINE-1s or L1s) are the most abundant retrotransposons in the human genome, and they serve as major sources of reverse transcriptase activity. Engineered L1s retrotranspose at high frequency in cultured human cells. Here it is shown that L1s insert into transcribed genes and retrotranspose sequences derived from their 3' flanks to new genomic locations. Thus, retrotransposition-competent L1s provide a vehicle to mobilize non-L1 sequences, such as exons or promoters, into existing genes and may represent a general mechanism for the evolution of new genes.

Codon, Initiator↗

PubMed2003

Glycoprotein of nonpathogenic rabies viruses is a major inducer of apoptosis in human jurkat T cells.

This study sought to identify the RV protein that causes apoptosis. For this purpose, we first compared the ability of G and N proteins of a pathogenic and a nonpathogenic strain to trigger apoptosis of Jurkat rtTA by using an inducible Tet-on expression system. Then we analyzed apoptosis induced by a reverse genetic-engineered recombinant rabies virus in which the G gene from a nonpathogenic strain was replaced by its pathogenic strain counterpart. No other virus proteins than G of nonpathogenic RV strains induce apoptosis, and the G polypeptide of RV is a critical determinant for apoptosis in human cells.

Antigens, Viral↗

PubMed2005

Apolipoprotein E is required for cell proliferation and survival in ovarian cancer.

Apolipoprotein E (ApoE) has been recently identified as a potential tumor-associated marker in ovarian cancer by serial analysis of gene expression. ApoE has long been known to play a key role in lipid transport, and its specific isoforms may participate in atherosclerogenesis. However, its role in human cancer is not known. In this study, apoE expression was frequently detected in ovarian serous carcinomas, the most common and lethal type of ovarian cancer. It was not detected in serous borderline tumors and normal ovarian surface epithelium. Inhibition of apoE expression using an apoE-specific siRNA led to G(2) cell cycle arrest and apoptosis in an apoE-expressing ovarian cancer cell line, OVCAR3, but not in apoE-negative cell lines. Furthermore, the phenotype of apoE siRNA-treated OVCAR3 cells was reversed by expressing engineered mutant apoE with introduced silent mutations in the siRNA target sequence. Expression of apoE in nuclei was significantly associated with a better survival in patients who presented peritoneal effusion at the time of diagnosis (5-year follow-up, P = 0.004). This study suggests a new role of apoE in cancer as apoE expression is important for the proliferation and survival in apoE-expressing ovarian cancer cells.

Apolipoproteins E↗

PubMed2006

Reversible thermal denaturation of a 60-kDa genetically engineered beta-sheet polypeptide.

A de novo 687-amino-acid residue polypeptide with a regular 32-amino-acid repeat sequence, (GA)(3)GY(GA)(3)GE(GA)(3)GH(GA)(3)GK, forms large beta-sheet assemblages that exhibit remarkable folding properties and, as well, form fibrillar structures. This construct is an excellent tool to explore the details of beta-sheet formation yielding intimate folding information that is otherwise difficult to obtain and may inform folding studies of naturally occurring materials. The polypeptide assumes a fully folded antiparallel beta-sheet/turn structure at room temperature, and yet is completely and reversibly denatured at 125 degrees C, adopting a predominant polyproline II conformation. Deep ultraviolet Raman spectroscopy indicated that melting/refolding occurred without any spectroscopically distinct intermediates, yet the relaxation kinetics depend on the initial polypeptide state, as would be indicative of a non-two-state process. Thermal denaturation and refolding on cooling appeared to be monoexponential with characteristic times of approximately 1 and approximately 60 min, respectively, indicating no detectable formation of hairpin-type nuclei in the millisecond timescale that could be attributed to nonlocal "nonnative" interactions. The polypeptide folding dynamics agree with a general property of beta-sheet proteins, i.e., initial collapse precedes secondary structure formation. The observed folding is much faster than expected for a protein of this size and could be attributed to a less frustrated free-energy landscape funnel for folding. The polypeptide sequence suggests an important balance between the absence of strong nonnative contacts (salt bridges or hydrophobic collapse) and limited repulsion of charged side chains.

Computer Simulation↗

PubMed2004

Taming plastids for a green future.

Plant genetic engineering will probably contribute to the required continued increase in agricultural productivity during the coming decades, and moreover, plants can potentially provide inexpensive production platforms for pharmaceuticals and nutraceuticals. With the advent of technologies for altering the genetic information inside chloroplasts, a new attractive target for genetic engineering has become available to biotechnologists. Potential advantages over conventional nuclear transformation include high transgene expression levels and increased biosafety because of maternal organelle inheritance in most crops. This review summarizes the state of the art in chloroplast genetic engineering and describes how reverse genetics approaches enhance our understanding of photosynthesis and other important chloroplast functions. Furthermore, promising strategies by which chloroplast genetic engineering might contribute to the successful modification of plant metabolism are discussed.

Chloroplasts↗

PubMed1997

Complementation of a primer binding site-impaired murine leukemia virus-derived retroviral vector by a genetically engineered tRNA-like primer.

Reverse transcription of retroviral genomes is primed by a tRNA annealed to an 18-nucleotide primer binding site. Here, we present a primer complementation system to study molecular interaction of the replication machinery with the primer and primer binding site in vivo. Introduction of eight base substitutions into the primer binding site of a murine leukemia virus-based vector allowed efficient RNA encapsidation but resulted in severely reduced vector replication capacity. Replication was restored upon complementation with a synthetic gene designed to encode a complementary tRNA-like primer, but not with a noncomplementary tRNA-like molecule. The engineered primer was shown to be involved in both the initiation of first-strand synthesis and second-strand transfer. These results provide an in vivo demonstration that the retroviral replication machinery may recognize sequence complementarity rather than actual primer binding site and 3' primer sequences. Use of mutated primer binding site vectors replicating via engineered primers may add additional control features to retroviral gene transfer technology.

Animals↗

PubMed1991

Engineering of functional supramacromolecular complexes of proteins (enzymes) using reversed micelles as matrix microreactors.

The size of the inner water cavity of reversed micelles formed in a triple system 'water-surfactant-organic solvent' can be widely varied by changing the degree of surfactant hydration. This gives grounds to use reversed micelles as matrix microreactors for the design of supramolecular complexes of proteins. Using ultracentrifugation analysis, it has been demonstrated that the oligomeric composition of various enzymes (ketoglutarate dehydrogenase, alkaline phosphatase, lactic dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase) solubilized in reversed micelles of Aerosol OT [sodium bis(2-ethylehexyl)sulfosuccinate] in octane changes upon variation of the degree of hydration. An oligomeric complex forms under conditions when the radius of the micelle inner cavity is big enough to incorporate this complex as a whole. At lower degrees of hydration the micelles 'uncouple' such complexes to their components. The catalytic properties of various oligomeric complexes have been studied. Possibilities of using reversed micelles for the separation of subunits of oligomeric enzymes under non-denaturating conditions have been demonstrated. In particular, the isolated subunits of alkaline phosphatase, lactic dehydrogenase and glyceraldehyde-3-phosphate have been found to be active in Aerosol OT reversed micelles. The dependences of the catalytic activity of oligomeric enzymes represent saw-like curves. The maxima of the catalytic activity observed at these curves relate to the functioning of various oligomeric forms of an enzyme. The radii of the micelle inner cavity under conditions when these maxima are observed correlate with the linear dimensions of the enzyme oligomeric forms. Correlation of the position of a maximum with the shape of an oligomeric complex is discussed.

Alkaline Phosphatase↗

PubMed1997

Mobility of yeast mitochondrial group II introns: engineering a new site specificity and retrohoming via full reverse splicing.

The mobile group II introns aI1 and aI2 of yeast mtDNA encode endonuclease activities that cleave intronless DNA target sites to initiate mobility by target DNA-primed reverse transcription. For aI2, sense-strand cleavage occurs mainly by a partial reverse splicing reaction, whereas for aI1, complete reverse splicing occurs, leading to insertion of the linear intron RNA into double-stranded DNA. Here, we show that aI1 homing and reverse splicing depend on the EBS1 (RNA)/IBS1(DNA) pairing and that target specificity can be changed by compensatory changes in the target site and the donor intron. Using well-marked strains to follow coconversion of flanking DNA, we show that homing occurs by both RT-dependent and -independent pathways. Remarkably, in most RT-dependent events, the reverse spliced intron is the initial template for first-strand cDNA synthesis.

Base Sequence↗

PubMed1990

Denaturation/refolding of purified recombinant HIV reverse transcriptase yields monomeric enzyme with high enzymatic activity.

We engineered a prokaryotic expression vector encoding the HIV reverse transcriptase (RT). We grew Escherichia coli JM109 carrying the vector in a 250-liter stirred tank fermentor and purified RT (p66) under native conditions to apparent homogeneity. Purified p66 (greater than or equal to 5 mg/ml) was not stable, and was rapidly processed to its 51 kD derivative (p51), until p66:p51 levels were approximately 1:1. These latter RT preparations were chromatographed as heterodimers and had approximately fivefold higher specific RT enzymatic activities compared with those containing predominantly p66. P66 purified under dilute concentrations (less than or equal to 0.5 mg/ml) was monomeric in solution, resistant to p51 processing for weeks at 4 degrees C, but also had low specific RT enzymatic activities. To attempt the preparation of homogeneous p66 with specific RT enzymatic activities equivalent to p66:p51 heterodimers, purified heterodimers were denatured and p66 was purified and refolded during extensive dialysis (refolded p66). Refolded p66 (less than or equal to 0.5 mg/ml) was monomeric in solution and had identical specific RT enzymatic activities, Km for dTTP, and inhibition by 3'-azido-3'-deoxythymidine triphosphate compared with heterodimeric p66:p51 RT. The data indicates that HIV RT obtained from recombinant E. coli under native conditions is extensively processed at concentrations promoting dimerization. Moreover, RT denaturation and refolding yields apparently homogeneous monomeric p66, with specific RT enzymatic activities equivalent to heterodimeric RT.

Base Sequence↗

PubMed2006

Engineering cyclic tetrapeptides containing chimeric amino acids as preferred reverse-turn scaffolds.

Four residues making almost a complete 180 degrees turn in the direction of the peptide chain define a reverse turn, a common motif and recognition site in proteins. Cyclization between residues i and i + 3 and incorporation of heterochiral dipeptides (such as d-Pro-l-Pro) in the i + 1 and i + 2 positions are used to constrain a peptide to a reverse-turn conformation. A combined approach, cyclic tetrapeptides (CTPs) based on heterochiral dipeptides of chimeric amino acids, is evaluated as minimalist scaffolds for reverse-turn conformations. Cyclo-(d-Pro-l-Pro-d-Pro-l-Pro) has been studied with density functional theory (DFT) calculations and molecular dynamics simulations. The all-trans amide conformer was the most stable in vacuo, while the cis-trans-cis-trans (ctct) or trans-cis-trans-cis (tctc) amide conformer was more favored in water due to its large dipole moment. Different conformations could be selectively stabilized by different substitutions on the proline rings. Due to the small 12-membered ring and exocyclic constraints, conformational interconversions could only occur at high temperature. The presence of seven hydrogens on each ring that could be functionalized offers an overwhelming diversity to design molecules to probe receptors. The spatial relationships of C(alpha)-C(beta) vectors of reverse turns in proteins were subjected to principal component analysis for determination of the relative orientation of the C(alpha)-C(beta) vectors. Most reverse-turn structures could be mimicked effectively with a subset of CTP scaffolds with an root-mean-square displacement (RMSD) of approximately 0.5 A. Structural diversity of CTP scaffolds could be enhanced by the incorporation of proline analogues, such as azaproline (azPro) or pipecolic (Pip), azapipecolic (azPip), nipecotic (Nip), and isonipecotic (Inp) acids.

Amino Acids↗

PubMed2005

Rational design of thermostable lactate oxidase by analyzing quaternary structure and prevention of deamidation.

Our current knowledge of protein unfolding is overwhelmingly related to reversible denaturation. However, to engineer thermostable enzymes for industrial applications and medical diagnostics, it is necessary to consider irreversible denaturation processes and/or the entire quaternary structure. In this study we have used lactate oxidase (LOD), which is employed in lactic acid sensors, as a model example to design thermostable variants by rational design. Twelve mutant proteins were tested and one of them displayed a markedly greater thermostability than all the mutants we had previously obtained by random mutagenesis. This mutant was designed so as to strengthen the interaction between the subunits and stabilize the quaternary structure. Since LOD is difficult to crystallize, its three-dimensional structure remains unknown. This study shows that it is possible to carry out rational design to improve thermostability using a computer-aided quaternary structure model based on the known tertiary structure of a related protein. Critical factors required for increasing the thermal stability of proteins by rational design, where the 3-D structure is not available, are discussed.

Amides↗

PubMed2004

Reversible site-selective labeling of membrane proteins in live cells.

Chemical and biological labeling is fundamental for the elucidation of the function of proteins within biochemical cellular networks. In particular, fluorescent probes allow detection of molecular interactions, mobility and conformational changes of proteins in live cells with high temporal and spatial resolution. We present a generic method to label proteins in vivo selectively, rapidly (seconds) and reversibly, with small molecular probes that can have a wide variety of properties. These probes comprise a chromophore and a metal-ion-chelating nitrilotriacetate (NTA) moiety, which binds reversibly and specifically to engineered oligohistidine sequences in proteins of interest. We demonstrate the feasibility of the approach by binding NTA-chromophore conjugates to a representative ligand-gated ion channel and G protein-coupled receptor, each containing a polyhistidine sequence. We investigated the ionotropic 5HT(3) serotonin receptor by fluorescence measurements to characterize in vivo the probe-receptor interactions, yielding information on structure and plasma membrane distribution of the receptor.

Animals↗

PubMed2002

New approaches to the development of live attenuated rabies vaccines.

In the United States, extensive reservoirs of the rabies virus exist in many diverse wild animal species, which continue to pose a serious risk of lethal infection of humans and cause an economic burden exceeding $1 billion annually. Previous experience with rabies control in foxes in Europe has clearly demonstrated that oral immunization with live vaccines is the only practical approach to eradicate rabies in free-ranging animals. However, unlike Europe where vulpine rabies was the only major reservoir, the Americas harbor a variety of species including raccoons, skunks, coyotes, and bats that serve as the primary reservoirs of rabies. Each of these animal reservoirs carries an antigenically distinct virus variant. The currently available modified-live rabies virus vaccines have either safety problems or do not induce sufficient protective immunity in particular wildlife species. Therefore, there is a need for the development of new live rabies virus vaccines that are very safe and highly effective in particular wildlife species. Based on previous observations indicating that the potency of a vaccine is significantly increased if the G protein of the vaccine strain is identical to that of the target virus, we have used a reverse genetics approach to engineer viruses that contain G proteins from virus strains associated with relevant wildlife species. Furthermore, because our recent data also indicate that the pathogenicity of a particular rabies virus strain is inversely proportional to its ability to induce apoptosis and that low-level apoptosis-inducing ability is associated with low anti-viral immune responses, we inserted genes encoding pro-apoptotic proteins to stimulate immunity or otherwise interfere with viral pathogenesis into these recombinant viruses to enhance their efficacy and safety.

Animals↗

PubMed1999

Studies on conditional gene expression in the brain.

This manuscript summarizes our recent attempts to regulate in vitro and in vivo the expression of genes encoding components and regulators of the postsynaptic machinery along with marker genes such as lacZ and GFP. In particular, we studied tTA-dependent regulation and utilized Cre in combination with reversible silencing by intron engineering of dominant negative alleles. We further present a "knockin" approach for on-site artificial regulation of chromosomal genes.

Animals↗